FMO DATABASE

FMODB ID: VRRY1

Calculation Name: 7T9W-F-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7T9W

Chain ID: F

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	109
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-595707.410352
FMO2-HF: Nuclear repulsion	560965.635669
FMO2-HF: Total energy	-34741.774682
FMO2-MP2: Total energy	-34843.230286

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(F:1241:LYS)

Summations of interaction energy for fragment #1(F: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.
-150.841	-145.728	21.055	-13.286	-12.879	-0.178

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.648 / q_NPA : 1.795

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	F	1243	VAL	0	0.012	0.004	3.756	-3.065	-1.604	-0.001	-0.544	-0.915	-0.001
4	F	1244	LEU	0	0.038	0.023	5.716	6.164	6.164	0.000	0.000	0.000	0.000
5	F	1245	GLU	-1	-0.890	-0.928	8.972	-43.282	-43.282	0.000	0.000	0.000	0.000
6	F	1246	CYS	0	-0.017	0.005	11.416	3.173	3.173	0.000	0.000	0.000	0.000
7	F	1247	ASN	0	0.035	0.002	13.936	1.823	1.823	0.000	0.000	0.000	0.000
8	F	1248	VAL	0	-0.008	0.005	12.806	2.271	2.271	0.000	0.000	0.000	0.000
9	F	1249	LYS	1	0.914	0.955	15.366	30.319	30.319	0.000	0.000	0.000	0.000
10	F	1250	THR	0	0.045	0.027	13.739	1.614	1.614	0.000	0.000	0.000	0.000
11	F	1251	THR	0	-0.019	-0.015	8.703	-0.301	-0.301	0.000	0.000	0.000	0.000
12	F	1252	GLU	-1	-0.842	-0.899	9.495	-43.432	-43.432	0.000	0.000	0.000	0.000
13	F	1253	VAL	0	-0.018	-0.014	3.384	-4.418	-4.128	0.005	-0.073	-0.222	-0.001
14	F	1254	VAL	0	-0.003	-0.010	5.447	8.504	8.504	0.000	0.000	0.000	0.000
15	F	1255	GLY	0	0.035	0.023	5.645	-4.111	-4.111	0.000	0.000	0.000	0.000
16	F	1256	ASP	-1	-0.817	-0.895	1.691	-167.241	-167.459	16.281	-9.991	-6.072	-0.127
17	F	1257	ILE	0	-0.066	-0.024	2.220	-19.869	-17.710	4.605	-2.370	-4.393	-0.045
18	F	1258	ILE	0	-0.038	-0.018	2.862	3.623	4.992	0.166	-0.300	-1.235	-0.004
19	F	1259	LEU	0	0.015	0.011	4.560	3.109	3.161	-0.001	-0.008	-0.042	0.000
20	F	1260	LYS	1	0.875	0.917	8.311	45.994	45.994	0.000	0.000	0.000	0.000
21	F	1261	PRO	0	-0.013	0.011	9.885	1.629	1.629	0.000	0.000	0.000	0.000
22	F	1262	ALA	0	0.039	0.012	13.702	-0.029	-0.029	0.000	0.000	0.000	0.000
23	F	1263	ASN	0	0.000	0.003	15.640	0.618	0.618	0.000	0.000	0.000	0.000
24	F	1264	ASN	0	-0.026	-0.011	19.261	-0.075	-0.075	0.000	0.000	0.000	0.000
25	F	1265	SER	0	0.047	0.032	16.376	-0.318	-0.318	0.000	0.000	0.000	0.000
26	F	1266	LEU	0	0.023	0.019	16.022	1.318	1.318	0.000	0.000	0.000	0.000
27	F	1267	LYS	1	0.972	0.970	17.137	25.421	25.421	0.000	0.000	0.000	0.000
28	F	1268	ILE	0	-0.008	-0.012	13.737	-1.148	-1.148	0.000	0.000	0.000	0.000
29	F	1269	THR	0	0.003	0.006	17.068	1.046	1.046	0.000	0.000	0.000	0.000
30	F	1270	GLU	-1	-0.777	-0.879	15.325	-38.891	-38.891	0.000	0.000	0.000	0.000
31	F	1271	GLU	-1	-0.805	-0.885	16.756	-29.951	-29.951	0.000	0.000	0.000	0.000
32	F	1272	VAL	0	-0.023	-0.001	19.400	0.905	0.905	0.000	0.000	0.000	0.000
33	F	1273	GLY	0	0.105	0.041	21.915	0.367	0.367	0.000	0.000	0.000	0.000
34	F	1274	HIS	0	0.044	0.042	25.507	-0.531	-0.531	0.000	0.000	0.000	0.000
35	F	1275	THR	0	0.051	0.017	27.966	0.119	0.119	0.000	0.000	0.000	0.000
36	F	1276	ASP	-1	-0.840	-0.877	23.924	-24.842	-24.842	0.000	0.000	0.000	0.000
37	F	1277	LEU	0	0.011	0.006	24.701	-0.287	-0.287	0.000	0.000	0.000	0.000
38	F	1278	MET	0	-0.016	0.005	27.257	0.168	0.168	0.000	0.000	0.000	0.000
39	F	1279	ALA	0	-0.005	0.000	27.481	0.401	0.401	0.000	0.000	0.000	0.000
40	F	1280	ALA	0	-0.006	-0.003	25.475	0.042	0.042	0.000	0.000	0.000	0.000
41	F	1281	TYR	0	0.002	-0.011	27.366	0.152	0.152	0.000	0.000	0.000	0.000
42	F	1282	VAL	0	-0.040	-0.020	30.501	0.467	0.467	0.000	0.000	0.000	0.000
43	F	1283	ASP	-1	-0.929	-0.957	28.518	-20.347	-20.347	0.000	0.000	0.000	0.000
44	F	1284	ASN	0	-0.118	-0.056	29.235	-0.521	-0.521	0.000	0.000	0.000	0.000
45	F	1285	SER	0	0.017	0.024	24.250	-0.768	-0.768	0.000	0.000	0.000	0.000
46	F	1286	SER	0	-0.061	-0.048	20.510	0.039	0.039	0.000	0.000	0.000	0.000
47	F	1287	LEU	0	0.011	-0.005	20.429	0.086	0.086	0.000	0.000	0.000	0.000
48	F	1288	THR	0	0.021	0.006	13.815	-1.451	-1.451	0.000	0.000	0.000	0.000
49	F	1289	ILE	0	0.015	0.013	16.479	-0.107	-0.107	0.000	0.000	0.000	0.000
50	F	1290	LYS	1	0.787	0.883	11.719	38.226	38.226	0.000	0.000	0.000	0.000
51	F	1291	LYS	1	0.860	0.918	11.767	37.626	37.626	0.000	0.000	0.000	0.000
52	F	1292	PRO	0	-0.009	0.008	13.883	1.756	1.756	0.000	0.000	0.000	0.000
53	F	1293	ASN	0	0.054	0.032	16.973	-0.050	-0.050	0.000	0.000	0.000	0.000
54	F	1294	GLU	-1	-0.883	-0.928	20.481	-22.049	-22.049	0.000	0.000	0.000	0.000
55	F	1295	LEU	0	0.032	0.025	23.755	0.156	0.156	0.000	0.000	0.000	0.000
56	F	1296	SER	0	0.032	-0.016	19.277	-0.358	-0.358	0.000	0.000	0.000	0.000
57	F	1297	ARG	1	0.872	0.925	17.911	29.491	29.491	0.000	0.000	0.000	0.000
58	F	1298	VAL	0	0.006	0.024	21.546	0.224	0.224	0.000	0.000	0.000	0.000
59	F	1299	LEU	0	-0.014	0.002	23.750	0.682	0.682	0.000	0.000	0.000	0.000
60	F	1300	GLY	0	-0.007	0.008	21.866	-0.074	-0.074	0.000	0.000	0.000	0.000
61	F	1301	LEU	0	-0.057	-0.028	19.344	-0.837	-0.837	0.000	0.000	0.000	0.000
62	F	1302	LYS	1	0.886	0.942	14.069	31.881	31.881	0.000	0.000	0.000	0.000
63	F	1303	THR	0	0.004	-0.009	13.660	0.411	0.411	0.000	0.000	0.000	0.000
64	F	1304	LEU	0	0.034	0.012	9.214	-2.106	-2.106	0.000	0.000	0.000	0.000
65	F	1305	ALA	0	-0.041	-0.019	8.442	-5.888	-5.888	0.000	0.000	0.000	0.000
66	F	1306	THR	0	-0.021	-0.032	9.161	-1.208	-1.208	0.000	0.000	0.000	0.000
67	F	1307	HIS	0	-0.004	0.018	10.446	0.078	0.078	0.000	0.000	0.000	0.000
68	F	1308	GLY	0	0.023	0.034	6.965	-1.513	-1.513	0.000	0.000	0.000	0.000
69	F	1309	LEU	0	0.034	-0.011	7.189	5.199	5.199	0.000	0.000	0.000	0.000
70	F	1310	ALA	0	0.009	0.012	8.941	4.543	4.543	0.000	0.000	0.000	0.000
71	F	1311	ALA	0	-0.009	-0.009	11.463	3.388	3.388	0.000	0.000	0.000	0.000
72	F	1312	VAL	0	-0.035	-0.016	11.145	2.216	2.216	0.000	0.000	0.000	0.000
73	F	1313	ASN	0	-0.016	0.004	13.898	1.155	1.155	0.000	0.000	0.000	0.000
74	F	1314	SER	0	0.003	0.012	15.916	1.161	1.161	0.000	0.000	0.000	0.000
75	F	1315	VAL	0	-0.064	-0.017	18.017	0.887	0.887	0.000	0.000	0.000	0.000
76	F	1316	PRO	0	-0.008	0.003	21.146	0.337	0.337	0.000	0.000	0.000	0.000
77	F	1317	TRP	0	0.059	0.013	24.112	0.093	0.093	0.000	0.000	0.000	0.000
78	F	1318	ASP	-1	-0.845	-0.897	27.338	-19.883	-19.883	0.000	0.000	0.000	0.000
79	F	1319	THR	0	0.054	0.004	24.964	0.458	0.458	0.000	0.000	0.000	0.000
80	F	1320	ILE	0	-0.019	0.017	24.571	0.323	0.323	0.000	0.000	0.000	0.000
81	F	1321	ALA	0	0.031	0.009	28.074	0.601	0.601	0.000	0.000	0.000	0.000
82	F	1322	ASN	0	-0.076	-0.038	30.595	1.163	1.163	0.000	0.000	0.000	0.000
83	F	1323	TYR	0	-0.029	-0.018	29.394	0.391	0.391	0.000	0.000	0.000	0.000
84	F	1324	ALA	0	0.073	0.012	31.447	0.479	0.479	0.000	0.000	0.000	0.000
85	F	1325	LYS	1	0.960	0.991	33.339	16.539	16.539	0.000	0.000	0.000	0.000
86	F	1326	PRO	0	-0.055	-0.019	35.123	0.476	0.476	0.000	0.000	0.000	0.000
87	F	1327	PHE	0	-0.039	-0.020	32.908	0.245	0.245	0.000	0.000	0.000	0.000
88	F	1328	LEU	-1	-0.941	-0.938	36.765	-15.073	-15.073	0.000	0.000	0.000	0.000
89	F	1401	HOH	0	-0.041	-0.034	18.137	0.377	0.377	0.000	0.000	0.000	0.000
90	F	1402	HOH	0	0.005	0.000	20.128	-0.550	-0.550	0.000	0.000	0.000	0.000
91	F	1403	HOH	0	-0.008	-0.018	5.730	3.683	3.683	0.000	0.000	0.000	0.000
92	F	1404	HOH	0	0.004	-0.004	35.698	-0.222	-0.222	0.000	0.000	0.000	0.000
93	F	1405	HOH	0	-0.017	-0.015	37.706	-0.183	-0.183	0.000	0.000	0.000	0.000
94	F	1406	HOH	0	-0.067	-0.057	18.928	0.495	0.495	0.000	0.000	0.000	0.000
95	F	1407	HOH	0	-0.020	-0.012	33.290	-0.042	-0.042	0.000	0.000	0.000	0.000
96	F	1408	HOH	0	0.003	-0.013	26.214	0.206	0.206	0.000	0.000	0.000	0.000
97	F	1409	HOH	0	-0.001	0.000	35.326	0.195	0.195	0.000	0.000	0.000	0.000
98	F	1410	HOH	0	-0.047	-0.039	33.681	0.098	0.098	0.000	0.000	0.000	0.000
99	F	1411	HOH	0	-0.036	-0.029	13.664	-0.824	-0.824	0.000	0.000	0.000	0.000
100	F	1412	HOH	0	-0.065	-0.050	26.159	-0.323	-0.323	0.000	0.000	0.000	0.000
101	F	1413	HOH	0	0.047	0.031	17.281	0.135	0.135	0.000	0.000	0.000	0.000
102	F	1414	HOH	0	-0.052	-0.048	30.938	-0.180	-0.180	0.000	0.000	0.000	0.000
103	F	1415	HOH	0	-0.045	-0.028	12.966	0.336	0.336	0.000	0.000	0.000	0.000
104	F	1416	HOH	0	-0.032	-0.024	24.524	0.336	0.336	0.000	0.000	0.000	0.000
105	F	1417	HOH	0	-0.015	-0.017	27.740	0.178	0.178	0.000	0.000	0.000	0.000
106	F	1418	HOH	0	-0.020	-0.030	21.936	0.222	0.222	0.000	0.000	0.000	0.000
107	F	1419	HOH	0	-0.027	-0.026	22.796	-0.565	-0.565	0.000	0.000	0.000	0.000
108	F	1420	HOH	0	-0.029	-0.014	24.264	0.078	0.078	0.000	0.000	0.000	0.000
109	F	1421	HOH	0	-0.027	-0.016	23.644	0.176	0.176	0.000	0.000	0.000	0.000

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