Maximum common subgraph (MCS)problems come in different variants. Both the maximum common induced subgraph (MCIS) problem and the maximum common edge subgraph (MCES) problem, as well as their restrictions to connected common subgraphs, are NP-hard . Nevertheless they can be solved efficiently for small pairs, and thus also for molecules. However, none of the variants of combinatorial optimization problem is guaranteed to identify the "chemically correct" common subgraph, i.e., the one that correctly identifies all bonds that change during a chemical reaction.