Comparing the sampled structures of the cis isomer with the DFT resolved GM, it is found that the putative GM of AMOEBA has a heavy-atom RMSD of only 0.5 Å (Fig. ). However, this is not the most similar structure found, as the GA was able to provide an even closer structure with an RMSD of 0.4 Å about 0.6 kcal/mol higher in energy that better reproduces the configuration of the proline cycle (Fig. ). At the GAFF level, although the lowest energy structure is more compact (Fig. ) and therefore shows a larger RMSD from the reference, a geometry almost equal to the DFT GM is also discovered about 1 kcal/mol higher in energy (Fig. ).