In Figure are shown as lines, and distance thresholds of 3Å (red line), 6Å (orange line), and 9Å (blue line) are used to determine the proximity and to connect these atoms. The edges were drawn from a single reference atom shown in dark blue to simplify the overall representation, but the same concept was applied to each ligand atom to create the entire graph. This approach resulted in the creation of three interaction spheres for each ligand atom, represented by the dashed circles within the distance thresholds of 3Å (red), 6Å (orange), and 9Å (blue). Using multiple distance thresholds results in a multigraph with different edge densities. The nodes closer together have a higher edge density, and the nodes farther apart have a lower edge density. The full grey circles in the graph denote atoms excluded from the graph because they did not meet the set distance thresholds. (b) This example shows the interaction between a small molecule and the GLN amino acid within a protein. The atom type annotations next to each atom act as identifiers, giving essential details about their connectivity and chemical identity. In the case of protein atoms, it also indicates whether they belong to the amino acid's side chain or backbone. Specifically, the interaction involves a hydrogen bond between the protein's amide hydrogen (H) atom and the sixth ligand's carbon-oxygen double bond (C=O). On the protein side, the 𝑁𝜖 notation specifies the nitrogen (N) atom in the amino acid's side chain. As for the ligand, the numbering system designates the positions of atoms within the molecule