Fig. 2
Systematic calibration of εX and RX. a A section of the VXO(r, εX, RX) LJ potential function at r = 2 Å. Scenarios Sc1-Sc3 are shown with the magnitude of the RX values corresponding to a short range repulsion of VXO ≈ 1 kcal/mol (dashed lines) b VXO LJ potential functions of scenarios Sc1-Sc3. VOO of an oxygen atom pair is also shown for comparison. c An example of excluded atoms X (red, Cycle 1, Rank 2, System 9). Docked ligand conformation, is presented with sticks and the binding pocket is shown as surface. d Ligand of System 2 (dark blue sticks) bound to its target farnesyl pyrophosphate synthase (grey lines and surface) after Shaker (MDF step). Explicit water molecules surrounding the ligand within 7 Å are shown with sticks and light blue surface