Table 3.

The average binding free energies calculated by MMGBSA method for the wild-type RBD and the E484K mutant, respectively, complexed with various neutralizing antibodies and nanobodies based on the five MD simulation trajectories for each system^a.

Neutralizing antibodies	RBD	$\Delta E_{vdw}$	$\Delta E_{ele}$	$\Delta G_{polar}$	$\Delta G_{nonpolar}$	$\Delta E_{vdw}+\Delta G_{nonpolar}$	$\Delta E_{ele}+\Delta G_{polar}$	$\Delta G_{bind}$	Standard deviation
BD23	WTb	−71.28	−122.61	149.54	−9.89	−81.17	26.93	−54.24	7.54
	MTc	−75.06	44.91	7.04	−9.85	−84.91	51.95	−32.96	7.71
Nanobody H11-D4	WT	−62.60	−2.90	26.09	−8.36	−70.96	23.19	−47.77	4.68
	MT	−64.60	271.64	−236.30	−7.89	−72.49	35.34	−37.15	4.63
BD368-2	WT	−74.68	−92.73	128.59	−9.59	−84.27	35.86	−48.41	5.76
	MT	−70.23	3.98	35.93	−9.21	−79.44	39.91	−39.53	6.14
Nanobody Nb20	WT	−82.75	−237.52	268.30	−12.09	−94.84	30.78	−64.06	6.09
	MT	−75.69	−47.65	85.08	−10.53	−86.22	37.43	−48.79	7.44
Nanobody MR17-K99Y	WT	−102.33	−299.26	344.51	−13.63	−115.96	45.25	−70.71	7.04
	MT	−106.09	−226.00	274.81	−13.94	−120.03	48.81	−71.22	7.11
S2M11	WT	−71.59	−74.16	97.06	−9.33	−80.92	22.90	−58.02	5.05
	MT	−72.79	31.18	8.59	−8.50	−81.29	39.77	−41.52	5.40

^aThe unit of the values is kcal/mol.

^bWT represents wild-type RBD.

^cMT represents the mutated RBD.