FMO DATABASE

FMODB ID: R5548

Calculation Name: 7T9W-H-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7T9W

Chain ID: H

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	125
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-656826.02186
FMO2-HF: Nuclear repulsion	619866.967592
FMO2-HF: Total energy	-36959.054268
FMO2-MP2: Total energy	-37066.816831

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(H:1239:ILE)

Summations of interaction energy for fragment #1(H:1239:ILE)

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.
-2.418	0.342	0.265	-1.229	-1.796	-0.005

Interaction energy analysis for fragmet #1(H:1239:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.021

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	H	1241	LYS	1	0.931	0.976	2.938	-0.875	1.745	0.266	-1.223	-1.663	-0.005
4	H	1242	ASP	-1	-0.788	-0.859	4.537	-0.415	-0.275	-0.001	-0.006	-0.133	0.000
5	H	1243	VAL	0	-0.014	-0.019	7.071	0.007	0.007	0.000	0.000	0.000	0.000
6	H	1244	LEU	0	0.024	0.016	10.278	0.062	0.062	0.000	0.000	0.000	0.000
7	H	1245	GLU	-1	-0.839	-0.903	13.745	-0.033	-0.033	0.000	0.000	0.000	0.000
8	H	1246	CYS	0	-0.026	0.008	16.797	0.002	0.002	0.000	0.000	0.000	0.000
9	H	1247	ASN	0	0.024	0.008	19.434	0.003	0.003	0.000	0.000	0.000	0.000
10	H	1248	VAL	0	0.008	0.008	17.961	0.011	0.011	0.000	0.000	0.000	0.000
11	H	1249	LYS	1	0.962	0.962	21.330	0.095	0.095	0.000	0.000	0.000	0.000
12	H	1250	THR	0	0.015	0.010	20.181	0.021	0.021	0.000	0.000	0.000	0.000
13	H	1251	THR	0	-0.004	-0.002	14.360	-0.013	-0.013	0.000	0.000	0.000	0.000
14	H	1252	GLU	-1	-0.805	-0.864	15.550	-0.259	-0.259	0.000	0.000	0.000	0.000
15	H	1253	VAL	0	0.002	0.002	10.444	-0.028	-0.028	0.000	0.000	0.000	0.000
16	H	1254	VAL	0	-0.010	-0.008	12.386	0.070	0.070	0.000	0.000	0.000	0.000
17	H	1255	GLY	0	0.037	0.026	12.027	-0.039	-0.039	0.000	0.000	0.000	0.000
18	H	1256	ASP	-1	-0.950	-0.961	7.024	-1.361	-1.361	0.000	0.000	0.000	0.000
19	H	1257	ILE	0	-0.025	-0.010	6.865	-0.289	-0.289	0.000	0.000	0.000	0.000
20	H	1258	ILE	0	-0.040	-0.028	8.331	0.047	0.047	0.000	0.000	0.000	0.000
21	H	1259	LEU	0	-0.006	0.000	10.968	0.053	0.053	0.000	0.000	0.000	0.000
22	H	1260	LYS	1	0.904	0.922	14.333	0.028	0.028	0.000	0.000	0.000	0.000
23	H	1261	PRO	0	-0.023	-0.006	15.979	0.009	0.009	0.000	0.000	0.000	0.000
24	H	1262	ALA	0	0.010	0.013	19.564	0.022	0.022	0.000	0.000	0.000	0.000
25	H	1263	ASN	0	-0.005	-0.017	21.375	-0.012	-0.012	0.000	0.000	0.000	0.000
26	H	1264	ASN	0	-0.064	-0.032	24.856	0.000	0.000	0.000	0.000	0.000	0.000
27	H	1265	SER	0	0.004	0.008	20.006	0.003	0.003	0.000	0.000	0.000	0.000
28	H	1266	LEU	0	0.015	0.013	18.751	0.004	0.004	0.000	0.000	0.000	0.000
29	H	1267	LYS	1	0.971	0.966	22.287	0.078	0.078	0.000	0.000	0.000	0.000
30	H	1268	ILE	0	-0.009	0.012	19.066	-0.008	-0.008	0.000	0.000	0.000	0.000
31	H	1269	THR	0	0.024	0.021	22.473	0.016	0.016	0.000	0.000	0.000	0.000
32	H	1270	GLU	-1	-0.776	-0.886	22.333	-0.232	-0.232	0.000	0.000	0.000	0.000
33	H	1271	GLU	-1	-0.819	-0.911	23.216	-0.189	-0.189	0.000	0.000	0.000	0.000
34	H	1272	VAL	0	-0.047	-0.012	25.801	0.011	0.011	0.000	0.000	0.000	0.000
35	H	1273	GLY	0	0.064	0.019	27.800	0.000	0.000	0.000	0.000	0.000	0.000
36	H	1274	HIS	0	0.026	0.033	31.543	-0.003	-0.003	0.000	0.000	0.000	0.000
37	H	1275	THR	0	0.001	-0.014	34.412	0.003	0.003	0.000	0.000	0.000	0.000
38	H	1276	ASP	-1	-0.847	-0.907	29.370	-0.113	-0.113	0.000	0.000	0.000	0.000
39	H	1277	LEU	0	0.006	0.003	29.704	-0.001	-0.001	0.000	0.000	0.000	0.000
40	H	1278	MET	0	-0.017	0.008	32.545	0.002	0.002	0.000	0.000	0.000	0.000
41	H	1279	ALA	0	0.003	0.006	33.187	0.004	0.004	0.000	0.000	0.000	0.000
42	H	1280	ALA	0	0.005	0.009	30.375	0.003	0.003	0.000	0.000	0.000	0.000
43	H	1281	TYR	0	-0.007	-0.005	32.260	0.002	0.002	0.000	0.000	0.000	0.000
44	H	1282	VAL	0	-0.054	-0.027	35.117	0.004	0.004	0.000	0.000	0.000	0.000
45	H	1283	ASP	-1	-0.882	-0.914	33.528	-0.065	-0.065	0.000	0.000	0.000	0.000
46	H	1284	ASN	0	-0.086	-0.038	34.000	-0.003	-0.003	0.000	0.000	0.000	0.000
47	H	1285	SER	0	0.010	0.009	29.292	0.001	0.001	0.000	0.000	0.000	0.000
48	H	1286	SER	0	-0.001	-0.016	25.649	-0.007	-0.007	0.000	0.000	0.000	0.000
49	H	1287	LEU	0	-0.011	-0.012	25.279	0.003	0.003	0.000	0.000	0.000	0.000
50	H	1288	THR	0	0.016	0.009	18.990	-0.012	-0.012	0.000	0.000	0.000	0.000
51	H	1289	ILE	0	0.001	0.002	21.606	0.003	0.003	0.000	0.000	0.000	0.000
52	H	1290	LYS	1	0.790	0.882	17.830	0.204	0.204	0.000	0.000	0.000	0.000
53	H	1291	LYS	1	0.816	0.905	18.455	0.225	0.225	0.000	0.000	0.000	0.000
54	H	1292	PRO	0	0.001	0.023	19.930	0.022	0.022	0.000	0.000	0.000	0.000
55	H	1293	ASN	0	-0.013	-0.010	22.957	0.000	0.000	0.000	0.000	0.000	0.000
56	H	1294	GLU	-1	-0.784	-0.871	26.586	-0.133	-0.133	0.000	0.000	0.000	0.000
57	H	1295	LEU	0	0.024	0.023	29.270	0.002	0.002	0.000	0.000	0.000	0.000
58	H	1296	SER	0	0.008	0.000	24.802	-0.007	-0.007	0.000	0.000	0.000	0.000
59	H	1297	ARG	1	0.902	0.944	21.264	0.239	0.239	0.000	0.000	0.000	0.000
60	H	1298	VAL	0	-0.014	0.011	26.318	0.000	0.000	0.000	0.000	0.000	0.000
61	H	1299	LEU	0	-0.005	0.005	28.773	0.006	0.006	0.000	0.000	0.000	0.000
62	H	1300	GLY	0	0.003	0.006	25.760	0.002	0.002	0.000	0.000	0.000	0.000
63	H	1301	LEU	0	-0.052	-0.022	24.242	-0.007	-0.007	0.000	0.000	0.000	0.000
64	H	1302	LYS	1	0.893	0.950	18.712	0.194	0.194	0.000	0.000	0.000	0.000
65	H	1303	THR	0	0.017	-0.004	18.721	0.014	0.014	0.000	0.000	0.000	0.000
66	H	1304	LEU	0	0.032	0.008	15.063	-0.032	-0.032	0.000	0.000	0.000	0.000
67	H	1305	ALA	0	-0.029	-0.014	13.986	-0.075	-0.075	0.000	0.000	0.000	0.000
68	H	1306	THR	0	-0.014	-0.021	14.438	-0.039	-0.039	0.000	0.000	0.000	0.000
69	H	1307	HIS	0	-0.004	0.028	14.198	-0.008	-0.008	0.000	0.000	0.000	0.000
70	H	1308	GLY	0	0.004	0.027	11.487	-0.022	-0.022	0.000	0.000	0.000	0.000
71	H	1309	LEU	0	0.015	-0.012	10.468	0.077	0.077	0.000	0.000	0.000	0.000
72	H	1310	ALA	0	0.009	0.011	13.237	0.061	0.061	0.000	0.000	0.000	0.000
73	H	1311	ALA	0	-0.055	-0.020	15.704	0.037	0.037	0.000	0.000	0.000	0.000
74	H	1312	VAL	0	0.005	-0.009	16.218	0.024	0.024	0.000	0.000	0.000	0.000
75	H	1313	ASN	0	-0.046	-0.025	18.765	0.010	0.010	0.000	0.000	0.000	0.000
76	H	1314	SER	0	0.050	0.047	20.226	0.006	0.006	0.000	0.000	0.000	0.000
77	H	1315	VAL	0	-0.041	0.001	22.343	0.003	0.003	0.000	0.000	0.000	0.000
78	H	1316	PRO	0	0.038	0.029	25.615	0.009	0.009	0.000	0.000	0.000	0.000
79	H	1317	TRP	0	0.078	0.029	28.137	0.000	0.000	0.000	0.000	0.000	0.000
80	H	1318	ASP	-1	-0.840	-0.917	31.460	-0.091	-0.091	0.000	0.000	0.000	0.000
81	H	1319	THR	0	-0.045	-0.015	29.388	-0.001	-0.001	0.000	0.000	0.000	0.000
82	H	1320	ILE	0	0.014	0.026	28.831	0.001	0.001	0.000	0.000	0.000	0.000
83	H	1321	ALA	0	0.017	0.007	32.670	0.004	0.004	0.000	0.000	0.000	0.000
84	H	1322	ASN	0	-0.101	-0.043	35.043	0.008	0.008	0.000	0.000	0.000	0.000
85	H	1323	TYR	0	-0.018	-0.012	34.262	0.001	0.001	0.000	0.000	0.000	0.000
86	H	1324	ALA	0	0.055	0.004	36.271	0.003	0.003	0.000	0.000	0.000	0.000
87	H	1325	LYS	1	0.983	0.998	38.138	0.068	0.068	0.000	0.000	0.000	0.000
88	H	1326	PRO	0	-0.046	-0.030	40.035	0.004	0.004	0.000	0.000	0.000	0.000
89	H	1327	PHE	0	-0.017	-0.011	38.218	0.002	0.002	0.000	0.000	0.000	0.000
90	H	1328	LEU	0	-0.108	-0.030	41.315	0.001	0.001	0.000	0.000	0.000	0.000
91	H	1329	ASN	-1	-0.953	-0.969	44.564	-0.044	-0.044	0.000	0.000	0.000	0.000
92	H	1503	HOH	0	0.009	0.005	22.922	-0.008	-0.008	0.000	0.000	0.000	0.000
93	H	1508	HOH	0	-0.016	-0.013	22.447	-0.006	-0.006	0.000	0.000	0.000	0.000
94	H	1511	HOH	0	-0.039	-0.034	17.753	0.013	0.013	0.000	0.000	0.000	0.000
95	H	1512	HOH	0	-0.033	-0.033	28.921	0.002	0.002	0.000	0.000	0.000	0.000
96	H	1514	HOH	0	0.018	0.007	24.165	-0.005	-0.005	0.000	0.000	0.000	0.000
97	H	1515	HOH	0	-0.080	-0.060	34.091	0.002	0.002	0.000	0.000	0.000	0.000
98	H	1517	HOH	0	-0.025	-0.020	20.630	0.008	0.008	0.000	0.000	0.000	0.000
99	H	1518	HOH	0	0.011	-0.014	24.325	0.003	0.003	0.000	0.000	0.000	0.000
100	H	1520	HOH	0	0.002	-0.005	10.115	0.028	0.028	0.000	0.000	0.000	0.000
101	H	1522	HOH	0	-0.054	-0.047	37.302	0.001	0.001	0.000	0.000	0.000	0.000
102	H	1523	HOH	0	-0.013	-0.015	20.015	0.001	0.001	0.000	0.000	0.000	0.000
103	H	1524	HOH	0	0.006	-0.008	22.365	-0.002	-0.002	0.000	0.000	0.000	0.000
104	H	1525	HOH	0	-0.010	-0.002	33.409	0.000	0.000	0.000	0.000	0.000	0.000
105	H	1526	HOH	0	-0.045	-0.026	30.537	-0.003	-0.003	0.000	0.000	0.000	0.000
106	H	1528	HOH	0	-0.038	-0.031	31.621	-0.003	-0.003	0.000	0.000	0.000	0.000
107	H	1529	HOH	0	-0.026	-0.023	31.249	0.000	0.000	0.000	0.000	0.000	0.000
108	H	1530	HOH	0	0.017	0.005	11.227	-0.037	-0.037	0.000	0.000	0.000	0.000
109	H	1532	HOH	0	-0.015	-0.010	11.734	0.016	0.016	0.000	0.000	0.000	0.000
110	H	1537	HOH	0	-0.001	-0.010	8.942	0.071	0.071	0.000	0.000	0.000	0.000
111	H	1538	HOH	0	-0.034	-0.020	17.608	0.006	0.006	0.000	0.000	0.000	0.000
112	H	1539	HOH	0	-0.012	-0.019	13.290	0.027	0.027	0.000	0.000	0.000	0.000
113	H	1540	HOH	0	0.010	0.000	30.337	-0.002	-0.002	0.000	0.000	0.000	0.000
114	H	1541	HOH	0	-0.020	-0.017	21.731	0.003	0.003	0.000	0.000	0.000	0.000
115	H	1545	HOH	0	-0.037	-0.025	27.518	-0.003	-0.003	0.000	0.000	0.000	0.000
116	H	1546	HOH	0	0.035	0.016	31.194	-0.002	-0.002	0.000	0.000	0.000	0.000
117	H	1549	HOH	0	-0.003	-0.014	32.444	0.002	0.002	0.000	0.000	0.000	0.000
118	H	1554	HOH	0	0.047	0.026	33.571	0.001	0.001	0.000	0.000	0.000	0.000
119	H	1557	HOH	0	0.004	-0.016	32.920	-0.002	-0.002	0.000	0.000	0.000	0.000
120	H	1559	HOH	0	-0.019	-0.022	11.098	0.034	0.034	0.000	0.000	0.000	0.000
121	H	1562	HOH	0	-0.012	-0.011	24.471	0.005	0.005	0.000	0.000	0.000	0.000
122	H	1565	HOH	0	-0.024	-0.024	34.474	0.003	0.003	0.000	0.000	0.000	0.000
123	H	1568	HOH	0	0.028	0.002	8.636	0.051	0.051	0.000	0.000	0.000	0.000
124	H	1572	HOH	0	-0.043	-0.031	32.411	-0.002	-0.002	0.000	0.000	0.000	0.000
125	H	1578	HOH	0	-0.004	-0.008	34.874	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(H:1239:ILE)