Bob,
Evidently, a fair number of PubChem's sdf's have partial charge data. I
know that I can parse the data with JavaScript and apply the charge
results, including implied zeros, to the model with Jmol script, but I want
to make sure I'm not reinventing the wheel. I've pasted the data for
ethanol below. Is Jmol able to read these partial charges directly?
Otis
702
-OEChem-01171122093D
9 8 0 0 0 0 0 0 0999 V2000
-1.1712 0.2997 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0463 -0.5665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2175 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0958 -1.2120 0.8819 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0952 -1.1938 -0.8946 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1050 -0.3720 -0.0177 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2426 0.9307 -0.8704 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2616 0.9052 0.8886 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1291 0.8364 0.8099 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 9 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 5 1 0 0 0 0
3 6 1 0 0 0 0
3 7 1 0 0 0 0
3 8 1 0 0 0 0
M END
> <PUBCHEM_COMPOUND_CID>
702
> <PUBCHEM_CONFORMER_RMSD>
0.4
> <PUBCHEM_CONFORMER_DIVERSEORDER>
1
> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
3
1 -0.68
2 0.28
9 0.4
> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
0
> <PUBCHEM_PHARMACOPHORE_FEATURES>
2
1 1 acceptor
1 1 donor
> <PUBCHEM_HEAVY_ATOM_COUNT>
3
> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
0
> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
0
> <PUBCHEM_BOND_DEF_STEREO_COUNT>
0
> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
0
> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
0
> <PUBCHEM_COMPONENT_COUNT>
1
> <PUBCHEM_CACTVS_TAUTO_COUNT>
1
> <PUBCHEM_CONFORMER_ID>
000002BE00000001
> <PUBCHEM_MMFF94_ENERGY>
-1.3096
> <PUBCHEM_FEATURE_SELFOVERLAP>
10.148
> <PUBCHEM_SHAPE_FINGERPRINT>
139733 1 18410856559692628036
21015797 1 18196933258125981446
> <PUBCHEM_SHAPE_MULTIPOLES>
55.87
1.48
0.75
0.58
0.11
-0.18
0
0
0.06
0.15
0
0
0.09
-0.67
> <PUBCHEM_SHAPE_SELFOVERLAP>
84.621
> <PUBCHEM_SHAPE_VOLUME>
41.5
> <PUBCHEM_COORDINATE_TYPE>
2
5
255
$$$$
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
------------------------------------------------------------------------------
Protect Your Site and Customers from Malware Attacks
Learn about various malware tactics and how to avoid them. Understand
malware threats, the impact they can have on your business, and how you
can protect your company and customers by using code signing.
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
