[buster-discuss] Grade2 Mogul_plane_rms_out_of_plane

[Wei-Chun Kao]

Dear BUSTER developers,

I am using grade2 version 1.6.0 with CCDC 2024.1. I am trying to generate restraints from a compound which undergoes E-Z conversion, therefore I created the two stereoisomers respectively in mol2 format and gave them to grade2. 

However, the output restraints as well as coordinates of the Z- and E-compound are the E-form, _chem_comp_plane_atom.plane_id and _chem_comp_tor.id <http://chem_comp_tor.id/> are trans-32 (I suppose that the one in the Z-form should be cis-32 ? as two substituents of the C=C of interest are hydrogen atoms), _chem_comp_plane_atom.source as well as _chem_comp_tor.source of four carbon atoms around the C=C of interest show 

Mogul_plane_rms_out_of_plane_torsion3.7_degs_282_hits_trans_98.6%_within_10degs

I wondered if the input coordinates in mol2 contain mistakes, hence I tried to use SMILES and explicitly assigned the stereochemistry (X/C=C/Y and X/C=C\Y). Interestingly, grade2 can write the Z-form coordinates correctly, but the restraints still contain the aforementioned out_of_plane information and _chem_comp_plane_atom.plane_id and _chem_comp_tor.id <http://chem_comp_tor.id/> are trans-32.

Another exercise I made was with cis-but-2-ene (C/C=C\C) and trans-but-2-ene (C/C=C/C). Grade2 wrote the coordinates of the respective stereoisomers correctly, and the _chem_comp_tor.source  in the restraints are both “unrestrained_default”. 

Could you please advise how to interpret these results? Thanks.

Best regards,

Wei-Chun Kao

—

Dr. rer. nat. Wei-Chun Kao
wei-chun.kao at biochemie.uni-freiburg.de
TEL: +49-761-203-5277 <tel:%2B49-761-203-5277>
orcid.org/0000-0001-8687-6334						

Institute for Biochemistry and Molecular Biology
AG Carola Hunte
Albert-Ludwigs-Universitaet Freiburg
Stefan-Meier-Str. 17
D-79104 Freiburg im Breisgau
Germany

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