Fig. 3. Comparison of predicted to experimental binding modes for the absolute binding free energy predictions.
A. & B. Two conformations of benzylacetate: A. X-ray result, 25:25 occupancy. 2Fo−Fc electron density map displayed at 1.0σ. B. Overlay of x-ray result (gray) with predicted geometry (green). C. & D. Two conformations of thiophene-2-carboxaldoxime: A. X-ray result, 50:50 occupancy. 2Fo−Fc electron density map displayed at 1.5σ. B. Overlay of x-ray result (gray) with predicted geometry (green).E. & F. Two conformations of thieno[3,2-b]thiophene: A. X-ray result, 50:50 occupancy. 2Fo−Fc electron density map displayed at 1.5σ. B. Overlay of x-ray result (gray) with predicted geometries (green & cyan).G. & H. Two conformations of 2-nitrothiophene: A. X-ray result, 50:50 occupancy. 2Fo−Fc electron density map displayed at 1.5σ. B. Overlay of x-ray result (gray) with predicted geometries (green & cyan). I. & J. Two molecules of 4-chloro-1H-pyrazole: A. X-ray result, two molecules (A & B) bound at 100% occupancy with two ordered water molecules. 2Fo−Fc electron density map displayed at 1.5σ. B. Overlay of x-ray result (gray) with predicted geometry (green). K. & L. N-phenylglycinonitrile: A. X-ray result, 100% occupancy. 2Fo−Fc electron density map displayed at 1.5σ. B. Overlay of x-ray result (gray) with predicted geometry (green). M. & N. 4,5,6,7-tetrahydroindole: A. X-ray result, 50% occupancy. 2Fo−Fc electron density map displayed at 1.0σ. B. Overlay of x-ray result (gray) with predicted geometries (green & cyan). O. & P. Two conformations of nitrosobenzene: A. X-ray result, 25:25 occupancy. 2Fo−Fc electron density map displayed at 1.0σ. B. Overlay of x-ray result (gray) with predicted geometry (green). Q. & R. 2-ethoxy-3,4-dihydro-2h-pyran: A. X-ray result, 25% occupancy. 2Fo−Fc electron density map displayed at 0.5σ. B. Overlay of x-ray result (gray) with predicted geometry (green).