3.6. MMGBSA Analysis

The molecular mechanics-generalised born surface area (MMGBSA) is a prominent method to calculate the free binding energy of a ligand to a particular protein target. To validate the complex stability, the prime MMGBSA 3.0 version tool (Schrödinger 2020-4 LLC, New York, NY, USA) was used for obtaining the trajectory of PtB against the 2YAC protein. The binding free energy was estimated through the thermal_mmgbsa.py command, which followed the MMGBSA equations.

where ΔE_MM is the difference between the total energy of a complex and the summation of ligand and receptor energies, ΔG_solvent is the difference between the total solvation energy and the energy summation of a ligand with the receptor, and ΔG_SA is the difference between the total energy of the surface area and the summation of energy surface area for the ligand and receptor [63,64].