Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

[David G. A. <ari...@cb...>]

OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/

> Hello, i'm trying to assign 3D coordinates to this SMILES structure
>
> OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3ccccc3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12
>
> obabel is unable to resolve the structure
>
> time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2
> 1 molecule converted
>
> real	6m8.107s
> user	6m7.947s
> sys	0m0.020s
>
> But the mol2 files looks like...
>
> @<TRIPOS>MOLECULE
> *****
>  65 70 0 0 0
> SMALL
> GASTEIGER
>
> @<TRIPOS>ATOM
>       1 O             -nan      -nan      -nan O.3     1  LIG1
> -0.3026
>       2 P             -nan      -nan      -nan P.3     1  LIG1
> 0.4724
>       3 O             -nan      -nan      -nan O.2     1  LIG1
> -0.2275
> (...)
>
> Any ideas, is this a known bug?
> Best
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