[phenixbb] phenix eLBOW and phosphorous stereochemistry

Nigel Moriarty nwmoriarty at lbl.gov
Thu Jun 11 12:50:09 PDT 2020


This should work. Can you send the SMILES and more details about the
symptom of the problem.



Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Thu, Jun 11, 2020 at 11:32 AM Xavier Brazzolotto <
xavier.brazzolotto at chemdef.fr> 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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