Our approach uses a modified dual topology scheme. This scheme involves selecting the maximal common substructure (MCS) for a given ligand pair which is structurally and chemically identical between the two ligands within the thresholds defined. The standard thresholds used are a 0.1e difference between the two ligands for atomic charges of individual atoms in MCS as well as their sums. First of all, a structurally identical MCS is identified.