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Opened 2 months ago
Closed 2 months ago
#18750 closed defect (not a bug)
Coulombic failure
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.11.dev202508260522 (2025-08-26 05:22:39 UTC)
Description
I loaded 4PYP GLUT1 protein, removed the ligand and added the glucose at the entrance (attached 4PYP_prepared_glucose0.pdb file). When I selected both protein and glucose AND in Molecule Display tab pressed electrostatic (equivalent to command coulombic sel) i see opened command window which is hanged with the error:
"(UNK) bash.exe: warning: could not find /tmp, please create!"
I don´t mind creating a /tmp file, but I do not know where!
Here is the output window:
coulombic sel
Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue UNK (net charge -7) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.11.dev202508260522/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\mbalc\AppData\Local\Temp\tmp9bs7aht5\ante.in.mol2 -fi mol2 -o C:\Users\mbalc\AppData\Local\Temp\tmp9bs7aht5\ante.out.mol2 -fo mol2 -c bcc -nc -7 -j 5 -s 2 -dr n (UNK) Cygwin WARNING: (UNK) Couldn't compute FAST_CWD pointer. This typically occurs if you're using (UNK) an older Cygwin version on a newer Windows. Please update to the latest (UNK) available Cygwin version from https://cygwin.com/. If the problem persists, (UNK) please see https://cygwin.com/problems.html (UNK) (UNK) (UNK) Welcome to antechamber 20.0: molecular input file processor. (UNK) (UNK) Info: Finished reading file (C:\Users\mbalc\AppData\Local\Temp\tmp9bs7aht5\ante.in.mol2); atoms read (17), bonds read (17). (UNK) Info: Determining atomic numbers from atomic symbols which are case sensitive. (UNK) Running: "C:/Program Files/ChimeraX 1.11.dev202508260522/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (UNK) bash.exe: warning: could not find /tmp, please create! (UNK) (UNK) (UNK) Running: "C:/Program Files/ChimeraX 1.11.dev202508260522/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (UNK) bash.exe: warning: could not find /tmp, please create! (UNK) Info: Total number of electrons: 96; net charge: -7 (UNK) (UNK) Running: "C:/Program Files/ChimeraX 1.11.dev202508260522/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out (UNK) bash.exe: warning: could not find /tmp, please create! Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 36
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 53
| QMMM: diag iterations used for timing = 15
| QMMM:
| QMMM: Internal diag routine = 0.005563 seconds
| QMMM: Dspev diag routine = 0.005183 seconds
| QMMM: Dspevd diag routine = 0.004217 seconds
| QMMM: Dspevx diag routine = 0.016751 seconds
| QMMM: Dsyev diag routine = 0.004829 seconds
| QMMM: Dsyevd diag routine = 0.022006 seconds
| QMMM: Dsyevr diag routine = 0.006645 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.000740 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 O 594.8880 -49.2410 190.0870
QMMM: 2 2 C 592.7210 -50.2600 190.5330
QMMM: 3 3 C 592.8010 -49.8380 192.0150
QMMM: 4 4 C 594.1520 -50.4520 189.9680
QMMM: 5 5 C 593.7220 -48.6140 192.1390
QMMM: 6 6 C 595.0780 -48.9030 191.4520
QMMM: 7 7 C 594.1060 -50.8520 188.4860
QMMM: 8 8 O 592.9940 -50.2760 187.8540
QMMM: 9 9 H 592.2250 -50.3810 188.4730
QMMM: 10 10 O 591.9530 -51.4310 190.3910
QMMM: 11 11 H 591.1170 -51.3060 190.9110
QMMM: 12 12 O 595.9140 -47.7780 191.5400
QMMM: 13 13 H 595.3670 -46.9840 191.3050
QMMM: 14 14 O 591.5290 -49.5140 192.5140
QMMM: 15 15 H 591.0340 -50.3650 192.6300
QMMM: 16 16 O 593.9000 -48.2500 193.4840
QMMM: 17 17 H 593.6950 -47.2810 193.5640
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 1762.0501 kcal/mol 68.1697 kcal/(mol*A)
xmin 20 1299.1693 kcal/mol 22.4071 kcal/(mol*A)
xmin 30 1070.8292 kcal/mol 12.4207 kcal/(mol*A)
xmin 40 944.8395 kcal/mol 9.6563 kcal/(mol*A)
xmin 50 864.9424 kcal/mol 8.7053 kcal/(mol*A)
xmin 60 808.0713 kcal/mol 7.0374 kcal/(mol*A)
xmin 70 765.5911 kcal/mol 5.6146 kcal/(mol*A)
xmin 80 732.9331 kcal/mol 4.9461 kcal/(mol*A)
xmin 90 706.9628 kcal/mol 4.1778 kcal/(mol*A)
xmin 100 685.9195 kcal/mol 4.0139 kcal/(mol*A)
xmin 110 668.5267 kcal/mol 4.0460 kcal/(mol*A)
xmin 120 653.8142 kcal/mol 3.9521 kcal/(mol*A)
xmin 130 641.2760 kcal/mol 4.0893 kcal/(mol*A)
xmin 140 630.4561 kcal/mol 4.1020 kcal/(mol*A)
xmin 150 621.0427 kcal/mol 4.0217 kcal/(mol*A)
xmin 160 612.7902 kcal/mol 4.4164 kcal/(mol*A)
xmin 170 605.3967 kcal/mol 4.2101 kcal/(mol*A)
xmin 180 598.6733 kcal/mol 3.9630 kcal/(mol*A)
xmin 190 592.6718 kcal/mol 3.7901 kcal/(mol*A)
xmin 200 587.4819 kcal/mol 6.5135 kcal/(mol*A)
xmin 210 583.3858 kcal/mol 11.6131 kcal/(mol*A)
xmin 220 579.6635 kcal/mol 13.4389 kcal/(mol*A)
xmin 230 576.0220 kcal/mol 13.4443 kcal/(mol*A)
xmin 240 572.1715 kcal/mol 9.8178 kcal/(mol*A)
xmin 250 568.6333 kcal/mol 7.8178 kcal/(mol*A)
xmin 260 565.2879 kcal/mol 8.3807 kcal/(mol*A)
xmin 270 561.8971 kcal/mol 6.0459 kcal/(mol*A)
xmin 280 558.9409 kcal/mol 5.2363 kcal/(mol*A)
xmin 290 556.4083 kcal/mol 5.0668 kcal/(mol*A)
xmin 300 554.0324 kcal/mol 4.7436 kcal/(mol*A)
xmin 310 551.9250 kcal/mol 4.6601 kcal/(mol*A)
xmin 320 549.9616 kcal/mol 4.3787 kcal/(mol*A)
xmin 330 548.2094 kcal/mol 4.2448 kcal/(mol*A)
xmin 340 546.6636 kcal/mol 4.0757 kcal/(mol*A)
xmin 350 545.1815 kcal/mol 4.1274 kcal/(mol*A)
xmin 360 543.8744 kcal/mol 3.9832 kcal/(mol*A)
xmin 370 542.8027 kcal/mol 3.8202 kcal/(mol*A)
xmin 380 541.6399 kcal/mol 3.6538 kcal/(mol*A)
xmin 390 540.1312 kcal/mol 3.0992 kcal/(mol*A)
xmin 400 538.6401 kcal/mol 3.0115 kcal/(mol*A)
xmin 410 537.4547 kcal/mol 2.8734 kcal/(mol*A)
xmin 420 535.9368 kcal/mol 2.5737 kcal/(mol*A)
xmin 430 534.2959 kcal/mol 2.4193 kcal/(mol*A)
xmin 440 532.6698 kcal/mol 3.0125 kcal/(mol*A)
xmin 450 531.3961 kcal/mol 3.5387 kcal/(mol*A)
xmin 460 530.3017 kcal/mol 3.4816 kcal/(mol*A)
xmin 470 529.3525 kcal/mol 3.4556 kcal/(mol*A)
xmin 480 528.5367 kcal/mol 3.7926 kcal/(mol*A)
xmin 490 527.8649 kcal/mol 4.5772 kcal/(mol*A)
xmin 500 527.1798 kcal/mol 4.7813 kcal/(mol*A)
xmin 510 526.4211 kcal/mol 4.5022 kcal/(mol*A)
xmin 520 525.6214 kcal/mol 3.9031 kcal/(mol*A)
xmin 530 524.9905 kcal/mol 4.2433 kcal/(mol*A)
xmin 540 523.7204 kcal/mol 2.8425 kcal/(mol*A)
xmin 550 522.7934 kcal/mol 2.0747 kcal/(mol*A)
xmin 560 521.9993 kcal/mol 1.7983 kcal/(mol*A)
xmin 570 521.2861 kcal/mol 1.6714 kcal/(mol*A)
xmin 580 520.6358 kcal/mol 1.6930 kcal/(mol*A)
xmin 590 519.9979 kcal/mol 1.6243 kcal/(mol*A)
xmin 600 519.4241 kcal/mol 1.3747 kcal/(mol*A)
xmin 610 518.8154 kcal/mol 1.1714 kcal/(mol*A)
xmin 620 518.2977 kcal/mol 1.4342 kcal/(mol*A)
xmin 630 517.7784 kcal/mol 1.6048 kcal/(mol*A)
xmin 640 517.2570 kcal/mol 1.6603 kcal/(mol*A)
xmin 650 516.7283 kcal/mol 1.7030 kcal/(mol*A)
xmin 660 516.1698 kcal/mol 1.6487 kcal/(mol*A)
xmin 670 515.6048 kcal/mol 1.6471 kcal/(mol*A)
xmin 680 515.0388 kcal/mol 1.6282 kcal/(mol*A)
xmin 690 514.4702 kcal/mol 1.5721 kcal/(mol*A)
xmin 700 513.8909 kcal/mol 1.5933 kcal/(mol*A)
xmin 710 513.2926 kcal/mol 1.5787 kcal/(mol*A)
xmin 720 512.6510 kcal/mol 1.7350 kcal/(mol*A)
xmin 730 512.0014 kcal/mol 1.7535 kcal/(mol*A)
xmin 740 511.3099 kcal/mol 1.8625 kcal/(mol*A)
xmin 750 510.6185 kcal/mol 2.2908 kcal/(mol*A)
xmin 760 509.8478 kcal/mol 2.2492 kcal/(mol*A)
xmin 770 509.0793 kcal/mol 2.2317 kcal/(mol*A)
xmin 780 508.4610 kcal/mol 2.0156 kcal/(mol*A)
xmin 790 507.7708 kcal/mol 1.1760 kcal/(mol*A)
xmin 800 507.1333 kcal/mol 1.0884 kcal/(mol*A)
xmin 810 506.5773 kcal/mol 1.2688 kcal/(mol*A)
xmin 820 506.0702 kcal/mol 1.1285 kcal/(mol*A)
xmin 830 505.5769 kcal/mol 1.1832 kcal/(mol*A)
xmin 840 505.1224 kcal/mol 1.1501 kcal/(mol*A)
xmin 850 504.7353 kcal/mol 1.4043 kcal/(mol*A)
xmin 860 504.3178 kcal/mol 1.0309 kcal/(mol*A)
xmin 870 503.9607 kcal/mol 0.8828 kcal/(mol*A)
xmin 880 503.6192 kcal/mol 0.6737 kcal/(mol*A)
xmin 890 503.3691 kcal/mol 1.0249 kcal/(mol*A)
xmin 900 503.1168 kcal/mol 0.8966 kcal/(mol*A)
xmin 910 502.8627 kcal/mol 0.5088 kcal/(mol*A)
xmin 920 502.6486 kcal/mol 1.5240 kcal/(mol*A)
xmin 930 502.4405 kcal/mol 1.8493 kcal/(mol*A)
xmin 940 502.2323 kcal/mol 1.6800 kcal/(mol*A)
xmin 950 502.0046 kcal/mol 1.2847 kcal/(mol*A)
xmin 960 501.8036 kcal/mol 1.2301 kcal/(mol*A)
xmin 970 501.6124 kcal/mol 1.1822 kcal/(mol*A)
xmin 980 501.4353 kcal/mol 1.3061 kcal/(mol*A)
xmin 990 501.1558 kcal/mol 1.3097 kcal/(mol*A)
xmin 1000 500.8523 kcal/mol 1.0356 kcal/(mol*A)
xmin 1010 500.6220 kcal/mol 1.1015 kcal/(mol*A)
xmin 1020 500.4097 kcal/mol 1.0022 kcal/(mol*A)
xmin 1030 500.2073 kcal/mol 0.9362 kcal/(mol*A)
xmin 1040 500.0102 kcal/mol 0.8850 kcal/(mol*A)
xmin 1050 499.8218 kcal/mol 0.9028 kcal/(mol*A)
xmin 1060 499.6350 kcal/mol 0.8668 kcal/(mol*A)
xmin 1070 499.4534 kcal/mol 0.8516 kcal/(mol*A)
xmin 1080 499.2749 kcal/mol 0.8583 kcal/(mol*A)
xmin 1090 499.0955 kcal/mol 0.9711 kcal/(mol*A)
xmin 1100 498.8014 kcal/mol 0.8729 kcal/(mol*A)
xmin 1110 498.6083 kcal/mol 0.9317 kcal/(mol*A)
xmin 1120 498.4224 kcal/mol 0.8334 kcal/(mol*A)
xmin 1130 498.2230 kcal/mol 0.9716 kcal/(mol*A)
xmin 1140 498.0373 kcal/mol 1.0666 kcal/(mol*A)
xmin 1150 497.8647 kcal/mol 0.8305 kcal/(mol*A)
xmin 1160 497.7040 kcal/mol 0.8766 kcal/(mol*A)
xmin 1170 497.5536 kcal/mol 0.9364 kcal/(mol*A)
xmin 1180 497.4155 kcal/mol 0.9063 kcal/(mol*A)
xmin 1190 497.2921 kcal/mol 1.1245 kcal/(mol*A)
xmin 1200 497.1651 kcal/mol 1.0800 kcal/(mol*A)
xmin 1210 497.0459 kcal/mol 1.1230 kcal/(mol*A)
xmin 1220 496.9227 kcal/mol 1.0175 kcal/(mol*A)
xmin 1230 496.8091 kcal/mol 1.0833 kcal/(mol*A)
xmin 1240 496.6894 kcal/mol 1.0254 kcal/(mol*A)
xmin 1250 496.5677 kcal/mol 0.9763 kcal/(mol*A)
xmin 1260 496.4438 kcal/mol 0.9350 kcal/(mol*A)
xmin 1270 496.3173 kcal/mol 0.8998 kcal/(mol*A)
xmin 1280 496.1373 kcal/mol 1.3163 kcal/(mol*A)
xmin 1290 495.9733 kcal/mol 1.1538 kcal/(mol*A)
xmin 1300 495.8141 kcal/mol 1.0920 kcal/(mol*A)
xmin 1310 495.6611 kcal/mol 1.0968 kcal/(mol*A)
xmin 1320 495.5121 kcal/mol 1.0206 kcal/(mol*A)
xmin 1330 495.3495 kcal/mol 1.2755 kcal/(mol*A)
xmin 1340 495.1844 kcal/mol 0.6214 kcal/(mol*A)
xmin 1350 495.0455 kcal/mol 0.7682 kcal/(mol*A)
xmin 1360 494.9069 kcal/mol 0.8096 kcal/(mol*A)
xmin 1370 494.7854 kcal/mol 0.7963 kcal/(mol*A)
xmin 1380 494.6772 kcal/mol 0.9751 kcal/(mol*A)
xmin 1390 494.5619 kcal/mol 0.6794 kcal/(mol*A)
xmin 1400 494.4350 kcal/mol 0.5220 kcal/(mol*A)
xmin 1410 494.3024 kcal/mol 0.6461 kcal/(mol*A)
xmin 1420 494.1841 kcal/mol 0.8680 kcal/(mol*A)
xmin 1430 494.0766 kcal/mol 0.9016 kcal/(mol*A)
xmin 1440 493.9728 kcal/mol 0.7345 kcal/(mol*A)
xmin 1450 493.8701 kcal/mol 0.6641 kcal/(mol*A)
xmin 1460 493.7615 kcal/mol 0.6062 kcal/(mol*A)
Failure running ANTECHAMBER for residue UNK Check reply log for details
QWindowsWindow::setGeometry: Unable to set geometry 1050x852+2163+1139 (frame: 1074x916+2151+1087) on QWidgetWindow/"QDockWidgetClassWindow" on "\\.\DISPLAY1". Resulting geometry: 1044x835+2166+1153 (frame: 1068x899+2154+1101) margins: 12, 52, 12, 12 minimum size: 600x333 maximum size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=917526, y=917566), mintrack=POINT(x=1074, y=647)))
Log:
Startup Messages
---
warning | Unknown Vendor ID: 0x4d4f4351
UCSF ChimeraX version: 1.11.dev202508260522 (2025-08-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP.pdb"
4PYP.pdb title:
Crystal structure of the human glucose transporter GLUT1 [more info...]
Chain information for 4PYP.pdb #1
---
Chain | Description | UniProt
A | solute carrier family 2, facilitated glucose transporter member 1 | GTR1_HUMAN 1-492
Non-standard residues in 4PYP.pdb #1
---
BNG — nonyl β-D-glucopyranoside (β-nonylglucoside; nonyl β-D-glucoside; nonyl
D-glucoside; nonyl glucoside)
3490 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> rainbow
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared_glucose0.pdb"
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared_glucose1.pdb"
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared_glucose2.pdb"
> hide #1 models
> show #1 models
> ui tool show "Side View"
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared_glucose3.pdb"
> hide #4 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show #4 models
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared_glucose4.pdb"
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared_glucose5.pdb"
> hide #6 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #7 models
> show #7 models
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared_glucose6.pdb"
> hide #7 models
> show #7 models
> hide #7 models
> hide #8 models
> show #8 models
> show #2 models
> hide #2 models
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared_glucose7.pdb"
> show #6 models
> hide #6 models
> show #6 models
> color #1,6,8-9 bychain
> rainbow #1,6,8-9
[Repeated 1 time(s)]
> nucleotides #1,6,8-9 atoms
> style nucleic & #1,6,8-9 stick
Changed 0 atom styles
> select #1/A
3490 atoms, 3573 bonds, 448 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select #1/A
3490 atoms, 3573 bonds, 448 residues, 1 model selected
> style sel stick
Changed 3490 atom styles
> show #2 models
> show #3 models
> hide #1 models
> show #4 models
> show #5 models
> show #7 models
> select subtract #1
Nothing selected
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> show #1 models
> show #2 models
> hide #2 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> hide #4 models
> show #4 models
> hide #6 models
> show #6 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> show #3 models
> hide #2 models
> show #2 models
> hide #3 models
> show #3 models
> hide #2 models
> hide #3 models
> show #9 models
> show #8 models
> show #7 models
> show #6 models
> hide #6 models
> hide #1 models
> hide #7 models
> hide #8 models
> hide #9 models
> show #9 models
> show #8 models
> show #7 models
> hide #9 models
> hide #8 models
> show #8 models
> show #9 models
> show #1 models
> nucleotides #1,7-9 atoms
> style nucleic & #1,7-9 stick
Changed 0 atom styles
> nucleotides #1,7-9 fill
> style nucleic & #1,7-9 stick
Changed 0 atom styles
> style #1,7-9 stick
Changed 3541 atom styles
> style #1,7-9 stick
Changed 3541 atom styles
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting simple
> lighting full
> view
> view orient
> lighting full
> hide #9 models
> hide #8 models
> hide #7 models
> show #2 models
> show #3 models
> hide #2 models
> hide #3 models
> show #2 models
> show #3 models
> hide #3 models
> style #1-2 stick
Changed 3507 atom styles
> label #1-2 attribute name
> ~label #1-2 residues
> select add #2
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel target ab
> view ligand
> label ligand
> label @@display
> select :UNK
136 atoms, 136 bonds, 8 residues, 8 models selected
> hbonds sel restrict cross reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 4PYP.pdb
2 4PYP_prepared_glucose0.pdb
3 4PYP_prepared_glucose1.pdb
4 4PYP_prepared_glucose2.pdb
5 4PYP_prepared_glucose3.pdb
6 4PYP_prepared_glucose4.pdb
7 4PYP_prepared_glucose5.pdb
8 4PYP_prepared_glucose6.pdb
9 4PYP_prepared_glucose7.pdb
28 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4PYP.pdb #1/A THR 62 OG1 4PYP_prepared_glucose0.pdb #2/N UNK 1 O no hydrogen 3.108 N/A
4PYP.pdb #1/A SER 80 OG 4PYP_prepared_glucose4.pdb #6/N UNK 1 O no hydrogen 3.203 N/A
4PYP.pdb #1/A SER 80 OG 4PYP_prepared_glucose4.pdb #6/N UNK 1 O no hydrogen 2.702 N/A
4PYP.pdb #1/A THR 137 OG1 4PYP_prepared_glucose4.pdb #6/N UNK 1 O no hydrogen 3.265 N/A
4PYP.pdb #1/A GLN 282 NE2 4PYP_prepared_glucose3.pdb #5/N UNK 1 O no hydrogen 3.003 N/A
4PYP.pdb #1/A GLN 283 NE2 4PYP_prepared_glucose3.pdb #5/N UNK 1 O no hydrogen 3.100 N/A
4PYP.pdb #1/A GLN 283 NE2 4PYP_prepared_glucose6.pdb #8/N UNK 1 O no hydrogen 3.060 N/A
4PYP.pdb #1/A ASN 288 ND2 4PYP_prepared_glucose2.pdb #4/N UNK 1 O no hydrogen 3.100 N/A
4PYP.pdb #1/A ASN 288 ND2 4PYP_prepared_glucose3.pdb #5/N UNK 1 O no hydrogen 3.114 N/A
4PYP.pdb #1/A ASN 288 ND2 4PYP_prepared_glucose7.pdb #9/N UNK 1 O no hydrogen 2.993 N/A
4PYP.pdb #1/A TRP 388 NE1 4PYP_prepared_glucose2.pdb #4/N UNK 1 O no hydrogen 3.010 N/A
4PYP.pdb #1/A TRP 388 NE1 4PYP_prepared_glucose3.pdb #5/N UNK 1 O no hydrogen 3.362 N/A
4PYP.pdb #1/A TRP 412 NE1 4PYP_prepared_glucose4.pdb #6/N UNK 1 O no hydrogen 3.053 N/A
4PYP.pdb #1/A ASN 415 ND2 4PYP_prepared_glucose2.pdb #4/N UNK 1 O no hydrogen 3.184 N/A
4PYP.pdb #1/A ASN 415 ND2 4PYP_prepared_glucose2.pdb #4/N UNK 1 O no hydrogen 3.122 N/A
4PYP.pdb #1/A ASN 415 ND2 4PYP_prepared_glucose7.pdb #9/N UNK 1 O no hydrogen 3.085 N/A
4PYP.pdb #1/A ASN 415 ND2 4PYP_prepared_glucose7.pdb #9/N UNK 1 O no hydrogen 2.799 N/A
4PYP.pdb #1/A GLN 427 NE2 4PYP_prepared_glucose0.pdb #2/N UNK 1 O no hydrogen 3.003 N/A
4PYP.pdb #1/A BNG 601 O6 4PYP_prepared_glucose5.pdb #7/N UNK 1 O no hydrogen 3.383 N/A
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A GLU 41 OE1 4PYP_prepared_glucose0.pdb #2/N UNK 1 H 2.928 2.031
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A GLN 37 OE1 4PYP_prepared_glucose1.pdb #3/N UNK 1 H 3.122 2.231
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A ASN 411 OD1 4PYP_prepared_glucose3.pdb #5/N UNK 1 H 2.993 2.066
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A GLN 283 OE1 4PYP_prepared_glucose3.pdb #5/N UNK 1 H 3.187 2.365
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A THR 137 OG1 4PYP_prepared_glucose4.pdb #6/N UNK 1 H 3.265 2.524
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A GLN 282 OE1 4PYP_prepared_glucose5.pdb #7/N UNK 1 H 2.799 1.862
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A ASN 288 OD1 4PYP_prepared_glucose6.pdb #8/N UNK 1 H 2.859 1.972
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A ASN 411 OD1 4PYP_prepared_glucose6.pdb #8/N UNK 1 H 2.863 1.940
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A ASN 288 OD1 4PYP_prepared_glucose7.pdb #9/N UNK 1 H 3.025 2.094
28 hydrogen bonds found
> label @@display
> contacts sel restrict cross reveal true log true select true
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
727 contacts
atom1 atom2 overlap distance
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 3.293 0.467
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 3.138 0.202
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 3.129 0.631
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 3.109 0.651
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 2.980 0.360
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 2.962 0.798
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.954 0.806
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.841 0.919
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 2.795 0.965
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 2.783 0.557
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 2.758 0.582
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.725 1.035
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 2.663 0.717
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 2.656 0.724
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 2.644 0.696
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.604 1.156
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 2.530 0.850
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 2.498 0.882
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 2.484 0.856
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.476 1.284
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.448 1.312
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 2.438 0.942
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 2.436 1.324
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 2.432 0.948
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 2.432 1.328
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.426 1.334
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 2.419 0.961
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 2.405 0.975
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 2.388 1.372
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.371 1.389
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.366 1.394
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 2.359 0.981
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 2.354 0.986
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.338 1.422
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 2.325 1.015
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 2.321 1.059
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 2.296 1.464
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 2.280 1.060
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 2.240 1.140
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.223 1.537
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.215 1.545
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 2.213 1.547
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.210 1.550
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4 2.206 0.674
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 2.183 1.157
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 2.182 1.198
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.175 1.585
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 2.153 1.227
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.147 1.613
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 2.125 1.255
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 2.117 1.643
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 2.115 1.225
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 2.096 1.664
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 2.094 1.666
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 2.084 1.256
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.077 1.683
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 2.067 1.693
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 2.058 1.282
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 2.044 1.296
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' 2.038 1.342
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 2.036 1.724
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 2.017 1.323
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 2.016 1.744
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.991 1.769
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O4 1.986 0.574
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 1.976 1.784
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 1.971 1.789
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 1.952 1.428
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 1.949 1.391
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 1.945 1.815
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.940 1.400
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4 1.915 0.965
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.907 1.473
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 1.899 1.441
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.897 1.483
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.892 1.868
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.847 1.913
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 1.847 0.713
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 1.838 1.922
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.836 1.504
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.808 1.952
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.803 1.577
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.799 1.961
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 1.796 0.764
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.788 1.972
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 1.777 1.603
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C6 1.760 1.620
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.755 1.585
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 1.748 1.592
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1' 1.746 1.134
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.742 2.018
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.733 2.027
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 1.728 1.612
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 1.716 2.044
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 1.705 1.675
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.696 2.064
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.669 2.091
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.646 1.734
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 1.639 1.701
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 1.638 0.922
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 1.617 2.143
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 1.615 1.725
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 1.614 1.266
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 1.604 1.736
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O4 1.603 0.957
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 1.590 0.970
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.590 1.750
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' 1.570 1.810
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 1.557 1.783
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.554 1.786
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 1.519 1.041
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2' 1.517 2.243
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C6 1.515 1.365
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 1.507 1.873
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 1.498 1.882
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2' 1.482 1.898
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 1.481 2.279
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.481 1.859
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 1.464 1.916
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 1.461 1.919
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 1.458 2.302
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.449 2.311
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.445 1.895
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1 1.442 1.438
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.440 1.940
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 1.432 1.908
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 O1 1.425 0.635
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 1.417 1.143
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 1.412 1.148
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.407 2.353
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 1.392 1.488
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 1.390 2.370
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.373 2.387
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 1.370 1.190
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.370 1.970
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 1.364 1.976
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.356 2.024
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.351 1.989
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1 1.350 1.530
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 1.348 1.212
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 1.342 2.038
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.339 2.421
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.338 2.042
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.337 2.043
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 1.333 2.007
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 1.324 2.436
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2' 1.318 2.442
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 1.309 1.651
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 1.307 2.453
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 1.306 2.074
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.293 2.467
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 1.287 2.473
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 1.286 2.474
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.285 2.475
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 1.283 2.097
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 1.273 2.107
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.264 2.076
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1' 1.261 1.619
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C5 1.260 1.620
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 1.256 2.504
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 1.250 2.090
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 1.242 2.138
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C5 1.234 1.646
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.229 2.531
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 1.227 2.113
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.224 2.536
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 1.217 2.543
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 1.216 2.164
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 1.214 2.126
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 1.213 2.167
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' 1.212 2.168
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.198 2.562
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.191 2.149
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2' 1.186 2.194
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.183 2.577
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.183 2.577
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 1.177 2.163
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 1.176 2.584
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4 1.171 1.709
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 1.164 2.176
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 1.162 2.218
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 1.157 2.603
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 1.150 2.230
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.145 2.615
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 1.142 2.198
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 O4 1.133 0.927
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 1.130 2.250
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4 1.122 1.758
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 O3 1.122 0.938
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O4 1.119 1.441
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.117 2.643
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 1.112 2.648
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 1.080 2.300
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 1.080 2.680
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 1.074 1.486
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 1.065 1.495
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 O4 1.042 1.018
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 1.036 2.724
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 1.030 2.310
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 1.025 2.315
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 1.007 2.753
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2' 1.005 1.875
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' 0.997 2.383
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 0.996 2.764
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 0.996 2.764
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 0.995 2.765
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.990 2.770
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 0.981 2.779
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O4 0.969 1.591
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 0.967 2.373
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 0.965 2.795
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 0.955 2.005
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1 0.954 1.926
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 0.951 2.809
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 0.951 2.429
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.949 2.811
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 0.946 1.614
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 0.932 2.408
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 0.931 2.829
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.918 2.422
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 0.916 2.424
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 0.916 2.464
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.912 2.848
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 0.906 2.474
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 0.901 2.479
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 0.896 2.864
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 0.894 2.866
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 0.877 2.003
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 0.866 2.514
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C6 0.865 2.895
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 0.852 2.908
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 0.842 2.498
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 0.842 2.918
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 0.829 2.931
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 O3 0.818 1.242
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 0.818 2.942
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 0.811 2.529
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 0.803 1.757
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 0.801 1.759
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 0.785 2.975
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 0.768 2.572
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 0.764 1.796
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2' 0.762 2.118
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 0.761 2.579
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 0.760 2.620
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.757 1.803
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.754 3.006
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 0.750 2.630
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 0.748 2.632
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 0.748 3.012
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.741 1.819
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 0.738 2.602
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.738 2.642
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 0.735 2.645
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 0.729 3.031
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 0.719 2.621
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.716 2.664
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 C5 0.705 2.175
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C5 0.705 2.175
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4 0.694 2.186
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.690 3.070
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 0.677 2.663
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 0.646 2.734
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 0.646 1.914
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.635 2.705
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A ASN 411 ND2 0.620 2.020
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C6 0.619 2.761
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 0.616 2.724
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 0.600 2.740
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 0.598 3.162
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 0.592 2.788
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 0.579 2.761
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 0.578 3.182
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.571 2.809
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 0.564 2.396
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 0.562 2.398
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 0.557 3.203
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 0.545 2.835
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 0.543 2.337
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 O5 0.542 1.518
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2 0.535 2.345
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 0.534 2.846
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.531 3.229
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 0.527 2.433
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.524 2.856
4PYP_prepared_glucose0.pdb #2/N UNK 1 H 4PYP.pdb #1/A GLN 423 NE2 0.502 2.138
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' 0.499 2.881
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 0.498 2.882
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.498 2.882
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 O4 0.494 1.566
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A GLN 283 NE2 0.492 2.148
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 0.491 3.269
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1' 0.489 2.391
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.488 2.852
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.482 3.278
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A ASN 288 ND2 0.482 2.158
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.477 2.863
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 O5 0.477 1.583
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 0.476 2.084
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 0.474 3.046
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 0.473 3.287
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.465 2.875
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.455 2.885
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.448 2.932
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.444 3.316
4PYP_prepared_glucose1.pdb #3/N UNK 1 H 4PYP.pdb #1/A LYS 38 N 0.443 2.197
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 0.440 2.900
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 0.439 2.941
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2 0.438 2.442
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 0.434 3.326
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.431 2.129
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 0.419 3.341
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.418 2.962
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A TRP 388 NE1 0.412 2.228
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.412 3.348
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C6 0.405 2.975
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C6 0.396 3.364
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C6 0.395 2.985
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 0.395 2.945
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O6 0.391 2.169
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 0.382 2.498
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2 0.381 3.379
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2' 0.376 3.004
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C6 0.374 3.386
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 O3 0.372 1.688
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.369 2.191
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.367 3.013
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 0.358 2.202
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4 0.357 2.523
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 0.356 2.204
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 0.353 2.987
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2' 0.348 3.032
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.342 2.998
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 0.340 2.220
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 0.339 3.001
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A ASN 415 ND2 0.332 2.308
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 0.320 3.440
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 0.317 2.243
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 0.308 3.032
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.307 2.253
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.304 3.036
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 0.300 2.580
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 0.296 3.084
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.296 3.044
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.279 2.281
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.272 3.488
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 0.238 3.142
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A GLN 282 NE2 0.229 3.291
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 0.224 3.116
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 0.222 3.298
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 O3 0.219 1.841
4PYP_prepared_glucose4.pdb #6/N UNK 1 H 4PYP.pdb #1/A SER 80 CB 0.216 2.664
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C5 0.208 2.672
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2' 0.198 2.682
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A GLY 408 CA 0.197 3.563
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.189 2.371
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A ILE 287 CD1 0.185 2.695
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.183 3.577
4PYP_prepared_glucose4.pdb #6/N UNK 1 H 4PYP.pdb #1/A THR 137 CB 0.181 2.699
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 0.179 3.581
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A ASN 415 ND2 0.175 2.465
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 O2 0.174 1.886
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4' 0.170 3.210
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2' 0.170 3.590
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 0.168 3.592
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 O5 0.165 1.895
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 0.165 2.715
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.162 3.218
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A THR 295 CG2 0.162 3.598
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.160 2.400
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A GLN 282 OE1 0.158 1.862
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 0.156 3.184
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 0.155 3.185
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 0.153 3.607
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 0.149 3.231
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 0.148 3.192
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 0.146 2.414
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A THR 295 CG2 0.142 3.618
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 0.138 3.242
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 0.137 3.623
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3' 0.137 3.243
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.136 3.244
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.130 3.250
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 0.129 3.211
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4 0.129 2.751
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 0.129 3.251
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A GLN 423 NE2 0.125 3.395
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 0.124 3.636
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 0.122 2.838
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A LYS 38 CD 0.114 3.646
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3' 0.104 3.656
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 0.102 3.238
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 0.102 3.658
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2 0.102 2.778
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 0.096 3.664
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 0.091 2.469
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C6 0.085 3.295
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 0.084 3.256
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A GLN 283 CD 0.083 2.527
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3' 0.080 3.300
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A ASN 411 OD1 0.080 1.940
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3' 0.074 3.686
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1' 0.072 3.688
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 0.072 3.308
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A SER 296 CB 0.070 3.690
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A SER 80 CB 0.069 3.311
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' 0.065 3.315
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A LYS 38 CD 0.064 3.696
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C6 0.058 3.702
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 0.057 3.323
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C5 0.056 2.824
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 0.055 3.325
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A THR 137 CG2 0.055 3.705
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 O3 0.053 2.007
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A ASN 288 OD1 0.048 1.972
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4' 0.043 3.337
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A GLY 408 CA 0.042 3.338
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 O1 0.033 2.027
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 0.030 3.730
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A SER 80 CB 0.025 3.735
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 0.022 3.738
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 0.022 3.498
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 0.020 3.320
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 O5 0.016 2.044
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 0.012 2.948
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A ASN 288 OD1 0.009 3.291
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C6 0.008 3.752
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2 0.007 2.873
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 O1 0.002 2.058
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A GLU 41 CD 0.002 3.378
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A THR 137 CB 0.001 3.759
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 -0.001 3.381
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A THR 30 CG2 -0.003 3.763
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 -0.005 2.965
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1' -0.005 2.885
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A ILE 287 CD1 -0.008 3.768
4PYP_prepared_glucose0.pdb #2/N UNK 1 H 4PYP.pdb #1/A GLU 41 OE1 -0.011 2.031
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' -0.014 3.394
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C6 -0.015 3.395
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A GLN 37 CG -0.015 3.775
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 -0.015 3.395
4PYP_prepared_glucose1.pdb #3/N UNK 1 H 4PYP.pdb #1/A LYS 38 CG -0.017 2.897
4PYP_prepared_glucose1.pdb #3/N UNK 1 H 4PYP.pdb #1/A SER 296 CB -0.020 2.900
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A GLU 299 CD -0.021 3.401
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 -0.021 3.541
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A SER 296 CA -0.024 3.784
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 -0.025 3.785
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A GLY 384 CA -0.031 2.911
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 -0.031 2.591
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 -0.041 3.381
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A SER 80 CB -0.046 3.806
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A ASN 411 OD1 -0.046 2.066
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C6 -0.047 3.427
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 -0.048 2.608
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 282 NE2 -0.050 3.570
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1' -0.051 2.931
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O2 -0.056 3.396
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 O3 -0.058 2.118
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A ASN 415 ND2 -0.059 2.799
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 -0.060 3.400
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 -0.060 3.440
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A THR 137 CB -0.061 3.441
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A LYS 38 CD -0.062 3.822
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 -0.064 3.584
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 -0.066 3.446
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 -0.068 3.448
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A ASN 288 OD1 -0.074 2.094
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A ILE 287 CD1 -0.079 3.459
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C5 -0.080 3.460
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2 -0.080 2.960
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 -0.081 3.421
4PYP_prepared_glucose1.pdb #3/N UNK 1 H 4PYP.pdb #1/A LYS 38 CB -0.082 2.962
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A GLN 282 NE2 -0.083 2.823
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A PHE 379 CE2 -0.087 3.727
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 -0.090 3.850
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A ASN 288 CG -0.092 2.702
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A ASN 411 CG -0.092 2.702
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A GLY 408 CA -0.092 3.472
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 -0.093 2.653
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A GLN 282 CD -0.095 2.705
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A GLN 283 CD -0.095 3.205
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' -0.096 3.476
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 O5 -0.104 3.064
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C6 -0.107 2.987
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 -0.107 3.447
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A LYS 38 CG -0.107 3.867
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A ALA 405 CA -0.108 3.488
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A GLY 138 CA -0.109 3.489
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 -0.114 2.674
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 O2 -0.116 2.176
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 -0.118 2.678
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 -0.123 3.003
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A GLN 427 NE2 -0.123 3.643
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 -0.124 3.504
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A LYS 300 NZ -0.126 3.646
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2' -0.127 3.887
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A ASN 415 ND2 -0.128 2.768
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' -0.132 3.512
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A ASN 411 CG -0.132 2.742
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 O6 -0.133 2.193
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 -0.133 3.893
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A GLN 37 NE2 -0.136 2.876
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2' -0.137 3.897
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 -0.137 3.657
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A THR 137 CB -0.137 3.517
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 282 OE1 -0.138 3.438
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A SER 80 OG -0.142 2.702
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A LYS 300 NZ -0.142 3.662
4PYP_prepared_glucose1.pdb #3/N UNK 1 H 4PYP.pdb #1/A LYS 38 CA -0.146 3.026
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A LYS 38 CB -0.151 3.911
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A ASN 415 ND2 -0.151 2.891
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A TRP 388 CH2 -0.152 3.792
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A PHE 379 CZ -0.153 3.793
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 -0.154 3.914
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A VAL 83 CG1 -0.154 3.534
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 -0.154 3.534
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 -0.155 3.675
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A THR 137 CB -0.156 3.916
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A ASN 415 ND2 -0.157 2.897
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 -0.158 3.498
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 -0.158 3.678
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A PHE 379 CZ -0.158 3.798
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A LYS 38 CG -0.159 3.919
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 -0.160 3.920
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A SER 296 CB -0.160 3.540
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A LYS 300 NZ -0.161 2.901
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A LYS 38 N -0.162 2.902
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A SER 80 CB -0.163 3.543
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A ASN 288 ND2 -0.163 2.903
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 -0.167 3.927
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A ASN 288 ND2 -0.168 2.808
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 283 NE2 -0.170 3.690
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 -0.170 3.550
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A GLN 37 N -0.173 2.913
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A THR 62 OG1 -0.173 3.513
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C6 -0.179 3.559
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 -0.181 3.521
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A ASN 411 OD1 -0.181 2.701
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A THR 295 CG2 -0.184 3.564
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 O3 -0.185 2.245
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A ALA 35 O -0.185 3.485
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 -0.186 3.946
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A THR 295 CB -0.188 3.568
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 -0.188 3.568
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A ASN 415 ND2 -0.189 3.709
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A GLN 427 CG -0.189 3.569
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 -0.190 3.530
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1 -0.191 3.071
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 -0.193 3.953
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 -0.194 3.954
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A ASN 411 OD1 -0.195 2.715
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 O3 -0.195 2.255
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A PHE 26 CE1 -0.198 3.838
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A PRO 58 O -0.199 2.719
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A ILE 287 CD1 -0.199 3.959
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A PRO 58 O -0.201 3.501
4PYP_prepared_glucose0.pdb #2/N UNK 1 H 4PYP.pdb #1/A GLU 41 CD -0.202 3.082
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A ASN 288 CG -0.203 2.813
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 -0.207 2.767
4PYP_prepared_glucose4.pdb #6/N UNK 1 H 4PYP.pdb #1/A SER 80 OG -0.208 2.268
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C2' -0.210 3.970
4PYP_prepared_glucose1.pdb #3/N UNK 1 H 4PYP.pdb #1/A GLN 37 OE1 -0.211 2.231
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 -0.211 3.591
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 O2 -0.213 2.773
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 -0.213 3.593
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A SER 296 CA -0.214 3.594
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A GLN 37 CA -0.215 3.595
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A SER 80 O -0.215 3.515
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A TRP 388 CH2 -0.225 3.865
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C5 -0.225 3.105
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 -0.225 3.565
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O6 -0.229 3.569
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A ASN 415 ND2 -0.233 3.753
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A ASN 411 ND2 -0.235 2.875
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A ILE 287 CD1 -0.236 3.996
4PYP_prepared_glucose0.pdb #2/N UNK 1 H 4PYP.pdb #1/A GLU 41 CD -0.236 3.116
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 282 NE2 -0.239 3.759
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A ASN 411 ND2 -0.239 3.759
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 -0.239 3.999
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C6 -0.240 4.000
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C1 -0.240 4.000
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A ILE 287 CD1 -0.244 4.004
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C6 -0.246 4.006
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4' -0.246 4.006
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A PHE 379 CE2 -0.248 3.888
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3' -0.252 3.632
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A PRO 306 CG -0.252 3.632
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 282 NE2 -0.253 3.773
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A ASN 288 ND2 -0.253 2.993
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A ASN 411 OD1 -0.253 3.553
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A THR 62 OG1 -0.254 3.594
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A GLU 299 CD -0.255 4.015
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3' -0.255 3.135
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A ASN 411 ND2 -0.257 2.997
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A ASN 411 OD1 -0.257 3.557
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 -0.258 4.018
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A ASN 411 ND2 -0.263 3.003
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A GLN 282 NE2 -0.263 3.003
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A GLN 427 NE2 -0.263 3.003
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A VAL 83 CG1 -0.264 4.024
4PYP_prepared_glucose0.pdb #2/N UNK 1 H 4PYP.pdb #1/A GLN 423 CD -0.266 2.876
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4' -0.267 3.147
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A ILE 404 CG2 -0.268 4.028
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C3 -0.268 4.028
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A ASN 415 ND2 -0.269 2.909
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A LEU 61 CD1 -0.270 3.650
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A TRP 388 NE1 -0.270 3.010
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A GLN 282 OE1 -0.274 3.574
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A BNG 601 C4 -0.275 3.155
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A GLN 423 CD -0.276 3.766
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A GLN 282 OE1 -0.278 3.578
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A GLY 408 CA -0.278 4.038
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A THR 295 CG2 -0.278 4.038
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A ASN 288 CG -0.279 3.389
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A GLN 282 OE1 -0.279 2.799
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A THR 62 OG1 -0.281 2.841
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A GLN 423 NE2 -0.281 3.021
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A THR 295 CG2 -0.283 4.043
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A GLU 41 OE1 -0.284 3.584
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A ASN 288 CG -0.285 3.395
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A THR 295 CG2 -0.287 4.047
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A GLN 37 OE1 -0.289 3.589
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A GLN 283 NE2 -0.290 3.030
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C3 -0.290 3.670
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 -0.291 3.671
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A ASN 415 ND2 -0.292 3.812
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C1 -0.293 3.173
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A GLU 299 OE2 -0.294 3.594
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A GLN 37 CB -0.294 4.054
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A GLN 282 NE2 -0.296 2.936
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A TRP 388 CZ2 -0.300 3.940
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A GLY 384 C -0.300 2.910
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A GLN 282 OE1 -0.301 3.601
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A ILE 404 O -0.303 3.603
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 -0.303 3.643
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 -0.304 4.064
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A GLU 299 CB -0.305 3.685
4PYP_prepared_glucose4.pdb #6/N UNK 1 C 4PYP.pdb #1/A ALA 405 CA -0.305 4.065
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A GLN 283 NE2 -0.306 3.046
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A ASN 411 CG -0.306 2.916
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A LYS 38 CG -0.306 4.066
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A TRP 388 NE1 -0.307 3.047
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A ALA 405 CA -0.308 3.688
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A GLN 282 CD -0.309 3.419
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 C6 -0.309 3.189
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A PRO 58 CB -0.310 4.070
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 C4 -0.310 4.070
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A GLN 283 NE2 -0.310 2.950
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C6 -0.312 3.192
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A TRP 412 NE1 -0.313 3.053
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A THR 137 CG2 -0.316 3.696
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 -0.317 3.657
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C4 -0.317 3.697
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 C6 -0.317 3.197
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A GLN 282 OE1 -0.318 2.838
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A ASN 411 OD1 -0.319 3.619
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A GLN 283 NE2 -0.320 3.060
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1' -0.322 3.702
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A GLU 380 CD -0.322 3.702
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A GLN 282 CD -0.322 3.432
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 -0.323 4.083
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 C5 -0.323 4.083
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A ASN 288 CG -0.325 2.935
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O3 -0.326 3.666
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A GLN 282 OE1 -0.327 2.847
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A ASN 288 ND2 -0.327 3.847
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A GLN 282 CD -0.327 3.437
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A GLN 282 CD -0.328 3.818
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A THR 295 CG2 -0.328 3.708
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A ASN 411 OD1 -0.329 2.349
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 O4 -0.332 2.392
4PYP_prepared_glucose2.pdb #4/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 -0.333 3.213
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 O3 -0.333 2.893
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A GLN 37 CB -0.333 3.713
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 -0.334 3.714
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 -0.335 3.715
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 -0.335 2.895
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A BNG 601 O4 -0.337 3.677
4PYP_prepared_glucose0.pdb #2/N UNK 1 H 4PYP.pdb #1/A LEU 61 CD1 -0.338 3.218
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A ASN 288 OD1 -0.339 2.859
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A BNG 601 O1 -0.339 3.299
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A THR 137 C -0.340 3.450
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A ASN 411 OD1 -0.343 2.863
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A GLN 282 NE2 -0.343 3.863
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A ASN 415 ND2 -0.345 3.085
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A GLN 283 OE1 -0.345 2.365
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 -0.345 3.725
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A ASN 415 ND2 -0.346 2.986
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A ASN 288 ND2 -0.346 3.866
4PYP_prepared_glucose6.pdb #8/N UNK 1 O 4PYP.pdb #1/A GLN 283 CD -0.348 3.458
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A ASN 415 ND2 -0.349 2.989
4PYP_prepared_glucose0.pdb #2/N UNK 1 O 4PYP.pdb #1/A GLU 426 OE1 -0.350 2.870
4PYP_prepared_glucose7.pdb #9/N UNK 1 O 4PYP.pdb #1/A ASN 288 CG -0.352 3.462
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A GLY 384 CA -0.352 3.732
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A BNG 601 O5 -0.353 3.693
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A GLN 282 NE2 -0.354 3.874
4PYP_prepared_glucose7.pdb #9/N UNK 1 C 4PYP.pdb #1/A ASN 288 OD1 -0.358 3.658
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A BNG 601 C2 -0.358 3.738
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A PRO 36 CA -0.359 3.739
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A GLN 283 NE2 -0.360 3.100
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A ASN 288 ND2 -0.360 3.100
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2 -0.367 3.247
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A PRO 58 CA -0.370 4.130
4PYP_prepared_glucose7.pdb #9/N UNK 1 H 4PYP.pdb #1/A BNG 601 C3 -0.370 3.250
4PYP_prepared_glucose6.pdb #8/N UNK 1 C 4PYP.pdb #1/A ASN 415 ND2 -0.374 3.894
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A ASN 288 ND2 -0.374 3.114
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A GLN 282 CD -0.377 3.487
4PYP_prepared_glucose4.pdb #6/N UNK 1 H 4PYP.pdb #1/A ALA 405 CA -0.377 3.257
4PYP_prepared_glucose6.pdb #8/N UNK 1 H 4PYP.pdb #1/A ASN 288 ND2 -0.379 3.019
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 282 OE1 -0.379 3.679
4PYP_prepared_glucose3.pdb #5/N UNK 1 O 4PYP.pdb #1/A GLN 283 CD -0.381 3.491
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A ASN 415 ND2 -0.382 3.122
4PYP_prepared_glucose2.pdb #4/N UNK 1 O 4PYP.pdb #1/A ASN 288 OD1 -0.383 2.903
4PYP_prepared_glucose4.pdb #6/N UNK 1 O 4PYP.pdb #1/A SER 80 CB -0.383 3.763
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2 -0.383 3.263
4PYP_prepared_glucose1.pdb #3/N UNK 1 C 4PYP.pdb #1/A SER 296 N -0.384 3.904
4PYP_prepared_glucose5.pdb #7/N UNK 1 C 4PYP.pdb #1/A GLU 380 OE1 -0.384 3.684
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A BNG 601 O1 -0.384 3.724
4PYP_prepared_glucose1.pdb #3/N UNK 1 O 4PYP.pdb #1/A PRO 36 C -0.386 3.496
4PYP_prepared_glucose2.pdb #4/N UNK 1 C 4PYP.pdb #1/A GLN 282 OE1 -0.389 3.689
4PYP_prepared_glucose1.pdb #3/N UNK 1 H 4PYP.pdb #1/A SER 296 N -0.389 3.029
4PYP_prepared_glucose5.pdb #7/N UNK 1 O 4PYP.pdb #1/A BNG 601 C1 -0.389 3.769
4PYP_prepared_glucose5.pdb #7/N UNK 1 H 4PYP.pdb #1/A BNG 601 C2 -0.390 3.270
4PYP_prepared_glucose3.pdb #5/N UNK 1 C 4PYP.pdb #1/A GLN 282 CD -0.390 3.880
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A TRP 388 NE1 -0.396 3.036
4PYP_prepared_glucose3.pdb #5/N UNK 1 H 4PYP.pdb #1/A BNG 601 O2 -0.399 2.459
4PYP_prepared_glucose0.pdb #2/N UNK 1 C 4PYP.pdb #1/A GLU 426 OE1 -0.400 3.700
727 contacts
> hide #10 models
> show #10 models
> label @@display
> ~contacts
> select clear
> labels delete
Unknown command: labels delete
> label delete
> ~hbonds
> ~clashes
> mlp
Map values for surface "4PYP.pdb_A SES surface": minimum -26.36, mean 0.3711,
maximum 24.51
> lighting full
> lighting shadows false
> lighting shadows true
> surface ligand @<6.3 visiblePatches 1
> surface ligand @<3.0 visiblePatches 1
> surface ligand @<8.0 visiblePatches 1
> mlp #2#!1
Map values for surface "4PYP.pdb_A SES surface": minimum -26.36, mean 0.3711,
maximum 24.51
To also show corresponding color key, enter the above mlp command and add key
true
> surface ligand @<8.0 visiblePatches 1
> mlp #2#!1
Map values for surface "4PYP.pdb_A SES surface": minimum -26.36, mean 0.3711,
maximum 24.51
To also show corresponding color key, enter the above mlp command and add key
true
> surface ligand @<1.0 visiblePatches 1
> surface ligand @<2.0 visiblePatches 1
> surface ligand @<3.0 visiblePatches 1
> surface ligand @<2.0 visiblePatches 1
> mlp #2#!1
Map values for surface "4PYP.pdb_A SES surface": minimum -26.36, mean 0.3711,
maximum 24.51
To also show corresponding color key, enter the above mlp command and add key
true
> surface ligand @<1.0 visiblePatches 1
> preset sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style ligand sphere
Changed 21 atom styles
> style UNK sphere
Expected a keyword
> select UNK
Expected an objects specifier or a keyword
> select :UNK
136 atoms, 136 bonds, 8 residues, 8 models selected
> style UNK sphere
Expected a keyword
> hide #2 models
> select subtract #2
119 atoms, 119 bonds, 7 residues, 12 models selected
> select subtract #3
102 atoms, 102 bonds, 6 residues, 11 models selected
> select add #1
3592 atoms, 3675 bonds, 454 residues, 12 models selected
> select subtract #4
3575 atoms, 3658 bonds, 453 residues, 13 models selected
> select subtract #5
3558 atoms, 3641 bonds, 452 residues, 11 models selected
> select subtract #6
3541 atoms, 3624 bonds, 451 residues, 9 models selected
> select subtract #7
3524 atoms, 3607 bonds, 450 residues, 8 models selected
> select subtract #8
3507 atoms, 3590 bonds, 449 residues, 6 models selected
> select subtract #9
3490 atoms, 3573 bonds, 448 residues, 4 models selected
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> show #2 models
> open "C:/Users/mbalc/OneDrive - UNIVERSIDAD DE SEVILLA/Ikerbasque/BNCT/New B
> compounds/Docking/GLUT1/4PYP_prepared.pdb"
4PYP_prepared.pdb title:
Crystal structure of the human glucose transporter GLUT1 [more info...]
Chain information for 4PYP_prepared.pdb #1
---
Chain | Description | UniProt
A | solute carrier family 2, facilitated glucose transporter member 1 | GTR1_HUMAN 1-492
3469 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> select ::name="UNK"
136 atoms, 136 bonds, 8 residues, 8 models selected
> coulombic sel & #2
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNK (net charge -7) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202508260522/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\mbalc\AppData\Local\Temp\tmpr_3o9uby\ante.in.mol2 -fi mol2 -o
C:\Users\mbalc\AppData\Local\Temp\tmpr_3o9uby\ante.out.mol2 -fo mol2 -c bcc
-nc -7 -j 5 -s 2 -dr n
(UNK) `Cygwin WARNING:`
(UNK) ` Couldn't compute FAST_CWD pointer. This typically occurs if you're
using`
(UNK) ` an older Cygwin version on a newer Windows. Please update to the
latest`
(UNK) ` available Cygwin version from https://cygwin.com/. If the problem
persists,`
(UNK) ` please see https://cygwin.com/problems.html`
(UNK) ``
(UNK) ``
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`
(UNK) ``
(UNK) `Info: Finished reading file
(C:\Users\mbalc\AppData\Local\Temp\tmpr_3o9uby\ante.in.mol2); atoms read (17),
bonds read (17).`
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNK) `Running: "C:/Program Files/ChimeraX
1.11.dev202508260522/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
(UNK) ``
(UNK) ``
(UNK) `Running: "C:/Program Files/ChimeraX
1.11.dev202508260522/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
(UNK) `Info: Total number of electrons: 96; net charge: -7`
(UNK) ``
(UNK) `Running: "C:/Program Files/ChimeraX
1.11.dev202508260522/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 36
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 53
| QMMM: diag iterations used for timing = 15
| QMMM:
| QMMM: Internal diag routine = 0.006435 seconds
| QMMM: Dspev diag routine = 0.006379 seconds
| QMMM: Dspevd diag routine = 0.004938 seconds
| QMMM: Dspevx diag routine = 0.021360 seconds
| QMMM: Dsyev diag routine = 0.006467 seconds
| QMMM: Dsyevd diag routine = 0.005388 seconds
| QMMM: Dsyevr diag routine = 0.005661 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.000939 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 O 594.8880 -49.2410 190.0870
QMMM: 2 2 C 592.7210 -50.2600 190.5330
QMMM: 3 3 C 592.8010 -49.8380 192.0150
QMMM: 4 4 C 594.1520 -50.4520 189.9680
QMMM: 5 5 C 593.7220 -48.6140 192.1390
QMMM: 6 6 C 595.0780 -48.9030 191.4520
QMMM: 7 7 C 594.1060 -50.8520 188.4860
QMMM: 8 8 O 592.9940 -50.2760 187.8540
QMMM: 9 9 H 592.2250 -50.3810 188.4730
QMMM: 10 10 O 591.9530 -51.4310 190.3910
QMMM: 11 11 H 591.1170 -51.3060 190.9110
QMMM: 12 12 O 595.9140 -47.7780 191.5400
QMMM: 13 13 H 595.3670 -46.9840 191.3050
QMMM: 14 14 O 591.5290 -49.5140 192.5140
QMMM: 15 15 H 591.0340 -50.3650 192.6300
QMMM: 16 16 O 593.9000 -48.2500 193.4840
QMMM: 17 17 H 593.6950 -47.2810 193.5640
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 1762.0501 kcal/mol 68.1697 kcal/(mol*A)
xmin 20 1299.1693 kcal/mol 22.4071 kcal/(mol*A)
xmin 30 1070.8292 kcal/mol 12.4207 kcal/(mol*A)
xmin 40 944.8395 kcal/mol 9.6563 kcal/(mol*A)
xmin 50 864.9424 kcal/mol 8.7053 kcal/(mol*A)
xmin 60 808.0713 kcal/mol 7.0374 kcal/(mol*A)
xmin 70 765.5911 kcal/mol 5.6146 kcal/(mol*A)
xmin 80 732.9331 kcal/mol 4.9461 kcal/(mol*A)
xmin 90 706.9628 kcal/mol 4.1778 kcal/(mol*A)
xmin 100 685.9195 kcal/mol 4.0139 kcal/(mol*A)
xmin 110 668.5267 kcal/mol 4.0460 kcal/(mol*A)
xmin 120 653.8142 kcal/mol 3.9521 kcal/(mol*A)
xmin 130 641.2760 kcal/mol 4.0893 kcal/(mol*A)
xmin 140 630.4561 kcal/mol 4.1020 kcal/(mol*A)
xmin 150 621.0427 kcal/mol 4.0217 kcal/(mol*A)
xmin 160 612.7902 kcal/mol 4.4164 kcal/(mol*A)
xmin 170 605.3967 kcal/mol 4.2101 kcal/(mol*A)
xmin 180 598.6733 kcal/mol 3.9630 kcal/(mol*A)
xmin 190 592.6718 kcal/mol 3.7901 kcal/(mol*A)
xmin 200 587.4819 kcal/mol 6.5135 kcal/(mol*A)
xmin 210 583.3858 kcal/mol 11.6131 kcal/(mol*A)
xmin 220 579.6635 kcal/mol 13.4389 kcal/(mol*A)
xmin 230 576.0220 kcal/mol 13.4443 kcal/(mol*A)
xmin 240 572.1715 kcal/mol 9.8178 kcal/(mol*A)
xmin 250 568.6333 kcal/mol 7.8178 kcal/(mol*A)
xmin 260 565.2879 kcal/mol 8.3807 kcal/(mol*A)
xmin 270 561.8971 kcal/mol 6.0459 kcal/(mol*A)
xmin 280 558.9409 kcal/mol 5.2363 kcal/(mol*A)
xmin 290 556.4083 kcal/mol 5.0668 kcal/(mol*A)
xmin 300 554.0324 kcal/mol 4.7436 kcal/(mol*A)
xmin 310 551.9250 kcal/mol 4.6601 kcal/(mol*A)
xmin 320 549.9616 kcal/mol 4.3787 kcal/(mol*A)
xmin 330 548.2094 kcal/mol 4.2448 kcal/(mol*A)
xmin 340 546.6636 kcal/mol 4.0757 kcal/(mol*A)
xmin 350 545.1815 kcal/mol 4.1274 kcal/(mol*A)
xmin 360 543.8744 kcal/mol 3.9832 kcal/(mol*A)
xmin 370 542.8027 kcal/mol 3.8202 kcal/(mol*A)
xmin 380 541.6399 kcal/mol 3.6538 kcal/(mol*A)
xmin 390 540.1312 kcal/mol 3.0992 kcal/(mol*A)
xmin 400 538.6401 kcal/mol 3.0115 kcal/(mol*A)
xmin 410 537.4547 kcal/mol 2.8734 kcal/(mol*A)
xmin 420 535.9368 kcal/mol 2.5737 kcal/(mol*A)
xmin 430 534.2959 kcal/mol 2.4193 kcal/(mol*A)
xmin 440 532.6698 kcal/mol 3.0125 kcal/(mol*A)
xmin 450 531.3961 kcal/mol 3.5387 kcal/(mol*A)
xmin 460 530.3017 kcal/mol 3.4816 kcal/(mol*A)
xmin 470 529.3525 kcal/mol 3.4556 kcal/(mol*A)
xmin 480 528.5367 kcal/mol 3.7926 kcal/(mol*A)
xmin 490 527.8649 kcal/mol 4.5772 kcal/(mol*A)
xmin 500 527.1798 kcal/mol 4.7813 kcal/(mol*A)
xmin 510 526.4211 kcal/mol 4.5022 kcal/(mol*A)
xmin 520 525.6214 kcal/mol 3.9031 kcal/(mol*A)
xmin 530 524.9905 kcal/mol 4.2433 kcal/(mol*A)
xmin 540 523.7204 kcal/mol 2.8425 kcal/(mol*A)
xmin 550 522.7934 kcal/mol 2.0747 kcal/(mol*A)
xmin 560 521.9993 kcal/mol 1.7983 kcal/(mol*A)
xmin 570 521.2861 kcal/mol 1.6714 kcal/(mol*A)
xmin 580 520.6358 kcal/mol 1.6930 kcal/(mol*A)
xmin 590 519.9979 kcal/mol 1.6243 kcal/(mol*A)
xmin 600 519.4241 kcal/mol 1.3747 kcal/(mol*A)
xmin 610 518.8154 kcal/mol 1.1714 kcal/(mol*A)
xmin 620 518.2977 kcal/mol 1.4342 kcal/(mol*A)
xmin 630 517.7784 kcal/mol 1.6048 kcal/(mol*A)
xmin 640 517.2570 kcal/mol 1.6603 kcal/(mol*A)
xmin 650 516.7283 kcal/mol 1.7030 kcal/(mol*A)
xmin 660 516.1698 kcal/mol 1.6487 kcal/(mol*A)
xmin 670 515.6048 kcal/mol 1.6471 kcal/(mol*A)
xmin 680 515.0388 kcal/mol 1.6282 kcal/(mol*A)
xmin 690 514.4702 kcal/mol 1.5721 kcal/(mol*A)
xmin 700 513.8909 kcal/mol 1.5933 kcal/(mol*A)
xmin 710 513.2926 kcal/mol 1.5787 kcal/(mol*A)
xmin 720 512.6510 kcal/mol 1.7350 kcal/(mol*A)
xmin 730 512.0014 kcal/mol 1.7535 kcal/(mol*A)
xmin 740 511.3099 kcal/mol 1.8625 kcal/(mol*A)
xmin 750 510.6185 kcal/mol 2.2908 kcal/(mol*A)
xmin 760 509.8478 kcal/mol 2.2492 kcal/(mol*A)
xmin 770 509.0793 kcal/mol 2.2317 kcal/(mol*A)
xmin 780 508.4610 kcal/mol 2.0156 kcal/(mol*A)
xmin 790 507.7708 kcal/mol 1.1760 kcal/(mol*A)
xmin 800 507.1333 kcal/mol 1.0884 kcal/(mol*A)
xmin 810 506.5773 kcal/mol 1.2688 kcal/(mol*A)
xmin 820 506.0702 kcal/mol 1.1285 kcal/(mol*A)
xmin 830 505.5769 kcal/mol 1.1832 kcal/(mol*A)
xmin 840 505.1224 kcal/mol 1.1501 kcal/(mol*A)
xmin 850 504.7353 kcal/mol 1.4043 kcal/(mol*A)
xmin 860 504.3178 kcal/mol 1.0309 kcal/(mol*A)
xmin 870 503.9607 kcal/mol 0.8828 kcal/(mol*A)
xmin 880 503.6192 kcal/mol 0.6737 kcal/(mol*A)
xmin 890 503.3691 kcal/mol 1.0249 kcal/(mol*A)
xmin 900 503.1168 kcal/mol 0.8966 kcal/(mol*A)
xmin 910 502.8627 kcal/mol 0.5088 kcal/(mol*A)
xmin 920 502.6486 kcal/mol 1.5240 kcal/(mol*A)
Failure running ANTECHAMBER for residue UNK Check reply log for details
> help help:user/preferences.html#startup
QWindowsWindow::setGeometry: Unable to set geometry 1477x1551+1950+789 (frame:
1501x1615+1938+737) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1471x1534+1953+803 (frame:
1495x1598+1941+751) margins: 12, 52, 12, 12 minimum size: 840x882 maximum
size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=917526, y=917566), mintrack=POINT(x=1494, y=1608)))
> select subtract #2
119 atoms, 119 bonds, 7 residues, 12 models selected
> select subtract #3
102 atoms, 102 bonds, 6 residues, 11 models selected
> select subtract #4
85 atoms, 85 bonds, 5 residues, 10 models selected
> select subtract #5
68 atoms, 68 bonds, 4 residues, 8 models selected
> select subtract #6
51 atoms, 51 bonds, 3 residues, 6 models selected
> select subtract #7
34 atoms, 34 bonds, 2 residues, 5 models selected
> select subtract #8
17 atoms, 17 bonds, 1 residue, 3 models selected
> select subtract #9
1 model selected
> select add #1
7063 atoms, 7146 bonds, 447 residues, 1 model selected
> hide #2 models
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 4PYP_prepared.pdb_A SES surface #1.1: minimum, -11.10,
mean 1.72, maximum 15.61
To also show corresponding color key, enter the above coulombic command and
add key true
> show #2 models
> help help:user/preferences.html#startup
QWindowsWindow::setGeometry: Unable to set geometry 1477x1551+1950+789 (frame:
1501x1615+1938+737) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1471x1534+1953+803 (frame:
1495x1598+1941+751) margins: 12, 52, 12, 12 minimum size: 840x882 maximum
size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=917526, y=917566), mintrack=POINT(x=1494, y=1608)))
> select add #2
7080 atoms, 7163 bonds, 448 residues, 3 models selected
> select add #1
7080 atoms, 7163 bonds, 448 residues, 5 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNK (net charge -7) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.11.dev202508260522/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\mbalc\AppData\Local\Temp\tmp9bs7aht5\ante.in.mol2 -fi mol2 -o
C:\Users\mbalc\AppData\Local\Temp\tmp9bs7aht5\ante.out.mol2 -fo mol2 -c bcc
-nc -7 -j 5 -s 2 -dr n
(UNK) `Cygwin WARNING:`
(UNK) ` Couldn't compute FAST_CWD pointer. This typically occurs if you're
using`
(UNK) ` an older Cygwin version on a newer Windows. Please update to the
latest`
(UNK) ` available Cygwin version from https://cygwin.com/. If the problem
persists,`
(UNK) ` please see https://cygwin.com/problems.html`
(UNK) ``
(UNK) ``
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`
(UNK) ``
(UNK) `Info: Finished reading file
(C:\Users\mbalc\AppData\Local\Temp\tmp9bs7aht5\ante.in.mol2); atoms read (17),
bonds read (17).`
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNK) `Running: "C:/Program Files/ChimeraX
1.11.dev202508260522/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
(UNK) ``
(UNK) ``
(UNK) `Running: "C:/Program Files/ChimeraX
1.11.dev202508260522/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
(UNK) `Info: Total number of electrons: 96; net charge: -7`
(UNK) ``
(UNK) `Running: "C:/Program Files/ChimeraX
1.11.dev202508260522/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 36
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 53
| QMMM: diag iterations used for timing = 15
| QMMM:
| QMMM: Internal diag routine = 0.005563 seconds
| QMMM: Dspev diag routine = 0.005183 seconds
| QMMM: Dspevd diag routine = 0.004217 seconds
| QMMM: Dspevx diag routine = 0.016751 seconds
| QMMM: Dsyev diag routine = 0.004829 seconds
| QMMM: Dsyevd diag routine = 0.022006 seconds
| QMMM: Dsyevr diag routine = 0.006645 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.000740 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 O 594.8880 -49.2410 190.0870
QMMM: 2 2 C 592.7210 -50.2600 190.5330
QMMM: 3 3 C 592.8010 -49.8380 192.0150
QMMM: 4 4 C 594.1520 -50.4520 189.9680
QMMM: 5 5 C 593.7220 -48.6140 192.1390
QMMM: 6 6 C 595.0780 -48.9030 191.4520
QMMM: 7 7 C 594.1060 -50.8520 188.4860
QMMM: 8 8 O 592.9940 -50.2760 187.8540
QMMM: 9 9 H 592.2250 -50.3810 188.4730
QMMM: 10 10 O 591.9530 -51.4310 190.3910
QMMM: 11 11 H 591.1170 -51.3060 190.9110
QMMM: 12 12 O 595.9140 -47.7780 191.5400
QMMM: 13 13 H 595.3670 -46.9840 191.3050
QMMM: 14 14 O 591.5290 -49.5140 192.5140
QMMM: 15 15 H 591.0340 -50.3650 192.6300
QMMM: 16 16 O 593.9000 -48.2500 193.4840
QMMM: 17 17 H 593.6950 -47.2810 193.5640
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 1762.0501 kcal/mol 68.1697 kcal/(mol*A)
xmin 20 1299.1693 kcal/mol 22.4071 kcal/(mol*A)
xmin 30 1070.8292 kcal/mol 12.4207 kcal/(mol*A)
xmin 40 944.8395 kcal/mol 9.6563 kcal/(mol*A)
xmin 50 864.9424 kcal/mol 8.7053 kcal/(mol*A)
xmin 60 808.0713 kcal/mol 7.0374 kcal/(mol*A)
xmin 70 765.5911 kcal/mol 5.6146 kcal/(mol*A)
xmin 80 732.9331 kcal/mol 4.9461 kcal/(mol*A)
xmin 90 706.9628 kcal/mol 4.1778 kcal/(mol*A)
xmin 100 685.9195 kcal/mol 4.0139 kcal/(mol*A)
xmin 110 668.5267 kcal/mol 4.0460 kcal/(mol*A)
xmin 120 653.8142 kcal/mol 3.9521 kcal/(mol*A)
xmin 130 641.2760 kcal/mol 4.0893 kcal/(mol*A)
xmin 140 630.4561 kcal/mol 4.1020 kcal/(mol*A)
xmin 150 621.0427 kcal/mol 4.0217 kcal/(mol*A)
xmin 160 612.7902 kcal/mol 4.4164 kcal/(mol*A)
xmin 170 605.3967 kcal/mol 4.2101 kcal/(mol*A)
xmin 180 598.6733 kcal/mol 3.9630 kcal/(mol*A)
xmin 190 592.6718 kcal/mol 3.7901 kcal/(mol*A)
xmin 200 587.4819 kcal/mol 6.5135 kcal/(mol*A)
xmin 210 583.3858 kcal/mol 11.6131 kcal/(mol*A)
xmin 220 579.6635 kcal/mol 13.4389 kcal/(mol*A)
xmin 230 576.0220 kcal/mol 13.4443 kcal/(mol*A)
xmin 240 572.1715 kcal/mol 9.8178 kcal/(mol*A)
xmin 250 568.6333 kcal/mol 7.8178 kcal/(mol*A)
xmin 260 565.2879 kcal/mol 8.3807 kcal/(mol*A)
xmin 270 561.8971 kcal/mol 6.0459 kcal/(mol*A)
xmin 280 558.9409 kcal/mol 5.2363 kcal/(mol*A)
xmin 290 556.4083 kcal/mol 5.0668 kcal/(mol*A)
xmin 300 554.0324 kcal/mol 4.7436 kcal/(mol*A)
xmin 310 551.9250 kcal/mol 4.6601 kcal/(mol*A)
xmin 320 549.9616 kcal/mol 4.3787 kcal/(mol*A)
xmin 330 548.2094 kcal/mol 4.2448 kcal/(mol*A)
xmin 340 546.6636 kcal/mol 4.0757 kcal/(mol*A)
xmin 350 545.1815 kcal/mol 4.1274 kcal/(mol*A)
xmin 360 543.8744 kcal/mol 3.9832 kcal/(mol*A)
xmin 370 542.8027 kcal/mol 3.8202 kcal/(mol*A)
xmin 380 541.6399 kcal/mol 3.6538 kcal/(mol*A)
xmin 390 540.1312 kcal/mol 3.0992 kcal/(mol*A)
xmin 400 538.6401 kcal/mol 3.0115 kcal/(mol*A)
xmin 410 537.4547 kcal/mol 2.8734 kcal/(mol*A)
xmin 420 535.9368 kcal/mol 2.5737 kcal/(mol*A)
xmin 430 534.2959 kcal/mol 2.4193 kcal/(mol*A)
xmin 440 532.6698 kcal/mol 3.0125 kcal/(mol*A)
xmin 450 531.3961 kcal/mol 3.5387 kcal/(mol*A)
xmin 460 530.3017 kcal/mol 3.4816 kcal/(mol*A)
xmin 470 529.3525 kcal/mol 3.4556 kcal/(mol*A)
xmin 480 528.5367 kcal/mol 3.7926 kcal/(mol*A)
xmin 490 527.8649 kcal/mol 4.5772 kcal/(mol*A)
xmin 500 527.1798 kcal/mol 4.7813 kcal/(mol*A)
xmin 510 526.4211 kcal/mol 4.5022 kcal/(mol*A)
xmin 520 525.6214 kcal/mol 3.9031 kcal/(mol*A)
xmin 530 524.9905 kcal/mol 4.2433 kcal/(mol*A)
xmin 540 523.7204 kcal/mol 2.8425 kcal/(mol*A)
xmin 550 522.7934 kcal/mol 2.0747 kcal/(mol*A)
xmin 560 521.9993 kcal/mol 1.7983 kcal/(mol*A)
xmin 570 521.2861 kcal/mol 1.6714 kcal/(mol*A)
xmin 580 520.6358 kcal/mol 1.6930 kcal/(mol*A)
xmin 590 519.9979 kcal/mol 1.6243 kcal/(mol*A)
xmin 600 519.4241 kcal/mol 1.3747 kcal/(mol*A)
xmin 610 518.8154 kcal/mol 1.1714 kcal/(mol*A)
xmin 620 518.2977 kcal/mol 1.4342 kcal/(mol*A)
xmin 630 517.7784 kcal/mol 1.6048 kcal/(mol*A)
xmin 640 517.2570 kcal/mol 1.6603 kcal/(mol*A)
xmin 650 516.7283 kcal/mol 1.7030 kcal/(mol*A)
xmin 660 516.1698 kcal/mol 1.6487 kcal/(mol*A)
xmin 670 515.6048 kcal/mol 1.6471 kcal/(mol*A)
xmin 680 515.0388 kcal/mol 1.6282 kcal/(mol*A)
xmin 690 514.4702 kcal/mol 1.5721 kcal/(mol*A)
xmin 700 513.8909 kcal/mol 1.5933 kcal/(mol*A)
xmin 710 513.2926 kcal/mol 1.5787 kcal/(mol*A)
xmin 720 512.6510 kcal/mol 1.7350 kcal/(mol*A)
xmin 730 512.0014 kcal/mol 1.7535 kcal/(mol*A)
xmin 740 511.3099 kcal/mol 1.8625 kcal/(mol*A)
xmin 750 510.6185 kcal/mol 2.2908 kcal/(mol*A)
xmin 760 509.8478 kcal/mol 2.2492 kcal/(mol*A)
xmin 770 509.0793 kcal/mol 2.2317 kcal/(mol*A)
xmin 780 508.4610 kcal/mol 2.0156 kcal/(mol*A)
xmin 790 507.7708 kcal/mol 1.1760 kcal/(mol*A)
xmin 800 507.1333 kcal/mol 1.0884 kcal/(mol*A)
xmin 810 506.5773 kcal/mol 1.2688 kcal/(mol*A)
xmin 820 506.0702 kcal/mol 1.1285 kcal/(mol*A)
xmin 830 505.5769 kcal/mol 1.1832 kcal/(mol*A)
xmin 840 505.1224 kcal/mol 1.1501 kcal/(mol*A)
xmin 850 504.7353 kcal/mol 1.4043 kcal/(mol*A)
xmin 860 504.3178 kcal/mol 1.0309 kcal/(mol*A)
xmin 870 503.9607 kcal/mol 0.8828 kcal/(mol*A)
xmin 880 503.6192 kcal/mol 0.6737 kcal/(mol*A)
xmin 890 503.3691 kcal/mol 1.0249 kcal/(mol*A)
xmin 900 503.1168 kcal/mol 0.8966 kcal/(mol*A)
xmin 910 502.8627 kcal/mol 0.5088 kcal/(mol*A)
xmin 920 502.6486 kcal/mol 1.5240 kcal/(mol*A)
xmin 930 502.4405 kcal/mol 1.8493 kcal/(mol*A)
xmin 940 502.2323 kcal/mol 1.6800 kcal/(mol*A)
xmin 950 502.0046 kcal/mol 1.2847 kcal/(mol*A)
xmin 960 501.8036 kcal/mol 1.2301 kcal/(mol*A)
xmin 970 501.6124 kcal/mol 1.1822 kcal/(mol*A)
xmin 980 501.4353 kcal/mol 1.3061 kcal/(mol*A)
xmin 990 501.1558 kcal/mol 1.3097 kcal/(mol*A)
xmin 1000 500.8523 kcal/mol 1.0356 kcal/(mol*A)
xmin 1010 500.6220 kcal/mol 1.1015 kcal/(mol*A)
xmin 1020 500.4097 kcal/mol 1.0022 kcal/(mol*A)
xmin 1030 500.2073 kcal/mol 0.9362 kcal/(mol*A)
xmin 1040 500.0102 kcal/mol 0.8850 kcal/(mol*A)
xmin 1050 499.8218 kcal/mol 0.9028 kcal/(mol*A)
xmin 1060 499.6350 kcal/mol 0.8668 kcal/(mol*A)
xmin 1070 499.4534 kcal/mol 0.8516 kcal/(mol*A)
xmin 1080 499.2749 kcal/mol 0.8583 kcal/(mol*A)
xmin 1090 499.0955 kcal/mol 0.9711 kcal/(mol*A)
xmin 1100 498.8014 kcal/mol 0.8729 kcal/(mol*A)
xmin 1110 498.6083 kcal/mol 0.9317 kcal/(mol*A)
xmin 1120 498.4224 kcal/mol 0.8334 kcal/(mol*A)
xmin 1130 498.2230 kcal/mol 0.9716 kcal/(mol*A)
xmin 1140 498.0373 kcal/mol 1.0666 kcal/(mol*A)
xmin 1150 497.8647 kcal/mol 0.8305 kcal/(mol*A)
xmin 1160 497.7040 kcal/mol 0.8766 kcal/(mol*A)
xmin 1170 497.5536 kcal/mol 0.9364 kcal/(mol*A)
xmin 1180 497.4155 kcal/mol 0.9063 kcal/(mol*A)
xmin 1190 497.2921 kcal/mol 1.1245 kcal/(mol*A)
xmin 1200 497.1651 kcal/mol 1.0800 kcal/(mol*A)
xmin 1210 497.0459 kcal/mol 1.1230 kcal/(mol*A)
xmin 1220 496.9227 kcal/mol 1.0175 kcal/(mol*A)
xmin 1230 496.8091 kcal/mol 1.0833 kcal/(mol*A)
xmin 1240 496.6894 kcal/mol 1.0254 kcal/(mol*A)
xmin 1250 496.5677 kcal/mol 0.9763 kcal/(mol*A)
xmin 1260 496.4438 kcal/mol 0.9350 kcal/(mol*A)
xmin 1270 496.3173 kcal/mol 0.8998 kcal/(mol*A)
xmin 1280 496.1373 kcal/mol 1.3163 kcal/(mol*A)
xmin 1290 495.9733 kcal/mol 1.1538 kcal/(mol*A)
xmin 1300 495.8141 kcal/mol 1.0920 kcal/(mol*A)
xmin 1310 495.6611 kcal/mol 1.0968 kcal/(mol*A)
xmin 1320 495.5121 kcal/mol 1.0206 kcal/(mol*A)
xmin 1330 495.3495 kcal/mol 1.2755 kcal/(mol*A)
xmin 1340 495.1844 kcal/mol 0.6214 kcal/(mol*A)
xmin 1350 495.0455 kcal/mol 0.7682 kcal/(mol*A)
xmin 1360 494.9069 kcal/mol 0.8096 kcal/(mol*A)
xmin 1370 494.7854 kcal/mol 0.7963 kcal/(mol*A)
xmin 1380 494.6772 kcal/mol 0.9751 kcal/(mol*A)
xmin 1390 494.5619 kcal/mol 0.6794 kcal/(mol*A)
xmin 1400 494.4350 kcal/mol 0.5220 kcal/(mol*A)
xmin 1410 494.3024 kcal/mol 0.6461 kcal/(mol*A)
xmin 1420 494.1841 kcal/mol 0.8680 kcal/(mol*A)
xmin 1430 494.0766 kcal/mol 0.9016 kcal/(mol*A)
xmin 1440 493.9728 kcal/mol 0.7345 kcal/(mol*A)
xmin 1450 493.8701 kcal/mol 0.6641 kcal/(mol*A)
xmin 1460 493.7615 kcal/mol 0.6062 kcal/(mol*A)
Failure running ANTECHAMBER for residue UNK Check reply log for details
QWindowsWindow::setGeometry: Unable to set geometry 1050x852+2163+1139 (frame:
1074x916+2151+1087) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1044x835+2166+1153 (frame:
1068x899+2154+1101) margins: 12, 52, 12, 12 minimum size: 600x333 maximum
size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=917526, y=917566), mintrack=POINT(x=1074, y=647)))
OpenGL version: 4.6 (Core Profile) Mesa 25.3.0-devel (git-4dfe2a8744)
OpenGL renderer: D3D12 (Qualcomm(R) Adreno(TM) X1-85 GPU)
OpenGL vendor: Microsoft Corporation
Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows
Manufacturer: Microsoft Corporation
Model: Microsoft Surface Pro with 5G, 11th Edition
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 16,760,201,216
MaxProcessMemory: 137,438,953,344
CPU: 12 Snapdragon(R) X 12-core X1E80100 @ 3.40 GHz
OSLanguage: en-GB
Installed Packages:
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appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.7.2
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.14
ChimeraX-AtomicLibrary: 14.1.22
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202508260522
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.3.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.4
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.48.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.10.5
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.3
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.19.1
fonttools: 4.59.1
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2025.4.15
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.4.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.5
matplotlib-inline: 0.1.7
msgpack: 1.1.1
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 311
pyzmq: 27.0.2
qtconsole: 5.6.1
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
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sortedcontainers: 2.4.0
soupsieve: 2.7
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sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
File attachment: 4PYP_prepared_glucose0.pdb
Attachments (1)
Change History (3)
by , 2 months ago
| Attachment: | 4PYP_prepared_glucose0.pdb added |
|---|
comment:1 by , 2 months ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Coulombic failure |
comment:2 by , 2 months ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
Hi Marcin,
Thanks for reporting this problem. You can ignore the "could not find /tmp" message -- it's a side effect of you not having the Cygwin environment on your machine, but having Cygwin installed is not necessary for ChimeraX to work. The real problem is that your UNK residue (glucose) only has some of the hydrogens it should have. If it had no hydrogens then coulombic would add hydrogens before trying to assign charges, but since you do have some hydrogens it assumes that's the protonation you actually want. Well, with that protonation the formal charge on the glucose is -7! So then the partial-charge computation step fails.
The solution is to add all hydrogens before running the electrostatic surface calculation, either with the Add Hydrogens tool (Tools→Structure Editing→Add Hydrogens) or with the "addh" command.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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