[Chimera-users] importing sdf files from PubChem
Elaine Meng
meng at cgl.ucsf.edu
Fri May 4 20:58:08 PDT 2007
Hi Mark,
I can open the SDF as shown in your mail (by cutting and pasting the
lines shown below into a file named test.sdf) successfully with
Chimera versions 1.2352, 1.2363, and 1.2382 on Mac OSX. It doesn't
sound like you were doing anything wrong, however. The only
possibilities I can think of are that the problem is platform-
specific or that cutting and pasting removed some deleterious
invisible character(s).
Note that SDF files from PubChem generally contain flatland molecules
(2-dimensional, with the Z-coordinate column all zeros, as you can
see below). I suspect you really wanted a 3-dimensional molecule.
Just a few weeks ago, I used the "Pub 3D" database as a source for 3D
coordinates of molecules, looked up by PID from PubChem searches.
Unfortunately this server seems to be unreachable right now (I'm
hoping it comes back!):
http://rguha.ath.cx/~rguha/p3d/
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
> 16048627
> -OEChem-05040716572D
>
> 113118 0 0 0 0 0 0 0999 V2000
> 3.4030 4.5407 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
> 11.7288 -2.2663 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
> 2.5369 5.0407 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 3.9030 5.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 2.9030 3.6746 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 11.7288 -3.2663 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
> 10.7288 -2.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 12.7288 -2.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 6.1864 -3.2991 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 17.1265 4.0641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 4.8972 -2.1423 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 16.7693 2.3693 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 6.6424 -5.4263 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 4.0223 -3.0754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 18.7407 5.5226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 18.0148 2.0782 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 6.9473 2.7359 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
> 11.5196 1.7056 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 5.5185 -4.0434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 18.1050 3.8579 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 6.9473 4.3454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.1258 0.9008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.5309 3.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.5309 1.8086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.0010 4.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.8628 0.2337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.0010 3.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 11.7288 0.7337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.7573 4.9318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.6399 5.2970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.2579 1.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 9.4553 0.1588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 9.2129 1.3091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 12.1874 2.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 8.5309 3.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.0309 2.6746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.1350 4.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.8628 -0.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.5901 1.0411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 13.1659 2.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.1350 2.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 12.5948 0.2337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 9.0309 2.6746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.2690 4.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 11.7288 -1.2663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.2690 3.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.9007 0.0906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 12.5948 -0.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 13.8338 2.9879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.2329 -0.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 14.8123 2.7817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.5436 -1.6042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 15.4801 3.5260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.8757 -2.3485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 16.4586 3.3198 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.7281 -5.0211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.5238 -3.9406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 18.8470 4.5283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 18.5133 2.9450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.8630 -5.5226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.1187 -4.8548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 19.7139 4.0298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 19.5076 3.0513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 8.1208 4.4296 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.2595 5.2953 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.3937 5.4340 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.2299 5.4876 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.4493 5.8870 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.0499 5.1064 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.8048 2.0774 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.6405 1.2975 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.9953 0.5745 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 9.0397 -0.3012 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 9.9154 -0.2568 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 9.4661 1.8751 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.6470 1.5623 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.9598 0.7432 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 11.6611 2.7775 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 12.4187 3.0251 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.8409 4.0776 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 10.3409 3.2116 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.1350 5.1607 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 10.3258 -1.0763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.0432 0.7491 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.2075 1.5290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 12.9347 1.6684 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.6923 1.9160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.1350 1.9207 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.1318 0.5437 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.7209 2.1377 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.7321 2.7307 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.2833 -0.3973 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.4477 0.3826 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.1318 -1.0763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 14.0650 3.5632 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.3074 3.3156 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.6860 -0.9457 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.8503 -0.1658 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 15.3386 2.4541 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 14.5810 2.2065 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.9261 -2.0921 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.0905 -1.3122 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 15.7114 4.1013 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 14.9538 3.8537 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.0000 4.7307 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.4029 -5.9383 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.2283 -6.0236 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.5812 -4.5457 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.7551 -5.3570 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 19.9651 4.5966 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 20.3038 3.8392 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 20.1244 2.9876 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 19.5087 2.4313 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 3 1 0 0 0 0
> 1 4 2 0 0 0 0
> 1 5 2 0 0 0 0
> 1 44 1 0 0 0 0
> 2 6 1 0 0 0 0
> 2 7 2 0 0 0 0
> 2 8 2 0 0 0 0
> 2 45 1 0 0 0 0
> 3105 1 0 0 0 0
> 9 19 1 0 0 0 0
> 9 54 1 0 0 0 0
> 10 20 1 0 0 0 0
> 10 55 1 0 0 0 0
> 11 54 2 0 0 0 0
> 12 55 2 0 0 0 0
> 13 56 2 0 0 0 0
> 14 57 2 0 0 0 0
> 15 58 2 0 0 0 0
> 16 59 2 0 0 0 0
> 17 23 2 0 0 0 0
> 17 27 1 0 0 0 0
> 17 31 1 0 0 0 0
> 18 24 1 0 0 0 0
> 18 28 1 0 0 0 0
> 18 34 1 0 0 0 0
> 19 56 1 0 0 0 0
> 19 57 1 0 0 0 0
> 20 58 1 0 0 0 0
> 20 59 1 0 0 0 0
> 21 23 1 0 0 0 0
> 21 25 1 0 0 0 0
> 21 29 1 0 0 0 0
> 21 30 1 0 0 0 0
> 22 24 1 0 0 0 0
> 22 26 1 0 0 0 0
> 22 32 1 0 0 0 0
> 22 33 1 0 0 0 0
> 23 35 1 0 0 0 0
> 24 36 2 0 0 0 0
> 25 27 2 0 0 0 0
> 25 37 1 0 0 0 0
> 26 28 2 0 0 0 0
> 26 38 1 0 0 0 0
> 27 41 1 0 0 0 0
> 28 42 1 0 0 0 0
> 29 64 1 0 0 0 0
> 29 65 1 0 0 0 0
> 29 66 1 0 0 0 0
> 30 67 1 0 0 0 0
> 30 68 1 0 0 0 0
> 30 69 1 0 0 0 0
> 31 39 1 0 0 0 0
> 31 70 1 0 0 0 0
> 31 71 1 0 0 0 0
> 32 72 1 0 0 0 0
> 32 73 1 0 0 0 0
> 32 74 1 0 0 0 0
> 33 75 1 0 0 0 0
> 33 76 1 0 0 0 0
> 33 77 1 0 0 0 0
> 34 40 1 0 0 0 0
> 34 78 1 0 0 0 0
> 34 79 1 0 0 0 0
> 35 43 2 0 0 0 0
> 35 80 1 0 0 0 0
> 36 43 1 0 0 0 0
> 36 81 1 0 0 0 0
> 37 44 2 0 0 0 0
> 37 82 1 0 0 0 0
> 38 45 2 0 0 0 0
> 38 83 1 0 0 0 0
> 39 47 1 0 0 0 0
> 39 84 1 0 0 0 0
> 39 85 1 0 0 0 0
> 40 49 1 0 0 0 0
> 40 86 1 0 0 0 0
> 40 87 1 0 0 0 0
> 41 46 2 0 0 0 0
> 41 88 1 0 0 0 0
> 42 48 2 0 0 0 0
> 42 89 1 0 0 0 0
> 43 90 1 0 0 0 0
> 44 46 1 0 0 0 0
> 45 48 1 0 0 0 0
> 46 91 1 0 0 0 0
> 47 50 1 0 0 0 0
> 47 92 1 0 0 0 0
> 47 93 1 0 0 0 0
> 48 94 1 0 0 0 0
> 49 51 1 0 0 0 0
> 49 95 1 0 0 0 0
> 49 96 1 0 0 0 0
> 50 52 1 0 0 0 0
> 50 97 1 0 0 0 0
> 50 98 1 0 0 0 0
> 51 53 1 0 0 0 0
> 51 99 1 0 0 0 0
> 51100 1 0 0 0 0
> 52 54 1 0 0 0 0
> 52101 1 0 0 0 0
> 52102 1 0 0 0 0
> 53 55 1 0 0 0 0
> 53103 1 0 0 0 0
> 53104 1 0 0 0 0
> 56 60 1 0 0 0 0
> 57 61 1 0 0 0 0
> 58 62 1 0 0 0 0
> 59 63 1 0 0 0 0
> 60 61 1 0 0 0 0
> 60106 1 0 0 0 0
> 60107 1 0 0 0 0
> 61108 1 0 0 0 0
> 61109 1 0 0 0 0
> 62 63 1 0 0 0 0
> 62110 1 0 0 0 0
> 62111 1 0 0 0 0
> 63112 1 0 0 0 0
> 63113 1 0 0 0 0
> M CHG 2 6 -1 17 1
> M END
>> <PUBCHEM_COMPOUND_CID>
> 16048627
>
>> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
> 15
>
>> <PUBCHEM_CACTVS_HBOND_DONOR>
> 1
>
>> <PUBCHEM_CACTVS_ROTATABLE_BOND>
> 19
>
>> <PUBCHEM_CACTVS_SUBSKEYS>
> AAADcfB/
> vABgAAAAAAAAAAAAAAAAAWLFiAAwYAAAAAAAAFgBQAAAHgQECAAADgjB2AQyyYMQAIKoAy
> XyXHDCAEAhAgAoiBk4ZJgIIDLAkZGEIAhkhCDIyAedyMAPgAQAgAACAAAACAEAAAQAAAAA
> AAAAAA==
>
>> <PUBCHEM_IUPAC_OPENEYE_NAME>
> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-
> [5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-
> sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate
>
>> <PUBCHEM_IUPAC_CAS_NAME>
> (2E)-1-[5-[(2,5-dioxopyrrolidin-1-yl)oxy-oxo-methyl]pentyl]-2-
> [(E)-3-[1-[5-[(2,5-dioxopyrrolidin-1-yl)oxy-oxo-methyl]pentyl]-3,3-
> dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-
> indoline-5-sulfonate
>
>> <PUBCHEM_IUPAC_NAME>
> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-
> [5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-
> sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indole-5-sulfonate
>
>> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-
> [5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-
> sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indole-5-sulfonate
>
>> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-
> [5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-
> sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate
>
>> <PUBCHEM_NIST_INCHI>
> InChI=1/C43H50N4O14S2/c1-42(2)30-26-28(62(54,55)56)16-18-32(30)44
> (24-9-5-7-14-40(52)60-46-36(48)20-21-37(46)49)34(42)12-11-13-35-43
> (3,4)31-27-29(63(57,58)59)17-19-33(31)45(35)25-10-6-8-15-41(53)
> 61-47-38(50)22-23-39(47)51/h11-13,16-19,26-27H,
> 5-10,14-15,20-25H2,1-4H3,(H-,54,55,56,57,58,59)/f/h54H
>
>> <PUBCHEM_CACTVS_EXACT_MASS>
> 910.276
>
>> <PUBCHEM_OPENEYE_MF>
> C43H50N4O14S2
>
>> <PUBCHEM_OPENEYE_MW>
> 911.008
>
>> <PUBCHEM_OPENEYE_CAN_SMILES>
> CC1(C2=C(C=CC(=C2)S(=O)(=O)O)[N+](=C1C=CC=C3C(C4=C(N3CCCCCC(=O)ON5C
> (=O)CCC5=O)C=CC(=C4)S(=O)(=O)[O-])(C)C)CCCCCC(=O)ON6C(=O)CCC6=O)C
>
>> <PUBCHEM_OPENEYE_ISO_SMILES>
> CC1(C2=C(C=CC(=C2)S(=O)(=O)O)[N+](=C1\C=C\C=C\3/C(C4=C(N3CCCCCC(=O)
> ON5C(=O)CCC5=O)C=CC(=C4)S(=O)(=O)[O-])(C)C)CCCCCC(=O)ON6C(=O)CCC6=O)C
>
>> <PUBCHEM_CACTVS_TPSA>
> 245
>
>> <PUBCHEM_OPENEYE_MONOISOTOPICWT>
> 910.276
>
>> <PUBCHEM_TOTAL_CHARGE>
> 0
>
>> <PUBCHEM_HEAVY_ATOM_COUNT>
> 63
>
>> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
> 0
>
>> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
> 0
>
>> <PUBCHEM_BOND_DEF_STEREO_COUNT>
> 2
>
>> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
> 0
>
>> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
> 0
>
>> <PUBCHEM_COMPONENT_COUNT>
> 1
>
>> <PUBCHEM_CACTVS_TAUTO_COUNT>
> 9
>
>> <PUBCHEM_BONDANNOTATIONS>
> 25 27 8
> 25 37 8
> 26 28 8
> 26 38 8
> 27 41 8
> 28 42 8
> 37 44 8
> 38 45 8
> 41 46 8
> 42 48 8
> 44 46 8
> 45 48 8
>
> $$$$
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