Xavier This should work. Can you send the SMILES and more details about the symptom of the problem. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Thu, Jun 11, 2020 at 11:32 AM Xavier Brazzolotto < [email protected]> wrote:

Dear all,

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 P*R* or P*R compound, *I always end up with the very same enantiomer…

Maybe eLBOW does not handle the phosphorous specific stereochemistry ?

Many thanks

Xavier Brazzolotto, PhD

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