I am trying to generate 3D coordinates with the correct stereochemistry from SMILES. For instance one of my molecules is:
c12c(O)c([C@H]5[C@H](O)[C@@H](O)[C@H](O)[C@H](O5)CO)c(O[C@H]4[C@H](O)[C@@H](O)[C@H](O)[C@H](O4)CO)cc1oc(c3ccc(O)cc3)cc2(=O)
I have tried:
Openbabel obgen (-> incorrect stereochemistry)
Pybel make3D (-> incorrect stereochemistry)
Balloon (-> incorrect stereochemistry)
smi23d (-> segmentation fault)
What tools can do this correctly? If there are no free tools, how about non-free tools (other than CORINA)?
Imported from: http://blueobelisk.stackexchange.com/questions/308
