Free energy is a state function i.e., it is independent of the pathway that connects a starting state to a final state (also referred to as end states) of the system. In the present separation of states approach to binding free energy calculations, we connected the phase spaces of our end states by a pathway that implements physical restraints and alchemical transformations in our system, ultimately resulting in a thermodynamic cycle. While designing the thermodynamic cycle, we aimed at optimizing three aspects-first, the overall computational efficiency of the calculations, i.e., the total computational resources required (CPU/GPU time); second, the time to solution (wall clock time); and third, the automation of the simulation workflow (setup and analysis of the thermodynamic cycle). Optimizing these aspects is crucial, especially in drug discovery pipelines that often involve large numbers of protein-ligand pairs for affinity calculations. Therefore, our goal here is to develop a simulation protocol requiring minimal human intervention for its setup and analysis. In the following subsections, we have described the two types of free energy estimates we used in this study.