<div dir="ltr"><p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif">Hi all, hope this message finds you well.
</p>
<p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif">As in a previous topic from 2018, I’m
having problems refining a covalent-bounded ligand.</p>
<p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif">The link shall be made between a carbon
atom that is double bonded to an oxigen </p>
<p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif">“SMILES <span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">C1=CC=C(C=C1)C=O”
and the SG group of a Cys residue. </span></p>
<p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">I generated a CIF dictionary through AceDRG in
COOT and CCP4i2. But after trying different approaches 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”).</span></p>
<p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"> </span></p>
<p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">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" style="color:rgb(5,99,193)">http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html</a>),
but is not the way I would like to follow.</span></p>
<p class="MsoNormal" style="margin:0cm;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">Any suggestions or ideas would be greatly
appreciated, thanks a lot for your time. Stay safe. </span></p><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><font color="#999999">“I’ve learned to think like a virus; no neurons, a lot of sex, and a lot of errors.”<br>John J. Holland<br><br><br>Biól. Sergio Aguirre Sampieri<br><br></font></div></div>