On 13/12/2024 08:06, Nicolas Bocquet wrote:
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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:
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.
1: It is not clear that you changed the bond order of the link. If the
valence seems to be 5, then the path forward would seem to be to
increase the bond order or delete an atom.
2: The link generation tool in CCP4i2 is more robust than the one in
Coot at the moment
https://www.youtube.com/watch?v=p4oTJ0bjD3M
Paul.
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