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. 2008 Sep 2;75(1):187–205. doi: 10.1002/prot.22234

Figure 1.

Figure 1

A diagram of a hypothetical macromolecular system. P consists of the atoms with known protonation state and geometry, A1, A2, and A3 denote chemical groups of atoms for which the protonation state is unknown; each group has a finite number of alternative states consisting of combinations of ionization, tautomer, flip, and rotamer configurations; in the diagram: four states for A1, two states for A2, and three states for A3.