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#869 Double bond geometry destroyed when generating 3D coordinates

2.3.x
open
nobody
None
1
2013-03-05
2013-03-05
upgrayedd
No

The following SMILES strings represent 16-membered rings, each containing two E-configured double bonds:

1.) O=C(OC@@HC(/C=C/1)=O)/C=C/C@@HC@HOC(CC@HOC1=O)=O
2.) O=C(OC@@HC@@H/C=C/C1=O)/C=C/C(C@HOC(CC@HO1)=O)=O

When generating coordinates using the --gen3d option, OpenBabel builds the correct structure in case of the first SMILES; but in case of the second SMILES, the geometry of one of the two endocyclic double bonds is changed from E to Z. Furthermore, the planarity of this double bond is destroyed.
The two SMILES strings were saved in a file called 'test.smi' and the following command was executed:
babel test.smi test.pdb --gen3d -m

The error also occures when the two molecules mentioned above are used as 2D-sdf files, so it seems to be an issue of 3D coordinates generation.

Version: 2.3.2 -- Oct 5 2012 -- 10:02:15
OS: Windows 7 (error also occures under Linux)

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Discussion

  • upgrayedd
    upgrayedd
    2013-03-05

    please excuse me, the two SMILES 1.) and 2.) are wrong.. - but the attached file 'test.smi' contains the correct SMILES.