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] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
