To calculate the free energy of binding and to score the inhibitors based on it, the molecular mechanics-Poisson-Boltzmann surface area (MM PBSA) method was carried out after simulation using the BIOVIA Discovery studio. Purposefully, the trajectories of the simulations were processed before the MM PBSA calculation and the trajectories of last 5 ns simulation data with frame increment of 250 was chosen for MM PBSA calculation. The MM PBSA calculation of free energy of binding is a slowest solvent approximation method based on continuum electrostatics and a summation of the calculation of potential energy, polar and non-polar solvation energy components and depends on the free energy of complex, ligand, and receptor as following as :