Our results indicate that, even without hyperparameter tuning of the environments, BuildAMol produced clash-free conformations reliably in almost all cases. The mode of clashes in optimized conformations was zero for all combinations of graph and environment except for the ResidueGraph+ForceFieldRotatron and Residue-Graph+OverlapRotatron (figure ). Inspection of the distributions of clashes in the final conformations shows that the AtomGraph+DistanceRotatron and Atom-Graph+ForceFieldRotatron markedly tend toward producing clash-free structures, while any combination with the OverlapRotatron yields poorer results due to the greater structural abstraction (figure ). A noticeably poor performance is exhibited by theResidueGraph+ForceFieldRotatron, where the worst conformation comprises 40 clashes.This lack of performance can be explained by the graph input. While the environment computes molecular energy, which should be a highly accurate metric for conformer evaluation, the input residue graph is not a valid chemical structure and, therefore, its molecular energy is a meaningless metric to optimize. Hence, we strongly discourage users from optimizing structures in this way.