Table 3. The occupancy of H-bond interactions during the simulations of 3CL^pro system and 3CL^pro-Indinavir system, respectively.

Interaction type	Residue 1	Residue 2	Occupancy (%) (3CLpro)	Occupancy (%) (3CLpro- Indinavir)
H bond	His41	Cys44	82.56	92.33
H bond	His41	Cys145	11.24	98.28
H bond	His41	His164	20.66	89.37
H bond	Cys145	Asn28	21.02	87.64
H bond	Cys145	Cys164	84.31	95.98
H bond	His164	Cys85	80.46	88.19
H bond	His164	Ala173	75.88	91.49