Hello,
I am looking into the molecular interactions between the docked pose of ligand and the protein, one of the bonds that show up in the 2d interaction map is named as an attractive charge which is formed between N of my ligand and O of my protein. I just wanted to confirm that this would be a covalent bond, right in which case it will definitely be stronger than the Hydrogen bond?
What functional groups are represented by the N and O? "attractive charge bond" is not an expression usually found in this context, but it may be an unusual way to describe a salt bridge (non-covalent interaction between groups carrying opposite charges). If the N e.g. is an amine, and the O part of a carboxylate group, you would have a salt bridge between the positively charged, protonated amine and the negatively charged, deprotonated carboxylate. Hydrogen bonds in a salt bridge are usually stronger than hydrogen bonds between uncharged groups.
Thank you very much Annemarie Honegger . You are right, it indeed is a salt bridge between an amine and a carboxylate group.
Since there is one carboxylate ion and one amonium ion, obviously, it is ionic interactions. However, -NH3+ hydrogen can form strong hydrogen bonding with the -COO- oxygen. The stabilization energy due to ionic interactions (salt bridge) is many fold higher than that of hydrogen bonding interactions.... So you can mention both the interactions (if you found) simultaneously in your manuscript.
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