FMO DATABASE

FMODB ID: GNNV1

Calculation Name: 7T9W-N-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7T9W

Chain ID: N

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2022-02-03

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHLSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Waters within average of the temperature factors of receptor.
Procedure	Auto-FMO protocol ver. 1.20200406

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-680937.88294
FMO2-HF: Nuclear repulsion	643125.367282
FMO2-HF: Total energy	-37812.515657
FMO2-MP2: Total energy	-37922.187001

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(N:1240:GLN)

Summations of interaction energy for fragment #1(N:1240:GLN)

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.
-1.622	-0.407	-0.014	-0.518	-0.684	0.002

Interaction energy analysis for fragmet #1(N:1240:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.025

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.	FCHARGEFormal charge [e].	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	N	1242	ASP	-1	-0.807	-0.871	3.798	-5.059	-3.844	-0.014	-0.518	-0.684	0.002
4	N	1243	VAL	0	-0.008	-0.021	5.980	0.909	0.909	0.000	0.000	0.000	0.000
5	N	1244	LEU	0	0.022	0.017	8.252	-0.077	-0.077	0.000	0.000	0.000	0.000
6	N	1245	GLU	-1	-0.822	-0.890	11.893	-0.422	-0.422	0.000	0.000	0.000	0.000
7	N	1246	CYS	0	-0.042	0.000	14.076	0.014	0.014	0.000	0.000	0.000	0.000
8	N	1247	ASN	0	0.013	-0.002	16.967	0.019	0.019	0.000	0.000	0.000	0.000
9	N	1248	VAL	0	0.055	0.036	14.652	0.025	0.025	0.000	0.000	0.000	0.000
10	N	1249	LYS	1	0.945	0.946	18.107	-0.053	-0.053	0.000	0.000	0.000	0.000
11	N	1250	THR	0	0.022	0.044	16.531	-0.019	-0.019	0.000	0.000	0.000	0.000
12	N	1251	THR	0	0.005	0.008	10.151	-0.055	-0.055	0.000	0.000	0.000	0.000
13	N	1252	GLU	-1	-0.740	-0.805	12.061	0.526	0.526	0.000	0.000	0.000	0.000
14	N	1253	VAL	0	0.013	0.001	8.307	0.002	0.002	0.000	0.000	0.000	0.000
15	N	1254	VAL	0	-0.025	-0.006	10.736	-0.109	-0.109	0.000	0.000	0.000	0.000
16	N	1255	GLY	0	0.035	0.031	11.786	-0.101	-0.101	0.000	0.000	0.000	0.000
17	N	1256	ASP	-1	-0.877	-0.910	8.082	1.689	1.689	0.000	0.000	0.000	0.000
18	N	1257	ILE	0	-0.029	-0.014	7.303	-0.076	-0.076	0.000	0.000	0.000	0.000
19	N	1258	ILE	0	-0.058	-0.033	5.250	0.510	0.510	0.000	0.000	0.000	0.000
20	N	1259	LEU	0	-0.005	-0.005	8.288	-0.404	-0.404	0.000	0.000	0.000	0.000
21	N	1260	LYS	1	0.895	0.924	10.468	0.613	0.613	0.000	0.000	0.000	0.000
22	N	1261	PRO	0	-0.031	0.003	12.266	-0.057	-0.057	0.000	0.000	0.000	0.000
23	N	1262	ALA	0	0.051	0.027	15.896	-0.048	-0.048	0.000	0.000	0.000	0.000
24	N	1263	ASN	0	-0.016	-0.017	17.961	0.045	0.045	0.000	0.000	0.000	0.000
25	N	1264	ASN	0	-0.045	-0.025	21.709	-0.012	-0.012	0.000	0.000	0.000	0.000
26	N	1265	SER	0	0.041	0.017	17.554	-0.030	-0.030	0.000	0.000	0.000	0.000
27	N	1266	LEU	0	0.023	0.025	17.751	0.034	0.034	0.000	0.000	0.000	0.000
28	N	1267	LYS	1	0.882	0.931	20.138	0.160	0.160	0.000	0.000	0.000	0.000
29	N	1268	ILE	0	0.011	0.008	17.436	-0.010	-0.010	0.000	0.000	0.000	0.000
30	N	1269	THR	0	0.004	0.018	20.918	0.014	0.014	0.000	0.000	0.000	0.000
31	N	1270	GLU	-1	-0.751	-0.849	20.461	0.250	0.250	0.000	0.000	0.000	0.000
32	N	1271	GLU	-1	-0.829	-0.896	22.411	0.248	0.248	0.000	0.000	0.000	0.000
33	N	1272	VAL	0	-0.002	0.016	25.153	-0.017	-0.017	0.000	0.000	0.000	0.000
34	N	1273	GLY	0	0.087	0.037	27.525	0.017	0.017	0.000	0.000	0.000	0.000
35	N	1274	HIS	0	0.020	0.035	31.107	-0.010	-0.010	0.000	0.000	0.000	0.000
36	N	1275	THR	0	0.032	0.008	32.091	-0.006	-0.006	0.000	0.000	0.000	0.000
37	N	1276	ASP	-1	-0.865	-0.909	28.260	0.028	0.028	0.000	0.000	0.000	0.000
38	N	1277	LEU	0	0.037	0.007	30.074	-0.018	-0.018	0.000	0.000	0.000	0.000
39	N	1278	MET	0	-0.027	0.000	32.313	-0.012	-0.012	0.000	0.000	0.000	0.000
40	N	1279	ALA	0	0.010	0.002	31.983	-0.008	-0.008	0.000	0.000	0.000	0.000
41	N	1280	ALA	0	-0.002	0.010	30.082	-0.010	-0.010	0.000	0.000	0.000	0.000
42	N	1281	TYR	0	-0.005	-0.012	31.771	-0.011	-0.011	0.000	0.000	0.000	0.000
43	N	1282	VAL	0	-0.027	-0.011	35.084	-0.009	-0.009	0.000	0.000	0.000	0.000
44	N	1283	ASP	-1	-0.879	-0.928	32.509	-0.079	-0.079	0.000	0.000	0.000	0.000
45	N	1284	ASN	0	-0.093	-0.039	33.403	-0.010	-0.010	0.000	0.000	0.000	0.000
46	N	1285	SER	0	-0.001	0.016	28.570	-0.017	-0.017	0.000	0.000	0.000	0.000
47	N	1286	SER	0	-0.012	-0.018	25.924	0.010	0.010	0.000	0.000	0.000	0.000
48	N	1287	LEU	0	-0.022	-0.017	25.120	0.010	0.010	0.000	0.000	0.000	0.000
49	N	1288	THR	0	0.027	0.010	18.316	-0.043	-0.043	0.000	0.000	0.000	0.000
50	N	1289	ILE	0	-0.005	0.005	21.216	0.022	0.022	0.000	0.000	0.000	0.000
51	N	1290	LYS	1	0.768	0.870	16.787	-0.267	-0.267	0.000	0.000	0.000	0.000
52	N	1291	LYS	1	0.876	0.921	17.572	-0.442	-0.442	0.000	0.000	0.000	0.000
53	N	1292	PRO	0	-0.007	0.013	20.395	-0.035	-0.035	0.000	0.000	0.000	0.000
54	N	1293	ASN	0	0.004	-0.014	23.447	0.017	0.017	0.000	0.000	0.000	0.000
55	N	1294	GLU	-1	-0.936	-0.978	27.027	0.119	0.119	0.000	0.000	0.000	0.000
56	N	1295	LEU	0	0.005	0.016	30.120	-0.014	-0.014	0.000	0.000	0.000	0.000
57	N	1296	SER	0	0.030	-0.017	25.085	-0.007	-0.007	0.000	0.000	0.000	0.000
58	N	1297	ARG	1	0.896	0.954	22.981	-0.258	-0.258	0.000	0.000	0.000	0.000
59	N	1298	VAL	0	0.010	0.024	27.490	-0.016	-0.016	0.000	0.000	0.000	0.000
60	N	1299	LEU	0	0.006	0.009	29.911	-0.013	-0.013	0.000	0.000	0.000	0.000
61	N	1300	GLY	0	0.000	0.012	27.456	-0.019	-0.019	0.000	0.000	0.000	0.000
62	N	1301	LEU	0	-0.044	-0.017	25.358	-0.026	-0.026	0.000	0.000	0.000	0.000
63	N	1302	LYS	1	0.894	0.951	19.722	0.199	0.199	0.000	0.000	0.000	0.000
64	N	1303	THR	0	0.017	0.003	19.569	0.012	0.012	0.000	0.000	0.000	0.000
65	N	1304	LEU	0	0.020	0.004	14.612	-0.003	-0.003	0.000	0.000	0.000	0.000
66	N	1305	ALA	0	-0.012	-0.003	14.557	0.055	0.055	0.000	0.000	0.000	0.000
67	N	1306	THR	0	-0.032	-0.030	15.151	0.095	0.095	0.000	0.000	0.000	0.000
68	N	1307	HIS	0	-0.018	0.012	15.749	0.014	0.014	0.000	0.000	0.000	0.000
69	N	1308	GLY	0	0.049	0.047	12.600	-0.116	-0.116	0.000	0.000	0.000	0.000
70	N	1309	LEU	0	0.014	-0.020	10.665	0.072	0.072	0.000	0.000	0.000	0.000
71	N	1310	ALA	0	0.004	0.015	14.010	0.013	0.013	0.000	0.000	0.000	0.000
72	N	1311	ALA	0	-0.021	0.003	16.615	0.035	0.035	0.000	0.000	0.000	0.000
73	N	1312	VAL	0	0.023	0.006	16.199	0.054	0.054	0.000	0.000	0.000	0.000
74	N	1313	ASN	0	-0.054	-0.028	19.115	-0.003	-0.003	0.000	0.000	0.000	0.000
75	N	1314	SER	0	-0.007	0.011	21.138	0.003	0.003	0.000	0.000	0.000	0.000
76	N	1315	VAL	0	-0.026	0.007	23.214	0.011	0.011	0.000	0.000	0.000	0.000
77	N	1316	PRO	0	0.044	0.028	26.499	-0.017	-0.017	0.000	0.000	0.000	0.000
78	N	1317	TRP	0	0.050	0.017	29.079	0.016	0.016	0.000	0.000	0.000	0.000
79	N	1318	ASP	-1	-0.865	-0.906	32.192	-0.061	-0.061	0.000	0.000	0.000	0.000
80	N	1319	THR	0	0.012	0.000	31.084	0.014	0.014	0.000	0.000	0.000	0.000
81	N	1320	ILE	0	-0.005	0.012	29.242	0.013	0.013	0.000	0.000	0.000	0.000
82	N	1321	ALA	0	0.015	0.006	33.377	0.009	0.009	0.000	0.000	0.000	0.000
83	N	1322	ASN	0	-0.083	-0.031	36.500	0.014	0.014	0.000	0.000	0.000	0.000
84	N	1323	TYR	0	0.043	0.000	35.086	0.011	0.011	0.000	0.000	0.000	0.000
85	N	1324	ALA	0	0.040	0.009	36.711	0.007	0.007	0.000	0.000	0.000	0.000
86	N	1325	LYS	1	0.931	0.967	38.600	0.055	0.055	0.000	0.000	0.000	0.000
87	N	1326	PRO	0	-0.012	-0.003	40.740	0.001	0.001	0.000	0.000	0.000	0.000
88	N	1327	PHE	0	-0.042	-0.030	38.825	0.005	0.005	0.000	0.000	0.000	0.000
89	N	1328	LEU	0	-0.122	-0.050	41.564	0.000	0.000	0.000	0.000	0.000	0.000
90	N	1329	ASN	-1	-0.931	-0.940	44.794	-0.012	-0.012	0.000	0.000	0.000	0.000
91	N	1401	HOH	0	-0.023	-0.030	32.356	0.000	0.000	0.000	0.000	0.000	0.000
92	N	1402	HOH	0	-0.038	-0.033	18.179	0.015	0.015	0.000	0.000	0.000	0.000
93	N	1403	HOH	0	-0.027	-0.030	14.792	-0.008	-0.008	0.000	0.000	0.000	0.000
94	N	1404	HOH	0	-0.038	-0.033	13.865	-0.036	-0.036	0.000	0.000	0.000	0.000
95	N	1406	HOH	0	-0.066	-0.058	28.046	-0.001	-0.001	0.000	0.000	0.000	0.000
96	N	1407	HOH	0	-0.002	-0.016	12.100	0.051	0.051	0.000	0.000	0.000	0.000
97	N	1408	HOH	0	0.015	0.009	35.548	0.004	0.004	0.000	0.000	0.000	0.000
98	N	1409	HOH	0	-0.003	-0.016	11.541	-0.024	-0.024	0.000	0.000	0.000	0.000
99	N	1410	HOH	0	-0.053	-0.048	14.804	-0.015	-0.015	0.000	0.000	0.000	0.000
100	N	1411	HOH	0	-0.005	-0.005	23.397	0.005	0.005	0.000	0.000	0.000	0.000
101	N	1412	HOH	0	-0.015	-0.011	21.030	0.006	0.006	0.000	0.000	0.000	0.000
102	N	1414	HOH	0	0.033	0.020	13.444	0.038	0.038	0.000	0.000	0.000	0.000
103	N	1415	HOH	0	0.008	-0.007	32.265	-0.001	-0.001	0.000	0.000	0.000	0.000
104	N	1416	HOH	0	-0.008	-0.004	19.841	0.011	0.011	0.000	0.000	0.000	0.000
105	N	1417	HOH	0	-0.019	-0.013	21.308	0.005	0.005	0.000	0.000	0.000	0.000
106	N	1418	HOH	0	0.003	0.005	29.280	0.006	0.006	0.000	0.000	0.000	0.000
107	N	1419	HOH	0	0.047	0.026	25.045	0.008	0.008	0.000	0.000	0.000	0.000
108	N	1422	HOH	0	0.006	-0.001	8.818	0.338	0.338	0.000	0.000	0.000	0.000
109	N	1424	HOH	0	-0.006	-0.013	23.479	0.012	0.012	0.000	0.000	0.000	0.000
110	N	1425	HOH	0	-0.020	-0.012	22.483	0.005	0.005	0.000	0.000	0.000	0.000
111	N	1426	HOH	0	-0.018	-0.007	19.801	0.005	0.005	0.000	0.000	0.000	0.000
112	N	1427	HOH	0	-0.007	-0.016	24.428	-0.012	-0.012	0.000	0.000	0.000	0.000
113	N	1429	HOH	0	-0.020	-0.028	9.945	0.102	0.102	0.000	0.000	0.000	0.000
114	N	1431	HOH	0	-0.016	-0.024	27.910	-0.005	-0.005	0.000	0.000	0.000	0.000
115	N	1433	HOH	0	-0.046	-0.038	29.359	-0.007	-0.007	0.000	0.000	0.000	0.000
116	N	1434	HOH	0	0.033	0.021	41.089	0.001	0.001	0.000	0.000	0.000	0.000
117	N	1435	HOH	0	-0.022	-0.021	16.679	-0.002	-0.002	0.000	0.000	0.000	0.000
118	N	1438	HOH	0	-0.043	-0.033	28.734	0.002	0.002	0.000	0.000	0.000	0.000
119	N	1441	HOH	0	0.005	-0.006	23.493	0.014	0.014	0.000	0.000	0.000	0.000
120	N	1442	HOH	0	0.031	0.017	29.943	0.001	0.001	0.000	0.000	0.000	0.000
121	N	1444	HOH	0	-0.010	-0.001	31.389	-0.002	-0.002	0.000	0.000	0.000	0.000
122	N	1445	HOH	0	-0.034	-0.031	30.522	-0.002	-0.002	0.000	0.000	0.000	0.000
123	N	1447	HOH	0	0.003	-0.006	31.016	0.001	0.001	0.000	0.000	0.000	0.000
124	N	1448	HOH	0	0.018	-0.002	33.777	0.002	0.002	0.000	0.000	0.000	0.000
125	N	1449	HOH	0	-0.017	-0.022	18.926	-0.021	-0.021	0.000	0.000	0.000	0.000
126	N	1451	HOH	0	-0.040	-0.032	12.005	-0.069	-0.069	0.000	0.000	0.000	0.000
127	N	1452	HOH	0	-0.029	-0.020	30.716	0.005	0.005	0.000	0.000	0.000	0.000
128	N	1453	HOH	0	-0.024	-0.022	35.812	0.003	0.003	0.000	0.000	0.000	0.000
129	N	1454	HOH	0	-0.014	-0.007	26.758	0.003	0.003	0.000	0.000	0.000	0.000
130	N	1456	HOH	0	-0.054	-0.047	20.166	0.006	0.006	0.000	0.000	0.000	0.000
131	N	1457	HOH	0	0.009	0.009	25.058	-0.012	-0.012	0.000	0.000	0.000	0.000
132	N	1462	HOH	0	0.006	0.001	15.992	-0.032	-0.032	0.000	0.000	0.000	0.000
133	N	1463	HOH	0	-0.057	-0.041	25.095	0.010	0.010	0.000	0.000	0.000	0.000
134	N	1464	HOH	0	-0.054	-0.033	29.789	-0.002	-0.002	0.000	0.000	0.000	0.000
135	N	1465	HOH	0	0.011	-0.006	21.832	0.016	0.016	0.000	0.000	0.000	0.000
136	N	1469	HOH	0	0.041	0.026	21.501	-0.004	-0.004	0.000	0.000	0.000	0.000
137	N	1470	HOH	0	0.000	0.000	24.398	-0.008	-0.008	0.000	0.000	0.000	0.000
138	N	1471	HOH	0	-0.051	-0.040	32.722	-0.005	-0.005	0.000	0.000	0.000	0.000
139	N	1472	HOH	0	0.000	0.000	11.803	0.071	0.071	0.000	0.000	0.000	0.000
140	N	1474	HOH	0	0.001	0.000	39.024	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(N:1240:GLN)