The PDBBind (Protein Data Bank Binding) dataset is a vital resource in drug research, primarily composed of high-quality protein-ligand (PL) complexes whose structural information is sourced from the Protein Data Bank (PDB). Each complex is experimentally measured under specific Given that our work primarily focuses on high-precision prediction of binding free energies, we mainly use FEP1 and FEP2 datasets for testing. The two challenging datasets are widely employed as important benchmarks by models such as GenScore, PBCNet, and PIGNET2. The FEP1 dataset includes eight targets: BACE, CDK2, Jnk1, MCL1, p38, PTP1B, Thrombin, and Tyk2, with a total of 199 data points. The FEP2 dataset comprises eight targets: cdk8, cmet, eg5, hif2a, pfkfb3, shp2, syk, and tnks2, with 264 data points. For all proteins, we select the portion where the distance to the ligand atoms is not more than 5 A as the molecular pocket and compute the distances between atoms within the protein. Atoms with distances less than 6 A and having a covalent bond are considered to be connected by an edge. Additionally, based on different interaction rules, we extract the corresponding atom indices for each energy term. The atom indices for the ligand atoms are also extracted accordingly.