However, while the model will be trained knowing the ionization center, predicting molecular pKa should not require this information. Our method was extended to evaluate various protonation states (microstates) as illustrated in Figure . We coded the train of thought a chemist would go through to estimate pKa values on any molecule. The protocol starts with the identification of all the potential acidic sites. Then, these are deprotonated, and the model predicts the pKa of each site and identifies the most basic one. The latter is then protonated and the pKa values of the other sites are recomputed, with the second most basic one identified and protonated. The process is iterated until all the basic sites are protonated and all the pKa values are computed. This method allows us not only to compute all these values but also to predict the most likely protonation state at a given pH (the pH can be given by the user), although we understand that multiple protonation states may co-exist. From this first set of models, we first observed that the error of the models ranges between 0.70 and 0.80 pKa unit as long as the sum of the GAT layers and mask size is at least 6 (Figure ). A marked decrease in error is observed when going from a size of 2 (number of GAT layers + mask size) with a median MAE of 1.0 on the testing set to a size of 3 (0.88-0.91), 4 (0.77-0.84), and a minor decrease is then observed with more GAT layers and/or increased mask size. This error reached a minimum with a total size of 7 or 8 (0.67-0.74) in line with the trends observed experimentally (Figures and). A size of 2 captures the nature of the ionization center (central atom and atoms directly bound). This layer depicts the necessary information to differentiate, for instance, a primary amine from a tertiary amine or an aniline. Additional long-range effects are captured with additional layers. These more subtle effects may at times be within the experimental error leading to negligible improvement of the accuracy when stacking more GAT layers or increasing the mask size.