The differences in the ABFEs of the trapped water between our study and the reference study of Barillari et al. can be attributed to a number of differences between the two studies. We have simulated water in our calculations using the TIP3P water model, whereas the reference study used the TIP4P water model. The reference study modeled the protonation states of the protein amino acids and ligands in their complex structures assuming a pH of 7, while we have taken the experimental pH for the respective complexes, as reported in the PDB database, to determine the protonation states. The reference study did not report the prepared structures of their simulated complexes, so comparison of the employed protonation states is not possible. Furthermore, the reference study used a hard-wall potential to restrain the trapped water at its approximate position in the binding site, as well as to prevent the surrounding (the solvent, the protein side chains, and the ligand) from occupying the binding site after the trapped water's decoupling. In our study, we have used a Lennard-Jones repulsion term to prevent solvent flooding, and harmonic positional restraints to prevent a potential binding site collapse in our thermodynamic cycle. Additionally, the reference study's use of the hard-wall potential for water means that the resulting free energy calculations are calculating a subtly different free energy. In particular, the prior study is essentially computing the binding free energy of a trapped water in a preexisting cavity, unlike our study, which computes the binding free energy of water to the target site in a protein including any contributions of displacing the surroundings.