Present approaches characterize protein-ligand interactions using ligand molecular graphs, wherein each node encodes the contacts as features. These interactions are acquired by considering proximitybased contacts and applying a defined cutoff distance . This work presents a novel approach to model the intricate structure of a protein-ligand interaction occurring across various distances. Features of both the ligand and the protein are included, creating a topological representation of the interactions. Specifically, our approach uses a multigraph-based methodology, which proves to be highly advantageous in capturing the importance of close molecular interactions that determine binding affinity. The multigraph is constructed based on a PDB file where the atoms are represented as nodes, while the edges describe the Euclidean distances between the ligand and the protein atoms within three distance ranges .