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Calculation of protein–ligand binding affinity is a cornerstone of drug discovery. Classic implicit solvent models, which have been widely used to accomplish this task, lack accuracy compared to experimental references. Emerging data-driven models, on the other hand, are often accurate yet not fully interpretable and also likely to be overfitted. In this research, we explore the application of Theory-Guided Data Science in studying protein–ligand binding. A hybrid model is introduced by integrating Graph Convolutional Network (data-driven model) with the GBNSR6 implicit solvent (physics-based model). The proposed physics-data model is tested on a dataset of 368 complexes from the PDBbind refined set and 72 host–guest systems. Results demonstrate that the proposed Physics-Guided Neural Network can successfully improve the “accuracy” of the pure data-driven model. In addition, the “interpretability” and “transferability” of our model have boosted compared to the purely data-driven model. Further analyses include evaluating model robustness and understanding relationships between the physical features.