We used covalent bond edges and proximity-based virtual edges to build the ligand-receptor proximity graphs. This approach mirrors virtual graph construction in PLEC fingerprints. We started building the graph representation from the ligand atoms. From each heavy atom, we added the protein atoms within a sphere of 4.5 Å radius (Figure ). Next, we added virtual "proximity" edges connecting the ligand and proximal protein atoms (Figure ) to allow information to flow between the ligand and the protein during message passing.