The mapping-based RMSD calculates the distance atoms need to travel from their original position to the resulting mapped position (refer to Figure ). This score seeks to penalize large atomic displacements which may require excess configurational sampling. MVR quantifies the shape overlap of the mapped region and the two molecules on average. In this case, a larger ratio is preferred, as it indicates a larger overlap of the two ligands in the mapping. For planar molecules, this score is expected to highly correlate with the MAR or the maximum common substructure rule from the Lomap scorer. However, if a molecule with a fold or significant 3D structure is involved, it might diverge from the simpler metric (refer to Figure ).