Revisiting the example in Fig. , we now note that while the interaction between the peptides groups highlighted in red and blue appears four times with a positive sign, it now also appears four times with a negative sign in the fragment-cap interactions (i.e., in the interaction of cap molecule AB with fragments D and E as well as in the interaction of cap molecule DE with fragments A and B) and once with a positive sign in the cap-cap interactions (i.e., in the interaction of cap molecule AB with cap molecule DE). Thus, in total it is correctly counted only once.