Clearly there is no way to simulate covalent bonding with any docking tools. I can't completely understand your question. But I think what you mean is you have a PDB file where the ligand is covalently attached to cysteine, and you'd like to use it for docking. I used to met a couple case where the ligand is covalently attached to Fe in heme moiety of CYP450 enzyme, in this case we decided to not use the PDB and use other PDB with another ligand where the ligand is not covalently attached to any part of the protein nor heme.

Just to be sure, you better check the paper relating to the PDB structure you're dealing with. Because to my knowledge there is no way that an oxygen could form three stable covalent bond. And there is a probability that what Ganesh said is correct, it may form hydrogen bond, the only problem is the oxygen and sulfur atom is close enough that your molecule visualization software predict that there is a bond between oxygen and sulfur. Perhaps telling the PDB ID may help other solving this problem quicker.

Hope that help,

Radif

Mr. Salah.

Typical formation of S-S bonding. 

Usually cystein itseft has ability to convert to cystin.

Please find a paper in this topic:

1. Linear-dichroic infrared spectral analysis of Cu(I)–homocysteine complex, Spectrochimica Acta Part A,  60, 2004, 855-862, B.B Ivanova, M.G Arnaudov, P.R Bontchev 

Dear,

thank you very much for your answeres, I appreciate this,

So experementally in some articles i have found that the covalent bonding to macromolecules, is involved in trypanocidal effects (against trypanosoma cruzain).

and after the docking of the best pose a covalent adduct with the sulfur of the active site cysteine thiol in this enzyme was shown in results.

So is that possible a covalent bonding or it is only a hydrogen bonding which is so strong (much closer to the sulfur of cystein)

Thank you in advance :)

"and after the docking of the best pose a covalent adduct with the sulfur of the active site cysteine thiol in this enzyme was shown in results."

Which software did you use for docking?

I'm asking, since in most (or even all) cases such a situation is simply impossible. Most docking software can't properly describe covalent bond between the protein and the ligand (as Muhammad suggested above).

If you see a "bond" drawn by a visualization software, when looking at the results, don't mistake it for a true covalent bond. Most visualization software draw bonds between atoms that are close - but it does not mean there's really a bond between them, it just meanst that there are close. PDB files usually don't have any information about the bonds. 

i am using molegro virtual docker

but this software dont describe well ligand receptor interactions

so i used the lingplot+ and it show some hydrogen bonding that are strong ( less than  3.2 angstrom and it shows a covalent bounding with Cys25 !!

here my email and skype maybe if you will have free time we can discuss about it

[email protected]

skype user: kamel.tifa

Thank you in advance :)

If I remember correctly, hydrogen bond between NH - O or OH - O is in the range of 2.8-3.2 Angstrom, distance range of SH - O could be slightly longer than that (around +0.2 or +0.3), so it could be a hydrogen bond. If it is a hydrogen bond then there is should be hydrogen atom from thiol group right between sulfur and oxygen atom.