Chiral Ligand Poses Differ Between CCD or SMILES Inputs

[rjrich]

I have a pair of enantiomeric ligands. Only the (R)-isomer is available as a CCD. If I run the prediction for both the (R)- and (S)-isomers using SMILES for both, the poses are superposed and in a site distant from published results for the (R)-isomer. If I run the prediction with the (R)-isomer on its own as a CCD, the pose is in good agreement with published results. Finally, if I run the prediction with the (R)-isomer on its own as a SMILES string, the pose is in the same apparently erroneous site as obtained when running both isomers as SMILES strings. I have triple-checked the CCD and SMILES structures, and they are correct. Suggestions? Thanks!