inputs - contains all the ligands as sdf files and the parameterised proteins (ff14SB)
networks - contains the networks (lomap/rbfenn), charged and neutral ligands are split
prep - contains the equilibrated solvated (TIP3P) ligands and protein-ligand complexes. tyk2, mcl1, p38 - ligands paramterised using Sage (OpenFF) syk, cmet, hif2a - ligands parameterised using GAFF2