FMO DATABASE

FMODB ID: 7GG4K

Calculation Name: 7T9W-L-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7T9W

Chain ID: L

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	127
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-636298.58786
FMO2-HF: Nuclear repulsion	600188.517659
FMO2-HF: Total energy	-36110.0702
FMO2-MP2: Total energy	-36215.122864

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(L:1241:LYS)

Summations of interaction energy for fragment #1(L:1241:LYS)

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.
-141.132	-136.343	21.308	-12.526	-13.568	-0.139

Interaction energy analysis for fragmet #1(L:1241:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.930

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

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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	L	1243	VAL	0	-0.003	-0.010	3.442	-4.592	-2.023	0.012	-1.308	-1.273	0.005
4	L	1244	LEU	0	0.014	0.010	5.979	2.768	2.768	0.000	0.000	0.000	0.000
5	L	1245	GLU	-1	-0.864	-0.924	9.120	-18.902	-18.902	0.000	0.000	0.000	0.000
6	L	1246	CYS	0	-0.046	-0.012	11.632	0.724	0.724	0.000	0.000	0.000	0.000
7	L	1247	ASN	0	0.022	0.016	14.458	-0.456	-0.456	0.000	0.000	0.000	0.000
8	L	1248	VAL	0	0.025	0.017	12.027	0.831	0.831	0.000	0.000	0.000	0.000
9	L	1249	LYS	1	0.979	0.979	15.475	14.438	14.438	0.000	0.000	0.000	0.000
10	L	1250	THR	0	0.001	-0.003	13.708	1.008	1.008	0.000	0.000	0.000	0.000
11	L	1251	THR	0	-0.006	-0.002	8.794	-0.170	-0.170	0.000	0.000	0.000	0.000
12	L	1252	GLU	-1	-0.781	-0.859	9.180	-25.348	-25.348	0.000	0.000	0.000	0.000
13	L	1253	VAL	0	0.006	0.002	3.573	-2.162	-1.798	0.011	-0.064	-0.311	0.000
14	L	1254	VAL	0	-0.001	0.000	5.514	4.311	4.311	0.000	0.000	0.000	0.000
15	L	1255	GLY	0	0.026	0.018	4.981	-1.541	-1.462	-0.001	-0.016	-0.061	0.000
16	L	1256	ASP	-1	-0.851	-0.932	1.776	-136.032	-136.796	16.690	-9.436	-6.490	-0.104
17	L	1257	ILE	0	-0.055	-0.013	2.306	-8.058	-6.639	4.514	-1.482	-4.451	-0.039
18	L	1258	ILE	0	-0.059	-0.031	3.014	-2.595	-1.489	0.083	-0.214	-0.974	-0.001
19	L	1259	LEU	0	0.007	0.002	4.612	3.627	3.643	-0.001	-0.006	-0.008	0.000
20	L	1260	LYS	1	0.856	0.910	8.291	19.482	19.482	0.000	0.000	0.000	0.000
21	L	1261	PRO	0	0.003	0.014	10.517	0.662	0.662	0.000	0.000	0.000	0.000
22	L	1262	ALA	0	0.030	0.019	14.285	0.290	0.290	0.000	0.000	0.000	0.000
23	L	1263	ASN	0	-0.033	-0.028	16.469	0.490	0.490	0.000	0.000	0.000	0.000
24	L	1264	ASN	0	-0.042	-0.017	20.143	0.274	0.274	0.000	0.000	0.000	0.000
25	L	1265	SER	0	0.042	0.034	15.572	0.192	0.192	0.000	0.000	0.000	0.000
26	L	1266	LEU	0	-0.001	0.005	14.332	0.642	0.642	0.000	0.000	0.000	0.000
27	L	1267	LYS	1	0.979	0.982	17.183	12.511	12.511	0.000	0.000	0.000	0.000
28	L	1268	ILE	0	0.003	0.008	13.655	-0.293	-0.293	0.000	0.000	0.000	0.000
29	L	1269	THR	0	-0.014	-0.001	16.943	1.018	1.018	0.000	0.000	0.000	0.000
30	L	1270	GLU	-1	-0.769	-0.865	14.565	-22.397	-22.397	0.000	0.000	0.000	0.000
31	L	1271	GLU	-1	-0.892	-0.928	16.012	-17.914	-17.914	0.000	0.000	0.000	0.000
32	L	1272	VAL	0	0.004	0.011	18.588	0.754	0.754	0.000	0.000	0.000	0.000
33	L	1273	GLY	0	0.086	0.033	21.306	0.143	0.143	0.000	0.000	0.000	0.000
34	L	1274	HIS	0	0.027	0.029	24.849	-0.268	-0.268	0.000	0.000	0.000	0.000
35	L	1275	THR	0	0.022	-0.008	27.972	0.205	0.205	0.000	0.000	0.000	0.000
36	L	1276	ASP	-1	-0.810	-0.874	23.685	-13.404	-13.404	0.000	0.000	0.000	0.000
37	L	1277	LEU	0	0.009	0.003	24.512	0.005	0.005	0.000	0.000	0.000	0.000
38	L	1278	MET	0	-0.027	0.005	27.216	0.194	0.194	0.000	0.000	0.000	0.000
39	L	1279	ALA	0	0.001	-0.002	27.936	0.278	0.278	0.000	0.000	0.000	0.000
40	L	1280	ALA	0	-0.007	-0.002	25.826	0.112	0.112	0.000	0.000	0.000	0.000
41	L	1281	TYR	0	0.013	0.002	27.751	0.180	0.180	0.000	0.000	0.000	0.000
42	L	1282	VAL	0	-0.040	-0.026	30.996	0.221	0.221	0.000	0.000	0.000	0.000
43	L	1283	ASP	-1	-0.851	-0.888	29.165	-10.211	-10.211	0.000	0.000	0.000	0.000
44	L	1284	ASN	0	-0.086	-0.032	29.942	0.240	0.240	0.000	0.000	0.000	0.000
45	L	1285	SER	0	-0.029	0.002	25.250	-0.289	-0.289	0.000	0.000	0.000	0.000
46	L	1286	SER	0	0.043	0.004	22.156	-0.217	-0.217	0.000	0.000	0.000	0.000
47	L	1287	LEU	0	-0.017	-0.008	20.802	0.022	0.022	0.000	0.000	0.000	0.000
48	L	1288	THR	0	0.023	0.006	14.410	-0.655	-0.655	0.000	0.000	0.000	0.000
49	L	1289	ILE	0	-0.008	0.002	15.922	-0.070	-0.070	0.000	0.000	0.000	0.000
50	L	1290	LYS	1	0.758	0.857	11.379	21.138	21.138	0.000	0.000	0.000	0.000
51	L	1291	LYS	1	0.827	0.900	10.630	22.273	22.273	0.000	0.000	0.000	0.000
52	L	1292	PRO	0	-0.010	0.016	12.713	1.485	1.485	0.000	0.000	0.000	0.000
53	L	1293	ASN	0	0.001	-0.004	15.797	-0.161	-0.161	0.000	0.000	0.000	0.000
54	L	1294	GLU	-1	-0.851	-0.907	19.190	-12.589	-12.589	0.000	0.000	0.000	0.000
55	L	1295	LEU	0	0.007	0.017	22.380	0.206	0.206	0.000	0.000	0.000	0.000
56	L	1296	SER	0	0.039	-0.002	18.678	-0.148	-0.148	0.000	0.000	0.000	0.000
57	L	1297	ARG	1	0.885	0.954	14.885	18.775	18.775	0.000	0.000	0.000	0.000
58	L	1298	VAL	0	-0.003	0.009	20.588	0.182	0.182	0.000	0.000	0.000	0.000
59	L	1299	LEU	0	-0.013	0.003	23.443	0.453	0.453	0.000	0.000	0.000	0.000
60	L	1300	GLY	0	-0.017	-0.001	21.503	0.015	0.015	0.000	0.000	0.000	0.000
61	L	1301	LEU	0	-0.038	-0.014	19.579	-0.383	-0.383	0.000	0.000	0.000	0.000
62	L	1302	LYS	1	0.898	0.958	15.054	16.235	16.235	0.000	0.000	0.000	0.000
63	L	1303	THR	0	0.016	0.007	12.845	0.322	0.322	0.000	0.000	0.000	0.000
64	L	1304	LEU	0	0.023	0.009	9.503	-1.380	-1.380	0.000	0.000	0.000	0.000
65	L	1305	ALA	0	-0.044	-0.023	7.599	-4.073	-4.073	0.000	0.000	0.000	0.000
66	L	1306	THR	0	-0.027	-0.035	7.901	-2.635	-2.635	0.000	0.000	0.000	0.000
67	L	1307	HIS	0	-0.006	0.005	10.279	-0.719	-0.719	0.000	0.000	0.000	0.000
68	L	1308	GLY	0	0.040	0.034	8.178	0.084	0.084	0.000	0.000	0.000	0.000
69	L	1309	LEU	0	0.030	-0.011	7.625	2.808	2.808	0.000	0.000	0.000	0.000
70	L	1310	ALA	0	-0.010	0.006	10.182	2.246	2.246	0.000	0.000	0.000	0.000
71	L	1311	ALA	0	-0.035	-0.012	12.742	1.776	1.776	0.000	0.000	0.000	0.000
72	L	1312	VAL	0	0.015	0.011	12.205	1.039	1.039	0.000	0.000	0.000	0.000
73	L	1313	ASN	0	-0.035	-0.023	14.937	0.597	0.597	0.000	0.000	0.000	0.000
74	L	1314	SER	0	0.002	0.022	17.234	0.782	0.782	0.000	0.000	0.000	0.000
75	L	1315	VAL	0	-0.046	-0.007	19.213	0.426	0.426	0.000	0.000	0.000	0.000
76	L	1316	PRO	0	0.024	0.021	22.002	0.285	0.285	0.000	0.000	0.000	0.000
77	L	1317	TRP	0	0.073	0.021	25.175	0.024	0.024	0.000	0.000	0.000	0.000
78	L	1318	ASP	-1	-0.853	-0.933	28.376	-11.132	-11.132	0.000	0.000	0.000	0.000
79	L	1319	THR	0	-0.035	-0.013	25.147	0.158	0.158	0.000	0.000	0.000	0.000
80	L	1320	ILE	0	0.006	0.020	24.943	0.102	0.102	0.000	0.000	0.000	0.000
81	L	1321	ALA	0	0.001	-0.011	28.521	0.302	0.302	0.000	0.000	0.000	0.000
82	L	1322	ASN	0	-0.045	-0.027	31.610	0.595	0.595	0.000	0.000	0.000	0.000
83	L	1323	TYR	0	-0.034	-0.026	29.170	0.122	0.122	0.000	0.000	0.000	0.000
84	L	1324	ALA	0	0.049	0.001	31.325	0.211	0.211	0.000	0.000	0.000	0.000
85	L	1325	LYS	1	0.912	0.971	33.201	8.572	8.572	0.000	0.000	0.000	0.000
86	L	1326	PRO	0	-0.011	0.003	34.954	0.260	0.260	0.000	0.000	0.000	0.000
87	L	1327	PHE	0	-0.010	0.001	32.507	0.181	0.181	0.000	0.000	0.000	0.000
88	L	1328	LEU	-1	-0.857	-0.862	36.693	-7.788	-7.788	0.000	0.000	0.000	0.000
89	L	1404	HOH	0	-0.035	-0.041	27.012	-0.155	-0.155	0.000	0.000	0.000	0.000
90	L	1405	HOH	0	-0.021	-0.025	16.618	0.367	0.367	0.000	0.000	0.000	0.000
91	L	1407	HOH	0	0.017	-0.008	17.273	0.262	0.262	0.000	0.000	0.000	0.000
92	L	1408	HOH	0	-0.008	-0.016	17.215	-0.241	-0.241	0.000	0.000	0.000	0.000
93	L	1410	HOH	0	0.004	0.001	18.754	-0.346	-0.346	0.000	0.000	0.000	0.000
94	L	1411	HOH	0	-0.071	-0.054	40.489	0.022	0.022	0.000	0.000	0.000	0.000
95	L	1412	HOH	0	0.015	0.006	19.162	-0.136	-0.136	0.000	0.000	0.000	0.000
96	L	1413	HOH	0	-0.010	-0.011	37.181	-0.100	-0.100	0.000	0.000	0.000	0.000
97	L	1416	HOH	0	0.005	-0.010	18.823	-0.043	-0.043	0.000	0.000	0.000	0.000
98	L	1417	HOH	0	0.000	-0.006	35.371	-0.124	-0.124	0.000	0.000	0.000	0.000
99	L	1418	HOH	0	0.017	0.002	21.275	-0.278	-0.278	0.000	0.000	0.000	0.000
100	L	1419	HOH	0	0.004	0.002	36.440	0.119	0.119	0.000	0.000	0.000	0.000
101	L	1420	HOH	0	0.026	0.019	17.502	-0.413	-0.413	0.000	0.000	0.000	0.000
102	L	1421	HOH	0	-0.018	-0.022	20.718	0.251	0.251	0.000	0.000	0.000	0.000
103	L	1422	HOH	0	-0.024	-0.026	14.892	-0.159	-0.159	0.000	0.000	0.000	0.000
104	L	1423	HOH	0	-0.020	-0.021	22.488	-0.184	-0.184	0.000	0.000	0.000	0.000
105	L	1425	HOH	0	-0.020	-0.018	29.256	0.137	0.137	0.000	0.000	0.000	0.000
106	L	1426	HOH	0	-0.007	-0.011	20.423	-0.317	-0.317	0.000	0.000	0.000	0.000
107	L	1428	HOH	0	-0.018	-0.008	20.250	-0.322	-0.322	0.000	0.000	0.000	0.000
108	L	1429	HOH	0	-0.045	-0.033	18.522	0.202	0.202	0.000	0.000	0.000	0.000
109	L	1430	HOH	0	0.028	0.018	26.442	0.009	0.009	0.000	0.000	0.000	0.000
110	L	1432	HOH	0	-0.008	-0.010	23.471	-0.221	-0.221	0.000	0.000	0.000	0.000
111	L	1435	HOH	0	-0.008	-0.011	19.577	-0.391	-0.391	0.000	0.000	0.000	0.000
112	L	1436	HOH	0	-0.002	-0.003	22.861	0.255	0.255	0.000	0.000	0.000	0.000
113	L	1437	HOH	0	-0.024	-0.024	42.301	0.078	0.078	0.000	0.000	0.000	0.000
114	L	1438	HOH	0	-0.044	-0.030	26.881	-0.095	-0.095	0.000	0.000	0.000	0.000
115	L	1440	HOH	0	-0.025	-0.023	23.679	0.125	0.125	0.000	0.000	0.000	0.000
116	L	1442	HOH	0	-0.034	-0.036	23.600	-0.301	-0.301	0.000	0.000	0.000	0.000
117	L	1443	HOH	0	-0.001	-0.014	20.535	0.029	0.029	0.000	0.000	0.000	0.000
118	L	1444	HOH	0	-0.051	-0.030	23.069	-0.088	-0.088	0.000	0.000	0.000	0.000
119	L	1445	HOH	0	-0.056	-0.042	41.926	0.009	0.009	0.000	0.000	0.000	0.000
120	L	1446	HOH	0	-0.024	-0.018	21.310	-0.177	-0.177	0.000	0.000	0.000	0.000
121	L	1447	HOH	0	0.009	0.005	20.375	0.223	0.223	0.000	0.000	0.000	0.000
122	L	1448	HOH	0	0.032	0.019	28.103	0.089	0.089	0.000	0.000	0.000	0.000
123	L	1449	HOH	0	-0.029	-0.026	31.007	0.074	0.074	0.000	0.000	0.000	0.000
124	L	1450	HOH	0	0.018	0.010	16.941	-0.237	-0.237	0.000	0.000	0.000	0.000
125	L	1451	HOH	0	-0.027	-0.018	33.811	0.123	0.123	0.000	0.000	0.000	0.000
126	L	1452	HOH	0	-0.025	-0.025	22.023	0.038	0.038	0.000	0.000	0.000	0.000
127	L	1453	HOH	0	-0.029	-0.019	34.388	0.090	0.090	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:1241:LYS)