While the size of an MCS is uniquely defined, neither the common subgraph nor its embedding is unique in general. In the example in Fig. the subgraph isomorphism for the red subgraph is not unique. This is a well-known issue for the construction of atom-atom-mapping tools. These ambiguities are not easily resolved because the combinatorial MCS problems operate on graphs rather than a more detailed model of the molecules that encompasses also e.g. hybridization or partial charges.