Additional sequence differences between nCOV-2019 and SARS-COV influence RBD/ACE2 binding. Residue D480 in SARS-COV contributes negatively to total binding energy (6.25 ± 0.14 kcal/mol) and mutating this residue to S494 in nCOV-2019 lowers this negative contribution to 1.17 ± 0.06 kcal/mol. D480 in SARS-COV is located in a region of high negative charge from residues E35, E37, and D38 on ACE2. Electrostatic repulsion between D480 on SARS-COV and the acidic residues on ACE2 is the reason for highly negative contribution of this residue to binding of SARS-COV to ACE2. Mutation to S494 in this location removes this highly negative contribution. Gao and co-workers26 computed the relative free energies of binding because of mutations from the RBD-ACE2 of SARS-COV to the corresponding residues in nCOV-2019. They used a FEP approach and showed that mutation D480S in SARS-COV changed the binding free energy by −1.9 ± 0.8 kcal/mol which is consistent with our study. Furthermore, we performed an additional simulation on D480A mutant in SARS-COV and found that this mutation has a binding affinity of 23.46 ± 3.07 kcal/mol which is about 5 kcal/mol higher than the wild-type SARS-COV RBD. In addition, experimental binding affinity measurements showed that mutations of S494 to an acidic residue highly reduce the binding affinity to ACE2 which confirms the hypothesis here.