In a next step in setting up the topology files, atoms for the Boresch-style restraints were selected ac-cording to the algorithm as described in Section 2.2. The restraints are defined in .itp files and added to the corresponding topology files. In this work, a force constant of 20 kcal mol -1 Å -2 was used for the bonds and 20 kcal mol -1 rad -2 for one of the angles and three dihedrals. The force constant for the other angle varied depending on the bond distance. We set it up such that for a bond distance of 5 Å a force constant of 40 kcal mol -1 rad -2 would be used for that angle restraint and with increasing distance that force constant was scaled quadratically. The contribution for releasing the orientational restraints when the ligands are noninteracting (Figure leg A and leg E) was calculated analytically using equation 32 from Boresch et al. 4.3. Setup for calculations in the solvent. For calculations in the solvent, we used two different protocols, depending on whether the ligands have a net charge. If all ligands in the dataset were neutral, we performed absolute hydration free energy calculations. If ligands were charged we performed an analogous 'separated topology' hydration free energy calculation, where the solvation of the two ligands were performed simultaneously in opposite directions. (As a test of this approach, we transformed a charged ligand into itself in solution and confirmed that the computed free energy converged to zero.) The two approaches required different scripts to generate the respective topology and coordinate files. For the absolute hydration free energy calculations the tool writes a topology file with a fully non-interacting ligand in the B state. For the charged ligands in the BACE1 dataset we ran SepTop calculations for the solvent part of the thermodynamic cycle in order to preserve the net charge throughout the simulation. We restrained the ligands to be half the box edge away from each other using a single harmonic distance restraint between the heavy atoms closest to the COM of the two ligands using a force constant of 2.4 kcal mol -1 Å -2 . One ligand was then fully decoupled while at the same time the other ligand was fully coupled using a similar protocol as in the binding site with the difference that in the solvent, the LJ-ϵ was scaled with a scaling factor γ = 0.3 rather than γ = 0.5 as in the binding site. The system was first equilibrated for 10 ps in the NVT ensemble at a force constant of 0.0024 kcal mol -1 Å -2 to allow the ligands to gently adjust to the distance restraint, followed by a 10 ps eqilibration in the NVT ensemble at the full restraint force constant.