I use phenix.elbow in order to generate mol2 files that will then be used in a docking process through autodock/vina.

I am facing a strange issue. While using a SMILES string bearing stereochemistry at a desired phosphorous atom as eLBOW input file, the correct stereochemistry is not respected in the output files.

While giving PR or PR compound, I always end up with the very same enantiomer…

Maybe eLBOW does not handle the phosphorous specific stereochemistry ?

Many thanks