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