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. Author manuscript; available in PMC: 2013 Jul 25.
Published in final edited form as: J Chem Theory Comput. 2012 Jul 25;8(9):3022–3033. doi: 10.1021/ct3003817

Fig. 3.

Fig. 3

The alchemical intermediate that we use. The black methyl group is shared between the two side chain analogs. The blue atoms are the rest of the ILE side chain analog. The red atoms are the remaining of the GLN side chain analog. While the black atoms interact with all the other atoms, blue and red particles do not interact with each other.