FMO DATABASE

FMODB ID: 4NZYN

Calculation Name: 7K3G-ABCDE-SolidNMR166-

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7K3G

Chain ID: ABCDE

ChEMBL ID:

UniProt ID:

Base Structure: SolidStateNMR

Registration Date: 2020-10-19

Reference: K. Fukuzawa, K. Kato, C. Watanabe et. Al., Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. J. Chem. Inf. Model. 2021, 61, 9, 4594-4612.

DOI: 10.1021/acs.jcim.1c00694

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSolvOptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1355132.880468
FMO2-HF: Nuclear repulsion	1298979.477677
FMO2-HF: Total energy	-56153.40279
FMO2-MP2: Total energy	-56325.102477

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:8:GLU )

Summations of interaction energy for fragment #1(A:8:GLU )

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
22.49	26.395	0.304	-1.483	-2.726	0.005

Interaction energy analysis for fragmet #1(A:8:GLU )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.053 / q_NPA : -0.033

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	10	GLY	0.074	0.047	2.701	5.141	8.654	0.276	-1.493	-2.296	0.005
4	A	11	THR	0.045	0.004	3.541	1.145	1.537	0.028	0.010	-0.430	0.000
5	A	12	LEU	-0.010	-0.005	6.130	0.895	0.895	0.000	0.000	0.000	0.000
6	A	13	ILE	0.022	0.023	6.272	1.057	1.057	0.000	0.000	0.000	0.000
7	A	14	VAL	0.005	0.007	8.968	0.877	0.877	0.000	0.000	0.000	0.000
8	A	15	ASN	0.002	-0.001	11.649	0.149	0.149	0.000	0.000	0.000	0.000
9	A	16	SER	0.062	0.011	12.400	0.220	0.220	0.000	0.000	0.000	0.000
10	A	17	VAL	-0.014	0.000	11.730	0.354	0.354	0.000	0.000	0.000	0.000
11	A	18	LEU	0.031	0.015	14.299	0.238	0.238	0.000	0.000	0.000	0.000
12	A	19	LEU	-0.003	0.015	16.866	0.125	0.125	0.000	0.000	0.000	0.000
13	A	20	PHE	-0.035	-0.021	17.828	0.126	0.126	0.000	0.000	0.000	0.000
14	A	21	LEU	-0.003	-0.011	19.597	0.105	0.105	0.000	0.000	0.000	0.000
15	A	22	ALA	0.015	0.005	22.309	0.048	0.048	0.000	0.000	0.000	0.000
16	A	23	PHE	-0.021	-0.012	23.143	0.042	0.042	0.000	0.000	0.000	0.000
17	A	24	VAL	0.020	0.008	24.893	0.038	0.038	0.000	0.000	0.000	0.000
18	A	25	VAL	-0.008	0.001	26.700	0.006	0.006	0.000	0.000	0.000	0.000
19	A	26	PHE	0.018	-0.008	28.808	0.018	0.018	0.000	0.000	0.000	0.000
20	A	27	LEU	-0.012	0.011	28.762	0.033	0.033	0.000	0.000	0.000	0.000
21	A	28	LEU	0.000	-0.004	31.041	0.019	0.019	0.000	0.000	0.000	0.000
22	A	29	VAL	0.004	0.000	32.901	0.009	0.009	0.000	0.000	0.000	0.000
23	A	30	THR	-0.031	-0.006	33.506	0.024	0.024	0.000	0.000	0.000	0.000
24	A	31	LEU	-0.017	-0.015	34.317	0.017	0.017	0.000	0.000	0.000	0.000
25	A	32	ALA	0.005	0.009	37.338	0.004	0.004	0.000	0.000	0.000	0.000
26	A	33	ILE	-0.007	-0.017	38.752	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	34	LEU	-0.071	-0.012	38.389	0.014	0.014	0.000	0.000	0.000	0.000
28	A	35	THR	0.009	0.002	41.217	0.011	0.011	0.000	0.000	0.000	0.000
29	A	36	ALA	-0.026	0.000	43.209	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	37	LEU	-0.050	-0.013	44.070	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	38	ARG	0.010	-0.002	40.260	-0.061	-0.061	0.000	0.000	0.000	0.000
32	B	8	GLU	-0.054	-0.033	11.293	1.484	1.484	0.000	0.000	0.000	0.000
33	B	9	THR	0.042	0.000	7.471	0.127	0.127	0.000	0.000	0.000	0.000
34	B	10	GLY	0.075	0.047	10.843	0.312	0.312	0.000	0.000	0.000	0.000
35	B	11	THR	0.045	0.004	14.553	0.090	0.090	0.000	0.000	0.000	0.000
36	B	12	LEU	-0.009	-0.004	8.387	-0.131	-0.131	0.000	0.000	0.000	0.000
37	B	13	ILE	0.021	0.023	12.618	0.022	0.022	0.000	0.000	0.000	0.000
38	B	14	VAL	0.004	0.007	14.218	0.282	0.282	0.000	0.000	0.000	0.000
39	B	15	ASN	0.000	-0.002	13.433	0.051	0.051	0.000	0.000	0.000	0.000
40	B	16	SER	0.062	0.012	12.919	0.093	0.093	0.000	0.000	0.000	0.000
41	B	17	VAL	-0.013	0.002	15.566	0.253	0.253	0.000	0.000	0.000	0.000
42	B	18	LEU	0.030	0.015	18.721	0.161	0.161	0.000	0.000	0.000	0.000
43	B	19	LEU	-0.004	0.014	16.418	0.094	0.094	0.000	0.000	0.000	0.000
44	B	20	PHE	-0.035	-0.020	19.644	0.140	0.140	0.000	0.000	0.000	0.000
45	B	21	LEU	-0.003	-0.012	22.450	0.081	0.081	0.000	0.000	0.000	0.000
46	B	22	ALA	0.013	0.004	22.750	0.049	0.049	0.000	0.000	0.000	0.000
47	B	23	PHE	-0.019	-0.012	24.709	0.040	0.040	0.000	0.000	0.000	0.000
48	B	24	VAL	0.019	0.008	27.286	0.019	0.019	0.000	0.000	0.000	0.000
49	B	25	VAL	-0.010	0.002	26.489	0.003	0.003	0.000	0.000	0.000	0.000
50	B	26	PHE	0.020	-0.007	27.621	0.019	0.019	0.000	0.000	0.000	0.000
51	B	27	LEU	-0.014	0.011	31.217	0.022	0.022	0.000	0.000	0.000	0.000
52	B	28	LEU	-0.001	-0.003	32.717	0.006	0.006	0.000	0.000	0.000	0.000
53	B	29	VAL	0.005	0.000	33.394	0.007	0.007	0.000	0.000	0.000	0.000
54	B	30	THR	-0.030	-0.007	34.867	0.026	0.026	0.000	0.000	0.000	0.000
55	B	31	LEU	-0.017	-0.016	37.136	0.011	0.011	0.000	0.000	0.000	0.000
56	B	32	ALA	0.005	0.008	38.760	0.005	0.005	0.000	0.000	0.000	0.000
57	B	33	ILE	-0.008	-0.017	38.538	0.006	0.006	0.000	0.000	0.000	0.000
58	B	34	LEU	-0.069	-0.011	40.965	0.016	0.016	0.000	0.000	0.000	0.000
59	B	35	THR	0.008	0.001	43.018	0.006	0.006	0.000	0.000	0.000	0.000
60	B	36	ALA	-0.025	0.001	42.917	0.004	0.004	0.000	0.000	0.000	0.000
61	B	37	LEU	-0.049	-0.013	44.640	0.016	0.016	0.000	0.000	0.000	0.000
62	B	38	ARG	0.011	-0.001	38.952	-0.065	-0.065	0.000	0.000	0.000	0.000
63	C	8	GLU	-0.054	-0.033	19.312	0.536	0.536	0.000	0.000	0.000	0.000
64	C	9	THR	0.041	-0.001	16.126	0.068	0.068	0.000	0.000	0.000	0.000
65	C	10	GLY	0.077	0.046	18.682	0.076	0.076	0.000	0.000	0.000	0.000
66	C	11	THR	0.043	0.004	19.219	0.051	0.051	0.000	0.000	0.000	0.000
67	C	12	LEU	-0.009	-0.003	13.656	-0.068	-0.068	0.000	0.000	0.000	0.000
68	C	13	ILE	0.022	0.023	17.915	-0.004	-0.004	0.000	0.000	0.000	0.000
69	C	14	VAL	0.004	0.007	18.994	0.131	0.131	0.000	0.000	0.000	0.000
70	C	15	ASN	0.000	-0.004	15.809	-0.010	-0.010	0.000	0.000	0.000	0.000
71	C	16	SER	0.063	0.013	19.377	0.094	0.094	0.000	0.000	0.000	0.000
72	C	17	VAL	-0.013	0.002	21.633	0.137	0.137	0.000	0.000	0.000	0.000
73	C	18	LEU	0.029	0.017	21.445	0.111	0.111	0.000	0.000	0.000	0.000
74	C	19	LEU	-0.005	0.013	22.301	0.092	0.092	0.000	0.000	0.000	0.000
75	C	20	PHE	-0.035	-0.021	24.608	0.106	0.106	0.000	0.000	0.000	0.000
76	C	21	LEU	-0.001	-0.011	27.008	0.070	0.070	0.000	0.000	0.000	0.000
77	C	22	ALA	0.013	0.005	28.154	0.064	0.064	0.000	0.000	0.000	0.000
78	C	23	PHE	-0.020	-0.013	29.701	0.054	0.054	0.000	0.000	0.000	0.000
79	C	24	VAL	0.018	0.007	31.334	0.034	0.034	0.000	0.000	0.000	0.000
80	C	25	VAL	-0.009	0.000	29.856	0.028	0.028	0.000	0.000	0.000	0.000
81	C	26	PHE	0.023	-0.006	33.008	0.033	0.033	0.000	0.000	0.000	0.000
82	C	27	LEU	-0.016	0.011	35.913	0.026	0.026	0.000	0.000	0.000	0.000
83	C	28	LEU	0.001	0.000	34.893	0.018	0.018	0.000	0.000	0.000	0.000
84	C	29	VAL	0.003	0.000	36.442	0.019	0.019	0.000	0.000	0.000	0.000
85	C	30	THR	-0.030	-0.008	38.991	0.023	0.023	0.000	0.000	0.000	0.000
86	C	31	LEU	-0.017	-0.016	41.021	0.013	0.013	0.000	0.000	0.000	0.000
87	C	32	ALA	0.006	0.007	40.980	0.013	0.013	0.000	0.000	0.000	0.000
88	C	33	ILE	-0.008	-0.017	41.793	0.014	0.014	0.000	0.000	0.000	0.000
89	C	34	LEU	-0.070	-0.012	44.521	0.011	0.011	0.000	0.000	0.000	0.000
90	C	35	THR	0.008	0.000	46.730	0.009	0.009	0.000	0.000	0.000	0.000
91	C	36	ALA	-0.025	0.002	45.684	0.011	0.011	0.000	0.000	0.000	0.000
92	C	37	LEU	-0.049	-0.013	47.740	0.016	0.016	0.000	0.000	0.000	0.000
93	C	38	ARG	0.010	-0.002	45.033	0.016	0.016	0.000	0.000	0.000	0.000
94	D	8	GLU	-0.053	-0.033	19.224	0.547	0.547	0.000	0.000	0.000	0.000
95	D	9	THR	0.040	0.000	18.198	0.093	0.093	0.000	0.000	0.000	0.000
96	D	10	GLY	0.077	0.046	19.563	0.089	0.089	0.000	0.000	0.000	0.000
97	D	11	THR	0.043	0.004	16.630	0.092	0.092	0.000	0.000	0.000	0.000
98	D	12	LEU	-0.009	-0.003	15.490	-0.096	-0.096	0.000	0.000	0.000	0.000
99	D	13	ILE	0.025	0.024	17.991	0.060	0.060	0.000	0.000	0.000	0.000
100	D	14	VAL	0.005	0.007	17.300	0.154	0.154	0.000	0.000	0.000	0.000
101	D	15	ASN	0.005	-0.002	17.006	-0.067	-0.067	0.000	0.000	0.000	0.000
102	D	16	SER	0.061	0.012	20.167	0.106	0.106	0.000	0.000	0.000	0.000
103	D	17	VAL	-0.014	0.001	23.300	0.123	0.123	0.000	0.000	0.000	0.000
104	D	18	LEU	0.029	0.017	20.469	0.114	0.114	0.000	0.000	0.000	0.000
105	D	19	LEU	-0.005	0.014	24.161	0.103	0.103	0.000	0.000	0.000	0.000
106	D	20	PHE	-0.034	-0.021	26.264	0.097	0.097	0.000	0.000	0.000	0.000
107	D	21	LEU	-0.002	-0.011	26.340	0.072	0.072	0.000	0.000	0.000	0.000
108	D	22	ALA	0.015	0.007	29.253	0.069	0.069	0.000	0.000	0.000	0.000
109	D	23	PHE	-0.023	-0.013	31.613	0.056	0.056	0.000	0.000	0.000	0.000
110	D	24	VAL	0.018	0.007	30.897	0.041	0.041	0.000	0.000	0.000	0.000
111	D	25	VAL	-0.007	-0.001	31.914	0.042	0.042	0.000	0.000	0.000	0.000
112	D	26	PHE	0.023	-0.006	34.465	0.037	0.037	0.000	0.000	0.000	0.000
113	D	27	LEU	-0.016	0.011	36.707	0.030	0.030	0.000	0.000	0.000	0.000
114	D	28	LEU	0.000	-0.001	34.293	0.029	0.029	0.000	0.000	0.000	0.000
115	D	29	VAL	0.001	0.001	37.814	0.027	0.027	0.000	0.000	0.000	0.000
116	D	30	THR	-0.030	-0.007	40.415	0.022	0.022	0.000	0.000	0.000	0.000
117	D	31	LEU	-0.018	-0.016	39.951	0.015	0.015	0.000	0.000	0.000	0.000
118	D	32	ALA	0.008	0.009	41.361	0.018	0.018	0.000	0.000	0.000	0.000
119	D	33	ILE	-0.006	-0.017	43.385	0.014	0.014	0.000	0.000	0.000	0.000
120	D	34	LEU	-0.073	-0.015	45.827	0.008	0.008	0.000	0.000	0.000	0.000
121	D	35	THR	0.009	0.000	46.824	0.013	0.013	0.000	0.000	0.000	0.000
122	D	36	ALA	-0.024	0.003	47.361	0.013	0.013	0.000	0.000	0.000	0.000
123	D	37	LEU	-0.050	-0.013	49.294	0.006	0.006	0.000	0.000	0.000	0.000
124	D	38	ARG	0.011	-0.001	48.359	0.024	0.024	0.000	0.000	0.000	0.000
125	E	8	GLU	-0.054	-0.034	11.192	1.549	1.549	0.000	0.000	0.000	0.000
126	E	9	THR	0.041	0.001	12.328	0.274	0.274	0.000	0.000	0.000	0.000
127	E	10	GLY	0.076	0.047	11.865	0.320	0.320	0.000	0.000	0.000	0.000
128	E	11	THR	0.045	0.004	7.594	0.507	0.507	0.000	0.000	0.000	0.000
129	E	12	LEU	-0.010	-0.003	10.692	0.051	0.051	0.000	0.000	0.000	0.000
130	E	13	ILE	0.024	0.024	12.863	0.361	0.361	0.000	0.000	0.000	0.000
131	E	14	VAL	0.005	0.007	12.332	0.382	0.382	0.000	0.000	0.000	0.000
132	E	15	ASN	-0.002	-0.006	14.934	0.005	0.005	0.000	0.000	0.000	0.000
133	E	16	SER	0.058	0.010	17.250	0.195	0.195	0.000	0.000	0.000	0.000
134	E	17	VAL	-0.013	0.000	18.034	0.188	0.188	0.000	0.000	0.000	0.000
135	E	18	LEU	0.030	0.016	17.067	0.187	0.187	0.000	0.000	0.000	0.000
136	E	19	LEU	-0.004	0.015	20.739	0.147	0.147	0.000	0.000	0.000	0.000
137	E	20	PHE	-0.034	-0.021	22.217	0.118	0.118	0.000	0.000	0.000	0.000
138	E	21	LEU	-0.002	-0.010	23.433	0.098	0.098	0.000	0.000	0.000	0.000
139	E	22	ALA	0.016	0.007	26.041	0.077	0.077	0.000	0.000	0.000	0.000
140	E	23	PHE	-0.024	-0.013	27.468	0.060	0.060	0.000	0.000	0.000	0.000
141	E	24	VAL	0.019	0.007	27.503	0.055	0.055	0.000	0.000	0.000	0.000
142	E	25	VAL	-0.007	0.000	29.978	0.046	0.046	0.000	0.000	0.000	0.000
143	E	26	PHE	0.020	-0.008	32.219	0.036	0.036	0.000	0.000	0.000	0.000
144	E	27	LEU	-0.014	0.011	32.090	0.035	0.035	0.000	0.000	0.000	0.000
145	E	28	LEU	0.001	-0.002	32.419	0.037	0.037	0.000	0.000	0.000	0.000
146	E	29	VAL	0.001	0.000	35.015	0.025	0.025	0.000	0.000	0.000	0.000
147	E	30	THR	-0.031	-0.006	37.537	0.021	0.021	0.000	0.000	0.000	0.000
148	E	31	LEU	-0.019	-0.015	35.860	0.019	0.019	0.000	0.000	0.000	0.000
149	E	32	ALA	0.006	0.009	39.463	0.016	0.016	0.000	0.000	0.000	0.000
150	E	33	ILE	-0.004	-0.017	41.277	0.008	0.008	0.000	0.000	0.000	0.000
151	E	34	LEU	-0.073	-0.014	42.073	0.007	0.007	0.000	0.000	0.000	0.000
152	E	35	THR	0.009	0.001	44.380	0.015	0.015	0.000	0.000	0.000	0.000
153	E	36	ALA	-0.023	0.002	45.907	0.007	0.007	0.000	0.000	0.000	0.000
154	E	37	LEU	-0.051	-0.014	47.426	-0.003	-0.003	0.000	0.000	0.000	0.000
155	E	38	ARG	0.011	-0.001	46.826	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:GLU )