To ensure that the correct perturbation is represented in the atom-mapping array, all atoms of the input ligands that change AMBER atom-type in the perturbation are stored. Then, by forcing the MCS on the six aromatic carbons of the benzene scaffold of the RBFE-Space derivatives, and generating the AMBER atom-type changes with that mapping, the atom-type change information is compared to the input ligands' atom-type information. By rotating the benzene scaffold forced MCS on one of the ligands (e.g. where {0:0, 1:1, 2:2, 3:3, 4:4, 5:5} is the initial forced MCS mapping, a first rotation would be {0:1, 1:2, 2:3, 3:4, 4:5, 5:0}) a second collection of RBFE-Space derivative atom-type changes is created. By repeating this process until all five rotations are completed and picking the mapping that matches the input ligands' mapping atom-type changes, the picked featurised atom-mapping array is ensured to correctly map the per-atom changes between the two ligands.