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. Author manuscript; available in PMC: 2013 Dec 1.
Published in final edited form as: J Chem Theory Comput. 2012 Oct 6;8(12):5092–5106. doi: 10.1021/ct3006826

Figure 2.

Figure 2

QM region 4: the PYP chromophore and the side chains of 11 surrounding residues. The MM region (not shown) includes the protein backbone of the 11 residues shown, the remaining protein, and an SPC/Fw water shell. Carbon atoms are orange, oxygen atoms are red, nitrogen atoms are blue, and sulfur atoms are yellow.