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<p class="MsoNormal"><span style="font-size:11.0pt">I recently did this for a covalently modified Cys. Follow these steps:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Generate a SMILES string for L-cysteine bonded the modification. Yours appears to be C1=CC=C(C=C1)C(=O)SCC(C(O)=O)N. https://pubchem.ncbi.nlm.nih.gov/compound/262741<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Input the SMILES string to PHENIX eLBOW using the graphical user interface with quantum optimization enabled to generate restraints (.cif) and coordinates
(.pdb). <o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Use the eLBOW graphical user interface to change the atom names for the backbone atoms of the modified cysteine to the standard ones for amino acids
(N, CA, C, O, CB).<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Save the new coordinates and restraints.<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Move the modified cysteine you saved in step 4 into the density using Coot.
<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Delete the extra O atom of the cysteine carboxylate and save the coordinates of the modified Cys.
<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Using a text editor, change the residue number and chain ID of the modified cysteine to those of the Cys in your structure. Save the file.
<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1"><span style="font-size:11.0pt">Using a text editor, replace the Cys coordinates of your structure with the coordinates of the modified Cys save in step 7. <o:p></o:p></span></li></ol>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">In subsequent refinements, PHENIX refine should automatically incorporate the modified cysteine into the polypeptide chain, assuming you correctly renamed the atoms in step 3 and deleted the correct O atom
in step 6.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">--<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">John J. Tanner </span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Professor of Biochemistry and Chemistry</span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Associate Chair of Biochemistry</span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Department of Biochemistry</span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">University of Missouri<br>
117 Schweitzer Hall</span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">503 S College Avenue<br>
Columbia, MO 65211<br>
Phone: 573-884-1280</span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black"><a href="mailto:tannerjj@missouri.edu" target="_blank" title="mailto:tannerjj@missouri.edu">Email: tannerjj@missouri.edu</a><br>
<a href="https://cafnrfaculty.missouri.edu/tannerlab/" title="https://cafnrfaculty.missouri.edu/tannerlab/">https://cafnrfaculty.missouri.edu/tannerlab/</a></span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.5pt;font-family:Helvetica;color:black">Lab: Schlundt Annex rooms 3,6,9, 203B, 203C</span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.5pt;font-family:Helvetica;color:black;background:white">Office: Schlundt Annex 203A</span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="ES-MX" style="font-size:12.0pt;color:black">From:
</span></b><span lang="ES-MX" style="font-size:12.0pt;color:black">phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Sergio A. Sampieri <sampieridae@gmail.com><br>
<b>Date: </b>Friday, January 21, 2022 at 10:39 PM<br>
<b>To: </b>phenixbb@phenix-online.org <phenixbb@phenix-online.org><br>
<b>Subject: </b>[phenixbb] refining a covalent-bound ligand (part 2)<o:p></o:p></span></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:#FFC7CE"><b><span lang="ES-MX" style="color:#9C0006">WARNING:</span></b><span lang="ES-MX" style="color:black"> This message has originated from an External Source. This may be a phishing expedition
that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="ES-MX" style="font-size:11.0pt"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES-MX" style="font-size:11.0pt">Hi all, hope this message finds you well.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES-MX" style="font-size:11.0pt">As in a previous topic from 2018, I�m having problems refining a covalent-bounded ligand.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES-MX" style="font-size:11.0pt">The link shall be made between a carbon atom that is double bonded to an oxigen
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES-MX" style="font-size:11.0pt">�SMILES </span><span lang="ES-MX" 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.
</span><span lang="ES-MX" style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES-MX" 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�).</span><span lang="ES-MX" style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES-MX" style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:#212121;background:white"> </span><span lang="ES-MX" style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES-MX" 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="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phenix-online.org%2Fpipermail%2Fphenixbb%2F2018-February%2F023718.html&data=04%7C01%7Ctannerjj%40missouri.edu%7C9ee2fb7d400b43ce4f2c08d9dd61150a%7Ce3fefdbef7e9401ba51a355e01b05a89%7C0%7C0%7C637784231772798225%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=jfdfpaNIDIvqF%2Foqqt1tlriMuWTRpL3%2F8CAz0oaVxS4%3D&reserved=0">http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html</a>),
but is not the way I would like to follow.</span><span lang="ES-MX" style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES-MX" 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.
</span><span lang="ES-MX" style="font-size:11.0pt"><o:p></o:p></span></p>
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