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, but sometimes, they do not actually contribute in binding affinity towards the catalytic residues, they may either be formed by the charge on the atoms of the ligand and/ protein, or 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.