To better analyze model performance and develop more accurate methods for classifying ligands and automating TMC structure generation, we require a measure of uncertainty that reliably indicates confidence in a model's prediction. We define confidence thresholds for each model in terms of a raw prediction's difference from a true negative (0) or true positive (1) label and use these thresholds as a means of quantifying prediction uncertainty (i.e., a threshold of 0.3 would include predictions less than 0.3 and greater than 0.7). As anticipated, we observe increased accuracy in both models at more restrictive thresholds, with the coordinating atoms count model reaching 97.4% overall accuracy and the coordinating atoms identification model reaching 97.1% molecular accuracy at the tightest threshold of 0.05 (SI Appendix, Figures and). Although such a threshold may seem stringent, for 68.4% of test set molecules, coordinating atom count predictions are within the threshold of 0.05 (SI Appendix, Figure ). We observe a lower level of confidence for coordinating atom identity predictions, with 51.9% of ligands in the test set having every atom prediction fall within this threshold (SI Appendix, Figure ). This difference between dataset percentages included by each model is preserved across various thresholds, suggesting that the model for predicting total number of coordinating atoms had slightly more confident predictions for than the model for predicting coordinating atom identities, which is consistent with the expectation of increased complexity of predicting coordinating atom identities.