[Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

[Gustavo S. <gus...@gm...>]

Hi all,

I run into an issue here, and I'd appreciate your input. I noticed that
compounds that differ only on the cis-trans isomerization around an sp2
nitrogen get the same InChI Key from RDKit. For example:

> inchi_cis =
Chem.inchi.MolToInchiKey(Chem.MolFromSmiles("C/N=C(/NC#N)NCCSCc1nc[nH]c1C"))
> inchi_cis
'AQIXAKUUQRKLND-UHFFFAOYSA-N'

> inchi_trans =
Chem.inchi.MolToInchiKey(Chem.MolFromSmiles("C/N=C(\\NC#N)NCCSCc1nc[nH]c1C"))
> inchi_trans
'AQIXAKUUQRKLND-UHFFFAOYSA-N'

> inchi_cis == inchi_trans
True

I wonder if this is a limitation of the InChI Key definition, or an
implementation issue.

Thanks a lot,
--
Gustavo Seabra.