<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><font face="Menlo">Dear BUSTER developers,</font><div><font face="Menlo"><br></font></div><div><font face="Menlo">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. </font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">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 _<a href="http://chem_comp_tor.id">chem_comp_tor.id</a> 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 </font></div><div><font face="Menlo"><br></font></div><div><p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; line-height: normal; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><span style="font-variant-ligatures: no-common-ligatures"><font face="Menlo">Mogul_plane_rms_out_of_plane_torsion3.7_degs_282_hits_trans_98.6%_within_10degs</font></span></p></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">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 _<a href="http://chem_comp_tor.id">chem_comp_tor.id</a> are trans-32.</font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">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”. </font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">Could you please advise how to interpret these results? Thanks.</font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">Best regards,</font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">Wei-Chun Kao</font></div><div><font face="Menlo"><span style="font-size: 11px;"><br></span></font><div>
<meta charset="UTF-8"><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="background-color: rgb(255, 255, 255);"><div style="color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">—</div><div style="color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px; min-height: 15px;"><br></div><div style="color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;">Dr. rer. nat. Wei-Chun Kao</div><div style="margin: 0px;"><div style="margin: 0px;"><font color="#888888" face="Proxima Nova Soft" size="2">wei-chun.kao@biochemie.uni-freiburg.de</font></div></div><div style="color: rgb(18, 85, 204); font-family: "Proxima Nova Soft"; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><span style="color: rgb(136, 136, 136);">TEL: <span style="color: rgb(18, 85, 204);"><a href="tel:%2B49-761-203-5277">+49-761-203-5277</a></span></span></div><div style="color: rgb(18, 85, 204); font-family: "Proxima Nova Soft"; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;"><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;"><div style="color: rgb(18, 85, 204); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;"><span style="color: rgb(145, 145, 145); font-size: small;">orcid.org/0000-0001-8687-6334<span class="Apple-tab-span" style="white-space: pre;"> </span></span></div></div></div></div></div></div></div></div></div></div></div></div></div><br><div style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none; color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Institute for Biochemistry and Molecular Biology</div><div style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none; color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">AG Carola Hunte</div><div style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none; color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Albert-Ludwigs-Universitaet Freiburg</div><div style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none; color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Stefan-Meier-Str. 17</div><div style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none; color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">D-79104 Freiburg im Breisgau</div><div style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none; color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Germany</div>
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