The molecular features (ionization formal charge and molecule net charge) added after the GAT layers were also removed one at a time (entries 16 and 17, median MAE = 0.68 and 0.67). The corresponding models showed accuracies similar to that of the original model. To test whether including features of both acids and bases was needed, we trained our model with either only the acid or only the base form (entries 19, MAE = 0.66 and 20, MAE = 0.64). These models appeared significantly more accurate than any models where both acids and bases were considered. However, the change in conjugation between acids and bases resulting in enhanced resonance stabilization of the base as observed in carboxylic acids is expected to be a major contributor which requires both acids and bases. Once more, the conjugation definition in the RDKit library may be the cause of this unexpected behavior. The new definition was used, the bases only were considered, and these new models (entry 21) showed similar accuracies as the full models (entry 20). It demonstrated that the newly implemented conjugation definition is significantly more appropriate for pKa prediction and likely a better feature for resonance effect modeling.