<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!--
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--></style></head><body lang=ES-MX link="#0563C1" vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi all, hope this message finds you well. </p><p class=MsoNormal>As in a previous topic from 2018, I’m having problems refining a covalent-bounded ligand.</p><p class=MsoNormal>The link shall be made between a carbon atom that is double bonded to an oxigen </p><p class=MsoNormal>“SMILES <span style='font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:#212121;background:white'>C1=CC=C(C=C1)C=O” and the SG group of a Cys residue. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:#212121;background:white'>I generated a CIF dictionary through AceDRG in COOT and CCP4i2. But after trying different aproaches during refinement, (Automatic Linking parameters, Atom selection, acceptor & donnor, ligand bond cut off and so) the result keeps being a non bounded enzyme-ligand complex (“Not linked: pdbres="LIG A 401”).<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:#212121;background:white'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:#212121;background:white'>I readed in the phenixbb that this was solved by changing the nature of the ligand (<a href="http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html">http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html</a>), but is not the way I would like to follow.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:#212121;background:white'>Any suggestions or ideas would be greately appreciated, thanks a lot for your time. Stay safe. <o:p></o:p></span></p></div></body></html>