Of the total 1755 mappings, the 2D Lomap approach 're-aligned' 891 mappings, 3D Lomap approach 're-aligned' 310 mappings, but no mapping was observed to be 're-aligned' in the Kartografs' atom mapping approach. In one case of the RHFE dataset, it was found that the ligand alignment was non-optimal, leading to a decreased number of atoms mapped by Kartograf (see SI-Figure ). This finding emphasizes the importance of the molecule input coordinates for Kartograf's atom mapper.