We next aimed to analyze the learned molecular representations of our trained models to gain further insight into model performance and the underlying chemistry governing ligand coordination. The D-MPNN phase of the model architecture uses message-passing operations between graph edges (i.e., bonds) to update node (i.e., atomic) embeddings based on the local graph (i.e., molecular) environment. The learned atomic embeddings are then aggregated into a single molecular embedding that represents the full ligand. We extracted the molecular representations of the test set ligands learned by the trained models, reducing the dimensionality via the t-distributed stochastic neighbor embedding (t-SNE) method. In the case of the multiclass coordinating atom count model, analysis of these representations shows distinct regions in latent space corresponding to the different classes of true number of coordinating atoms (Figure ). The separation between the learned representations of one-, two-, and three-coordinate ligands is most evident. This is to be expected since these classes are the most well-represented in the dataset and are the classes on which the trained model is the most accurate. In the case of the higher-denticity ligands with four, five, and six coordinating atoms, the distinction between classes in latent space is less well-defined, with significant overlap occurring in learned representations (Figure ). This is consistent with the observed decrease in model accuracy on these less frequent classes and is indicative of the model's difficulty in distinguishing between these chemically similar ligands with high numbers of coordinating atoms. Visualizing the learned representations by the average atomic number of coordinating atoms in each ligand from 6 (i.e., all C) to 16 (i.e., all S), we observe that the majority of ligands of all classes have low average atomic numbers of coordinating atoms (Figure ). The few distinct groups with higher coordinating atom atomic numbers are all observed in regions corresponding to lower denticities, primarily monodentate and bidentate ligands (Figure ). This observed trend of higher-denticity ligands primarily coordinating with 2p atoms and only lower-denticity ligands observed coordinating with both 2p and 3p atoms in large numbers suggests higher-denticity ligands coordinating with 3p atoms are less abundant in the CSD, which may indicate their being relatively under-sampled.