FMO DATABASE

FMODB ID: 6665Z

Calculation Name: 7T9W-A-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7T9W

Chain ID: A

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	130
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-645821.957306
FMO2-HF: Nuclear repulsion	609483.702224
FMO2-HF: Total energy	-36338.255082
FMO2-MP2: Total energy	-36443.899897

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:1241:LYS)

Summations of interaction energy for fragment #1(A: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.
-94.738	-85.628	12.798	-8.415	-13.489	-0.082

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.916 / q_NPA : 0.965

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	A	1243	VAL	0	-0.029	-0.025	3.350	-5.837	-3.010	0.023	-1.484	-1.365	0.004
4	A	1244	LEU	0	0.026	0.015	5.954	2.800	2.800	0.000	0.000	0.000	0.000
5	A	1245	GLU	-1	-0.821	-0.890	9.087	-20.302	-20.302	0.000	0.000	0.000	0.000
6	A	1246	CYS	0	-0.057	-0.015	11.457	0.626	0.626	0.000	0.000	0.000	0.000
7	A	1247	ASN	0	0.046	0.027	14.248	-0.658	-0.658	0.000	0.000	0.000	0.000
8	A	1248	VAL	0	0.043	0.038	11.839	1.012	1.012	0.000	0.000	0.000	0.000
9	A	1249	LYS	1	0.915	0.945	15.242	15.464	15.464	0.000	0.000	0.000	0.000
10	A	1250	THR	0	0.009	-0.007	13.729	0.502	0.502	0.000	0.000	0.000	0.000
11	A	1251	THR	0	-0.001	-0.009	8.327	-0.119	-0.119	0.000	0.000	0.000	0.000
12	A	1252	GLU	-1	-0.787	-0.861	8.319	-27.710	-27.710	0.000	0.000	0.000	0.000
13	A	1253	VAL	0	-0.026	-0.014	1.993	-5.063	-5.485	3.294	-0.923	-1.949	-0.011
14	A	1254	VAL	0	-0.023	-0.004	4.720	4.097	4.200	-0.001	-0.007	-0.094	0.000
15	A	1255	GLY	0	0.038	0.025	4.392	-0.102	0.077	-0.001	-0.072	-0.105	0.000
16	A	1256	ASP	-1	-0.880	-0.926	2.212	-95.344	-93.334	6.246	-4.146	-4.109	-0.050
17	A	1257	ILE	0	-0.025	-0.004	2.785	-1.221	1.592	1.213	-0.884	-3.142	-0.022
18	A	1258	ILE	0	-0.042	-0.031	2.259	-7.875	-6.301	2.025	-0.892	-2.707	-0.003
19	A	1259	LEU	0	0.002	-0.002	4.777	4.553	4.579	-0.001	-0.007	-0.018	0.000
20	A	1260	LYS	1	0.872	0.907	8.495	21.065	21.065	0.000	0.000	0.000	0.000
21	A	1261	PRO	0	-0.026	-0.008	10.340	1.019	1.019	0.000	0.000	0.000	0.000
22	A	1262	ALA	0	0.023	0.022	14.122	0.635	0.635	0.000	0.000	0.000	0.000
23	A	1263	ASN	0	-0.002	-0.012	16.331	-0.405	-0.405	0.000	0.000	0.000	0.000
24	A	1264	ASN	0	-0.013	-0.006	19.977	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	1265	SER	0	0.039	0.036	15.843	0.317	0.317	0.000	0.000	0.000	0.000
26	A	1266	LEU	0	0.010	0.009	14.369	0.609	0.609	0.000	0.000	0.000	0.000
27	A	1267	LYS	1	0.921	0.943	17.053	13.379	13.379	0.000	0.000	0.000	0.000
28	A	1268	ILE	0	0.022	0.024	13.704	-0.530	-0.530	0.000	0.000	0.000	0.000
29	A	1269	THR	0	0.027	0.042	16.948	1.051	1.051	0.000	0.000	0.000	0.000
30	A	1270	GLU	-1	-0.757	-0.858	13.932	-23.324	-23.324	0.000	0.000	0.000	0.000
31	A	1271	GLU	-1	-0.802	-0.892	15.539	-18.310	-18.310	0.000	0.000	0.000	0.000
32	A	1272	VAL	0	-0.010	0.010	18.155	0.759	0.759	0.000	0.000	0.000	0.000
33	A	1273	GLY	0	0.088	0.037	20.890	0.079	0.079	0.000	0.000	0.000	0.000
34	A	1274	HIS	0	0.034	0.031	24.479	-0.272	-0.272	0.000	0.000	0.000	0.000
35	A	1275	THR	0	0.043	0.011	27.342	0.295	0.295	0.000	0.000	0.000	0.000
36	A	1276	ASP	-1	-0.813	-0.864	22.960	-13.665	-13.665	0.000	0.000	0.000	0.000
37	A	1277	LEU	0	0.009	0.003	24.147	-0.061	-0.061	0.000	0.000	0.000	0.000
38	A	1278	MET	0	-0.028	-0.002	26.734	0.211	0.211	0.000	0.000	0.000	0.000
39	A	1279	ALA	0	-0.003	-0.002	27.289	0.285	0.285	0.000	0.000	0.000	0.000
40	A	1280	ALA	0	-0.005	0.007	25.303	0.117	0.117	0.000	0.000	0.000	0.000
41	A	1281	TYR	0	0.025	0.000	27.320	0.252	0.252	0.000	0.000	0.000	0.000
42	A	1282	VAL	0	-0.031	-0.016	30.573	0.282	0.282	0.000	0.000	0.000	0.000
43	A	1283	ASP	-1	-0.908	-0.952	28.474	-10.763	-10.763	0.000	0.000	0.000	0.000
44	A	1284	ASN	0	-0.101	-0.043	29.722	-0.115	-0.115	0.000	0.000	0.000	0.000
45	A	1285	SER	0	0.013	0.014	24.430	-0.331	-0.331	0.000	0.000	0.000	0.000
46	A	1286	SER	0	0.012	-0.003	22.144	-0.175	-0.175	0.000	0.000	0.000	0.000
47	A	1287	LEU	0	-0.033	-0.030	20.382	0.095	0.095	0.000	0.000	0.000	0.000
48	A	1288	THR	0	-0.003	0.005	14.564	-0.483	-0.483	0.000	0.000	0.000	0.000
49	A	1289	ILE	0	-0.014	-0.010	15.830	-0.294	-0.294	0.000	0.000	0.000	0.000
50	A	1290	LYS	1	0.765	0.860	10.913	23.209	23.209	0.000	0.000	0.000	0.000
51	A	1291	LYS	1	0.824	0.890	10.250	23.400	23.400	0.000	0.000	0.000	0.000
52	A	1292	PRO	0	-0.011	0.011	12.551	1.414	1.414	0.000	0.000	0.000	0.000
53	A	1293	ASN	0	0.005	0.005	15.563	-0.188	-0.188	0.000	0.000	0.000	0.000
54	A	1294	GLU	-1	-0.846	-0.920	18.930	-12.504	-12.504	0.000	0.000	0.000	0.000
55	A	1295	LEU	0	0.007	0.012	22.104	0.166	0.166	0.000	0.000	0.000	0.000
56	A	1296	SER	0	0.003	-0.014	18.262	-0.302	-0.302	0.000	0.000	0.000	0.000
57	A	1297	ARG	1	0.844	0.910	14.909	18.655	18.655	0.000	0.000	0.000	0.000
58	A	1298	VAL	0	-0.014	0.003	20.483	0.222	0.222	0.000	0.000	0.000	0.000
59	A	1299	LEU	0	-0.020	-0.001	23.185	0.466	0.466	0.000	0.000	0.000	0.000
60	A	1300	GLY	0	-0.007	0.003	21.485	0.096	0.096	0.000	0.000	0.000	0.000
61	A	1301	LEU	0	-0.043	-0.015	19.296	-0.260	-0.260	0.000	0.000	0.000	0.000
62	A	1302	LYS	1	0.936	0.974	15.043	16.328	16.328	0.000	0.000	0.000	0.000
63	A	1303	THR	0	0.005	-0.001	12.500	0.050	0.050	0.000	0.000	0.000	0.000
64	A	1304	LEU	0	0.009	-0.005	9.306	-0.990	-0.990	0.000	0.000	0.000	0.000
65	A	1305	ALA	0	-0.019	-0.003	7.527	-3.738	-3.738	0.000	0.000	0.000	0.000
66	A	1306	THR	0	-0.048	-0.039	7.942	-2.287	-2.287	0.000	0.000	0.000	0.000
67	A	1307	HIS	0	0.012	0.035	10.395	0.060	0.060	0.000	0.000	0.000	0.000
68	A	1308	GLY	0	0.081	0.054	8.150	0.576	0.576	0.000	0.000	0.000	0.000
69	A	1309	LEU	0	0.036	-0.003	7.755	2.716	2.716	0.000	0.000	0.000	0.000
70	A	1310	ALA	0	-0.007	0.014	10.312	2.311	2.311	0.000	0.000	0.000	0.000
71	A	1311	ALA	0	-0.044	-0.019	12.894	1.710	1.710	0.000	0.000	0.000	0.000
72	A	1312	VAL	0	0.012	-0.008	12.573	1.008	1.008	0.000	0.000	0.000	0.000
73	A	1313	ASN	0	-0.027	-0.006	15.269	0.791	0.791	0.000	0.000	0.000	0.000
74	A	1314	SER	0	0.004	0.023	17.339	0.678	0.678	0.000	0.000	0.000	0.000
75	A	1315	VAL	0	-0.020	0.001	19.359	0.427	0.427	0.000	0.000	0.000	0.000
76	A	1316	PRO	0	0.057	0.035	21.632	0.375	0.375	0.000	0.000	0.000	0.000
77	A	1317	TRP	0	0.030	0.010	24.882	0.035	0.035	0.000	0.000	0.000	0.000
78	A	1318	ASP	-1	-0.860	-0.934	28.116	-11.293	-11.293	0.000	0.000	0.000	0.000
79	A	1319	THR	0	-0.022	-0.004	24.851	0.104	0.104	0.000	0.000	0.000	0.000
80	A	1320	ILE	0	0.015	0.017	24.560	0.167	0.167	0.000	0.000	0.000	0.000
81	A	1321	ALA	0	-0.029	-0.014	28.068	0.315	0.315	0.000	0.000	0.000	0.000
82	A	1322	ASN	0	-0.063	-0.030	31.146	0.579	0.579	0.000	0.000	0.000	0.000
83	A	1323	TYR	0	0.001	-0.017	28.872	0.130	0.130	0.000	0.000	0.000	0.000
84	A	1324	ALA	0	0.062	0.016	30.938	0.219	0.219	0.000	0.000	0.000	0.000
85	A	1325	LYS	1	0.928	0.974	32.702	9.158	9.158	0.000	0.000	0.000	0.000
86	A	1326	PRO	0	-0.021	-0.005	34.652	0.269	0.269	0.000	0.000	0.000	0.000
87	A	1327	PHE	0	-0.043	-0.006	32.071	0.116	0.116	0.000	0.000	0.000	0.000
88	A	1328	LEU	-1	-0.901	-0.913	35.769	-7.948	-7.948	0.000	0.000	0.000	0.000
89	A	1401	HOH	0	-0.011	-0.011	36.541	-0.102	-0.102	0.000	0.000	0.000	0.000
90	A	1402	HOH	0	0.022	0.022	14.460	0.040	0.040	0.000	0.000	0.000	0.000
91	A	1403	HOH	0	-0.014	-0.026	19.789	-0.309	-0.309	0.000	0.000	0.000	0.000
92	A	1404	HOH	0	-0.033	-0.030	23.854	-0.178	-0.178	0.000	0.000	0.000	0.000
93	A	1405	HOH	0	-0.031	-0.028	21.684	0.148	0.148	0.000	0.000	0.000	0.000
94	A	1406	HOH	0	-0.035	-0.043	21.327	0.086	0.086	0.000	0.000	0.000	0.000
95	A	1407	HOH	0	0.017	0.002	22.546	-0.300	-0.300	0.000	0.000	0.000	0.000
96	A	1408	HOH	0	-0.029	-0.036	20.436	0.213	0.213	0.000	0.000	0.000	0.000
97	A	1409	HOH	0	-0.012	-0.008	17.753	0.261	0.261	0.000	0.000	0.000	0.000
98	A	1411	HOH	0	-0.026	-0.029	6.199	-0.661	-0.661	0.000	0.000	0.000	0.000
99	A	1412	HOH	0	-0.001	-0.013	16.636	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	1413	HOH	0	-0.022	-0.016	16.442	0.290	0.290	0.000	0.000	0.000	0.000
101	A	1414	HOH	0	0.027	0.012	7.003	-0.916	-0.916	0.000	0.000	0.000	0.000
102	A	1415	HOH	0	-0.002	-0.001	16.910	-0.377	-0.377	0.000	0.000	0.000	0.000
103	A	1416	HOH	0	-0.007	-0.013	14.307	0.079	0.079	0.000	0.000	0.000	0.000
104	A	1417	HOH	0	0.002	-0.006	34.858	-0.121	-0.121	0.000	0.000	0.000	0.000
105	A	1418	HOH	0	-0.016	-0.003	17.050	0.453	0.453	0.000	0.000	0.000	0.000
106	A	1419	HOH	0	-0.004	-0.005	28.741	0.161	0.161	0.000	0.000	0.000	0.000
107	A	1420	HOH	0	-0.024	-0.024	32.603	0.031	0.031	0.000	0.000	0.000	0.000
108	A	1421	HOH	0	-0.012	-0.022	18.838	0.043	0.043	0.000	0.000	0.000	0.000
109	A	1422	HOH	0	0.000	-0.006	17.180	-0.378	-0.378	0.000	0.000	0.000	0.000
110	A	1424	HOH	0	-0.015	-0.021	25.113	0.239	0.239	0.000	0.000	0.000	0.000
111	A	1425	HOH	0	0.001	-0.004	19.717	0.308	0.308	0.000	0.000	0.000	0.000
112	A	1427	HOH	0	-0.064	-0.040	40.024	0.059	0.059	0.000	0.000	0.000	0.000
113	A	1428	HOH	0	-0.016	-0.017	19.148	0.422	0.422	0.000	0.000	0.000	0.000
114	A	1429	HOH	0	-0.074	-0.049	26.925	0.143	0.143	0.000	0.000	0.000	0.000
115	A	1430	HOH	0	-0.064	-0.040	6.008	2.777	2.777	0.000	0.000	0.000	0.000
116	A	1431	HOH	0	0.017	0.006	23.454	-0.196	-0.196	0.000	0.000	0.000	0.000
117	A	1432	HOH	0	-0.014	-0.018	20.532	-0.226	-0.226	0.000	0.000	0.000	0.000
118	A	1433	HOH	0	-0.029	-0.021	16.112	0.112	0.112	0.000	0.000	0.000	0.000
119	A	1434	HOH	0	-0.003	0.006	23.147	0.211	0.211	0.000	0.000	0.000	0.000
120	A	1435	HOH	0	-0.002	-0.005	14.521	0.118	0.118	0.000	0.000	0.000	0.000
121	A	1436	HOH	0	-0.016	-0.012	17.692	0.136	0.136	0.000	0.000	0.000	0.000
122	A	1437	HOH	0	-0.030	-0.023	13.147	-0.103	-0.103	0.000	0.000	0.000	0.000
123	A	1438	HOH	0	0.006	0.010	22.219	-0.337	-0.337	0.000	0.000	0.000	0.000
124	A	1439	HOH	0	0.028	0.019	18.447	-0.177	-0.177	0.000	0.000	0.000	0.000
125	A	1440	HOH	0	-0.047	-0.031	26.544	-0.194	-0.194	0.000	0.000	0.000	0.000
126	A	1441	HOH	0	-0.015	-0.015	19.343	0.251	0.251	0.000	0.000	0.000	0.000
127	A	1442	HOH	0	-0.025	-0.026	23.680	0.260	0.260	0.000	0.000	0.000	0.000
128	A	1443	HOH	0	-0.033	-0.017	33.706	0.088	0.088	0.000	0.000	0.000	0.000
129	A	1444	HOH	0	-0.026	-0.021	19.118	0.293	0.293	0.000	0.000	0.000	0.000
130	A	1445	HOH	0	0.026	0.021	17.848	-0.159	-0.159	0.000	0.000	0.000	0.000

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