2.3. MD trajectory analysis and prime MM-GBSA calculations

The simulation interactions diagram panel in the Maestro software was utilized to follow the interactions' contributions to the ligand–protein stability. Hence to calculate the ligand binding free energies and ligand strain energies for the docked compounds, the molecular mechanics generalized Born/solvent accessibility (MM-GBSA) was carried out over the 100 ns period with the thermal_mmgbsa.py python script provided by Schrödinger, which takes a Desmond trajectory file, splits it into individual snapshots, runs the MM-GBSA calculations on each frame, and outputs the average computed binding energy along with the standard deviation.