[Chimera-users] Inquiry about hydrogen bond analysis- important

Mohamed S. Nafie mohamed_nafie at science.suez.edu.eg
Sun Jan 7 05:33:56 PST 2018

Chimera team.

I made the hydrogen bond analysis for the co-crystallized ligand for 1DB1 receptor. it makes on the PDB 6 hydrogen bonds through both oxygen and hydrogen of the hydroxyl group (three of both) with the amino acids residues in the binding site, Also chimera forms 6 but through oxygen of hydroxyl group only. This my first question why?

The second question is the structure of the Co crystallized Ligand is not correct, when I adjust the bond order of it by Maestro and save it as pdb and reopen it by Chimera, it forms only two hydrogen binds why?

Please try to help me in this question, because I need it necessary


Mohamed S. Nafie
Assistant lecturer Chemistry Department,
Faculty of Science,  Suez Canal University
Ismailia, P.O(41522), Egypt
Mobile: +201065072524
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