{{{ The following bug report has been submitted: Platform: Linux-5.10.0-1034-oem-x86_64-with-glibc2.14 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/ucsf-commands.cxc > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3EI4.pdbqt Chain information for 3EI4.pdbqt #1 --- Chain | Description A C E | No description available B D F | No description available Opened 3EI4.pdbqt containing 1 structures (70284 atoms, 71031 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 3EI4.pdbqt #1 --- warnings | Not adding hydrogens to /A GLU 368 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A ARG 369 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLN 759 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 779 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A THR 780 CB because it is missing heavy-atom bond partners 49 messages similar to the above omitted notes | No usable SEQRES records for 3EI4.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 3EI4.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 3EI4.pdbqt (#1) chain C; guessing termini instead No usable SEQRES records for 3EI4.pdbqt (#1) chain D; guessing termini instead No usable SEQRES records for 3EI4.pdbqt (#1) chain E; guessing termini instead 1 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B TRP 54, /C MET 1, /D TRP 54, /E MET 1, /F TRP 54 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 1140, /B GLU 421, /C HIS 1140, /D GLU 421, /E HIS 1140, /F GLU 421 Chain-final residues that are not actual C termini: 2812 hydrogen bonds 114 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3EI4-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3EI4--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.8 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 3EI4--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 40 contacts atom1 atom2 overlap distance 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 HE 0.326 2.554 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 458 O 0.049 3.311 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 NE -0.005 3.510 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 HN -0.006 2.886 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HB2 -0.009 2.889 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 O -0.028 3.388 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 HN -0.045 2.065 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 O -0.050 3.410 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 O -0.056 3.416 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 HG2 -0.071 2.831 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 CG1 -0.071 3.531 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C VAL 637 2HG1 -0.089 2.509 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 C -0.092 3.672 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 HB2 -0.115 2.995 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 CB -0.121 3.701 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HD2 -0.131 2.891 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C SER 590 HA -0.193 2.613 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 HB2 -0.227 3.107 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C TYR 678 HD2 -0.237 2.997 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 CG -0.240 3.700 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C TYR 678 CD2 -0.246 3.706 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ILE 591 O -0.258 3.618 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 HE -0.271 3.031 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 O -0.284 3.184 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 O -0.286 3.226 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CD2 -0.291 3.751 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CD2 -0.291 3.751 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 HB2 -0.296 3.176 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HD2 -0.312 3.072 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C MET 679 O -0.331 3.691 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 2HH2 -0.331 3.211 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C SER 590 CA -0.344 3.464 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 2HG1 -0.350 3.110 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 C -0.357 3.937 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 CB -0.367 3.947 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 N -0.374 3.019 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 CG1 -0.386 3.696 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 N -0.387 3.892 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CB -0.394 3.974 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 HB1 -0.394 3.274 40 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3EI4.pdbqt 2.1 3EI4--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 3EI4.pdbqt #1/C ILE 591 N 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 HN 3.019 2.065 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.8 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "3EI4 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2PA2.pdbqt Chain information for 2PA2.pdbqt #1 --- Chain | Description A B | No description available Opened 2PA2.pdbqt containing 1 structures (3578 atoms, 3614 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2PA2.pdbqt #1 --- notes | No usable SEQRES records for 2PA2.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 2PA2.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A LYS 40, /B LYS 40 Chain-initial residues that are not actual N termini: /A GLY 124, /B GLY 124 Chain-final residues that are actual C termini: /A PHE 176, /B PHE 176 Chain-final residues that are not actual C termini: /A PHE 94, /B PHE 94 173 hydrogen bonds Adding 'H' to /A GLY 124 Adding 'H' to /B GLY 124 /A PHE 94 is not terminus, removing H atom from 'C' /B PHE 94 is not terminus, removing H atom from 'C' 0 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2PA2-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2PA2--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.4 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2PA2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 42 contacts atom1 atom2 overlap distance 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH1 0.226 2.384 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 0.203 1.817 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 0.129 2.481 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 HB2 0.110 2.650 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE1 0.107 2.773 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 0.007 2.753 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 0.001 2.759 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 -0.038 2.648 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 -0.039 2.649 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH2 -0.042 2.922 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH2 -0.049 2.109 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B HIS 92 O -0.078 3.438 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 CE1 -0.094 3.674 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH2 -0.105 2.985 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 CG1 -0.107 3.687 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A PRO 47 HA -0.111 2.531 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HD1 -0.114 2.874 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HD1 -0.119 2.879 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B ARG 128 O -0.121 3.481 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/B HIS 130 HE1 -0.121 2.581 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 NH1 -0.139 2.784 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 NH1 -0.150 3.385 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.172 3.557 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 -0.175 2.785 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CD1 -0.211 3.671 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A LYS 169 O -0.229 3.319 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 NH2 -0.235 3.740 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A VAL 43 O -0.237 3.137 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.243 3.478 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 HD2 -0.251 3.011 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CB -0.266 3.576 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A TRP 171 HB2 -0.278 2.698 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A PRO 47 CB -0.283 3.863 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 CB -0.291 3.751 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 1HG1 -0.297 3.177 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B HIS 92 HN -0.300 3.180 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CD1 -0.306 3.766 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CB -0.325 3.785 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.331 3.566 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HN -0.354 3.234 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 HB -0.364 2.974 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 -0.383 3.143 42 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2PA2.pdbqt 2.1 2PA2--WRM-16.result.pdbqt 4 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 2PA2.pdbqt #1/A ARG 139 NH1 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 3.380 2.525 2PA2.pdbqt #1/A ARG 139 NH1 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 2.784 1.817 2PA2.pdbqt #1/A ARG 139 NH2 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH2 3.087 2.109 2PA2.pdbqt #1/A TRP 171 N 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A TRP 171 HN 3.576 2.621 4 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2PA2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KV2.pdbqt Chain information for 2KV2.pdbqt #1 --- Chain | Description A | No description available Opened 2KV2.pdbqt containing 1 structures (1351 atoms, 1361 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2KV2.pdbqt #1 --- notes | No usable SEQRES records for 2KV2.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASP 85 Chain-final residues that are not actual C termini: 61 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KV2-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KV2--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.4 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2KV2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 52 contacts atom1 atom2 overlap distance 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 0.640 2.240 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 0.469 2.291 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB 0.306 3.274 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 0.278 2.482 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 HB 0.207 2.673 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 CE 0.105 3.055 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HD2 0.105 2.655 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 CB 0.100 3.360 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HB2 0.075 2.685 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 CB 0.039 3.541 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CD2 -0.031 3.491 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HE3 -0.057 2.817 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HD1 -0.060 2.820 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CE3 -0.080 3.540 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CD1 -0.084 3.544 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HZ3 -0.099 2.979 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CD1 -0.106 3.686 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A THR 80 HB -0.115 2.875 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 -0.131 3.011 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE2 -0.136 2.596 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HA -0.165 2.775 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HA -0.207 2.817 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 CD -0.208 3.668 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 OG1 -0.214 3.594 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CB -0.214 3.674 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 -0.227 2.837 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CE3 -0.237 3.547 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 -0.262 3.142 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 C -0.263 3.723 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 CE3 -0.272 3.852 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 CZ3 -0.273 3.853 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 HZ3 -0.277 3.157 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 HE3 -0.280 3.160 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB -0.297 3.607 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CD2 -0.310 3.890 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB -0.317 3.897 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 O -0.323 3.563 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE2 -0.324 2.744 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 75 HB3 -0.325 2.785 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 O -0.329 3.569 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 75 CB -0.330 3.490 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 -0.331 2.941 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 O -0.336 3.576 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A TRP 79 CG -0.355 3.515 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HE3 -0.360 2.970 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 NZ -0.373 3.878 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CG -0.376 3.956 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A VAL 72 3HG2 -0.383 2.803 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE3 -0.388 2.848 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 -0.388 3.148 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 -0.391 3.151 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 8 HE2 -0.399 3.009 52 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2KV2.pdbqt 2.1 2KV2--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2KV2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3CO6.pdbqt Chain information for 3CO6.pdbqt #1 --- Chain | Description A | No description available B | No description available C | No description available Opened 3CO6.pdbqt containing 1 structures (2476 atoms, 2572 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 3CO6.pdbqt #1 --- warnings | Not adding hydrogens to /C LYS 192 CB because it is missing heavy- atom bond partners Not adding hydrogens to /C LYS 198 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C ASN 204 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C GLU 242 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for 3CO6.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 3CO6.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 3CO6.pdbqt (#1) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A DT -4, /B DC 13, /C SER 154 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A DG 12, /B DA 28, /C GLY 244 Chain-final residues that are not actual C termini: 127 hydrogen bonds 4 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3CO6-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3CO6--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 3CO6--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 57 contacts atom1 atom2 overlap distance 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3CO6.pdbqt #1/A DT 4 H4' 0.285 2.595 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 234 HA 0.279 2.481 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C GLN 227 OE1 0.215 3.025 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 O3' 0.090 3.290 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 2HH1 0.039 2.721 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 NH1 0.011 3.374 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 C5' 0.002 3.578 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 24 H3 0.000 2.880 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 O4' -0.016 3.396 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 H4' -0.026 2.906 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 1H5' -0.041 2.921 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C2 -0.066 3.226 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 234 CA -0.080 3.540 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H22 -0.090 2.850 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H3 -0.095 2.155 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C LYS 233 O -0.116 3.356 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3CO6.pdbqt #1/A DT 4 C4' -0.123 3.703 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H3 -0.125 2.885 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 OG -0.180 3.440 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H22 -0.187 2.947 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 H4' -0.190 2.800 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 23 H2 -0.212 2.632 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 2H5' -0.212 3.092 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 OG -0.222 3.482 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 N3 -0.223 2.908 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 23 C2 -0.223 3.343 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 C4' -0.229 3.809 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 C4' -0.230 3.810 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H2 -0.237 2.697 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 P -0.239 3.990 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 O4' -0.260 3.180 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 H4' -0.264 2.724 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 H4' -0.269 2.879 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C LYS 233 O -0.273 3.513 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 24 N3 -0.286 3.791 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 O4' -0.296 3.216 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H2 -0.297 2.717 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 C4' -0.299 3.759 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C GLN 227 CD -0.302 3.762 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 H4' -0.308 2.918 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 N3 -0.316 3.701 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H4' -0.322 3.202 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 N2 -0.323 3.708 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 H4' -0.326 3.086 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 NH1 -0.332 3.717 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C4 -0.337 3.457 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 O2 -0.341 3.281 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 2HH1 -0.352 3.112 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 O4' -0.360 3.620 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 N3 -0.360 3.005 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 C5' -0.366 3.946 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 C4' -0.374 3.684 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 N -0.392 3.777 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C1' -0.394 3.514 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 N -0.394 3.779 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 OP1 -0.397 3.777 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 C4' -0.400 3.980 57 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3CO6.pdbqt 2.1 3CO6--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 3CO6.pdbqt #1/B DA 24 N3 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H3 2.908 2.155 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -9.1 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "3CO6 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1D7G.pdbqt Chain information for 1D7G.pdbqt #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available Opened 1D7G.pdbqt containing 1 structures (2929 atoms, 3008 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1D7G.pdbqt #1 --- warnings | Not adding hydrogens to /A G 5 C2' because it is missing heavy-atom bond partners Not adding hydrogens to /A C 6 C2' because it is missing heavy-atom bond partners Not adding hydrogens to /A C 7 C2' because it is missing heavy-atom bond partners Not adding hydrogens to /A C 8 C2' because it is missing heavy-atom bond partners Not adding hydrogens to /A A 10 C2' because it is missing heavy-atom bond partners 19 messages similar to the above omitted notes | No usable SEQRES records for 1D7G.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1D7G.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 1D7G.pdbqt (#1) chain C; guessing termini instead No usable SEQRES records for 1D7G.pdbqt (#1) chain D; guessing termini instead Chain-initial residues that are actual N termini: /A G 5, /B G 5, /C GLU 1, /D SER 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A C 18, /B C 18, /C THR 59, /D LEU 59 Chain-final residues that are not actual C termini: 153 hydrogen bonds 4 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1D7G-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1D7G--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1D7G--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 39 contacts atom1 atom2 overlap distance 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HE 0.329 2.431 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 1H2' 0.256 2.624 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 HG1 0.119 2.641 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 2HH1 0.015 2.005 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 NE -0.009 3.394 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D LYS 5 CG -0.009 3.589 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HB2 -0.018 2.778 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 H7 -0.024 2.044 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 H7 -0.025 2.045 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D LYS 5 HG1 -0.045 2.925 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H7 -0.079 2.959 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 CZ -0.085 3.245 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 C2' -0.096 3.676 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D SER 1 O -0.112 3.472 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 2HH1 -0.121 2.731 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HB2 -0.137 2.897 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 N7 -0.144 3.649 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B C 18 H41 -0.162 3.042 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 NH1 -0.162 3.397 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 17 H7 -0.174 2.784 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 15 C8 -0.195 3.315 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 HG1 -0.207 2.817 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 NH1 -0.209 2.894 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H7 -0.210 2.820 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 C8 -0.227 3.387 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 C8 -0.227 3.807 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 CG -0.232 3.692 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 N7 -0.234 3.469 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 O2P -0.237 3.197 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 CB -0.252 3.712 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 N -0.277 3.662 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 O2P -0.310 3.570 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H8 -0.331 3.211 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 NH1 -0.333 2.978 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 C8 -0.337 3.647 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HE -0.343 2.953 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 N7 -0.347 2.992 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 N7 -0.366 3.011 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 O6 -0.397 3.297 39 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1D7G.pdbqt 2.1 1D7G--WRM-16.result.pdbqt 3 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1D7G.pdbqt #1/B G 16 N7 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 H7 2.992 2.045 1D7G.pdbqt #1/B G 17 N7 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 H7 3.011 2.044 1D7G.pdbqt #1/D ARG 4 NH1 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 2HH1 2.978 2.005 3 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1D7G WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1GXC.pdbqt Chain information for 1GXC.pdbqt #1 --- Chain | Description A D G J | No description available B E H K | No description available Opened 1GXC.pdbqt containing 1 structures (8116 atoms, 8224 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1GXC.pdbqt #1 --- warnings | Not adding hydrogens to /A ASP 111 CB because it is missing heavy- atom bond partners Not adding hydrogens to /D ASP 111 CB because it is missing heavy-atom bond partners Not adding hydrogens to /G ASP 111 CB because it is missing heavy-atom bond partners Not adding hydrogens to /H ARG 7 CB because it is missing heavy-atom bond partners Not adding hydrogens to /J ASP 111 CB because it is missing heavy-atom bond partners 1 messages similar to the above omitted notes | No usable SEQRES records for 1GXC.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1GXC.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 1GXC.pdbqt (#1) chain D; guessing termini instead No usable SEQRES records for 1GXC.pdbqt (#1) chain E; guessing termini instead No usable SEQRES records for 1GXC.pdbqt (#1) chain G; guessing termini instead 3 messages similar to the above omitted Chain-initial residues that are actual N termini: /A PRO 92, /B HIS 0, /D PRO 92, /E HIS 0, /G PRO 92, /H HIS 0, /J PRO 92, /K HIS 0 Chain-initial residues that are not actual N termini: /B TYR 4, /E TYR 4, /H TYR 4, /K TYR 4 Chain-final residues that are actual C termini: /A ASP 207, /B ARG 7, /D ASP 207, /E ARG 7, /G ASP 207, /H ARG 7, /J ASP 207, /K ARG 7 Chain-final residues that are not actual C termini: /B ASP 2, /E ASP 2, /H ASP 2, /K ASP 2 388 hydrogen bonds Adding 'H' to /B TYR 4 Adding 'H' to /E TYR 4 Adding 'H' to /H TYR 4 Adding 'H' to /K TYR 4 /B ASP 2 is not terminus, removing H atom from 'C' /E ASP 2 is not terminus, removing H atom from 'C' /H ASP 2 is not terminus, removing H atom from 'C' /K ASP 2 is not terminus, removing H atom from 'C' 0 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1GXC-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1GXC--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.0 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1GXC--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 30 contacts atom1 atom2 overlap distance 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 184 HB2 0.193 2.567 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HA 0.144 2.736 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 0.103 2.657 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 HN 0.074 2.806 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 HB2 0.014 2.866 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HA -0.111 2.721 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 CB -0.140 3.720 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CA -0.141 3.721 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 186 O -0.141 3.381 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 -0.151 2.761 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G ARG 132 HD1 -0.159 2.619 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 O -0.179 3.539 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 184 CB -0.181 3.641 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 N -0.199 3.584 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 HB2 -0.204 2.964 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G LEU 129 HA -0.211 2.631 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 O -0.218 3.458 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G ARG 132 CD -0.232 3.392 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 186 HB1 -0.235 2.995 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G LEU 129 O -0.252 3.152 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 HN -0.264 3.024 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.264 3.724 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 N -0.278 3.783 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 -0.301 3.061 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HB1 -0.310 3.070 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 N -0.338 3.843 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.354 3.664 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G ARG 132 HD1 -0.355 3.235 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/D ASN 186 HB2 -0.377 2.837 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.396 3.856 30 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1GXC.pdbqt 2.1 1GXC--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1GXC WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1KO6.pdbqt Chain information for 1KO6.pdbqt #1 --- Chain | Description A | No description available B D | No description available C | No description available Opened 1KO6.pdbqt containing 1 structures (4955 atoms, 5004 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1KO6.pdbqt #1 --- warnings | Not adding hydrogens to /A MET 712 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A LYS 814 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C THR 737 CB because it is missing heavy-atom bond partners Not adding hydrogens to /D ASP 870 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for 1KO6.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1KO6.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 1KO6.pdbqt (#1) chain C; guessing termini instead No usable SEQRES records for 1KO6.pdbqt (#1) chain D; guessing termini instead Chain-initial residues that are actual N termini: /A MET 712, /B LYS 865, /C HIS 713, /D LYS 865 Chain-initial residues that are not actual N termini: /C GLU 742 Chain-final residues that are actual C termini: /A PHE 863, /B ASP 870, /C PHE 863, /D ASP 870 Chain-final residues that are not actual C termini: /C ASN 738 223 hydrogen bonds Adding 'H' to /C GLU 742 /C ASN 738 is not terminus, removing H atom from 'C' 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1KO6-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1KO6--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.3 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1KO6--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 36 contacts atom1 atom2 overlap distance 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 0.149 2.461 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 0.075 2.535 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 0.038 2.722 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 0.022 2.738 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 -0.109 2.869 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A VAL 783 2HG1 -0.121 2.731 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 NH2 -0.144 3.649 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CD2 -0.149 3.459 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 CE1 -0.153 3.613 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HD1 -0.165 2.925 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 C -0.168 3.628 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C GLU 848 OE2 -0.172 3.412 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HD1 -0.179 2.939 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 CZ -0.190 3.770 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 CZ -0.200 3.780 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A ARG 778 CZ -0.201 3.361 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A LEU 786 3HD2 -0.234 2.694 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 ND1 -0.236 3.621 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CD2 -0.243 3.553 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HE1 -0.244 3.004 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 C -0.255 3.715 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 NE -0.258 3.763 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 N -0.265 3.650 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A ARG 778 CZ -0.299 3.419 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 ND1 -0.302 3.687 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 HB2 -0.308 3.068 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 HB2 -0.317 3.077 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C ARG 850 HD1 -0.328 3.088 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C ARG 850 CD -0.334 3.794 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 CE1 -0.338 3.798 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 CB -0.340 3.800 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CB -0.345 3.805 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 O -0.353 3.593 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A VAL 783 CG1 -0.358 3.668 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CB -0.362 3.822 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 -0.365 3.125 36 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1KO6.pdbqt 2.1 1KO6--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.3 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1KO6 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2I2Y.pdbqt Chain information for 2I2Y.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 2I2Y.pdbqt containing 1 structures (2441 atoms, 2472 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2I2Y.pdbqt #1 --- notes | No usable SEQRES records for 2I2Y.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 2I2Y.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1, /B C 151 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ARG 150, /B C 154 Chain-final residues that are not actual C termini: 171 hydrogen bonds 10 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2I2Y-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2I2Y--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2I2Y--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 42 contacts atom1 atom2 overlap distance 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 O 0.082 3.158 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 0.042 2.568 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD1 0.038 2.722 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 0.018 2.592 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 0.002 2.608 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 -0.056 2.936 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HA -0.087 2.847 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 HG2 -0.102 2.862 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD1 -0.104 2.864 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 N -0.108 3.613 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.117 2.877 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 O 2I2Y.pdbqt #1/A ASP 73 O -0.129 3.029 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HA -0.132 3.012 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.137 3.717 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CA -0.151 3.731 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HB3 -0.156 2.916 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 -0.160 2.920 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 OD1 -0.177 3.417 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HB3 -0.188 2.798 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.194 3.504 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 C -0.215 3.795 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 CZ -0.217 3.797 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 NH1 -0.264 3.769 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.268 3.578 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.274 3.034 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD1 -0.276 3.736 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.297 3.877 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A VAL 127 CG1 -0.301 3.761 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.306 3.616 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A VAL 127 CG1 -0.313 3.773 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.320 2.930 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 NH2 -0.323 3.828 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 HG2 -0.332 3.092 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 68 O -0.337 3.577 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 CB -0.338 3.648 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 CB -0.338 3.918 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 CG -0.343 3.803 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 O 2I2Y.pdbqt #1/A SER 69 OG -0.346 2.866 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CA -0.358 3.818 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A SER 69 OG -0.359 3.469 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.367 3.677 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 HB2 -0.389 3.269 42 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2I2Y.pdbqt 2.1 2I2Y--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2I2Y WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2CPE.pdbqt Chain information for 2CPE.pdbqt #1 --- Chain | Description A | No description available Opened 2CPE.pdbqt containing 1 structures (1663 atoms, 1680 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2CPE.pdbqt #1 --- notes | No usable SEQRES records for 2CPE.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 346 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A GLY 458 Chain-final residues that are not actual C termini: 43 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CPE-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CPE--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.4 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2CPE--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 45 contacts atom1 atom2 overlap distance 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 HB2 0.239 2.521 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A ILE 400 H 0.104 2.776 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB 0.090 2.670 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A VAL 372 O 0.010 2.930 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.008 2.768 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 ND1 -0.011 3.516 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 O -0.023 3.263 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CD1 -0.043 3.503 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 2HG2 -0.051 2.511 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 CE1 -0.060 3.640 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 CB -0.065 3.525 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.072 2.832 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.104 2.714 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 H -0.106 2.126 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 2HD2 -0.122 3.002 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.144 2.754 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 3HD1 -0.145 2.755 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A VAL 372 O -0.165 3.525 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.165 3.625 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A GLY 407 O -0.173 3.413 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.190 2.800 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 402 3HD1 -0.198 2.658 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A ILE 400 N -0.226 3.731 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.233 2.993 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.257 3.717 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.296 3.176 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.306 3.766 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 HA -0.312 3.192 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.326 3.086 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A THR 373 2HG2 -0.326 3.206 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 HA -0.326 2.746 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 H -0.328 2.938 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A THR 373 HA -0.343 3.223 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.348 3.808 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CG1 -0.351 3.811 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.367 2.977 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 HB2 -0.373 3.133 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 CG2 -0.376 3.536 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A ASP 370 O -0.382 3.282 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 1HD1 -0.384 3.144 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 N -0.385 3.030 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.390 3.850 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A GLY 407 O -0.392 3.632 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CD1 -0.398 3.708 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.400 3.710 45 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2CPE.pdbqt 2.1 2CPE--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 2CPE.pdbqt #1/A LEU 374 N 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 H 3.030 2.126 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2CPE WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XQZ.pdbqt Chain information for 1XQZ.pdbqt #1 --- Chain | Description A | No description available Opened 1XQZ.pdbqt containing 1 structures (4460 atoms, 4520 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1XQZ.pdbqt #1 --- notes | No usable SEQRES records for 1XQZ.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLU 32 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A SER 308 Chain-final residues that are not actual C termini: 219 hydrogen bonds 5 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XQZ-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XQZ--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1XQZ--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 84 contacts atom1 atom2 overlap distance 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.680 2.080 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.609 2.151 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 2HG1 0.394 2.366 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 0.391 3.069 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN 0.374 2.386 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HB1 0.366 2.514 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 0.197 3.263 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CE1 0.188 3.392 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 0.163 2.597 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 2HG1 0.161 2.599 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N 0.156 3.229 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 HZ3 0.141 2.619 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ARG 122 HG1 0.131 2.289 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 0.128 2.752 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG1 0.076 3.384 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 44 3HD1 0.076 2.684 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A GLU 121 O 0.067 3.293 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN 0.067 2.693 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.066 2.694 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A LEU 174 1HD1 0.058 2.402 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CB 0.050 3.530 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CZ 0.039 3.541 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD2 0.018 2.742 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN -0.011 2.771 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ALA 65 CB -0.021 3.601 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HA -0.021 2.781 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG1 -0.024 3.484 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 -0.026 3.486 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.033 2.913 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.053 2.513 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N -0.056 3.441 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CA -0.060 3.520 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 -0.062 2.822 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CD1 -0.070 3.650 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD2 -0.091 3.551 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.091 2.701 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG1 -0.109 3.569 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 NZ -0.112 3.497 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A PHE 49 CE1 -0.120 3.280 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CA -0.125 3.585 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.127 2.887 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 174 1HD1 -0.155 3.035 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 -0.155 2.765 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HA -0.161 2.921 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG1 -0.171 3.631 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CD1 -0.174 3.634 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.176 3.636 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ARG 122 CG -0.191 3.311 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CD1 -0.193 3.773 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ALA 65 HB3 -0.203 3.083 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 -0.203 2.813 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A LEU 174 CD1 -0.209 3.369 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 -0.219 2.829 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 HD1 -0.229 2.989 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 -0.241 2.851 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CB -0.253 3.713 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.285 2.895 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.295 3.605 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 2HG2 -0.296 2.906 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1XQZ.pdbqt #1/A VAL 126 O -0.301 3.661 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CB -0.302 3.612 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CG -0.304 3.884 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG2 -0.306 3.886 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A VAL 52 1HG1 -0.309 2.769 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N -0.313 3.698 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD1 -0.313 3.073 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ARG 122 HD2 -0.324 3.084 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 52 1HG1 -0.325 2.935 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 44 CD1 -0.326 3.786 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 185 2HG2 -0.327 2.787 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 174 1HD2 -0.328 3.208 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.336 3.096 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CD1 -0.337 3.647 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CE2 -0.340 3.920 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.342 3.652 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD1 -0.346 3.106 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 52 1HG2 -0.351 2.961 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CG -0.363 3.823 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 1HG2 -0.366 3.126 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 185 CG2 -0.373 3.533 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CB -0.387 3.967 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 HB2 -0.393 3.273 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CB -0.393 3.853 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG2 -0.396 3.856 84 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1XQZ.pdbqt 2.1 1XQZ--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -9.1 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1XQZ WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1Z00.pdbqt Chain information for 1Z00.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 1Z00.pdbqt containing 1 structures (2620 atoms, 2640 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1Z00.pdbqt #1 --- notes | No usable SEQRES records for 1Z00.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1Z00.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A MET 219, /B MET 822 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 302, /B LYS 905 Chain-final residues that are not actual C termini: 131 hydrogen bonds 0 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1Z00-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1Z00--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.8 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1Z00--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 52 contacts atom1 atom2 overlap distance 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB2 0.383 2.377 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 222 3HD2 0.372 2.388 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB 0.368 3.092 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 HA 0.193 2.687 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 O 0.163 3.197 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 0.104 2.656 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 HB3 0.064 2.696 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 CB 0.063 3.397 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 222 CD2 0.020 3.440 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB 0.011 3.449 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CD1 -0.010 3.470 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CA -0.022 3.602 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.036 3.496 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.039 2.649 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HZ3 -0.040 2.800 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HZ3 -0.042 2.802 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 -0.083 2.843 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 HB2 -0.087 2.507 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB2 -0.092 2.852 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HB2 -0.100 2.860 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 HB3 -0.122 2.882 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 3HD1 -0.124 2.884 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.127 3.367 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB3 -0.147 2.907 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CB -0.189 3.349 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 O -0.208 3.568 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB -0.211 3.671 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.218 2.828 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CD -0.225 3.685 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.228 3.688 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB1 -0.260 3.020 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 NZ -0.264 3.649 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CB -0.269 3.729 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/B GLN 885 OE1 -0.287 3.227 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CD1 -0.288 3.868 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HB3 -0.291 3.051 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1Z00.pdbqt #1/A LEU 222 CD2 -0.295 3.875 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.302 3.762 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A MET 219 O -0.310 3.400 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 -0.324 3.084 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.326 3.086 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CG -0.329 3.489 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 NZ -0.336 3.721 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 N -0.340 3.845 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CA -0.348 3.658 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 HB3 -0.357 2.817 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CB -0.359 3.819 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB -0.362 3.822 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 CB -0.369 3.829 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.371 3.461 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.380 3.470 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CB -0.386 3.506 52 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1Z00.pdbqt 2.1 1Z00--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.8 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1Z00 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2N1I.pdbqt Chain information for 2N1I.pdbqt #1 --- Chain | Description A | No description available Opened 2N1I.pdbqt containing 1 structures (2650 atoms, 2682 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2N1I.pdbqt #1 --- notes | No usable SEQRES records for 2N1I.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 51 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A GLU 226 Chain-final residues that are not actual C termini: 70 hydrogen bonds 0 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2N1I-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2N1I--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2N1I--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 54 contacts atom1 atom2 overlap distance 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 H 0.318 2.562 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 0.108 2.652 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 HB3 0.091 2.789 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 0.063 2.547 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 O 0.016 3.344 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 0.000 2.760 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 -0.025 2.635 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 N -0.031 3.536 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 HA -0.034 2.794 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 -0.037 2.797 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A ARG 102 NH2 -0.075 3.580 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.088 3.548 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 H -0.095 2.975 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 NH1 -0.100 3.605 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 O -0.123 3.483 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 2HH1 -0.129 3.009 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB2 -0.146 2.756 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 83 OD1 -0.153 3.513 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 CB -0.155 3.735 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.170 2.780 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 HE2 -0.171 3.051 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB3 -0.175 2.935 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 CG -0.213 3.673 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.216 3.526 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A ARG 102 CZ -0.232 3.812 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HA -0.236 3.116 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.246 3.006 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 105 H -0.256 3.016 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 NH1 -0.256 3.641 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 N -0.266 3.771 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 O -0.268 3.208 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 O -0.271 3.631 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CA -0.275 3.855 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HA -0.288 3.048 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A CYS 157 O -0.304 3.544 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.306 3.616 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB2 -0.307 3.187 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A MET 104 SD -0.309 3.511 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 H -0.310 2.370 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.311 3.891 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A MET 104 HA -0.317 3.197 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.327 3.787 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 CE -0.328 3.908 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 CG -0.330 3.790 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CA -0.338 3.798 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.339 3.099 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 NH1 -0.340 3.845 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.369 2.979 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.369 3.679 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A VAL 158 CG1 -0.385 3.545 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 C -0.387 3.547 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HA -0.391 3.001 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 83 OD2 -0.395 3.635 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ARG 109 O -0.398 3.298 54 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2N1I.pdbqt 2.1 2N1I--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 2N1I.pdbqt #1/A ASP 159 N 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 H 3.116 2.370 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2N1I WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1P4U.pdbqt Chain information for 1P4U.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 1P4U.pdbqt containing 1 structures (2389 atoms, 2419 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1P4U.pdbqt #1 --- notes | No usable SEQRES records for 1P4U.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1P4U.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 579, /B ASP -1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A LEU 723, /B ALA 6 Chain-final residues that are not actual C termini: 95 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1P4U-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1P4U--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.2 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1P4U--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 55 contacts atom1 atom2 overlap distance 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A THR 677 2HG2 0.351 2.409 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PRO 593 HA 0.208 2.212 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ALA 614 HA 0.167 2.253 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 O 0.103 3.257 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 HB 0.100 2.320 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 3HG2 0.090 2.790 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 0.056 2.704 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HA 0.043 2.567 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A THR 677 CG2 0.014 3.446 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.042 2.652 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 2HG1 -0.044 2.804 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 3HG2 -0.081 2.501 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 CG2 -0.090 3.670 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 N -0.098 3.603 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A SER 594 OG -0.119 3.499 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.120 2.730 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.124 3.004 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.157 2.917 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PRO 593 CA -0.173 3.293 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.186 2.796 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ALA 614 CA -0.187 3.307 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.198 2.808 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.204 3.439 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 CG2 -0.210 3.370 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 3HG2 -0.214 2.674 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 CB -0.242 3.362 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PHE 613 O -0.248 3.148 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A ALA 596 O -0.255 3.615 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD2 -0.257 3.717 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.261 3.021 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 HG -0.270 3.030 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.273 3.033 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.277 3.782 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A LYS 592 O -0.287 3.187 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CB -0.297 3.877 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CE1 -0.299 3.879 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD1 -0.303 3.763 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 3HG2 -0.306 2.916 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 -0.312 2.922 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A SER 594 HN -0.324 3.204 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1P4U.pdbqt #1/A LEU 588 1HD2 -0.333 3.213 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 CA -0.342 3.652 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 HN -0.343 3.223 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A SER 594 HN -0.343 2.403 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.350 3.735 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.352 2.962 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 CG2 -0.367 3.527 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HA -0.370 2.980 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CA -0.376 3.956 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 -0.379 3.139 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.389 3.624 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 C -0.391 3.971 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CG -0.391 3.851 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD2 -0.395 3.705 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HB2 -0.395 3.005 55 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1P4U.pdbqt 2.1 1P4U--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1P4U.pdbqt #1/A SER 594 N 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A SER 594 HN 3.335 2.403 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1P4U WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KCX.pdbqt Chain information for 2KCX.pdbqt #1 --- Chain | Description A | No description available Opened 2KCX.pdbqt containing 1 structures (1066 atoms, 1073 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2KCX.pdbqt #1 --- notes | No usable SEQRES records for 2KCX.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A SER 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A LYS 74 Chain-final residues that are not actual C termini: 56 hydrogen bonds 10 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KCX-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KCX--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.4 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2KCX--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 41 contacts atom1 atom2 overlap distance 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 0.106 2.504 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.085 2.675 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.014 2.596 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.013 2.747 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 HD3 0.006 2.874 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 HE2 -0.031 2.091 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.034 3.344 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A ALA 55 HB2 -0.081 2.961 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 -0.125 2.885 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 HA -0.126 2.886 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A ALA 55 CB -0.136 3.716 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 CB -0.155 3.615 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 NE2 -0.167 3.402 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CA -0.168 3.628 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 CD -0.169 3.749 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.185 3.645 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 -0.195 2.955 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 CG -0.207 3.787 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 CB -0.220 3.800 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 HA -0.222 2.982 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 -0.225 3.105 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 55 CB -0.229 3.689 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 HA -0.239 2.999 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 -0.246 3.126 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.247 3.557 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 HG3 -0.250 3.130 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.250 3.560 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 HB1 -0.258 3.018 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.260 3.720 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 NE2 -0.261 3.766 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A GLU 52 OE1 -0.267 3.507 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A THR 46 O -0.276 3.516 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.276 3.736 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.281 3.591 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CB -0.323 3.783 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CD2 -0.340 3.800 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 N -0.347 3.732 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CB -0.361 3.941 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 HB2 -0.382 3.142 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 NE2 -0.387 3.072 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 55 HB3 -0.388 3.148 41 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2KCX.pdbqt 2.1 2KCX--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 2KCX.pdbqt #1/A HIS 61 NE2 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 HE2 3.072 2.091 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2KCX WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1VR2.pdbqt Chain information for 1VR2.pdbqt #1 --- Chain | Description A | No description available Opened 1VR2.pdbqt containing 1 structures (4310 atoms, 4361 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1VR2.pdbqt #1 --- warnings | Not adding hydrogens to /A LYS 838 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A ARG 842 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A PHE 845 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A TYR 938 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 939 CB because it is missing heavy-atom bond partners 6 messages similar to the above omitted notes | No usable SEQRES records for 1VR2.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 820 Chain-initial residues that are not actual N termini: /A ASP 998, /A ASP 1064 Chain-final residues that are actual C termini: /A ALA 1168 Chain-final residues that are not actual C termini: /A LYS 939, /A PHE 1047 222 hydrogen bonds Adding 'H' to /A ASP 998 Adding 'H' to /A ASP 1064 /A LYS 939 is not terminus, removing H atom from 'C' /A PHE 1047 is not terminus, removing H atom from 'C' 2 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1VR2-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1VR2--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1VR2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 47 contacts atom1 atom2 overlap distance 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLY 846 HA1 0.221 2.659 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A LYS 868 HB1 0.195 2.685 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 HN 0.178 2.582 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 0.116 2.764 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 HN 0.070 2.690 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLN 847 HN 0.070 2.810 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 0.032 3.548 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 3HG2 0.032 2.428 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 HB3 -0.025 2.785 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A LYS 868 CB -0.077 3.657 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 CB -0.081 3.541 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLY 846 CA -0.093 3.673 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.095 2.855 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 CB -0.107 3.567 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLN 847 N -0.119 3.624 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HE1 -0.150 2.910 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 CD1 -0.161 3.621 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 HA -0.164 2.924 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 N -0.209 3.594 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A GLN 847 N -0.223 3.608 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HG2 -0.224 2.984 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 N -0.239 3.624 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A LEU 840 O -0.244 3.184 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 2HG1 -0.254 2.714 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 O -0.260 3.500 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.269 3.729 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.280 3.740 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 -0.284 2.894 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CE -0.291 3.751 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 2HG1 -0.295 2.905 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CG -0.303 3.763 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.308 3.068 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.310 3.070 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 CG2 -0.320 3.480 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.324 2.934 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 CE1 -0.326 3.786 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HE1 -0.332 3.092 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.343 3.803 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.351 3.811 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 -0.354 2.964 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 1HG2 -0.357 3.117 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 1HG2 -0.371 3.131 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 HB1 -0.375 3.135 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 2HG2 -0.383 3.143 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.387 2.997 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CD -0.393 3.853 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.399 3.159 47 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1VR2.pdbqt 2.1 1VR2--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.7 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1VR2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5AX3.pdbqt Chain information for 5AX3.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 5AX3.pdbqt containing 1 structures (5669 atoms, 5733 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 5AX3.pdbqt #1 --- notes | No usable SEQRES records for 5AX3.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 5AX3.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 1, /B LEU 349 Chain-initial residues that are not actual N termini: /A TYR 27, /A PHE 174, /A THR 181, /A GLY 194, /A LEU 248 Chain-final residues that are actual C termini: /A TYR 348, /B GLU 360 Chain-final residues that are not actual C termini: /A GLU 24, /A ALA 165, /A VAL 179, /A LEU 191, /A ASP 241 195 hydrogen bonds Adding 'H' to /A TYR 27 Adding 'H' to /A PHE 174 Adding 'H' to /A THR 181 Adding 'H' to /A GLY 194 Adding 'H' to /A LEU 248 /A GLU 24 is not terminus, removing H atom from 'C' /A ALA 165 is not terminus, removing H atom from 'C' /A VAL 179 is not terminus, removing H atom from 'C' /A LEU 191 is not terminus, removing H atom from 'C' /A ASP 241 is not terminus, removing H atom from 'C' -9 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5AX3-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5AX3--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.2 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 5AX3--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 52 contacts atom1 atom2 overlap distance 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 HG1 0.154 2.606 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 0.099 2.661 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 HD1 0.056 2.404 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 CG2 0.037 3.543 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 3HG2 0.002 2.878 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 HD1 -0.003 2.423 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HG2 -0.004 2.764 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A GLY 13 HA1 -0.068 2.488 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.084 2.844 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.109 2.719 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 13 HA1 -0.127 3.007 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 CD -0.127 3.247 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 15 HE -0.129 2.889 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 82 O -0.141 3.501 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HD2 -0.141 2.901 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 2HG2 -0.151 3.031 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 HG1 -0.154 2.914 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.158 2.768 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.158 2.768 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 CB -0.174 3.294 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 CG -0.181 3.641 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.184 2.794 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ASP 79 OD2 -0.194 3.434 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.210 2.970 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CB -0.218 3.528 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.235 2.845 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 13 HA1 -0.241 3.121 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.249 2.859 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 CG -0.250 3.710 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 82 O -0.279 3.519 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A GLY 13 CA -0.284 3.404 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 HN -0.284 3.044 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.287 3.047 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ILE 81 CG2 -0.288 3.448 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HB1 -0.297 2.717 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 CD -0.304 3.464 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.311 3.771 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 15 HE -0.322 2.932 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CB -0.324 3.634 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HN -0.330 2.350 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.346 3.806 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 HN -0.347 3.107 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.353 3.663 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 N -0.365 3.750 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HG2 -0.368 3.128 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 346 HB2 -0.371 2.831 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.379 2.989 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.386 2.996 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.388 3.698 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.391 3.851 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HD2 -0.396 3.006 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HA -0.399 3.159 52 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 5AX3.pdbqt 2.1 5AX3--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 5AX3.pdbqt #1/A ARG 15 N 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HN 3.304 2.350 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "5AX3 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KMU.pdbqt Chain information for 2KMU.pdbqt #1 --- Chain | Description A | No description available Opened 2KMU.pdbqt containing 1 structures (957 atoms, 963 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2KMU.pdbqt #1 --- notes | No usable SEQRES records for 2KMU.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A GLN 56 Chain-final residues that are not actual C termini: 40 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KMU-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KMU--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.8 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2KMU--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 55 contacts atom1 atom2 overlap distance 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB2 0.691 2.069 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB 0.326 3.134 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 1HH2 0.311 2.449 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NH2 0.233 3.152 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB2 0.185 2.575 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 HE2 0.153 2.727 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 1HH2 0.129 2.631 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HE3 0.035 2.575 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 0.021 2.589 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 OH -0.037 3.147 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A TRP 16 HA -0.042 2.502 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD3 -0.069 2.829 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 HH -0.072 2.682 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 CE2 -0.105 3.685 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD3 -0.109 2.869 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ARG 12 NH1 -0.111 2.796 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB -0.121 3.581 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NE -0.127 3.512 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 HB1 -0.128 2.738 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 NH1 -0.135 3.370 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 HE -0.136 2.896 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A THR 40 2HG2 -0.154 2.914 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.168 3.628 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NH2 -0.173 3.558 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.176 2.786 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.188 3.648 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HE3 -0.191 2.801 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 NH1 -0.202 3.587 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CE3 -0.202 3.512 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB -0.205 3.785 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 CZ -0.217 3.677 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 C -0.231 3.691 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 15 O -0.232 3.592 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 HB1 -0.241 3.121 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CZ3 -0.251 3.561 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB1 -0.264 3.144 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.289 3.749 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.305 3.065 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A THR 40 OG1 -0.306 3.566 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.310 3.770 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A TRP 16 CA -0.310 3.470 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD2 -0.313 3.073 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PHE 20 N -0.315 3.700 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CG -0.334 3.794 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KMU.pdbqt #1/A PRO 37 HG3 -0.336 3.216 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ALA 15 O -0.344 3.284 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ARG 12 2HH1 -0.344 2.404 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 C -0.359 3.819 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PHE 20 N -0.363 3.748 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.364 3.674 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CZ3 -0.366 3.676 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 CB -0.371 3.681 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 OH -0.376 3.756 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 1HH1 -0.384 3.144 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.391 3.001 55 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2KMU.pdbqt 2.1 2KMU--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.8 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2KMU WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2D68.pdbqt Chain information for 2D68.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 2D68.pdbqt containing 1 structures (2419 atoms, 2436 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2D68.pdbqt #1 --- warnings | Not adding hydrogens to /A LYS 69 CD because it is missing heavy- atom bond partners Not adding hydrogens to /B LYS 69 CG because it is missing heavy-atom bond partners notes | No usable SEQRES records for 2D68.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 2D68.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A VAL 58, /B ASN 59 Chain-initial residues that are not actual N termini: /A LEU 104 Chain-final residues that are actual C termini: /A TRP 135, /B TRP 135 Chain-final residues that are not actual C termini: /A THR 100 143 hydrogen bonds Adding 'H' to /A LEU 104 /A THR 100 is not terminus, removing H atom from 'C' -3 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D68-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D68--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.5 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2D68--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 45 contacts atom1 atom2 overlap distance 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD2 0.473 2.407 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD1 0.376 2.384 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HB1 0.240 2.640 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HA 0.211 2.669 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD 0.179 3.281 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B PHE 65 HD1 0.147 2.733 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD 0.095 3.485 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD1 0.057 2.703 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HD1 0.023 2.437 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HA 0.004 2.456 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CB -0.002 3.582 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HD1 -0.029 2.449 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CD1 -0.031 3.151 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 85 HZ -0.041 2.461 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.069 2.829 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CZ -0.108 3.568 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A GLY 124 O -0.108 3.468 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 O -0.119 3.479 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CA -0.139 3.719 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.157 2.917 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 O -0.164 3.404 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CA -0.169 3.329 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 85 CZ -0.174 3.294 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B PHE 65 CD1 -0.195 3.775 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 84 HE2 -0.224 2.684 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CE2 -0.261 3.721 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CD1 -0.269 3.429 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CZ -0.272 3.582 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD -0.275 3.735 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.282 2.892 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.283 3.043 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.310 3.070 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 CE1 -0.322 3.902 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A GLY 124 O -0.324 3.414 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD2 -0.344 3.104 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B SER 61 HB1 -0.355 2.815 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A GLY 124 O -0.356 3.296 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CB -0.368 3.828 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 CD1 -0.372 3.952 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CB -0.384 3.844 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.385 2.995 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CA -0.390 3.970 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HB1 -0.391 3.151 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CB -0.395 3.705 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CB -0.395 3.555 45 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2D68.pdbqt 2.1 2D68--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.5 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2D68 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1OW1.pdbqt Chain information for 1OW1.pdbqt #1 --- Chain | Description A | No description available Opened 1OW1.pdbqt containing 1 structures (2619 atoms, 2644 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1OW1.pdbqt #1 --- notes | No usable SEQRES records for 1OW1.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A PRO 3495 Chain-initial residues that are not actual N termini: /A PRO 3545 Chain-final residues that are actual C termini: /A VAL 3664 Chain-final residues that are not actual C termini: /A SER 3541 124 hydrogen bonds /A SER 3541 is not terminus, removing H atom from 'C' 0 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OW1-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OW1--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1OW1--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 54 contacts atom1 atom2 overlap distance 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 0.457 2.423 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A HIS 3656 HE1 0.285 2.595 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 0.241 2.639 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 HD2 0.208 2.552 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A HIS 3656 CE1 0.058 3.522 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 ND2 0.047 3.188 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB 0.042 3.538 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 1HD2 0.027 2.583 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 1HE2 0.008 2.602 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 1HE2 0.006 2.054 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 OE2 -0.046 3.286 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 CG2 -0.051 3.511 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HG2 -0.056 2.936 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 CD -0.060 3.520 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 -0.069 2.679 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 HG1 -0.070 2.490 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 2HD1 -0.102 2.982 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 ND2 -0.113 2.798 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 HG1 -0.117 2.537 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 CG2 -0.123 3.703 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OW1.pdbqt #1/A THR 3601 OG1 -0.128 3.508 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 1HD2 -0.143 2.203 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 OE1 -0.160 3.400 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.161 3.471 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 CD -0.162 3.622 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.171 2.781 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 -0.189 2.799 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 CG -0.210 3.330 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 -0.214 2.974 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A SER 3651 HA -0.252 3.132 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.262 2.872 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN -0.264 2.284 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.265 3.575 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.274 3.584 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 CG -0.287 3.407 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 OE1 -0.287 3.527 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 CB -0.295 3.415 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN -0.297 2.357 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CG -0.300 3.880 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.312 2.922 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 CD -0.313 3.773 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 CG -0.322 3.782 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 HB1 -0.332 3.092 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 N -0.332 2.977 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 NE2 -0.343 3.578 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 3HG2 -0.343 3.103 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 CA -0.344 3.464 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 HN -0.347 3.227 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 NE2 -0.358 3.043 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 CD -0.367 3.487 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 NE2 -0.367 3.752 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 1HD2 -0.377 2.987 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 -0.377 2.987 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 HN -0.390 3.000 54 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1OW1.pdbqt 2.1 1OW1--WRM-16.result.pdbqt 2 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1OW1.pdbqt #1/A GLN 3604 NE2 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 1HE2 3.043 2.054 1OW1.pdbqt #1/A ASN 3652 N 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN 3.284 2.357 2 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.1 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1OW1 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1RJB.pdbqt Chain information for 1RJB.pdbqt #1 --- Chain | Description A | No description available Opened 1RJB.pdbqt containing 1 structures (4781 atoms, 4839 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1RJB.pdbqt #1 --- notes | No usable SEQRES records for 1RJB.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A TYR 572 Chain-initial residues that are not actual N termini: /A ARG 655, /A LEU 783 Chain-final residues that are actual C termini: /A LEU 947 Chain-final residues that are not actual C termini: /A GLU 648, /A PHE 710 249 hydrogen bonds Adding 'H' to /A ARG 655 Adding 'H' to /A LEU 783 /A GLU 648 is not terminus, removing H atom from 'C' /A PHE 710 is not terminus, removing H atom from 'C' 3 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RJB-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RJB--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.6 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1RJB--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 51 contacts atom1 atom2 overlap distance 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 2HE2 0.378 2.502 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 2HG2 0.292 2.468 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 0.238 3.267 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A PHE 621 HE2 0.094 2.666 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A TYR 865 HH 0.037 2.723 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O 0.021 3.069 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 1HG1 -0.003 2.763 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CG -0.016 3.596 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ALA 848 HB3 -0.091 2.851 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.091 2.701 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.093 3.403 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 CG2 -0.117 3.577 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG1 -0.148 2.908 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 HD2 -0.162 2.582 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HN -0.174 2.784 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG1 -0.178 2.938 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 1HD2 -0.179 2.939 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A TYR 842 CE1 -0.179 3.339 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 1HD2 -0.188 2.948 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A PHE 621 CE2 -0.192 3.652 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 2HG2 -0.200 2.960 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ALA 848 HA -0.214 2.674 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 CD -0.219 3.339 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 HG2 -0.221 3.101 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 CG -0.223 3.683 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ASP 811 HB2 -0.228 2.648 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A GLN 575 HG2 -0.230 2.650 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 CG -0.243 3.703 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 CD2 -0.254 3.714 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 HG1 -0.259 3.139 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.259 3.839 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A TYR 865 OH -0.259 3.519 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.268 3.358 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.269 3.359 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ALA 848 CB -0.277 3.737 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.297 3.387 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.301 3.391 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG2 -0.313 3.073 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 -0.318 3.553 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.331 3.091 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.332 3.692 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 -0.352 3.857 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.357 3.667 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.366 3.726 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A TYR 842 HE1 -0.375 2.835 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 CZ -0.376 3.496 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ASP 811 OD1 -0.387 3.747 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.389 3.969 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.395 3.005 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 CG1 -0.395 3.855 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ASP 811 CB -0.397 3.517 51 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1RJB.pdbqt 2.1 1RJB--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.6 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1RJB WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1IFR.pdbqt Chain information for 1IFR.pdbqt #1 --- Chain | Description A | No description available Opened 1IFR.pdbqt containing 1 structures (1747 atoms, 1765 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1IFR.pdbqt #1 --- notes | No usable SEQRES records for 1IFR.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 432 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A VAL 544 Chain-final residues that are not actual C termini: 96 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1IFR-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1IFR--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1IFR--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 43 contacts atom1 atom2 overlap distance 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 HE1 0.513 2.367 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 CE1 0.243 3.337 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 HA 0.157 2.723 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HD2 0.117 2.643 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 HE1 0.011 2.869 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.034 3.494 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A TRP 514 HD1 -0.075 2.495 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ALA 516 HB1 -0.130 3.010 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ALA 516 CB -0.132 3.712 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.132 3.442 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.156 3.616 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 CA -0.164 3.744 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CD -0.170 3.630 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A VAL 513 O -0.173 3.533 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.177 2.937 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A LYS 515 HN -0.199 2.809 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 HG1 -0.203 2.963 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.212 2.972 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A VAL 513 O -0.218 3.458 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 NE1 -0.230 3.735 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.238 3.698 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LYS 515 HB2 -0.256 2.676 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LEU 512 HB1 -0.279 2.699 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.284 3.044 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 OH -0.290 3.670 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 HD1 -0.300 2.910 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A PRO 484 HG1 -0.303 2.723 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.312 3.772 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 NE2 -0.315 3.700 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A PRO 484 HA -0.316 2.776 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.321 3.781 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A ALA 516 HN -0.348 2.368 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.362 3.822 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HD2 -0.363 3.123 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.365 3.125 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 ND1 -0.367 3.752 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 CZ -0.368 3.948 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB2 -0.368 3.128 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CD -0.382 3.842 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 HE1 -0.384 2.994 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A HIS 506 HE1 -0.385 2.805 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A TRP 514 CD1 -0.396 3.516 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 O -0.398 3.488 43 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1IFR.pdbqt 2.1 1IFR--WRM-16.result.pdbqt 2 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1IFR.pdbqt #1/A LYS 515 N 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LYS 515 HN 3.558 2.542 1IFR.pdbqt #1/A ALA 516 N 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A ALA 516 HN 3.125 2.368 2 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1IFR WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1DNQ.pdbqt Chain information for 1DNQ.pdbqt #1 --- Chain | Description A | No description available Opened 1DNQ.pdbqt containing 1 structures (4770 atoms, 4812 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1DNQ.pdbqt #1 --- notes | No usable SEQRES records for 1DNQ.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A VAL 312 Chain-final residues that are not actual C termini: 155 hydrogen bonds 26 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1DNQ-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1DNQ--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1DNQ--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 44 contacts atom1 atom2 overlap distance 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 HN 0.298 2.582 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CD1 0.113 3.467 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 0.112 2.648 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 1HD2 0.109 1.911 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HG2 0.095 2.665 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 HB2 0.074 2.686 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 N 0.071 3.434 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.020 2.780 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 HB1 -0.041 2.921 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HA -0.076 2.836 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.088 2.698 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.089 2.849 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 HD1 -0.098 2.978 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HA -0.117 2.877 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A TYR 45 HE1 -0.135 2.555 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CE2 -0.142 3.452 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 CB -0.172 3.632 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 CG -0.199 3.659 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.208 2.968 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 1HD2 -0.212 2.822 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 CB -0.218 3.798 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 104 C -0.227 3.687 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 CA -0.229 3.689 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CA -0.237 3.697 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 N -0.252 3.637 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.253 3.713 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A ALA 68 HB3 -0.257 3.137 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.260 3.720 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A ALA 68 CB -0.260 3.840 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 ND2 -0.271 2.916 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 OD1 -0.279 3.519 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 CA -0.290 3.870 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HA -0.291 3.051 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CD2 -0.304 3.614 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.326 2.936 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CZ -0.334 3.644 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.353 3.663 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HB1 -0.356 2.966 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 OD1 -0.365 3.455 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CE2 -0.368 3.678 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.383 3.843 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.385 3.845 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 C -0.385 3.845 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 103 O -0.388 3.628 44 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1DNQ.pdbqt 2.1 1DNQ--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1DNQ.pdbqt #1/A ASN 70 ND2 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 1HD2 2.916 1.911 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1DNQ WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3U84.pdbqt Chain information for 3U84.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 3U84.pdbqt containing 1 structures (15424 atoms, 15596 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 3U84.pdbqt #1 --- warnings | Not adding hydrogens to /B ARG 206 CB because it is missing heavy- atom bond partners Not adding hydrogens to /B ARG 207 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for 3U84.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 3U84.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A SER 1, /B GLY 2 Chain-initial residues that are not actual N termini: /A SER 402, /A THR 534, /A GLY 548, /A SER 596, /B LEU 75, /B ARG 206, /B SER 402, /B ALA 523, /B GLY 548 Chain-final residues that are actual C termini: /A LYS 608, /B ALA 581 Chain-final residues that are not actual C termini: /A GLY 386, /A GLY 528, /A ALA 539, /A ALA 581, /B ASP 70, /B HIS 199, /B ALA 385, /B SER 459, /B GLY 528 784 hydrogen bonds Adding 'H' to /A SER 402 Adding 'H' to /A THR 534 Adding 'H' to /A GLY 548 Adding 'H' to /A SER 596 Adding 'H' to /B LEU 75 4 messages similar to the above omitted /A GLY 386 is not terminus, removing H atom from 'C' /A GLY 528 is not terminus, removing H atom from 'C' /A ALA 539 is not terminus, removing H atom from 'C' /A ALA 581 is not terminus, removing H atom from 'C' /B ASP 70 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted -13 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3U84-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3U84--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.5 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 3U84--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 37 contacts atom1 atom2 overlap distance 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 HB2 0.433 2.027 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TRP 341 HZ2 0.260 2.620 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B VAL 371 1HG1 0.250 2.630 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLY 326 HA1 0.185 2.695 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B CYS 329 HG 0.091 2.789 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 CB 0.060 3.100 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLU 363 OE2 -0.030 3.390 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CD2 -0.086 3.546 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B VAL 371 CG1 -0.103 3.683 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TRP 341 HE1 -0.116 2.136 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TRP 341 CZ2 -0.126 3.706 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 HB1 -0.165 2.585 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLY 326 CA -0.175 3.755 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 HB2 -0.189 3.069 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 O -0.208 3.148 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CE1 -0.214 3.674 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B VAL 371 1HG2 -0.215 2.675 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CE2 -0.234 3.694 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B CYS 329 SG -0.241 3.903 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 CB -0.245 3.365 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 HA -0.261 3.141 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 C -0.269 3.429 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CE2 -0.282 3.742 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.292 3.752 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.312 3.772 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TYR 323 CD2 -0.317 3.437 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 C -0.325 3.445 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.327 3.587 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.330 3.440 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 C -0.334 3.914 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CG -0.349 3.809 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.353 3.613 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.360 3.670 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TYR 323 N -0.378 3.023 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 HB2 -0.382 2.992 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLU 363 OE2 -0.387 3.477 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 O -0.399 3.759 37 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3U84.pdbqt 2.1 3U84--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 3U84.pdbqt #1/B TRP 341 NE1 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TRP 341 HE1 3.103 2.136 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "3U84 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2YSM.pdbqt Chain information for 2YSM.pdbqt #1 --- Chain | Description A | No description available Opened 2YSM.pdbqt containing 1 structures (1584 atoms, 1601 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2YSM.pdbqt #1 --- notes | No usable SEQRES records for 2YSM.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A GLY 111 Chain-final residues that are not actual C termini: 29 hydrogen bonds 15 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2YSM-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2YSM--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.5 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2YSM--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 58 contacts atom1 atom2 overlap distance 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 HG2 0.549 2.331 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 HB2 0.263 2.617 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 CG 0.262 3.318 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 2HG1 0.200 2.560 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 H 0.194 2.566 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 CA 0.171 3.409 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 HA 0.167 2.713 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 2HG1 0.075 2.685 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 3HD2 0.068 2.692 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 52 HB3 0.066 2.814 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 CB 0.017 3.563 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 55 HZ1 0.014 2.866 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 C -0.022 3.602 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG1 -0.039 2.919 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG2 -0.053 3.633 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.053 2.933 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 N -0.094 3.599 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.109 2.719 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A MET 69 O -0.119 3.479 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.129 2.739 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 3HD2 -0.130 2.890 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.136 3.716 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 CB -0.142 3.722 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.142 2.752 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A GLY 95 N -0.146 3.651 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 CG1 -0.151 3.611 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 O -0.156 3.516 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 N -0.158 3.543 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 92 O -0.216 3.456 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.219 2.829 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.219 3.529 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A THR 93 C -0.221 3.801 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 CD2 -0.255 3.715 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 CD2 -0.258 3.718 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 76 OD1 -0.259 3.499 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 C -0.264 3.844 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.266 3.146 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 CG1 -0.271 3.731 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.280 2.890 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 52 CB -0.282 3.862 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.286 2.896 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 HA -0.289 3.049 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 73 OD1 -0.292 3.532 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 N -0.297 3.802 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.297 3.877 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.299 3.609 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 HB2 -0.302 3.182 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.309 3.069 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A TRP 96 CB -0.331 3.791 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 H -0.335 3.215 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.338 3.648 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 45 HZ3 -0.358 3.118 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 92 HG2 -0.359 2.969 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A THR 93 O -0.359 3.599 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 N -0.383 3.888 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 55 NZ -0.384 3.889 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.385 3.695 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 76 OD1 -0.395 3.635 58 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2YSM.pdbqt 2.1 2YSM--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2YSM WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2LNK.pdbqt Chain information for 2LNK.pdbqt #1 --- Chain | Description A B | No description available C | No description available Opened 2LNK.pdbqt containing 1 structures (3899 atoms, 3931 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2LNK.pdbqt #1 --- notes | No usable SEQRES records for 2LNK.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 2LNK.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 2LNK.pdbqt (#1) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C GLN 1897 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A LYS 101, /B LYS 101, /C ALA 1935 Chain-final residues that are not actual C termini: 191 hydrogen bonds 0 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LNK-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LNK--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.0 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2LNK--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 34 contacts atom1 atom2 overlap distance 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 0.362 2.518 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 0.342 3.238 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 1HD2 0.261 2.349 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/C THR 1906 2HG2 0.132 2.628 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 0.076 2.534 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A GLU 88 HB2 0.041 2.379 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 0.005 3.230 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.072 2.952 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.095 3.637 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A MET 84 O -0.109 3.049 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 ND2 -0.119 2.804 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 1HD2 -0.126 2.146 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/C THR 1906 CG2 -0.131 3.591 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CD1 -0.159 3.619 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 1HD2 -0.162 2.222 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.219 2.829 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CD1 -0.222 3.682 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CZ -0.228 3.688 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A GLU 88 CB -0.228 3.348 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 -0.254 3.564 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CE2 -0.261 3.841 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 HB3 -0.283 3.043 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.288 3.830 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 -0.291 3.796 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.298 3.608 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 -0.300 3.880 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.300 3.760 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.318 3.778 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.356 2.966 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/B PHE 27 CD2 -0.368 3.488 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CG -0.376 3.836 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE2 -0.386 3.846 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.386 3.928 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 -0.390 3.895 34 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2LNK.pdbqt 2.1 2LNK--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2LNK WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XUM.pdbqt Chain information for 1XUM.pdbqt #1 --- Chain | Description A | No description available Opened 1XUM.pdbqt containing 1 structures (2876 atoms, 2908 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1XUM.pdbqt #1 --- notes | No usable SEQRES records for 1XUM.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A THR 54 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A THR 236 Chain-final residues that are not actual C termini: 96 hydrogen bonds 59 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XUM-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XUM--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.8 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1XUM--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 50 contacts atom1 atom2 overlap distance 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 HD2 0.493 2.387 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 HG1 0.216 2.664 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 CD 0.190 3.390 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CE2 0.101 3.359 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 134 HG 0.100 2.660 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 HZ2 0.069 2.691 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 CD 0.018 3.102 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 CE 0.016 3.104 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.001 2.761 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 HD2 -0.002 2.422 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASP 160 OD2 -0.014 2.914 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 CB -0.062 3.372 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 HG1 -0.100 2.980 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 OG1 -0.102 3.482 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 110 2HD2 -0.109 2.869 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A GLU 157 OE1 -0.125 3.485 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.126 2.886 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 HD2 -0.128 2.888 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 NZ -0.138 3.523 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 HE2 -0.140 2.900 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CD2 -0.142 3.602 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 HB2 -0.156 2.766 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A GLU 157 CD -0.190 3.770 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 HB2 -0.198 2.618 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 CD2 -0.208 3.368 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 HE1 -0.225 2.645 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 HD2 -0.234 2.994 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 CD -0.246 3.706 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.257 3.762 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 134 OG -0.264 3.524 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CD2 -0.267 3.727 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 110 ND2 -0.276 3.661 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 1HG2 -0.283 3.163 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.289 2.899 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASP 160 CG -0.294 3.414 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 186 ND2 -0.305 3.540 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.309 3.694 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 CE2 -0.315 3.475 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A THR 159 OG1 -0.321 2.841 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.331 3.716 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.334 3.719 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 CG -0.343 3.653 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 CG2 -0.352 3.932 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.358 3.743 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A THR 159 HG1 -0.360 2.380 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CE2 -0.371 3.831 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 234 HG -0.378 3.258 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 CE -0.381 3.841 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 OG1 -0.387 3.767 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.390 3.150 50 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1XUM.pdbqt 2.1 1XUM--WRM-16.result.pdbqt 2 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1XUM.pdbqt #1/A ASN 186 ND2 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASN 186 1HD2 3.170 2.565 1XUM.pdbqt #1/A ASN 208 ND2 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASN 208 2HD2 3.318 2.547 2 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.8 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1XUM WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/6LTH.pdbqt Chain information for 6LTH.pdbqt #1 --- Chain | Description I | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available Opened 6LTH.pdbqt containing 1 structures (30136 atoms, 30416 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 6LTH.pdbqt #1 --- warnings | Not adding hydrogens to /M LYS 199 CD because it is missing heavy- atom bond partners Not adding hydrogens to /M LYS 211 CG because it is missing heavy-atom bond partners notes | No usable SEQRES records for 6LTH.pdbqt (#1) chain I; guessing termini instead No usable SEQRES records for 6LTH.pdbqt (#1) chain L; guessing termini instead No usable SEQRES records for 6LTH.pdbqt (#1) chain M; guessing termini instead No usable SEQRES records for 6LTH.pdbqt (#1) chain N; guessing termini instead No usable SEQRES records for 6LTH.pdbqt (#1) chain O; guessing termini instead 3 messages similar to the above omitted Chain-initial residues that are actual N termini: /I SER 350, /L ILE 1639, /M SER 7, /N HIS 423, /O HIS 423, /P LYS 125, /Q SER 172, /R GLY 13 Chain-initial residues that are not actual N termini: /I LEU 396, /L GLU 1802, /L ILE 1954, /L GLU 2047, /L PRO 2225, /M ASP 78, /M ASP 172, /M GLN 257, /M PRO 332, /N THR 602, /N ASN 671, /N LEU 858, /O THR 598, /O LEU 656, /O ALA 867, /P GLN 291, /P THR 399 Chain-final residues that are actual C termini: /I LEU 476, /L SER 2285, /M THR 357, /N GLN 952, /O GLN 952, /P GLU 505, /Q LEU 276, /R LYS 82 Chain-final residues that are not actual C termini: /I LEU 388, /L ASP 1746, /L LYS 1862, /L LYS 2025, /L GLN 2210, /M SER 67, /M ASP 101, /M PRO 249, /M TYR 326, /N ASP 515, /N ARG 641, /N MET 703, /O GLN 545, /O ASP 651, /O ARG 717, /P LYS 177, /P GLU 369 1386 hydrogen bonds Adding 'H' to /I LEU 396 Adding 'H' to /L GLU 1802 Adding 'H' to /L ILE 1954 Adding 'H' to /L GLU 2047 Adding 'H' to /M ASP 78 10 messages similar to the above omitted /I LEU 388 is not terminus, removing H atom from 'C' /L ASP 1746 is not terminus, removing H atom from 'C' /L LYS 1862 is not terminus, removing H atom from 'C' /L LYS 2025 is not terminus, removing H atom from 'C' /L GLN 2210 is not terminus, removing H atom from 'C' 12 messages similar to the above omitted -24 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LTH-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LTH--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.3 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 6LTH--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 48 contacts atom1 atom2 overlap distance 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HG1 0.557 2.203 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CG 0.147 3.313 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 HG2 0.113 2.647 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L PHE 1999 HE1 0.078 2.342 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HG1 0.071 2.689 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 OH 0.045 3.215 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 HA 0.021 2.399 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HA 0.009 2.871 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 CE1 0.003 3.577 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CA 0.002 3.578 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HG2 -0.053 2.813 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.064 2.824 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 CZ -0.085 3.665 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L PRO 2075 HB1 -0.087 2.967 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 CG -0.091 3.551 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 OH -0.096 3.476 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.114 2.874 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L ASP 2072 HB1 -0.134 3.014 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.135 2.895 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CB -0.137 3.717 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 HG2 -0.165 2.775 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HG2 -0.175 2.785 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 CD -0.176 3.336 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.189 2.949 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HB2 -0.190 2.950 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L PRO 2075 CB -0.197 3.777 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HB2 -0.207 3.087 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2128 OE1 -0.214 3.304 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.215 2.825 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 CG -0.225 3.685 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 CA -0.232 3.352 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PHE 1999 HE1 -0.235 2.845 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 CD -0.238 3.358 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 CG -0.240 3.700 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 N -0.245 3.750 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L ASP 2072 CB -0.251 3.831 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L PHE 1999 CE1 -0.258 3.378 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CG -0.263 3.723 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 CZ -0.264 3.724 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 HH -0.283 3.043 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2128 2HE2 -0.292 2.902 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PHE 1999 HE1 -0.313 3.193 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 CG -0.322 3.782 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2070 NE2 -0.333 3.568 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.349 2.959 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLU 465 HG2 -0.380 3.140 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 OE1 -0.393 3.333 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 CG -0.397 3.857 48 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 6LTH.pdbqt 2.1 6LTH--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 6LTH.pdbqt #1/L GLN 2128 NE2 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 2HE2 3.227 2.606 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.3 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "6LTH WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3H9R.pdbqt Chain information for 3H9R.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 3H9R.pdbqt containing 1 structures (6620 atoms, 6691 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 3H9R.pdbqt #1 --- warnings | Not adding hydrogens to /A ARG 218 CD because it is missing heavy- atom bond partners Not adding hydrogens to /A SER 276 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 499 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B ARG 14 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for 3H9R.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 3H9R.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A THR 172, /B GLY 2 Chain-initial residues that are not actual N termini: /A SER 276, /A ARG 375 Chain-final residues that are actual C termini: /A ASP 499, /B GLU 108 Chain-final residues that are not actual C termini: /A SER 272, /A HIS 361 360 hydrogen bonds Adding 'H' to /A SER 276 Adding 'H' to /A ARG 375 /A SER 272 is not terminus, removing H atom from 'C' /A HIS 361 is not terminus, removing H atom from 'C' 7 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3H9R-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3H9R--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -10.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 3H9R--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 56 contacts atom1 atom2 overlap distance 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A GLY 215 HA2 0.237 2.643 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A LYS 340 HE1 0.199 2.681 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A SER 290 HG 0.131 2.629 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 0.091 2.669 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 OH 0.084 3.296 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 0.026 2.734 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.001 2.611 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.040 3.500 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HE1 -0.051 2.811 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HE1 -0.053 2.663 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A GLY 215 CA -0.076 3.656 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 2HD1 -0.077 2.687 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.104 3.344 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HH -0.112 2.992 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 214 1HG2 -0.136 2.896 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.146 3.506 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HH -0.154 2.914 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 -0.157 2.767 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.158 2.768 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A ASP 293 OD2 -0.168 3.528 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CZ -0.169 3.749 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 214 CG2 -0.171 3.631 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 CD1 -0.171 3.631 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A SER 290 OG -0.174 3.434 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CE -0.180 3.640 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.205 2.815 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A LYS 340 CE -0.206 3.786 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HE2 -0.256 3.016 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CE2 -0.259 3.839 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CG -0.261 3.721 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A LEU 343 2HD1 -0.276 2.736 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 CD2 -0.279 3.589 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A ALA 353 HB1 -0.284 2.704 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 -0.287 3.047 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 -0.287 2.897 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB1 -0.289 3.049 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB2 -0.297 3.177 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB1 -0.298 3.058 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 CD2 -0.307 3.617 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A TYR 292 CD2 -0.308 3.888 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 3HG2 -0.317 2.927 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB2 -0.319 3.079 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 CE1 -0.325 3.785 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A TYR 292 HD2 -0.326 3.206 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.326 3.786 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 -0.350 3.110 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 CG1 -0.350 3.810 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CE2 -0.367 3.677 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CE -0.368 3.678 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HE2 -0.371 2.981 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.374 3.464 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.376 3.956 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 263 1HD2 -0.382 3.262 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A LEU 263 CD2 -0.384 3.544 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 HD1 -0.388 3.148 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 CG1 -0.390 3.970 56 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3H9R.pdbqt 2.1 3H9R--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -10.1 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "3H9R WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1A5E.pdbqt Chain information for 1A5E.pdbqt #1 --- Chain | Description A | No description available Opened 1A5E.pdbqt containing 1 structures (2306 atoms, 2328 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1A5E.pdbqt #1 --- notes | No usable SEQRES records for 1A5E.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASP 156 Chain-final residues that are not actual C termini: 64 hydrogen bonds 0 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1A5E-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1A5E--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.6 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1A5E--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 45 contacts atom1 atom2 overlap distance 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 0.185 2.695 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 1HH1 0.171 1.889 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 HA3 0.148 2.732 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HD3 0.134 2.626 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A LEU 117 2HD1 0.063 2.817 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 CA 0.033 3.547 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 NH1 0.030 3.475 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD2 -0.013 3.593 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A LEU 117 CD1 -0.018 3.598 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.022 2.782 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CG -0.036 3.616 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A PRO 151 HD3 -0.038 2.918 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.064 2.824 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.074 3.384 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.085 2.845 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 NH1 -0.090 2.775 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A LEU 117 3HD1 -0.118 2.538 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 87 NH2 -0.119 3.624 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.131 2.891 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A PRO 151 CD -0.159 3.739 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.161 2.771 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.174 3.634 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ASP 108 OD2 -0.193 3.133 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A GLY 111 N -0.213 3.598 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.218 3.678 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.221 3.681 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 N -0.227 3.732 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 CD -0.234 3.694 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CZ3 -0.255 3.565 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD1 -0.273 3.853 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A LEU 117 CD1 -0.275 3.395 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CE2 -0.277 3.857 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CZ3 -0.277 3.587 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.289 3.599 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HD3 -0.299 3.059 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.303 2.913 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A GLY 111 C -0.323 3.783 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 -0.339 2.949 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A TRP 110 C -0.352 3.932 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HB2 -0.359 3.119 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 46 NH2 -0.361 3.746 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 87 2HH2 -0.361 3.241 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD1 -0.370 3.830 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.386 3.846 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 -0.399 3.009 45 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1A5E.pdbqt 2.1 1A5E--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1A5E.pdbqt #1/A ARG 112 NH1 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 1HH1 2.775 1.889 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.6 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1A5E WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1ES7.pdbqt Chain information for 1ES7.pdbqt #1 --- Chain | Description A C | No description available B | No description available D | No description available Opened 1ES7.pdbqt containing 1 structures (5745 atoms, 5815 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1ES7.pdbqt #1 --- notes | No usable SEQRES records for 1ES7.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1ES7.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 1ES7.pdbqt (#1) chain C; guessing termini instead No usable SEQRES records for 1ES7.pdbqt (#1) chain D; guessing termini instead Chain-initial residues that are actual N termini: /A LYS 11, /B THR 232, /C LYS 511, /D THR 732 Chain-initial residues that are not actual N termini: /B GLU 270, /D GLU 770 Chain-final residues that are actual C termini: /A ARG 114, /B PRO 317, /C ARG 614, /D ILE 820 Chain-final residues that are not actual C termini: /B ASP 266, /D ASP 766 270 hydrogen bonds Adding 'H' to /B GLU 270 Adding 'H' to /D GLU 770 /B ASP 266 is not terminus, removing H atom from 'C' /D ASP 766 is not terminus, removing H atom from 'C' 28 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1ES7-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1ES7--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.5 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1ES7--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 46 contacts atom1 atom2 overlap distance 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HN 0.266 2.614 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 HN 0.165 1.855 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B PRO 245 HB2 0.115 2.645 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 ND1 0.101 3.404 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HD1 0.099 2.781 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 HN 0.038 2.022 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HB2 -0.021 2.781 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.077 2.687 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 N -0.107 3.612 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 1HD2 -0.114 2.134 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B PRO 245 CB -0.134 3.594 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 HN -0.134 2.744 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ASN 56 1HD2 -0.156 2.766 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 N -0.177 2.822 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HN -0.181 2.791 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 CB -0.198 3.658 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HN -0.206 2.966 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A GLY 110 HA1 -0.216 2.636 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD1 -0.230 3.470 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 OD2 -0.233 3.473 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.234 2.994 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 CB -0.239 3.699 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HB2 -0.244 3.004 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.248 3.128 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HB2 -0.253 3.013 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 O -0.274 3.364 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A GLY 110 CA -0.280 3.400 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 O -0.305 3.205 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 CB -0.311 3.771 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD1 -0.316 3.556 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A LYS 15 CA -0.326 3.446 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 O -0.327 3.567 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 2HD2 -0.328 2.388 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A LYS 15 HA -0.330 2.750 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD2 -0.331 3.571 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 CB -0.338 3.648 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 N -0.338 3.573 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 N -0.339 3.024 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 O -0.361 3.301 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ASN 56 ND2 -0.363 3.598 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 N -0.363 3.748 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 ND2 -0.369 3.014 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 CG -0.374 3.834 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.375 2.985 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 ND2 -0.381 3.066 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 HN -0.394 3.274 46 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1ES7.pdbqt 2.1 1ES7--WRM-16.result.pdbqt 4 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1ES7.pdbqt #1/A ARG 16 N 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 HN 2.822 1.855 1ES7.pdbqt #1/A ASN 56 ND2 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 1HD2 3.014 2.134 1ES7.pdbqt #1/A ASN 56 ND2 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 2HD2 3.066 2.388 1ES7.pdbqt #1/A CYS 111 N 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 HN 3.024 2.022 4 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1ES7 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3TGX.pdbqt Chain information for 3TGX.pdbqt #1 --- Chain | Description A M O | No description available B | No description available C G I K | No description available D | No description available E | No description available F | No description available H | No description available J | No description available L | No description available N | No description available P | No description available Opened 3TGX.pdbqt containing 1 structures (41174 atoms, 41719 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 3TGX.pdbqt #1 --- warning | Not adding hydrogens to /J ARG 126 CB because it is missing heavy- atom bond partners notes | No usable SEQRES records for 3TGX.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 3TGX.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 3TGX.pdbqt (#1) chain C; guessing termini instead No usable SEQRES records for 3TGX.pdbqt (#1) chain D; guessing termini instead No usable SEQRES records for 3TGX.pdbqt (#1) chain E; guessing termini instead 11 messages similar to the above omitted Chain-initial residues that are actual N termini: /A CYS 1, /B GLY 2, /C CYS 1, /D GLY 2, /E CYS 1, /F GLY 2, /G CYS 1, /H ASP 4, /I CYS 1, /J GLY 2, /K CYS 1, /L ASP 4, /M CYS 1, /N ASP 4, /O CYS 1, /P ASP 4 Chain-initial residues that are not actual N termini: /B HIS 89, /D LEU 91, /F THR 92, /H GLN 87, /J LEU 91, /L LEU 91, /N THR 92, /P THR 92 Chain-final residues that are actual C termini: /A SER 208, /B LEU 123, /C GLU 209, /D LEU 123, /E GLN 207, /F LEU 123, /G GLU 209, /H LEU 123, /I GLU 209, /J ARG 126, /K GLU 209, /L HIS 122, /M SER 208, /N HIS 120, /O SER 208, /P LEU 123 Chain-final residues that are not actual C termini: /B THR 81, /D ARG 85, /F ASN 82, /H ASN 82, /J THR 81, /L THR 81, /N THR 81, /P THR 81 1792 hydrogen bonds Adding 'H' to /B HIS 89 Adding 'H' to /D LEU 91 Adding 'H' to /F THR 92 Adding 'H' to /H GLN 87 Adding 'H' to /J LEU 91 3 messages similar to the above omitted /B THR 81 is not terminus, removing H atom from 'C' /D ARG 85 is not terminus, removing H atom from 'C' /F ASN 82 is not terminus, removing H atom from 'C' /H ASN 82 is not terminus, removing H atom from 'C' /J THR 81 is not terminus, removing H atom from 'C' 3 messages similar to the above omitted 80 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3TGX-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3TGX--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.5 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 3TGX--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 84 contacts atom1 atom2 overlap distance 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 0.702 2.058 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 2HD2 0.553 2.327 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 HB2 0.512 2.368 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 0.484 2.901 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASP 81 OD1 0.349 3.011 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 HH 0.297 2.463 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/E ALA 127 HB1 0.227 2.533 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 1HE2 0.207 2.403 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 0.181 2.579 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CB 0.180 3.400 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 OH 0.166 3.094 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 ND2 0.163 3.342 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CB 0.149 3.431 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 CD1 0.133 3.447 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 NE 0.132 3.373 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB1 0.131 2.749 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 HD1 0.115 2.765 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CB 0.110 3.470 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 0.094 2.786 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 CG1 0.089 3.491 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HN 0.077 2.683 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/E ALA 127 CB 0.016 3.444 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 NE1 0.005 3.500 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 2HG1 0.001 2.879 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.001 2.611 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 CB -0.006 3.586 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASP 81 OD1 -0.008 3.248 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 1HG1 -0.043 2.923 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HN -0.056 2.816 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 HE1 -0.056 2.936 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 ND2 -0.057 3.292 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 1HE2 -0.067 2.127 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CG -0.098 3.678 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 NE2 -0.104 3.339 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.107 3.612 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 HD2 -0.112 2.872 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB1 -0.119 2.879 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB1 -0.134 3.014 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 HB1 -0.143 3.023 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.158 2.768 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CG -0.159 3.619 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 -0.159 3.039 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/F ASN 62 HB2 -0.163 2.623 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 -0.178 2.938 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 -0.185 3.690 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CG -0.188 3.648 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 N -0.192 3.577 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.208 2.818 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.228 3.108 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB2 -0.235 3.115 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.240 3.000 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CE1 -0.248 3.708 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 HH -0.249 3.009 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CG -0.260 3.840 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CB -0.262 3.842 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CD -0.265 3.845 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CZ -0.271 3.851 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 N -0.274 3.779 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB1 -0.281 3.161 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 HE -0.296 3.176 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB2 -0.296 3.176 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.298 3.533 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/A ASP 81 OD1 -0.308 3.248 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 HB2 -0.313 3.193 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.319 2.929 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 OH -0.336 3.596 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 CD -0.339 3.799 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.343 2.953 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 CB -0.346 3.806 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 -0.347 3.107 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CD2 -0.354 3.814 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 HB2 -0.356 2.816 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 HB2 -0.357 3.117 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 -0.361 3.746 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.361 3.121 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 CG -0.362 3.522 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.368 3.603 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 -0.370 3.250 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CB -0.370 3.680 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 1HE2 -0.388 3.268 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 NE2 -0.389 3.774 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HB2 -0.390 3.150 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 ND1 -0.394 3.779 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/A ASN 22 ND2 -0.395 3.080 84 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3TGX.pdbqt 2.1 3TGX--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 3TGX.pdbqt #1/M GLN 82 NE2 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 1HE2 3.121 2.127 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.5 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "3TGX WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/4JUP.pdbqt Chain information for 4JUP.pdbqt #1 --- Chain | Description A B | No description available Opened 4JUP.pdbqt containing 1 structures (2664 atoms, 2690 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 4JUP.pdbqt #1 --- notes | No usable SEQRES records for 4JUP.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 4JUP.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 22, /B LEU 22 Chain-initial residues that are not actual N termini: /A ASN 71, /B ASN 71 Chain-final residues that are actual C termini: /A GLY 108, /B GLY 108 Chain-final residues that are not actual C termini: /A ALA 63, /B ALA 63 116 hydrogen bonds Adding 'H' to /A ASN 71 Adding 'H' to /B ASN 71 /A ALA 63 is not terminus, removing H atom from 'C' /B ALA 63 is not terminus, removing H atom from 'C' -2 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/4JUP-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/4JUP--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 4JUP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 77 contacts atom1 atom2 overlap distance 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 HA 0.493 1.967 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 HA 0.445 2.315 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 HB1 0.307 2.573 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG 0.303 2.457 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 O 0.286 3.074 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 HB1 0.217 2.663 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 HD2 0.197 2.683 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CA 0.183 2.977 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG2 0.161 2.599 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B HIS 31 CE1 0.142 3.018 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG 0.130 2.630 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH2 0.110 2.770 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CB 0.083 3.497 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 HA 0.074 2.686 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 CA 0.055 3.405 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 CG 0.047 3.413 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 2HH2 0.027 1.993 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 HG1 -0.010 2.770 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 HB1 -0.017 2.777 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG -0.018 2.778 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.024 2.634 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH2 -0.029 3.534 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CB -0.049 3.629 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.079 3.339 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 HG1 -0.087 2.697 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A THR 82 HG1 -0.105 2.985 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CD -0.111 3.691 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 HA -0.119 2.999 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.153 3.243 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 NH2 -0.159 2.804 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.165 3.255 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A THR 82 1HG2 -0.181 3.061 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 OG1 -0.189 3.449 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 HA -0.191 2.951 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 CE1 -0.199 3.779 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 HD2 -0.203 2.963 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 CD -0.205 3.665 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 1HG1 -0.205 2.965 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH2 -0.206 2.816 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH1 -0.210 3.445 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG2 -0.213 2.973 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASN 71 2HD2 -0.213 3.093 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 CA -0.215 3.675 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HB1 -0.220 3.100 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A ILE 79 CG1 -0.228 3.808 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.243 3.503 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CG -0.244 3.824 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.246 2.856 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A ILE 79 1HG1 -0.248 3.128 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.258 3.498 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 OD1 -0.262 3.622 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 CB -0.272 3.732 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 HB2 -0.297 2.717 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CB -0.302 3.422 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B HIS 31 ND1 -0.304 2.989 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASN 71 ND2 -0.305 3.810 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 C -0.306 3.886 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CG -0.306 3.426 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CB -0.308 3.768 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 C -0.314 3.774 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.315 3.575 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 CG -0.316 3.776 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 C -0.326 3.786 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG -0.329 3.089 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 ND1 -0.343 3.848 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD1 -0.346 3.706 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG1 -0.355 3.115 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH2 -0.360 3.595 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CA -0.362 3.942 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CG -0.365 3.675 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HB1 -0.370 3.130 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 HA -0.375 2.985 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 CZ -0.378 3.498 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 NH1 -0.384 3.769 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 C -0.385 3.845 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 CB -0.388 3.698 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.396 3.276 77 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 4JUP.pdbqt 2.1 4JUP--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 4JUP.pdbqt #1/A ARG 75 NH2 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 2HH2 2.804 1.993 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "4JUP WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1FLI.pdbqt Chain information for 1FLI.pdbqt #1 --- Chain | Description A | No description available Opened 1FLI.pdbqt containing 1 structures (1589 atoms, 1612 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1FLI.pdbqt #1 --- notes | No usable SEQRES records for 1FLI.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A PRO 276 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A PRO 373 Chain-final residues that are not actual C termini: 38 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1FLI-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1FLI--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.4 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1FLI--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 45 contacts atom1 atom2 overlap distance 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 HE1 0.444 2.316 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 1HD2 0.247 2.513 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 1HD2 0.080 2.680 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 CE1 0.065 3.395 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 0.055 2.555 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 0.017 3.563 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 0.004 2.606 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 HA -0.026 2.786 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 CD1 -0.029 3.609 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 HZ3 -0.038 2.918 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.055 3.515 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 CA -0.065 3.525 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 CG -0.089 3.669 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 CD2 -0.091 3.551 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 O -0.144 3.384 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 2HD1 -0.165 2.925 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.166 3.476 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 -0.197 2.957 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 CD2 -0.206 3.666 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CH2 -0.224 3.684 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 -0.228 3.688 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 HH2 -0.228 2.838 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 N -0.247 3.632 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE2 -0.250 3.710 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A TRP 302 HH2 -0.251 2.671 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 C -0.269 3.729 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A SER 292 CB -0.272 3.392 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 3HD2 -0.277 2.887 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CD2 -0.286 3.596 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CD1 -0.287 3.747 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 3HD2 -0.291 2.901 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.294 3.604 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE3 -0.311 3.771 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ2 -0.324 3.784 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE3 -0.330 3.790 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 2HD1 -0.331 3.091 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 HE1 -0.348 3.108 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CD1 -0.365 3.825 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CD2 -0.368 3.828 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB2 -0.373 3.133 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 -0.388 3.698 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A TRP 302 CH2 -0.390 3.550 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A LEU 288 C -0.393 3.553 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 NE1 -0.396 3.901 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A GLN 370 C -0.400 3.860 45 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1FLI.pdbqt 2.1 1FLI--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.4 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1FLI WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5LTY.pdbqt Chain information for 5LTY.pdbqt #1 --- Chain | Description A B | No description available E F | No description available K | No description available M | No description available Opened 5LTY.pdbqt containing 1 structures (4847 atoms, 5029 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 5LTY.pdbqt #1 --- warnings | Not adding hydrogens to /A DT 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /B DT 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /F DG 19 P because it is missing heavy-atom bond partners Not adding hydrogens to /E DG 19 P because it is missing heavy-atom bond partners notes | No usable SEQRES records for 5LTY.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 5LTY.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 5LTY.pdbqt (#1) chain E; guessing termini instead No usable SEQRES records for 5LTY.pdbqt (#1) chain F; guessing termini instead No usable SEQRES records for 5LTY.pdbqt (#1) chain K; guessing termini instead 1 messages similar to the above omitted Chain-initial residues that are actual N termini: /A DT 1, /B DT 1, /E DG 19, /F DG 19, /K THR 185, /M LYS 186 Chain-initial residues that are not actual N termini: /A DG 12, /B DG 12, /E DG 26, /F DG 26 Chain-final residues that are actual C termini: /A DC 18, /B DC 18, /E DA 36, /F DA 36, /K GLN 255, /M GLN 255 Chain-final residues that are not actual C termini: /A DA 10, /B DA 10, /E DT 24, /F DT 24 250 hydrogen bonds 4 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5LTY-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5LTY--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.4 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 5LTY--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 53 contacts atom1 atom2 overlap distance 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 HZ2 0.418 2.462 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 0.241 2.639 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 HB1 0.235 2.645 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 NZ 0.227 3.278 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 0.212 1.808 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 HB2 0.183 2.577 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 HB1 0.168 2.592 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 9 H71 0.135 2.625 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H71 0.114 2.766 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 0.090 2.670 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 28 H61 0.080 2.530 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 CB 0.033 3.427 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H71 0.003 2.877 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 29 H61 -0.009 2.889 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 C7 -0.033 3.613 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 H73 -0.045 2.505 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 -0.046 2.806 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.051 2.931 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 CB -0.069 3.529 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 CB -0.072 3.652 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 OP2 -0.079 3.459 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 9 C7 -0.099 3.559 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 -0.100 2.710 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 -0.122 3.002 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 HB2 -0.125 2.735 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.130 2.740 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.133 2.743 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M LYS 240 HB2 -0.145 3.025 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.147 3.727 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 O4 -0.148 3.508 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 29 N6 -0.149 3.654 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.153 3.613 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 N6 -0.168 2.813 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.179 3.489 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 28 N6 -0.183 3.418 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.193 3.503 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/B DT 9 C7 -0.198 3.778 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.209 3.669 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 C -0.248 3.828 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 CG -0.262 3.722 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 C7 -0.285 3.595 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H71 -0.289 2.899 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M LYS 240 HD2 -0.299 3.179 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 -0.302 2.912 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H71 -0.305 3.185 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.311 3.891 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 O -0.320 3.560 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 C5 -0.325 3.445 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.349 3.929 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 HZ3 -0.354 3.234 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 O -0.369 3.729 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 C7 -0.383 3.543 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 HB1 -0.396 3.006 53 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 5LTY.pdbqt 2.1 5LTY--WRM-16.result.pdbqt 3 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 5LTY.pdbqt #1/E DA 28 N6 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 3.435 2.808 5LTY.pdbqt #1/E DA 28 N6 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 2.813 1.808 5LTY.pdbqt #1/E DA 28 N7 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H7 3.287 2.424 3 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "5LTY WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1JDH.pdbqt Chain information for 1JDH.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 1JDH.pdbqt containing 1 structures (8191 atoms, 8243 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1JDH.pdbqt #1 --- warnings | Not adding hydrogens to /A ILE 140 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A ARG 151 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 158 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 163 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLN 177 CB because it is missing heavy-atom bond partners 28 messages similar to the above omitted notes | No usable SEQRES records for 1JDH.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1JDH.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A ALA 135, /B LEU 12 Chain-initial residues that are not actual N termini: /A ARG 151, /A PHE 560 Chain-final residues that are actual C termini: /A SER 663, /B VAL 49 Chain-final residues that are not actual C termini: /A ILE 140, /A GLN 548 502 hydrogen bonds Adding 'H' to /A ARG 151 Adding 'H' to /A PHE 560 /A ILE 140 is not terminus, removing H atom from 'C' /A GLN 548 is not terminus, removing H atom from 'C' 5 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1JDH-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1JDH--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1JDH--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 49 contacts atom1 atom2 overlap distance 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 2HG1 0.358 2.522 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE 0.338 2.542 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HE 0.255 1.805 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 HA 0.243 2.517 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 HA 0.123 2.757 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HB2 0.103 2.357 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 3HG2 0.097 2.783 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HB2 0.055 2.555 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 CG1 0.046 3.534 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 CA 0.013 3.567 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 NE 0.003 3.502 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 CB -0.018 3.598 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 HA -0.027 2.487 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 CB -0.038 3.198 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 2HH2 -0.088 2.968 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.090 2.850 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.106 3.611 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLN 165 1HE2 -0.115 2.995 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 NE -0.118 2.803 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 HA -0.118 2.538 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 1HD2 -0.126 2.736 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 CG2 -0.146 3.726 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HB2 -0.155 3.035 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 CA -0.159 3.619 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 HA -0.171 2.781 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 CB -0.177 3.487 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 CB -0.204 3.664 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 HB2 -0.206 3.086 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 1HD2 -0.213 2.823 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 OG1 -0.218 2.738 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASP 162 O -0.235 3.475 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 CB -0.251 3.561 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 NH2 -0.267 3.772 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 CA -0.284 3.404 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLN 165 OE1 -0.287 3.647 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE -0.295 3.175 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 161 O -0.303 3.543 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.310 3.545 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 CZ -0.336 3.496 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.340 2.950 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE -0.356 2.966 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 O -0.363 3.723 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A LEU 160 O -0.365 3.725 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.368 3.128 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.369 3.604 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A THR 201 2HG2 -0.380 3.260 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 CA -0.385 3.545 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 CB -0.389 3.969 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 -0.395 2.415 49 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1JDH.pdbqt 2.1 1JDH--WRM-16.result.pdbqt 4 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1JDH.pdbqt #1/A ASN 161 ND2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 1HD2 3.118 2.516 1JDH.pdbqt #1/A ARG 200 NE 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HE 2.803 1.805 1JDH.pdbqt #1/A ARG 200 NH2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 3.325 2.546 1JDH.pdbqt #1/A ARG 200 NH2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 3.343 2.415 4 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1JDH WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/6LZP.pdbqt Chain information for 6LZP.pdbqt #1 --- Chain | Description A | No description available Opened 6LZP.pdbqt containing 1 structures (1381 atoms, 1395 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 6LZP.pdbqt #1 --- notes | No usable SEQRES records for 6LZP.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A HIS 171 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A SER 258 Chain-final residues that are not actual C termini: 35 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LZP-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LZP--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.5 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 6LZP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 42 contacts atom1 atom2 overlap distance 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 HE3 0.364 2.516 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 0.319 2.441 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 HE1 0.260 2.620 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 CE3 0.181 3.399 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 HA 0.168 2.712 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 0.150 2.460 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 CA 0.145 3.435 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 CE1 0.125 3.455 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 N 0.050 3.455 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HE1 0.040 2.840 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 H 0.034 1.986 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 H -0.009 2.619 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HE1 -0.027 2.637 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CG -0.029 3.489 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A THR 214 C -0.067 3.647 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 HG1 -0.077 2.687 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HB2 -0.091 2.701 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 -0.093 2.703 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HB2 -0.114 2.874 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.120 2.880 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 CZ3 -0.132 3.712 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 HG1 -0.139 2.159 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 -0.146 2.906 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.174 3.484 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 O -0.176 3.116 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.179 2.789 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HE1 -0.191 2.951 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CE -0.193 3.773 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 CE1 -0.195 3.505 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.234 2.844 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 CB -0.256 3.836 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.256 3.566 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 N -0.271 3.506 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A TRP 206 HE3 -0.271 3.031 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CB -0.294 3.754 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CG -0.298 3.758 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 CB -0.314 3.894 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 N -0.320 2.965 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 HZ3 -0.324 3.204 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 CZ -0.337 3.917 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 OG1 -0.354 3.464 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.361 3.821 42 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 6LZP.pdbqt 2.1 6LZP--WRM-16.result.pdbqt 2 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 6LZP.pdbqt #1/A THR 205 N 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 H 2.965 1.986 6LZP.pdbqt #1/A THR 205 OG1 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 HG1 3.071 2.159 2 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.5 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "6LZP WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2CS1.pdbqt Chain information for 2CS1.pdbqt #1 --- Chain | Description A | No description available Opened 2CS1.pdbqt containing 1 structures (1441 atoms, 1451 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2CS1.pdbqt #1 --- notes | No usable SEQRES records for 2CS1.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A GLY 92 Chain-final residues that are not actual C termini: 43 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CS1-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CS1--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.0 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2CS1--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 50 contacts atom1 atom2 overlap distance 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 14 HB2 0.371 2.389 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 HG 0.226 1.834 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 HB1 0.195 2.685 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HD2 0.150 2.610 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 HG2 0.131 2.629 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HG2 0.080 2.680 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HD2 0.072 2.688 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 14 CB 0.013 3.447 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.019 3.599 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.028 2.908 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 HG2 -0.041 2.801 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 3HD1 -0.049 2.929 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.068 2.948 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 OG -0.074 3.454 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CE2 -0.090 3.550 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CG -0.104 3.564 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CD -0.117 3.577 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.124 2.734 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 HZ1 -0.129 3.009 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 OG -0.138 2.698 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 CB -0.158 3.738 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 CG -0.166 3.626 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 CD -0.172 3.632 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 HD3 -0.195 3.075 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 HN -0.208 2.968 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 O -0.211 3.571 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.220 3.530 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 OE1 -0.227 3.467 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HG2 -0.229 3.109 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CD2 -0.237 3.697 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A ALA 61 HB3 -0.242 2.662 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 HA2 -0.267 3.147 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 CG -0.272 3.732 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 OE1 -0.276 3.516 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HA -0.296 3.176 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HD2 -0.304 3.064 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 2HD1 -0.327 2.937 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CD -0.330 3.790 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HB3 -0.331 3.091 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 CB -0.332 3.912 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.334 3.644 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CZ -0.337 3.797 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 NZ -0.359 3.864 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 OG -0.373 3.483 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HD2 -0.378 3.138 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 N -0.379 3.764 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CG -0.380 3.840 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TRP 46 HZ2 -0.386 3.146 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A ALA 61 CB -0.386 3.506 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD2 -0.388 3.968 50 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2CS1.pdbqt 2.1 2CS1--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 2CS1.pdbqt #1/A SER 13 OG 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 HG 2.698 1.834 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2CS1 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2GU8.pdbqt Chain information for 2GU8.pdbqt #1 --- Chain | Description A | No description available C | No description available Opened 2GU8.pdbqt containing 1 structures (5803 atoms, 5874 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2GU8.pdbqt #1 --- warnings | Not adding hydrogens to /A VAL 15 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A LYS 16 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 17 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 21 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for 2GU8.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 2GU8.pdbqt (#1) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A SER 14, /C THR 505 Chain-initial residues that are not actual N termini: /A LEU 198, /A ILE 339 Chain-final residues that are actual C termini: /A PHE 350, /C ASP 524 Chain-final residues that are not actual C termini: /A TRP 196, /A VAL 337 290 hydrogen bonds Adding 'H' to /A LEU 198 Adding 'H' to /A ILE 339 /A TRP 196 is not terminus, removing H atom from 'C' /A VAL 337 is not terminus, removing H atom from 'C' -2 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2GU8-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2GU8--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2GU8--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 57 contacts atom1 atom2 overlap distance 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HG2 0.382 2.498 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 O 0.347 3.013 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HN 0.332 2.428 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 HD1 0.278 2.602 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 HA 0.244 2.516 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A VAL 310 3HG2 0.217 2.663 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 CG2 0.191 3.269 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 HB2 0.173 2.707 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HE 0.160 1.900 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HE 0.104 2.506 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 1HG2 0.094 2.666 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 CD 0.077 3.503 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A ASP 301 HB2 0.074 2.806 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HN 0.042 2.718 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 HG1 0.035 1.985 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 CG 0.002 3.578 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 O -0.001 3.241 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 N -0.038 3.423 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 HA -0.045 2.655 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CB -0.051 3.631 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 1HH2 -0.078 2.098 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A PRO 141 HA -0.089 2.549 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A VAL 310 CG2 -0.106 3.686 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A ASP 301 CB -0.132 3.712 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 CA -0.133 3.593 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 3HG2 -0.136 2.896 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 1HH2 -0.140 2.750 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 NE -0.171 2.856 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 3HG2 -0.210 2.970 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A GLU 311 O -0.241 3.601 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 CG -0.249 3.829 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CD1 -0.251 3.831 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 CD -0.252 3.372 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 C -0.252 3.832 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 O -0.253 3.493 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 NE -0.260 3.495 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 N -0.268 3.653 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 HB -0.289 3.169 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HG2 -0.290 3.170 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CG -0.293 3.873 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A PRO 141 CA -0.296 3.456 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A VAL 310 CG1 -0.301 3.461 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HE -0.306 3.186 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 CG2 -0.311 3.771 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 300 CA -0.313 3.433 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HB2 -0.319 3.079 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 N -0.333 3.838 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 CA -0.337 3.917 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CA -0.342 3.922 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ILE 305 1HD1 -0.361 3.121 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 C -0.363 3.483 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 HB2 -0.372 2.982 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 NH2 -0.373 3.018 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 OG1 -0.378 2.898 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 OG1 -0.384 3.494 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HG2 -0.393 2.813 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 HA -0.395 3.275 57 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2GU8.pdbqt 2.1 2GU8--WRM-16.result.pdbqt 3 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 2GU8.pdbqt #1/A ARG 144 NE 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HE 2.856 1.900 2GU8.pdbqt #1/A ARG 144 NH2 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 1HH2 3.018 2.098 2GU8.pdbqt #1/A THR 299 OG1 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 HG1 2.898 1.985 3 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.1 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2GU8 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5VTB.pdbqt Chain information for 5VTB.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 5VTB.pdbqt containing 1 structures (5433 atoms, 5510 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 5VTB.pdbqt #1 --- warnings | Not adding hydrogens to /A LYS 25 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A LYS 26 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A VAL 35 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 52 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 59 CB because it is missing heavy-atom bond partners 32 messages similar to the above omitted notes | No usable SEQRES records for 5VTB.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 5VTB.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A LYS 25, /B ARG 3 Chain-initial residues that are not actual N termini: /A LYS 59, /A GLY 113, /A PRO 363 Chain-final residues that are actual C termini: /A ASP 411, /B GLU 16 Chain-final residues that are not actual C termini: /A THR 54, /A ASN 88, /A GLU 352 287 hydrogen bonds Adding 'H' to /A LYS 59 Adding 'H' to /A GLY 113 /A THR 54 is not terminus, removing H atom from 'C' /A ASN 88 is not terminus, removing H atom from 'C' /A GLU 352 is not terminus, removing H atom from 'C' -2 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VTB-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VTB--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.4 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 5VTB--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 47 contacts atom1 atom2 overlap distance 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 2HE2 0.542 2.338 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 HB2 0.411 2.469 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 NE2 0.359 3.146 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A TRP 382 O 0.261 3.099 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 HN 0.260 2.500 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CB 0.243 3.337 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 HB2 0.217 2.543 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 HG1 0.111 2.769 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 HA 0.106 2.654 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 HB2 0.056 2.554 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 HG -0.008 2.028 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CA -0.067 3.647 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 280 HA -0.085 2.505 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 CG -0.089 3.669 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A TRP 325 HB1 -0.103 2.523 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 2HE2 -0.108 2.988 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 N -0.114 3.499 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 2HE2 -0.124 2.734 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 OG -0.150 3.410 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 234 HG -0.157 2.767 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 HB2 -0.165 3.045 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 CB -0.167 3.747 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 382 HB2 -0.167 2.927 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 CA -0.177 3.637 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 HA -0.183 2.943 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 CB -0.192 3.652 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 CB -0.197 3.507 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A LEU 183 O -0.205 3.565 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 N -0.232 3.737 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 OG -0.239 2.759 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CD -0.256 3.836 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 325 O -0.266 3.506 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 1HE2 -0.291 3.051 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 HN -0.309 3.069 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A GLN 324 OE1 -0.311 3.251 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A VAL 233 O -0.314 3.674 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 CD -0.319 3.899 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 234 OG -0.319 3.429 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 OG -0.328 2.888 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 NE2 -0.330 3.715 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 HA -0.334 3.214 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 CB -0.341 3.461 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 NE2 -0.343 3.728 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 CB -0.350 3.510 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A LEU 279 O -0.370 3.270 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 1HE2 -0.379 3.139 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CG -0.388 3.968 47 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 5VTB.pdbqt 2.1 5VTB--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 5VTB.pdbqt #1/A SER 234 OG 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 HG 2.759 2.028 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "5VTB WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2D3J.pdbqt Chain information for 2D3J.pdbqt #1 --- Chain | Description A | No description available Opened 2D3J.pdbqt containing 1 structures (2441 atoms, 2470 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2D3J.pdbqt #1 --- notes | No usable SEQRES records for 2D3J.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A GLU 157 Chain-final residues that are not actual C termini: 134 hydrogen bonds 2 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D3J-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D3J--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2D3J--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 45 contacts atom1 atom2 overlap distance 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D3J.pdbqt #1/A LEU 85 2HD1 0.384 2.496 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 55 HB3 0.246 2.514 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ 0.218 2.542 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D3J.pdbqt #1/A LEU 85 CD1 0.198 3.382 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 3HG1 0.151 2.609 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 N 0.137 3.368 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CZ 0.129 3.451 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HD1 0.115 2.645 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HG2 0.068 2.692 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 HB3 0.051 2.829 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.008 2.888 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 55 CB -0.044 3.504 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.047 2.657 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.064 2.824 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 CA -0.071 3.651 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD2 -0.087 3.667 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.097 2.977 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 CB -0.100 3.680 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CE2 -0.125 3.705 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.137 3.717 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.142 2.752 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CZ -0.164 3.624 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 CD1 -0.196 3.656 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CB -0.221 3.681 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 CG1 -0.221 3.681 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 3HG1 -0.232 2.992 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CG -0.235 3.695 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PRO 54 HB2 -0.236 2.996 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD2 -0.247 3.557 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A LYS 48 C -0.250 3.830 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HG2 -0.280 3.040 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 CG2 -0.287 3.747 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HD2 -0.289 3.169 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD1 -0.292 3.752 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CE1 -0.296 3.876 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D3J.pdbqt #1/A ARG 47 NH1 -0.304 2.949 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.325 3.085 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D3J.pdbqt #1/A ARG 47 1HH1 -0.329 2.349 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.348 3.658 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CG -0.349 3.659 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CB -0.352 3.812 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HE2 -0.357 3.237 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.365 3.825 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 O -0.370 3.730 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HB3 -0.374 3.134 45 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2D3J.pdbqt 2.1 2D3J--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.9 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2D3J WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2E50.pdbqt Chain information for 2E50.pdbqt #1 --- Chain | Description A | No description available B | No description available P | No description available Q | No description available Opened 2E50.pdbqt containing 1 structures (11470 atoms, 11602 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2E50.pdbqt #1 --- warning | Not adding hydrogens to /B MET 145 CB because it is missing heavy- atom bond partners notes | No usable SEQRES records for 2E50.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 2E50.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 2E50.pdbqt (#1) chain P; guessing termini instead No usable SEQRES records for 2E50.pdbqt (#1) chain Q; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1, /B SER 24, /P MET 1, /Q SER 24 Chain-initial residues that are not actual N termini: /A ASP 21, /A SER 152, /A PHE 189, /A ALA 201, /B SER 152, /B PHE 189, /B GLY 200, /P ALA 20, /P SER 152, /P PHE 189, /P GLY 200, /Q SER 152, /Q PHE 189, /Q ALA 201 Chain-final residues that are actual C termini: /A VAL 222, /B PRO 223, /P VAL 222, /Q PRO 223 Chain-final residues that are not actual C termini: /A SER 15, /A HIS 144, /A MET 166, /A THR 194, /B MET 145, /B MET 166, /B THR 194, /P ASN 16, /P HIS 144, /P THR 167, /P THR 194, /Q HIS 144, /Q TRP 160, /Q THR 194 568 hydrogen bonds Adding 'H' to /A ASP 21 Adding 'H' to /A SER 152 Adding 'H' to /A PHE 189 Adding 'H' to /A ALA 201 Adding 'H' to /B SER 152 9 messages similar to the above omitted /A SER 15 is not terminus, removing H atom from 'C' /A HIS 144 is not terminus, removing H atom from 'C' /A MET 166 is not terminus, removing H atom from 'C' /A THR 194 is not terminus, removing H atom from 'C' /B MET 145 is not terminus, removing H atom from 'C' 9 messages similar to the above omitted -41 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2E50-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2E50--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.8 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2E50--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 49 contacts atom1 atom2 overlap distance 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HB2 0.217 2.543 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 HG1 0.160 2.720 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HN 0.145 2.735 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A GLN 65 HB2 0.121 2.339 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HB1 0.092 2.668 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 HD1 0.078 2.682 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 O 0.052 3.308 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 CD1 -0.046 3.506 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 CG -0.080 3.660 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASP 117 HN -0.136 2.896 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.144 3.024 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A GLN 65 CB -0.152 3.312 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 N -0.156 3.541 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 CB -0.162 3.622 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HB2 -0.168 2.928 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE1 -0.182 3.642 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 CB -0.188 3.768 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 N -0.196 3.701 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.198 2.808 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 HE1 -0.224 2.984 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.225 2.835 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HB1 -0.236 3.116 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.245 3.705 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 CB -0.258 3.718 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.261 3.721 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 NE -0.263 3.648 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 CZ -0.277 3.737 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE2 -0.278 3.738 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 NH1 -0.279 3.664 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A ASN 61 O -0.292 3.232 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 HD2 -0.294 3.054 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HN -0.296 3.056 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 O -0.298 3.538 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 HD2 -0.303 3.063 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 OD1 -0.315 3.405 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 N -0.318 3.703 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 CB -0.319 3.899 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 CD -0.323 3.783 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 CB -0.323 3.903 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 ND2 -0.330 3.835 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 OD1 -0.332 3.422 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE2 -0.337 3.797 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.340 3.650 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 CA -0.362 3.942 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 NE1 -0.364 3.749 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.365 3.825 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.379 3.839 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 CB -0.383 3.843 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 NE1 -0.385 3.770 49 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2E50.pdbqt 2.1 2E50--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.8 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2E50 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5VBN.pdbqt Chain information for 5VBN.pdbqt #1 --- Chain | Description A E | No description available B F | No description available Opened 5VBN.pdbqt containing 1 structures (17529 atoms, 17769 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 5VBN.pdbqt #1 --- notes | No usable SEQRES records for 5VBN.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 5VBN.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 5VBN.pdbqt (#1) chain E; guessing termini instead No usable SEQRES records for 5VBN.pdbqt (#1) chain F; guessing termini instead Chain-initial residues that are actual N termini: /A HIS 84, /B SER 2150, /E HIS 84, /F SER 2150 Chain-initial residues that are not actual N termini: /A PHE 163, /B PRO 2183, /E PHE 163, /F PRO 2183 Chain-final residues that are actual C termini: /A PHE 527, /B PRO 2282, /E PHE 527, /F PRO 2282 Chain-final residues that are not actual C termini: /A GLU 145, /B SER 2174, /E GLU 145, /F SER 2174 854 hydrogen bonds Adding 'H' to /A PHE 163 Adding 'H' to /E PHE 163 /A GLU 145 is not terminus, removing H atom from 'C' /B SER 2174 is not terminus, removing H atom from 'C' /E GLU 145 is not terminus, removing H atom from 'C' /F SER 2174 is not terminus, removing H atom from 'C' 35 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VBN-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VBN--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.3 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 5VBN--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 63 contacts atom1 atom2 overlap distance 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 1HD2 0.442 2.438 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 HB2 0.235 2.525 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 CD2 0.213 3.367 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLN 189 O 0.052 3.308 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 0.023 2.737 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 0.015 2.595 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.011 2.621 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 HG -0.027 2.787 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 3HG2 -0.054 2.814 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.055 2.815 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.081 2.841 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HA -0.095 2.855 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.121 3.581 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.126 2.886 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CZ -0.136 3.596 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 HB1 -0.136 2.896 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.139 3.019 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 HB1 -0.152 2.912 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.156 3.616 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 CE -0.163 3.623 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HD1 -0.168 3.048 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 CB -0.173 3.633 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 OG -0.175 3.555 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HA -0.177 2.937 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLN 189 C -0.183 3.763 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CA -0.202 3.662 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.204 3.664 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CG -0.206 3.666 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.216 2.826 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 CB -0.222 3.682 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 OG -0.228 3.488 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 HA -0.229 3.109 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 456 3HD1 -0.231 3.111 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CE2 -0.231 3.691 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 HE2 -0.236 2.996 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VBN.pdbqt #1/A GLU 220 OE2 -0.242 3.182 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 HG -0.247 3.007 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 3HD1 -0.254 3.014 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 HB -0.257 3.137 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CE2 -0.260 3.720 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.262 3.722 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.265 3.725 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.268 3.578 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VBN.pdbqt #1/B LEU 2216 O -0.275 3.175 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LYS 126 HE2 -0.301 3.181 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB1 -0.303 3.063 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CA -0.313 3.773 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.313 3.773 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 CB -0.323 3.783 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 HE2 -0.328 3.088 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 CG2 -0.330 3.790 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLU 220 OE2 -0.346 3.586 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 O -0.348 3.588 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.353 3.663 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 -0.363 3.123 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HE1 -0.366 2.976 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 -0.374 3.134 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LYS 126 CE -0.382 3.962 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CG -0.383 3.843 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB1 -0.385 2.995 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CG -0.387 3.847 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CD1 -0.395 3.975 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 HB2 -0.398 3.158 63 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 5VBN.pdbqt 2.1 5VBN--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.3 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "5VBN WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3ALN.pdbqt Chain information for 3ALN.pdbqt #1 --- Chain | Description A | No description available B | No description available C | No description available Opened 3ALN.pdbqt containing 1 structures (11428 atoms, 11539 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 3ALN.pdbqt #1 --- warnings | Not adding hydrogens to /A SER 83 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A LYS 86 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 88 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LEU 105 C because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 138 CB because it is missing heavy-atom bond partners 30 messages similar to the above omitted The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /A PRO 308 N notes | No usable SEQRES records for 3ALN.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 3ALN.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 3ALN.pdbqt (#1) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A SER 83, /B SER 84, /C GLU 100 Chain-initial residues that are not actual N termini: /A TYR 284, /A THR 318, /B TYR 284, /B ASP 324, /C ASN 117, /C ILE 127, /C CYS 158, /C CYS 174, /C LYS 231, /C SER 288, /C PRO 325 Chain-final residues that are actual C termini: /A PRO 389, /B ALA 390, /C ALA 390 Chain-final residues that are not actual C termini: /A GLN 253, /A TRP 310, /B LEU 254, /B PRO 308, /C GLU 107, /C VAL 120, /C THR 136, /C TYR 165, /C LYS 224, /C PHE 248, /C PHE 305 465 hydrogen bonds Adding 'H' to /A TYR 284 Adding 'H' to /A THR 318 Adding 'H' to /B TYR 284 Adding 'H' to /B ASP 324 Adding 'H' to /C ASN 117 5 messages similar to the above omitted /A GLN 253 is not terminus, removing H atom from 'C' /A TRP 310 is not terminus, removing H atom from 'C' /B LEU 254 is not terminus, removing H atom from 'C' /B PRO 308 is not terminus, removing H atom from 'C' /C GLU 107 is not terminus, removing H atom from 'C' 6 messages similar to the above omitted -6 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3ALN-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3ALN--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 3ALN--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 50 contacts atom1 atom2 overlap distance 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A TYR 113 HN 0.426 2.454 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.385 2.375 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 HE1 0.145 2.615 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 HA 0.134 2.626 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.097 2.513 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A TYR 113 N 0.090 3.415 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 3HG2 0.087 2.523 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 187 HE1 0.085 2.795 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A LYS 131 HZ1 0.045 2.835 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 0.033 2.727 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.027 2.733 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A MET 181 O -0.005 3.245 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.019 3.479 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 3HD1 -0.024 2.904 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 CE -0.041 3.501 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A MET 178 SD -0.068 3.730 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 CD1 -0.070 3.650 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A VAL 116 3HG2 -0.075 2.495 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 233 HG -0.104 2.864 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 -0.125 2.885 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A ALA 112 N -0.153 3.658 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 187 CE -0.159 3.739 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 NZ -0.161 3.546 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CG2 -0.166 3.626 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A LYS 131 NZ -0.194 3.699 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 -0.208 2.968 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 CA -0.221 3.681 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A ALA 129 CB -0.224 3.384 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 -0.224 2.984 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CG2 -0.237 3.697 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A ALA 129 HB2 -0.237 2.697 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.248 3.558 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.257 3.717 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 HA -0.278 3.038 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A SER 233 OG -0.287 2.807 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 CG2 -0.305 3.615 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 233 OG -0.305 3.565 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A GLY 114 N -0.308 3.813 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 112 HN -0.324 3.084 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A VAL 116 CG2 -0.327 3.447 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 129 CB -0.329 3.909 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 3HD1 -0.337 3.097 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A ALA 112 HN -0.339 3.219 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 2HD1 -0.352 3.112 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 2HD1 -0.353 3.233 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 182 O -0.357 3.597 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 114 O -0.359 3.599 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CD1 -0.382 3.842 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 3HG2 -0.398 3.008 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 129 HB3 -0.400 3.280 50 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN-- > WRM-16.hbonds.txt The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 3ALN.pdbqt #1/A PRO 308 N Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3ALN.pdbqt 2.1 3ALN--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.7 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "3ALN WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1BJ8.pdbqt Chain information for 1BJ8.pdbqt #1 --- Chain | Description A | No description available Opened 1BJ8.pdbqt containing 1 structures (1763 atoms, 1786 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1BJ8.pdbqt #1 --- notes | No usable SEQRES records for 1BJ8.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ARG 109 Chain-final residues that are not actual C termini: 53 hydrogen bonds 1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1BJ8-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1BJ8--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -6.1 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1BJ8--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 46 contacts atom1 atom2 overlap distance 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HN 0.407 2.473 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 0.307 2.573 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CD1 0.188 3.392 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HD2 0.101 2.659 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HD2 0.099 2.661 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TRP 94 HD1 0.093 2.367 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 N 0.055 3.450 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 0.042 2.568 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HA 0.032 2.848 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1BJ8.pdbqt #1/A TYR 93 HE1 0.021 2.859 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A ARG 84 1HH1 -0.035 2.915 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HD1 -0.079 2.959 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1BJ8.pdbqt #1/A TYR 93 CE1 -0.079 3.659 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 -0.085 2.965 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A GLY 92 O -0.136 3.496 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CG -0.149 3.609 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 CD -0.166 3.626 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 -0.172 2.782 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.174 3.264 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 1HH1 -0.175 2.235 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CE1 -0.177 3.487 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 -0.200 2.810 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HE1 -0.226 2.836 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.231 3.471 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CB -0.254 3.714 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A GLY 92 O -0.270 3.510 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CE1 -0.273 3.733 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CA -0.283 3.863 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TRP 94 CD1 -0.288 3.448 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HZ2 -0.299 3.059 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 HG2 -0.302 3.062 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 CD -0.307 3.767 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 91 O -0.315 3.555 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 HB2 -0.317 2.777 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 NH1 -0.328 3.013 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 -0.331 2.941 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CD -0.332 3.792 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 HD1 -0.338 2.798 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 HD2 -0.347 3.107 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CD1 -0.352 3.662 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 CZ -0.358 3.478 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 CB -0.364 3.524 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CB -0.372 3.682 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A ARG 84 NH1 -0.385 3.890 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 CA -0.392 3.552 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.399 3.489 46 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1BJ8.pdbqt 2.1 1BJ8--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1BJ8.pdbqt #1/A ARG 84 NH1 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 1HH1 3.013 2.235 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -6.1 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1BJ8 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2LX7.pdbqt Chain information for 2LX7.pdbqt #1 --- Chain | Description A | No description available Opened 2LX7.pdbqt containing 1 structures (931 atoms, 945 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 2LX7.pdbqt #1 --- notes | No usable SEQRES records for 2LX7.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A LEU 60 Chain-final residues that are not actual C termini: 24 hydrogen bonds 0 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LX7-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LX7--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.2 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 2LX7--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 35 contacts atom1 atom2 overlap distance 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2LX7.pdbqt #1/A TRP 39 HH2 0.191 2.689 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 HH 0.132 1.888 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 HZ 0.130 2.750 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 HH2 0.115 2.645 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 O 0.112 3.128 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HE2 0.053 2.707 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 HG3 0.042 2.718 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HH 0.010 2.600 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2LX7.pdbqt #1/A TRP 39 CH2 -0.011 3.591 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 HG3 -0.060 2.820 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 CH2 -0.068 3.528 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 HA3 -0.079 2.959 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CZ -0.105 3.685 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLU 15 O -0.118 3.058 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 CA -0.132 3.712 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 CE2 -0.179 3.639 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 CZ3 -0.207 3.787 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 HH2 -0.232 2.842 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 CH2 -0.241 3.821 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 HA2 -0.243 3.003 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLU 15 O -0.254 3.154 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CZ -0.296 3.606 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 OH -0.300 2.820 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 CG -0.319 3.779 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 CG -0.323 3.783 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 OH -0.323 3.583 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 HE1 -0.324 2.934 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 C -0.328 3.908 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 CZ3 -0.350 3.810 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLY 14 H -0.369 2.389 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 CA -0.372 3.832 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A SER 13 CB -0.376 3.496 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 OH -0.387 3.497 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CE1 -0.391 3.701 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HE2 -0.398 3.008 35 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2LX7.pdbqt 2.1 2LX7--WRM-16.result.pdbqt 2 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 2LX7.pdbqt #1/A GLY 14 N 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLY 14 H 3.315 2.389 2LX7.pdbqt #1/A TYR 56 OH 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 HH 2.820 1.888 2 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "2LX7 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1SM3.pdbqt Chain information for 1SM3.pdbqt #1 --- Chain | Description H | No description available L | No description available P | No description available Opened 1SM3.pdbqt containing 1 structures (6388 atoms, 6469 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1SM3.pdbqt #1 --- warnings | Not adding hydrogens to /L ASP 41 CB because it is missing heavy- atom bond partners Not adding hydrogens to /L GLU 123 CB because it is missing heavy-atom bond partners Not adding hydrogens to /L GLN 163 CB because it is missing heavy-atom bond partners Not adding hydrogens to /H GLN 1 CB because it is missing heavy-atom bond partners Not adding hydrogens to /H GLU 42 CB because it is missing heavy-atom bond partners 7 messages similar to the above omitted notes | No usable SEQRES records for 1SM3.pdbqt (#1) chain H; guessing termini instead No usable SEQRES records for 1SM3.pdbqt (#1) chain L; guessing termini instead No usable SEQRES records for 1SM3.pdbqt (#1) chain P; guessing termini instead Chain-initial residues that are actual N termini: /H GLN 1, /L ILE 3, /P SER 2 Chain-initial residues that are not actual N termini: /H SER 134 Chain-final residues that are actual C termini: /H ARG 213, /L ARG 208, /P PRO 10 Chain-final residues that are not actual C termini: /H GLY 127 327 hydrogen bonds Adding 'H' to /H SER 134 /H GLY 127 is not terminus, removing H atom from 'C' 6 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1SM3-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1SM3--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1SM3--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 44 contacts atom1 atom2 overlap distance 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H LEU 45 O 0.370 2.990 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN 0.367 2.393 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 0.353 2.257 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 3HG2 0.128 2.632 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 N 0.075 3.310 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 2HG1 0.056 2.404 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN 0.000 2.610 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H ALA 60 HB1 -0.008 2.428 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H ALA 60 HA -0.009 2.769 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H TRP 47 HN -0.048 2.068 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG1 -0.053 3.363 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 3HG2 -0.115 2.995 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.116 3.501 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 HD1 -0.124 3.004 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H GLU 46 HA -0.129 2.549 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 -0.148 2.758 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 3HG2 -0.173 2.933 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L ILE 3 O -0.179 3.419 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CG -0.185 3.645 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN -0.187 2.797 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 HA -0.215 2.635 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L ILE 3 O -0.217 3.457 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 -0.234 2.844 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CE1 -0.246 3.706 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 CG1 -0.256 3.416 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CG -0.264 3.724 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 HA -0.282 2.892 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 CG2 -0.283 3.743 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H ALA 60 CA -0.291 3.751 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CE1 -0.319 3.779 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H ALA 60 CB -0.325 3.445 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L PHE 98 O -0.325 3.265 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.328 3.713 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 HG1 -0.347 2.957 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 CG -0.354 3.664 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H TRP 47 HN -0.354 2.964 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 HG2 -0.363 3.243 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.366 3.601 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.369 3.874 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG1 -0.375 3.685 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 HA -0.380 3.140 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 N -0.390 3.625 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG2 -0.393 3.973 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H GLU 46 CA -0.398 3.518 44 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1SM3.pdbqt 2.1 1SM3--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1SM3.pdbqt #1/H TRP 47 N 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H TRP 47 HN 3.052 2.068 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.7 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1SM3 WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1RRP.pdbqt Chain information for 1RRP.pdbqt #1 --- Chain | Description A | No description available B D | No description available C | No description available Opened 1RRP.pdbqt containing 1 structures (10655 atoms, 10785 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1RRP.pdbqt #1 --- notes | No usable SEQRES records for 1RRP.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1RRP.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 1RRP.pdbqt (#1) chain C; guessing termini instead No usable SEQRES records for 1RRP.pdbqt (#1) chain D; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 8, /B HIS 17, /C GLN 8, /D HIS 17 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASP 211, /B ILE 150, /C VAL 187, /D ILE 150 Chain-final residues that are not actual C termini: 454 hydrogen bonds 12 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RRP-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RRP--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1RRP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 73 contacts atom1 atom2 overlap distance 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 0.550 2.210 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ALA 151 HB2 0.329 2.431 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 HA2 0.286 2.594 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 ND2 0.178 3.207 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 CA 0.103 3.477 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ 0.101 2.509 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 0.066 2.694 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HE1 0.052 2.708 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 0.026 2.734 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ 0.015 2.745 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C ILE 126 1HD1 0.006 2.454 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C THR 25 HG1 -0.002 2.882 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HD2 -0.018 2.898 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1RRP.pdbqt #1/C ILE 126 1HG2 -0.020 2.900 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HB2 -0.024 2.784 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ALA 151 CB -0.043 3.503 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.053 2.663 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.087 2.847 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.100 2.710 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.113 2.723 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HG2 -0.115 2.875 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.120 2.730 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CE1 -0.126 3.586 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HA -0.140 2.900 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.150 3.030 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1RRP.pdbqt #1/C ILE 126 CG2 -0.172 3.752 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 CD -0.173 3.753 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ1 -0.173 3.053 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HZ3 -0.182 3.062 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HB2 -0.189 2.949 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.193 3.073 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C THR 25 HG1 -0.195 2.255 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CE1 -0.197 3.657 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C THR 25 OG1 -0.198 3.578 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.208 3.668 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.213 2.973 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CE -0.220 3.800 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.220 3.680 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.221 3.726 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.225 3.685 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.232 2.992 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASP 125 OD1 -0.239 3.479 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 -0.242 3.002 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.254 3.564 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.263 3.498 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.264 3.724 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.270 3.730 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.272 2.882 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 ND2 -0.275 3.660 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HE1 -0.275 3.035 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.277 3.587 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CE -0.281 3.591 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 CB -0.282 3.742 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HG2 -0.293 3.053 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.294 3.754 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 NZ -0.297 3.802 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.298 3.058 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 N -0.311 3.816 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.319 3.079 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 N -0.321 3.706 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CG -0.336 3.796 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 1HG2 -0.341 2.951 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.346 3.656 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 37 O -0.351 3.441 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CG -0.355 3.815 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASP 125 OD1 -0.356 3.596 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.358 3.118 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 20 O -0.362 3.722 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C ILE 126 CD1 -0.365 3.525 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.372 3.832 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CD -0.385 3.845 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.393 3.628 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.399 3.009 73 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1RRP.pdbqt 2.1 1RRP--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1RRP.pdbqt #1/C THR 25 OG1 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C THR 25 HG1 3.164 2.255 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1RRP WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1OQD.pdbqt Chain information for 1OQD.pdbqt #1 --- Chain | Description A B C D E F G H I J | No description available K L M O P Q R | No description available N | No description available Opened 1OQD.pdbqt containing 1 structures (27310 atoms, 27575 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1OQD.pdbqt #1 --- notes | No usable SEQRES records for 1OQD.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1OQD.pdbqt (#1) chain B; guessing termini instead No usable SEQRES records for 1OQD.pdbqt (#1) chain C; guessing termini instead No usable SEQRES records for 1OQD.pdbqt (#1) chain D; guessing termini instead No usable SEQRES records for 1OQD.pdbqt (#1) chain E; guessing termini instead 13 messages similar to the above omitted Chain-initial residues that are actual N termini: /A VAL 1, /B VAL 1, /C VAL 1, /D VAL 1, /E VAL 1, /F VAL 1, /G VAL 1, /H VAL 1, /I VAL 1, /J VAL 1, /K CYS 1, /L CYS 1, /M CYS 1, /N CYS 1, /O CYS 1, /P CYS 1, /Q CYS 1, /R CYS 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A LEU 144, /B LEU 144, /C LEU 144, /D LEU 144, /E LEU 144, /F LEU 144, /G LEU 144, /H LEU 144, /I LEU 144, /J LEU 144, /K THR 39, /L THR 39, /M THR 39, /N CYS 21, /O THR 39, /P THR 39, /Q THR 39, /R THR 39 Chain-final residues that are not actual C termini: 1396 hydrogen bonds 76 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OQD-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OQD--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -8.0 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1OQD--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 59 contacts atom1 atom2 overlap distance 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HB2 0.581 2.179 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 2HD2 0.325 2.555 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CB 0.263 3.197 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 HB1 0.221 2.659 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 ND2 0.083 3.422 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/B PRO 96 HA 0.046 2.374 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 0.043 2.717 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 HG1 0.040 2.720 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 HG1 0.021 2.739 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 O 0.012 3.348 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 HB2 0.008 2.872 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 OG1 -0.005 3.265 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.011 3.101 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/C GLU 97 HB2 -0.026 2.486 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.055 2.665 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HB2 -0.060 2.820 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 HB1 -0.061 2.821 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 CB -0.062 3.642 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.072 2.682 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 HG1 -0.076 2.956 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CB -0.091 3.551 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.093 2.853 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.135 3.495 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 OD1 -0.141 3.501 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 C -0.144 3.724 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 HB1 -0.150 2.610 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C GLU 97 HN -0.158 2.768 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CA -0.160 3.620 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.168 2.778 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.196 2.956 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/B PRO 96 CA -0.202 3.322 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HA -0.204 2.964 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.212 3.452 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A ASN 94 HB2 -0.215 2.975 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 CB -0.218 3.798 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.248 3.338 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 CB -0.254 3.414 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B ASN 94 O -0.260 3.500 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.262 3.142 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A ASN 94 CB -0.270 3.730 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 CG -0.275 3.855 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 O -0.277 3.517 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 OG1 -0.281 3.541 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CA -0.285 3.745 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 HB2 -0.287 3.047 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CG -0.291 3.751 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CB -0.306 3.766 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.316 3.076 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.318 3.778 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HA -0.322 3.082 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CG -0.332 3.912 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.340 3.800 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.340 3.430 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/C GLU 97 CB -0.345 3.465 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 CG -0.346 3.506 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C GLU 97 OE1 -0.350 3.710 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 HG1 -0.351 2.811 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B MET 95 C -0.360 3.820 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.383 3.843 59 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1OQD.pdbqt 2.1 1OQD--WRM-16.result.pdbqt 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -8.0 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1OQD WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1S9J.pdbqt Chain information for 1S9J.pdbqt #1 --- Chain | Description A | No description available Opened 1S9J.pdbqt containing 1 structures (4567 atoms, 4613 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1S9J.pdbqt #1 --- notes | No usable SEQRES records for 1S9J.pdbqt (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A MET 61 Chain-initial residues that are not actual N termini: /A VAL 224, /A PRO 306 Chain-final residues that are actual C termini: /A ASN 382 Chain-final residues that are not actual C termini: /A ALA 220, /A PHE 275 207 hydrogen bonds Adding 'H' to /A VAL 224 /A ALA 220 is not terminus, removing H atom from 'C' /A PHE 275 is not terminus, removing H atom from 'C' -1 hydrogens added > wait 5 > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1S9J-- > WRM-16.result.pdbqt Summary of feedback from opening /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1S9J--WRM-16.result.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -9.2 0.000 0.000 Ignored bad PDB record found on line 3 REMARK 5 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C_9 and O_15 Ignored bad PDB record found on line 6 REMARK 2 A between atoms: C_10 and O_17 184 messages similar to the above omitted Opened 1S9J--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279 bonds) > wait 5 > close #2.2-9 > wait 5 > contacts :UNL radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J-- > WRM-16.contacts.txt Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 47 contacts atom1 atom2 overlap distance 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 146 HN 0.179 2.581 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 1HG1 0.131 2.329 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A ASN 78 HB1 0.073 2.807 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 149 HA1 0.062 2.818 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 0.042 2.718 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 HB2 0.034 2.846 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ALA 95 CB 0.029 3.431 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLN 153 OE1 0.015 3.345 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.055 2.815 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 HE1 -0.069 2.949 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.092 3.552 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 O -0.118 3.478 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LYS 97 HE1 -0.119 2.999 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A VAL 82 1HG2 -0.133 2.743 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.148 3.608 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A GLY 149 HA1 -0.156 2.616 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 CE -0.158 3.278 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ASP 208 OD2 -0.164 3.524 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 149 CA -0.173 3.753 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 146 N -0.179 3.564 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 CE -0.181 3.761 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A CYS 207 SG -0.191 3.853 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 SD -0.205 3.747 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A SER 194 HG -0.211 2.971 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 HG -0.219 2.979 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 CG1 -0.246 3.406 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.247 3.707 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.262 3.022 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A SER 150 OG -0.269 2.789 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A ASN 78 CB -0.271 3.851 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 O -0.279 3.519 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ASP 208 OD1 -0.291 3.651 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A VAL 82 1HG2 -0.310 2.920 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 HE2 -0.310 2.730 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LYS 97 CE -0.316 3.896 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A GLY 149 CA -0.320 3.480 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 -0.323 3.083 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 -0.326 2.936 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.341 3.801 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 CB -0.348 3.928 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 CA -0.350 3.810 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A LYS 192 NZ -0.352 3.857 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.353 2.963 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 2HD2 -0.368 3.128 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A SER 194 HB2 -0.376 3.136 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 2HD2 -0.385 3.145 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 1HG2 -0.389 2.849 47 contacts > hbonds :UNL showDist true radius 0.05 log true saveFile > /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J-- > WRM-16.hbonds.txt Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 1S9J.pdbqt 2.1 1S9J--WRM-16.result.pdbqt 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 1S9J.pdbqt #1/A LYS 97 NZ 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 HZ1 3.189 2.451 1 hydrogen bonds found > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > label sel text "Ligand " > label height 1 > ~select Nothing selected > 2dlabels text "Binding Energy: -9.2 kcal/mol" color red size 18 xpos .03 > ypos .95 > 2dlabels text "1S9J WRM-16 Complex" color gray size 18 xpos .03 ypos .91 > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J-- > WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground > true > select :UNL 28 atoms, 31 bonds, 1 residue, 1 model selected > view sel > save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J-- > WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground > true > close > wait 5 > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XJV.pdbqt Chain information for 1XJV.pdbqt #1 --- Chain | Description A | No description available B | No description available Opened 1XJV.pdbqt containing 1 structures (4991 atoms, 5066 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to 1XJV.pdbqt #1 --- notes | No usable SEQRES records for 1XJV.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1XJV.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A ALA 6, /B DT 1 Chain-initial residues that are not actual N termini: /A THR 149 Chain-final residues that are actual C termini: /A ALA 299, /B DG 10 Chain-final residues that are not actual C termini: /A SER 145 244 hydrogen bonds Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/cmd_line/tool.py", line 280, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/open_command/cmd.py", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/open_command/cmd.py", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/open_command/cmd.py", line 404, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core_formats/__init__.py", line 37, in open return open_command_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/scripting.py", line 161, in open_command_script run(session, text) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/cmd.py", line 63, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/hbond.py", line 447, in add_hydrogens did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by, processed) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/hbond.py", line 1098, in _try_finish pos = at_pos + nearest * h_len TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/hbond.py", line 1098, in _try_finish pos = at_pos + nearest * h_len See log for complete Python traceback. > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/ucsf-commands.cxc > set bgColor white > open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3EI4.pdbqt Chain information for 3EI4.pdbqt #2 --- Chain | Description A C E | No description available B D F | No description available Opened 3EI4.pdbqt containing 1 structures (70284 atoms, 71031 bonds) > wait 5 > hide surfaces > hide atoms > show cartoons > wait 5 > addh Summary of feedback from adding hydrogens to multiple structures --- notes | No usable SEQRES records for 1XJV.pdbqt (#1) chain A; guessing termini instead No usable SEQRES records for 1XJV.pdbqt (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: 1XJV.pdbqt #1/A ALA 6, 1XJV.pdbqt #1/B DT 1 Chain-initial residues that are not actual N termini: 1XJV.pdbqt #1/A THR 149 Chain-final residues that are actual C termini: 1XJV.pdbqt #1/A ALA 299, 1XJV.pdbqt #1/B DG 10 Chain-final residues that are not actual C termini: 1XJV.pdbqt #1/A SER 145 244 hydrogen bonds Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/cmd_line/tool.py", line 280, in execute cmd.run(cmd_text) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/open_command/cmd.py", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/open_command/cmd.py", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/open_command/cmd.py", line 404, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core_formats/__init__.py", line 37, in open return open_command_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/scripting.py", line 161, in open_command_script run(session, text) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/cmd.py", line 63, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/cmd.py", line 162, in hbond_add_hydrogens hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info, File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/hbond.py", line 447, in add_hydrogens did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by, processed) File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/hbond.py", line 1098, in _try_finish pos = at_pos + nearest * h_len TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' File "/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/addh/hbond.py", line 1098, in _try_finish pos = at_pos + nearest * h_len See log for complete Python traceback. OpenGL version: 4.6 (Core Profile) Mesa 20.2.6 OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2) OpenGL vendor: Intel Manufacturer: HP Model: HP Desktop Pro G1 MT OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virutal Machine: none CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz Cache Size: 9216 KB Memory: total used free shared buff/cache available Mem: 11Gi 5.2Gi 2.7Gi 401Mi 3.7Gi 5.7Gi Swap: 31Gi 5.2Gi 26Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop) [8086:3e92] DeviceName: Onboard - Video Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop) [103c:843c] Locale: ('en_IN', 'ISO8859-1') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.2.0 }}}