The active-site of the SARS-CoV-2 M pro consists of catalytic dyad residues (His41/Cys145) which are responsible for the proteolytic activity and function of the protease. Among the residues involved in the enzymatic activity of the M pro , His41 is suggested to act as a proton carrier of the thiol hydrogen of Cys145 66,67 -enabling nucleophilic attack on the reactive center of the inhibitor by the activated Cys145 thiolate formed. Recent work by Gumbart and coworkers have shown that the protonation state of His41 of the M pro is sensitive to the presence of a ligand, which can influence the structural stability and dynamics of the M pro complex. Therefore, for each of the protein-ligand complexes studied, we investigated the preferred protonation state for His41 to inform our binding energy simulations.