I am making the restraints file (CIF) for a ligand with two chiral carbons, using eLBOW (AM1 QM, output: retain original chirality) from a SMILES description and obtain the following:

Atom   input_chirality   input_smiles   output_vol_sign   output_R/S   output_chirality_pdb

C20    S                       C@H               negative               S                  S

C37    R                       C@@H            positive                S                  S

Although the volume_sign in the output cif file correspond to the input chiralities, the output pdb has the wrong chirality for the carbon C37: S instead of the desired R.

I think the "retain original chirality" option is what I need to keep the input chirality, but apparently it doesn't. How should I proceed to get a pdb with the correct chiralities?

Best regards,

Lionel

PS: phenix version 1.9-1692, linux X86_64

PS2: in REEL, the action "Find unique code" make phenix (not REEL) crash (all windows close) without error message