For the protein, it is also abstracted into a topological graph. Unlike many models, we still represent each atom as a node rather than using residues. This is done to facilitate the calculation of atomic pair energy terms in the subsequent steps. Although there are a large number of atoms in proteins, not all of them actively participate in the binding between the protein and ligand. Therefore, a protein pocket is extracted to reduce the computational load. Additionally, in the processing of edges, due to the complex protein structures, using only covalent bonds as edges to describe the connectivity of the entire topological graph may cause information loss. Hence, we consider not only covalent bonds as edges but also atom pairs within a 6Å distance as connected edges. To differentiate them, we assign a feature value of 1 to covalent bond edges and 0 to non-covalent bond edges. Finally, the protein is represented as ,𝐺 " = -𝐻 " , 𝐸 " , 𝑋 " ./, where 𝐻 " denotes node features, 𝐸 " denotes edge features, and 𝑋 " denotes atomic coordinates.