The further four saaPCVA schemes have in common that they are performed in vacuum, which means the solvation shell is completely removed from the system to decrease the computational cost. As for the standard variant, the QM region contains the three ligands only. In the first scheme (vac), we simply removed all water molecules from the equilibrated COMT starting structure and performed saaPCVA based on the resulting vacuum system. Since in this case the whole system is geometry-optimized in vacuum without a fixed water environment we additionally tested an approach with a completely fixed MM protein environment (vac fix ), i.e., only the QM region is optimized. The two remaining schemes (cryst and cryst fix ) are similar to the aforementioned ones, except for the fact that the optimization is directly performed based on the crystal structure (PDB: 3BWM) without the previous equilibration steps to assess the need of pre-processing.