Dear community,

I try to create a covalent bond between a nitrile warhead and a cysteine. 
Therefore, the final product should be S-C=NH2 (of course the C is also 
connected to the rest of my ligand). The triple bond between C and N of the 
ligand should lose one order and pass to a double one and gain the covalent 
bond with the SG of the Cysteine. Unfortunately, I am unable to make it with 
the "Make a link" module in coot despite all possible entries I could think of. 
It is always complaining about the valence of the C of my ligand. Somehow, the 
module believes that the C will have a valence of 5 which is of course not 
possible. I probably do not write properly the command about the bond order in 
the following window:
[cid:image002.png@01DB4D3D.C0777680]

Does anyone could give me a hand? Would be very much appreciated. The bond 
should happen between the C29 of my ligand and the SG of the protein cysteine. 
Triple bond between C29 and N5 of my ligand should become double bond.

Many thanks for your help!
Best,


Nicolas Bocquet, PhD
FoRx Therapeutics
----------------------------
Lichtstrasse, 35 WSJ-350.3.13
4056 Basel, Switzerland
Tel +41782312920

[cid:image001.png@01DB4D3C.D3A67680]


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