Assumed pH 7.4
Maestro's prepwizard was used to add hydrogens using default parameters.
All the waters were retained
The binding site residue HIS 451 was used in a flipped, and "open" alternative configuration, and doubly protonated (HIP)
Ligand conformational libraries were generated using LigPrep.
Preparation for docking with Vina was done using MGLTools with the ligand pdb files from ligprep.
Exhaustiveness=32 #exhaustiveness of global search (default=8)
Poses were predicted using the deepest energy pose from qpld, and where this did not produce a pose, then either XP poses were used (FXR_16), or Vina poses (FXR_65, 79, 80, 97, and 101)