We trained one GNN for each molecule-, atom-, and bondlevel descriptor individually, and evaluated model accuracy using the withheld test sets for both the acids and amines. For the primary and secondary amines, models for the conserved descriptors for both functional groups (e.g., HOMO, N 1 NMR, N 1 NBO, etc.) were trained using the combined dataset, while models for descriptors that were only collected for primary amines (i.e., Sterimol values, C 4 NMR, C 4 NBO) or secondary amines (i.e., H NMR and H 4 NBO) were trained solely on their respective libraries. For each molecule-level descriptor, the models achieved high accuracy (R 2 > 0.95) across the condensed descriptor set for both acids and amines, with the exception of the dipole moment. For the atom-level descriptors of acids, the models obtained higher accuracy (R 2 > 0.94) for NBO partial charges on C 1 and C 4 compared to those on O 2 , O , and H 5 (0.61 < R 2 < 0.91). Upon analyzing the outliers for NBO partial charges, we noted that hydrogen-bonding had a significant impact on the charges of O 2 , O , and H 5 . To investigate prediction failures, the lowest energy conformers were considered, as they have the greatest influence on the Boltzmann-averaged descriptor. For example, the acid molecule with the maximum deviation showed that our model underpredicts the charge on H and may not account for the increase in positive charge on the H 5 atom attributed to H-bonding (1, Figure ). Similar trends were observed for NMR chemical shifts, where we noted enhanced performance for C 1 and C 4 compared to H 5 (R 2 > 0.96 vs. R 2 < 0.73), which can again be ascribed to the presence of an intramolecular H-bond (2). Models for amine atom-level descriptors such as NBO partial charges on N 1 and C 2 achieved high accuracy (R 2 > 0.94) but exhibited poorer performance for H 4 (R 2 < 0.74). Similar to the carboxylic acids, H-bonding impacts the charge on the H 4 atom of amine 3. Additionally, model performance was compromised for the lone pair energy of the N 1 atom. Upon analyzing the most extreme outlier (4), destabilizing interactions due to eclipsing lone pair and methyl substituents increase the lone pair energy. With respect to NMR chemical shifts, while adequate performance is obtained for N 1 and C 2 (R 2 > 0.85), H 4 shifts had significantly lower R 2 values (< 0.69). The most extreme outlier was due to an anomeric effect caused by the back donation of LPN1 to s * (C-S) (interaction energy of 18.88 kcal.mol -1 obtained from second-order perturbation analysis of the Fock matrix in the NBO basis), which deshields the proton (H 4 ) (5). The same compound was also an outlier in the prediction of N 1 lone pair occupancy, wherein the reduction in occupancy is found due to back-donation. These examples highlight the limitations of using simple 2D representations that may fail to capture critical stereoelectronic effects.