(1) complexes.tar - All the protein-ligand complexes (several orientations of each ligand, whether crystallographic or not). This is in GROMACS top and gro format. Some of the top and gro files show five atoms which are fully decoupled, labeled "MR1"-"MR5".  These were used in our free energy protocol (the "reference" topology described in the paper methods) but are not physical.  The compounds are labeled c1-c20 based on the numbering in the paper/Table 1.

(2) ligands_in_solution.tar - Top and gro files of the free ligands in solution.

(3) net9.tar - We mention in the paper that all of the relative calculations were performed with a probably-incorrectly protonated receptor with a net charge of -5.  Obviously we don't know the actual protonation states of any residues except the binding site aspartate, but based on the protein pI the protein net charge is probably positive and not negative.  We corrected these problems by performing all absolute charging calculations in a re-parameterized receptor with net charge +9.  This receptor shows the net +9 topology we employed.