Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein

Table 2

Occupancy time of hydrogen bonds in the binding domain of the LRDPSO-docked complex at different temperatures.

Donor	Acceptor	Occupancy time (%) (300 K)	Occupancy time (%) (400 K)	Occupancy time (%) (500 K)	Occupancy time (%) (600 K)
ARG413-side	LYS3-side	100	100	100	100
LYS1-main	ASP419-side	100	100	92.79	92.39
ARG404-side	TYR2-side	100	72.53	2.92	1.51
ARG413-side	LYS3-main	100	54.61	76.1	68.13
LYS1-main	TRP416-side	100	100	31.5	13.51
CYS417-main	LYS1-main	89.58	86	77.86	66.16
LYS3-main	GLY415-main	89.35	83.7	65.39	46.06
LYS1-side	ASN506-side	87.25	37.96	3.19	2.46
LYS1-main	CYS417-main	85.43	76.36	39.27	49.8
TYR2-main	GLU32-main	79.58	50.61	45.56	20.99
LYS1-side	ASP419-side	66.58	61.30	64.63	35.96
VAL34-main	TYR2-main	63.90	68.97	34.23	30.07
LYS1-side	LEU504-main	59.15	26.52	2.95	3.95
LYS3-side	HSD371-side	52.33	0.61	0.16	1.04