Fig 6. Free energy along the ΔRMSD coordination and the low free energies representative structures.

(A), the free energy along the one dimensional coordination together with error bars. (B), the representative structure (gray color) in the local minimum 1, where ΔRMSD = -1.3 nm. (C), 10 representative intermediate structures in a local minimum 2 (the ΔRMSD range 0.3 nm to 0.5 nm). In panel B and C, the PR LBD crystal agonistic conformation (green) and the crystal antagonist conformation (cyan) are also superimposed with the representative structures.