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(a) Hydrogen bond distances between 3′OH and the Y416 backbone during the FEP calculation for structures. (b) The distance between 2′O and Cγ of the side chain of Y416 during the FEP calculation. Three cases were tested with the original structure (red), with the structure processed by water flooding (blue), and the same structure by water flooding but the hydrogen bond 3′O and HN is forced by a 4.0 kcal/mol Å2 harmonic constraint at 2 Å (green).
