I am using the SARS-CoV-2 RBD domain and human ACE2 (PDB ID:6LZG) receptor in HADDOCK server to predict top model and compare with existing PDB to validate HADDOCK method.
By giving known active site residues of RBD and ACE2 from PDB.
Note: There is a presence of 3 glycans attached on ACE2 protein and 1 glycan on RBD protein.
Glycan attached to nitrogen atom of Asparagine(Asn-N) residue by glycosidic bond (type of covalent bond).
After protein-protein docking, the bond breaks between glycan and Asn residue and all NAGs moved away from protein.
How to restraint to keep bond without breaking after protein-protein docking?
Why is there a break in covalent bond even though it is very strong?