Do all residues showing attachment to ligand contribute to the binding energy?
While doing docking, if, in addition to the known binding site attachments, the ligand is showing few more attachments with some residues. Do they contribute to the binding energy ?? if Yes, do I need to dock the ligand in such a way so that, it shows attachments with the ligand as it is showing in PDB file when viewed in Pymol?
Sometimes ligand shows some additional polar bonds with the other residues which may occur because of the different ligand of choice. If you are using different ligands than the one present in PDB entry, then you may see additional bonds that contribute to the binding affinity. Hence, they may either be formed by the charge on the atoms of the ligand and/ protein or sometimes, the software reads them as the polar bond, hence, they appear. But, you need to dock the ligand in the specific binding site and not to worry about the additional bonds.