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

Table 3

Occupancy time of hydrogen bonds in the binding domain of the LGA-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	85.78
ARG404-side	TYR2-side	100	100	11.58	5.8
LYS1-main	TRP416-side	100	100	67.93	14.29
ARG413-side	LYS3-main	100	100	93.55	51.71
LYS1-main	ASP419-side	94.37	100	99.3	46.38
CYS417-main	LYS1-main	92.25	87.1	80.22	41.29
LYS1-main	CYS417-main	85.62	67.95	61.67	24.05
LYS1-side	ASP419-side	83.87	86.03	62.23	34.33
LYS3-main	GLY415-main	80.48	62.68	61.62	30.8
VAL34-main	TYR2-main	74.75	80.47	20.37	27.76
TYR485-side	LYS3-side	70.33	11.2	16.12	3.4
TYR2-main	GLU32-main	68.58	44.52	58.4	21.9
LYS1-side	HSD161-side	61.48	8.3	34.8	1.14