Superimposes structures of the same molecule whose atom names, atom order and conformation differ, where a plain Kabsch fit cannot: the atoms are first matched by an exact correspondence of the molecular graphs (element, connectivity, hydrogens, formal charge) that must also preserve the 3D configuration at every stereocentre, double bond and hindered axis, and the structure is then fitted by a proper rotation (never a reflection). Among symmetry-equivalent correspondences the lowest-RMSD one is chosen. If no such correspondence exists the tool says why rather than guess. RMSD values are in Å.