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What (free) tools will generate 3D coordinates with correct stereochemistry from SMILES?

Asked by [ Editor ]

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

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2 answers

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baoilleach [ Admin ]

For the structure quoted, the dev version of OpenBabel should do it fine, but not the current release (as you note). Where the dev version will run into problems is where there is a ring system with internal stereochemistry (e.g. a bridged ring, or two cyclohexanes joined along an edge). There it may or may not work depending on the ring templates available, but should issue a warning if the stereochem was not achieved.

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