Fig. 3. Interpretation of the predicted outcomes. (a) Substructural analysis of ligands for two target proteins. Protein-tyrosine phosphatase non-receptor type 1 (PTPN1) and platelet activating factor acetylhydrolase (PAF-AH). The blue and red circles indicate common and different substructures, respectively, and the predicted energy contribution (unit: kcal mol⁻¹) of each substructure is annotated. The inhibitory constant, K_i, indicates how potent the ligand binds to the target protein. (b) A distance–energy plot of carbon–carbon pairwise van der Waals (vdW) energy components in the test set. The red solid line illustrates the original distance-energy relation without any deviation induced by learnable parameters. The closer the color of a data point to yellow, the larger the number of corresponding carbon–carbon pairs. (c) The average value of the corrected sum of vdW radii, , corresponding to different carbon–carbon pair types. C_sp²–C_sp², C_sp²–C_sp³, and C_sp³–C_sp³ pairs are compared. The results include 95% confidence intervals.