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. Author manuscript; available in PMC: 2018 Jan 1.
Published in final edited form as: J Comput Aided Mol Des. 2016 Sep 30;31(1):29–44. doi: 10.1007/s10822-016-9956-6

Fig. 2.

Fig. 2

a Position of the hydration spheres added to AGBNP2 parameters for each hosts, b the carbon atoms used to position the hydration sphere in all three hosts; the carbon atoms marked in magenta are used for positioning the water sites on the top cavity of octa-acids; in CB-clip, those carbons are used to position water site in between two naphthalene rings; the center of masses of carbons marked in green were used to position water-sites in the middle cavity of the octa-acids; carbons marked in orange were used to model a water site at the bottom cavity of the octa-acids; in CB-clip, a water site is positioned at the center of mass of those four carbons