[phenixbb] phenix eLBOW and phosphorous stereochemistry

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


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 : 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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