Table 4.

Docking scores and energies of ferulic acid with crystal structure of H. pylori 4HI0.

Mol (Five Poses of Ferulic Acid)	rseq	mseq	S	rmsd_refine	E_conf	E_place	E_score1	E_refine	E_score2
	1	1	−5.58	3.35	−42.86	−61.32	−11.22	−27.30	−5.58
	1	1	−5.35	1.81	−40.17	−64.29	−11.15	−29.20	−5.35
	1	1	−5.31	2.06	−41.95	−63.97	−9.95	−28.10	−5.31
	1	1	−5.29	1.73	−41.47	−67.91	−10.93	−27.96	−5.29
	1	1	−5.24	2.00	−40.25	−74.10	−9.96	−28.98	−5.24

S, the final score (score of the last stage that was not set to none); rmsd, the root-mean-square deviation of the pose, in Å, from the original ligand; rmsd_refine, the root-mean-square deviation among the pose before refinement and the pose after refinement; E_conf, the energy of the conformer; E_place, the score from the placement stage; E_score 1 and E_score 2, the score from rescoring stages 1 and 2, respectively; E_refine, the score from the refinement stage, which is determined to be the totality of the solvation energies and van der Waals electrostatics, according to the generalized Born solvation model.