FMO DATABASE

FMODB ID: V5VQ1

Calculation Name: 5F4Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F4Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q13796

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1570499.822358
FMO2-HF: Nuclear repulsion	1502854.379839
FMO2-HF: Total energy	-67645.442519
FMO2-MP2: Total energy	-67843.889075

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:1436:LYS)

Summations of interaction energy for fragment #1(A:1436: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.
-126.537	-122.486	0.493	-1.428	-3.116	-0.002

Interaction energy analysis for fragmet #1(A:1436:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.032 / q_NPA : 0.993

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	A	1438	GLU	-1	-0.888	-0.944	3.511	-29.301	-27.224	-0.008	-0.844	-1.225	-0.001
4	A	1439	LEU	0	-0.016	-0.014	2.743	2.307	3.633	0.489	-0.488	-1.327	-0.001
5	A	1440	ILE	0	0.036	0.025	3.442	2.150	2.692	0.013	-0.088	-0.466	0.000
6	A	1441	GLU	-1	-0.847	-0.888	5.884	-17.450	-17.450	0.000	0.000	0.000	0.000
7	A	1442	SER	0	-0.019	-0.012	8.261	2.562	2.562	0.000	0.000	0.000	0.000
8	A	1443	ILE	0	0.017	0.002	8.190	2.214	2.214	0.000	0.000	0.000	0.000
9	A	1444	SER	0	0.013	-0.004	9.606	1.920	1.920	0.000	0.000	0.000	0.000
10	A	1445	ARG	1	0.836	0.904	11.784	18.990	18.990	0.000	0.000	0.000	0.000
11	A	1446	LYS	1	0.958	0.980	13.349	18.944	18.944	0.000	0.000	0.000	0.000
12	A	1447	LEU	0	0.015	0.014	13.542	0.980	0.980	0.000	0.000	0.000	0.000
13	A	1448	GLN	0	0.001	-0.021	15.563	0.743	0.743	0.000	0.000	0.000	0.000
14	A	1449	VAL	0	-0.043	-0.012	17.778	0.769	0.769	0.000	0.000	0.000	0.000
15	A	1450	LEU	0	0.000	-0.008	17.350	0.642	0.642	0.000	0.000	0.000	0.000
16	A	1451	ARG	1	0.815	0.904	19.868	13.132	13.132	0.000	0.000	0.000	0.000
17	A	1452	GLU	-1	-0.877	-0.946	21.627	-11.824	-11.824	0.000	0.000	0.000	0.000
18	A	1453	ALA	0	-0.019	0.003	23.369	0.520	0.520	0.000	0.000	0.000	0.000
19	A	1454	ARG	1	0.818	0.889	24.005	12.001	12.001	0.000	0.000	0.000	0.000
20	A	1455	GLU	-1	-0.764	-0.858	25.548	-11.083	-11.083	0.000	0.000	0.000	0.000
21	A	1456	SER	0	-0.050	-0.029	27.865	0.410	0.410	0.000	0.000	0.000	0.000
22	A	1457	LEU	0	0.056	0.027	28.271	0.306	0.306	0.000	0.000	0.000	0.000
23	A	1458	LEU	0	-0.056	-0.027	29.563	0.245	0.245	0.000	0.000	0.000	0.000
24	A	1459	GLU	-1	-0.920	-0.956	31.773	-8.394	-8.394	0.000	0.000	0.000	0.000
25	A	1460	ASP	-1	-0.895	-0.940	33.321	-8.667	-8.667	0.000	0.000	0.000	0.000
26	A	1461	VAL	0	-0.057	-0.032	33.194	0.284	0.284	0.000	0.000	0.000	0.000
27	A	1462	GLN	0	0.003	0.020	35.790	0.196	0.196	0.000	0.000	0.000	0.000
28	A	1463	ALA	0	0.006	-0.003	37.920	0.265	0.265	0.000	0.000	0.000	0.000
29	A	1464	ASN	0	-0.008	-0.024	38.908	0.355	0.355	0.000	0.000	0.000	0.000
30	A	1465	THR	0	-0.063	-0.046	38.909	0.169	0.169	0.000	0.000	0.000	0.000
31	A	1466	VAL	0	-0.050	-0.021	41.494	0.172	0.172	0.000	0.000	0.000	0.000
32	A	1467	LEU	0	0.055	0.039	43.668	0.147	0.147	0.000	0.000	0.000	0.000
33	A	1468	GLY	0	0.026	0.001	44.205	0.156	0.156	0.000	0.000	0.000	0.000
34	A	1469	ALA	0	-0.032	-0.019	45.684	0.156	0.156	0.000	0.000	0.000	0.000
35	A	1470	GLU	-1	-0.934	-0.965	47.773	-6.342	-6.342	0.000	0.000	0.000	0.000
36	A	1471	VAL	0	0.017	0.005	48.399	0.170	0.170	0.000	0.000	0.000	0.000
37	A	1472	GLU	-1	-0.914	-0.956	49.392	-6.214	-6.214	0.000	0.000	0.000	0.000
38	A	1473	ALA	0	-0.042	-0.034	51.383	0.152	0.152	0.000	0.000	0.000	0.000
39	A	1474	ILE	0	0.019	0.010	52.685	0.149	0.149	0.000	0.000	0.000	0.000
40	A	1475	VAL	0	0.030	0.014	53.288	0.137	0.137	0.000	0.000	0.000	0.000
41	A	1476	LYS	1	0.877	0.939	55.493	5.642	5.642	0.000	0.000	0.000	0.000
42	A	1477	GLY	0	-0.046	-0.017	57.289	0.094	0.094	0.000	0.000	0.000	0.000
43	A	1478	VAL	0	-0.036	-0.022	58.699	0.103	0.103	0.000	0.000	0.000	0.000
44	A	1479	CYS	0	-0.051	0.010	58.733	0.048	0.048	0.000	0.000	0.000	0.000
45	A	1480	LYS	1	0.855	0.905	60.778	5.033	5.033	0.000	0.000	0.000	0.000
46	A	1481	PRO	0	0.037	0.010	60.043	-0.088	-0.088	0.000	0.000	0.000	0.000
47	A	1482	SER	0	0.038	0.009	58.755	-0.104	-0.104	0.000	0.000	0.000	0.000
48	A	1483	GLU	-1	-0.793	-0.843	58.314	-5.231	-5.231	0.000	0.000	0.000	0.000
49	A	1484	PHE	0	0.046	0.028	53.758	-0.096	-0.096	0.000	0.000	0.000	0.000
50	A	1485	ASP	-1	-0.842	-0.925	54.244	-5.871	-5.871	0.000	0.000	0.000	0.000
51	A	1486	LYS	1	0.840	0.910	53.340	5.354	5.354	0.000	0.000	0.000	0.000
52	A	1487	PHE	0	0.065	0.024	49.598	-0.115	-0.115	0.000	0.000	0.000	0.000
53	A	1488	ARG	1	0.841	0.909	49.582	5.939	5.939	0.000	0.000	0.000	0.000
54	A	1489	MET	0	-0.055	-0.032	48.644	-0.123	-0.123	0.000	0.000	0.000	0.000
55	A	1490	PHE	0	0.036	0.031	46.089	-0.160	-0.160	0.000	0.000	0.000	0.000
56	A	1491	ILE	0	0.051	0.027	45.322	-0.190	-0.190	0.000	0.000	0.000	0.000
57	A	1492	GLY	0	-0.015	0.003	43.840	-0.212	-0.212	0.000	0.000	0.000	0.000
58	A	1493	ASP	-1	-0.803	-0.896	43.165	-6.981	-6.981	0.000	0.000	0.000	0.000
59	A	1494	LEU	0	-0.005	0.001	41.399	-0.208	-0.208	0.000	0.000	0.000	0.000
60	A	1495	ASP	-1	-0.789	-0.866	39.105	-8.363	-8.363	0.000	0.000	0.000	0.000
61	A	1496	LYS	1	0.778	0.888	38.330	7.506	7.506	0.000	0.000	0.000	0.000
62	A	1497	VAL	0	0.035	0.007	38.154	-0.256	-0.256	0.000	0.000	0.000	0.000
63	A	1498	VAL	0	0.000	0.010	35.546	-0.180	-0.180	0.000	0.000	0.000	0.000
64	A	1499	ASN	0	0.001	-0.013	33.577	-0.566	-0.566	0.000	0.000	0.000	0.000
65	A	1500	LEU	0	-0.023	-0.016	33.380	-0.316	-0.316	0.000	0.000	0.000	0.000
66	A	1501	LEU	0	0.018	0.015	34.369	-0.230	-0.230	0.000	0.000	0.000	0.000
67	A	1502	LEU	0	0.045	0.034	29.395	-0.177	-0.177	0.000	0.000	0.000	0.000
68	A	1503	SER	0	-0.002	-0.002	29.720	-0.343	-0.343	0.000	0.000	0.000	0.000
69	A	1504	LEU	0	-0.071	-0.039	29.782	-0.374	-0.374	0.000	0.000	0.000	0.000
70	A	1505	SER	0	0.042	0.021	29.893	-0.114	-0.114	0.000	0.000	0.000	0.000
71	A	1506	GLY	0	0.036	0.028	26.677	-0.279	-0.279	0.000	0.000	0.000	0.000
72	A	1507	ARG	1	0.838	0.919	25.998	9.589	9.589	0.000	0.000	0.000	0.000
73	A	1508	LEU	0	-0.015	0.000	27.316	-0.267	-0.267	0.000	0.000	0.000	0.000
74	A	1509	ALA	0	0.038	0.017	25.492	-0.194	-0.194	0.000	0.000	0.000	0.000
75	A	1510	ARG	1	0.968	0.988	21.665	12.738	12.738	0.000	0.000	0.000	0.000
76	A	1511	VAL	0	-0.056	-0.027	23.382	-0.451	-0.451	0.000	0.000	0.000	0.000
77	A	1512	GLU	-1	-0.825	-0.903	25.570	-11.234	-11.234	0.000	0.000	0.000	0.000
78	A	1513	ASN	0	-0.033	-0.017	19.857	-0.703	-0.703	0.000	0.000	0.000	0.000
79	A	1514	ALA	0	0.020	0.007	21.006	-0.515	-0.515	0.000	0.000	0.000	0.000
80	A	1515	LEU	0	-0.044	-0.036	22.075	-0.155	-0.155	0.000	0.000	0.000	0.000
81	A	1516	ASN	0	-0.058	-0.029	23.218	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	1517	ASN	0	-0.031	0.000	16.197	-0.798	-0.798	0.000	0.000	0.000	0.000
83	A	1518	LEU	0	-0.063	-0.028	19.384	-0.614	-0.614	0.000	0.000	0.000	0.000
84	A	1519	ASP	-1	-0.883	-0.939	21.965	-12.309	-12.309	0.000	0.000	0.000	0.000
85	A	1520	ASP	-1	-0.927	-0.945	19.395	-15.167	-15.167	0.000	0.000	0.000	0.000
86	A	1521	GLY	0	-0.032	-0.007	20.284	-0.737	-0.737	0.000	0.000	0.000	0.000
87	A	1522	ALA	0	-0.020	-0.019	20.972	0.822	0.822	0.000	0.000	0.000	0.000
88	A	1523	SER	0	-0.028	-0.022	21.980	-0.707	-0.707	0.000	0.000	0.000	0.000
89	A	1524	PRO	0	-0.026	0.005	24.286	0.388	0.388	0.000	0.000	0.000	0.000
90	A	1525	GLY	0	0.041	0.008	27.889	0.385	0.385	0.000	0.000	0.000	0.000
91	A	1526	ASP	-1	-0.891	-0.948	25.418	-12.069	-12.069	0.000	0.000	0.000	0.000
92	A	1527	ARG	1	0.921	0.934	27.379	11.371	11.371	0.000	0.000	0.000	0.000
93	A	1528	GLN	0	0.009	0.009	28.226	0.146	0.146	0.000	0.000	0.000	0.000
94	A	1529	SER	0	-0.030	-0.013	29.021	0.352	0.352	0.000	0.000	0.000	0.000
95	A	1530	LEU	0	0.028	0.008	24.320	0.219	0.219	0.000	0.000	0.000	0.000
96	A	1531	LEU	0	0.035	0.027	28.860	0.111	0.111	0.000	0.000	0.000	0.000
97	A	1532	GLU	-1	-0.816	-0.893	31.822	-8.589	-8.589	0.000	0.000	0.000	0.000
98	A	1533	LYS	1	0.869	0.918	30.147	9.825	9.825	0.000	0.000	0.000	0.000
99	A	1534	GLN	0	-0.002	-0.011	30.649	0.359	0.359	0.000	0.000	0.000	0.000
100	A	1535	ARG	1	0.875	0.932	32.108	8.442	8.442	0.000	0.000	0.000	0.000
101	A	1536	VAL	0	-0.032	-0.024	34.555	0.195	0.195	0.000	0.000	0.000	0.000
102	A	1537	LEU	0	-0.020	-0.012	29.959	0.107	0.107	0.000	0.000	0.000	0.000
103	A	1538	ILE	0	0.034	0.015	34.081	0.090	0.090	0.000	0.000	0.000	0.000
104	A	1539	GLN	0	-0.090	-0.045	36.034	0.170	0.170	0.000	0.000	0.000	0.000
105	A	1540	GLN	0	0.043	0.007	35.900	-0.109	-0.109	0.000	0.000	0.000	0.000
106	A	1541	HIS	0	0.025	0.015	34.190	0.125	0.125	0.000	0.000	0.000	0.000
107	A	1542	GLU	-1	-0.815	-0.890	36.939	-8.097	-8.097	0.000	0.000	0.000	0.000
108	A	1543	ASP	-1	-0.864	-0.915	40.261	-7.417	-7.417	0.000	0.000	0.000	0.000
109	A	1544	ALA	0	-0.023	-0.022	38.036	0.141	0.141	0.000	0.000	0.000	0.000
110	A	1545	LYS	1	0.807	0.884	37.381	8.285	8.285	0.000	0.000	0.000	0.000
111	A	1546	GLU	-1	-0.755	-0.857	40.877	-6.613	-6.613	0.000	0.000	0.000	0.000
112	A	1547	LEU	0	-0.046	-0.021	42.702	0.173	0.173	0.000	0.000	0.000	0.000
113	A	1548	LYS	1	0.798	0.874	39.546	7.782	7.782	0.000	0.000	0.000	0.000
114	A	1549	GLU	-1	-0.833	-0.906	42.795	-6.779	-6.779	0.000	0.000	0.000	0.000
115	A	1550	ASN	0	-0.089	-0.052	45.526	0.300	0.300	0.000	0.000	0.000	0.000
116	A	1551	LEU	0	-0.048	-0.023	43.512	0.146	0.146	0.000	0.000	0.000	0.000
117	A	1552	ASP	-1	-0.781	-0.862	43.613	-7.311	-7.311	0.000	0.000	0.000	0.000
118	A	1553	ARG	1	0.767	0.842	46.758	6.676	6.676	0.000	0.000	0.000	0.000
119	A	1554	ARG	1	0.775	0.874	48.536	6.631	6.631	0.000	0.000	0.000	0.000
120	A	1555	GLU	-1	-0.786	-0.855	46.697	-6.398	-6.398	0.000	0.000	0.000	0.000
121	A	1556	ARG	1	0.816	0.885	49.432	6.365	6.365	0.000	0.000	0.000	0.000
122	A	1557	ILE	0	0.016	0.021	52.261	0.121	0.121	0.000	0.000	0.000	0.000
123	A	1558	VAL	0	-0.046	-0.021	51.113	0.121	0.121	0.000	0.000	0.000	0.000
124	A	1559	PHE	0	0.024	0.006	51.704	0.087	0.087	0.000	0.000	0.000	0.000
125	A	1560	ASP	-1	-0.879	-0.949	53.611	-5.590	-5.590	0.000	0.000	0.000	0.000
126	A	1561	ILE	0	-0.110	-0.061	55.977	0.131	0.131	0.000	0.000	0.000	0.000
127	A	1562	LEU	0	0.013	0.000	52.761	0.093	0.093	0.000	0.000	0.000	0.000
128	A	1563	ALA	0	0.015	0.011	56.920	0.061	0.061	0.000	0.000	0.000	0.000
129	A	1564	ASN	0	-0.128	-0.051	58.426	0.139	0.139	0.000	0.000	0.000	0.000
130	A	1565	TYR	0	-0.096	-0.079	59.708	0.139	0.139	0.000	0.000	0.000	0.000
131	A	1566	LEU	0	-0.042	-0.011	54.238	0.018	0.018	0.000	0.000	0.000	0.000
132	A	1567	SER	0	-0.007	-0.018	56.820	0.058	0.058	0.000	0.000	0.000	0.000
133	A	1568	GLU	-1	-0.903	-0.970	55.677	-5.541	-5.541	0.000	0.000	0.000	0.000
134	A	1569	GLU	-1	-0.911	-0.924	52.907	-5.730	-5.730	0.000	0.000	0.000	0.000
135	A	1570	SER	0	0.048	0.015	51.669	-0.079	-0.079	0.000	0.000	0.000	0.000
136	A	1571	LEU	0	-0.039	-0.006	51.736	-0.103	-0.103	0.000	0.000	0.000	0.000
137	A	1572	ALA	0	0.032	0.018	49.195	-0.136	-0.136	0.000	0.000	0.000	0.000
138	A	1573	ASP	-1	-0.885	-0.946	47.451	-6.537	-6.537	0.000	0.000	0.000	0.000
139	A	1574	TYR	0	-0.077	-0.069	46.698	-0.183	-0.183	0.000	0.000	0.000	0.000
140	A	1575	GLU	-1	-0.834	-0.914	46.550	-6.547	-6.547	0.000	0.000	0.000	0.000
141	A	1576	HIS	0	-0.025	-0.011	41.490	-0.292	-0.292	0.000	0.000	0.000	0.000
142	A	1577	PHE	0	-0.002	0.022	42.290	-0.220	-0.220	0.000	0.000	0.000	0.000
143	A	1578	VAL	0	0.012	0.007	41.816	-0.233	-0.233	0.000	0.000	0.000	0.000
144	A	1579	LYS	1	0.954	0.986	39.788	7.549	7.549	0.000	0.000	0.000	0.000
145	A	1580	MET	0	0.019	0.012	36.315	-0.275	-0.275	0.000	0.000	0.000	0.000
146	A	1581	LYS	1	0.879	0.934	36.975	7.606	7.606	0.000	0.000	0.000	0.000
147	A	1582	SER	0	-0.094	-0.062	36.460	-0.243	-0.243	0.000	0.000	0.000	0.000
148	A	1583	ALA	0	0.022	0.000	34.551	-0.247	-0.247	0.000	0.000	0.000	0.000
149	A	1584	LEU	0	0.032	0.015	32.643	-0.333	-0.333	0.000	0.000	0.000	0.000
150	A	1585	ILE	0	-0.019	-0.006	31.502	-0.336	-0.336	0.000	0.000	0.000	0.000
151	A	1586	ILE	0	-0.026	-0.017	30.155	-0.300	-0.300	0.000	0.000	0.000	0.000
152	A	1587	GLU	-1	-0.908	-0.951	28.010	-11.122	-11.122	0.000	0.000	0.000	0.000
153	A	1588	GLN	0	-0.002	0.008	26.767	-0.393	-0.393	0.000	0.000	0.000	0.000
154	A	1589	ARG	1	0.822	0.897	26.160	9.996	9.996	0.000	0.000	0.000	0.000
155	A	1590	GLU	-1	-0.797	-0.880	23.520	-12.819	-12.819	0.000	0.000	0.000	0.000
156	A	1591	LEU	0	-0.023	-0.022	22.363	-0.833	-0.833	0.000	0.000	0.000	0.000
157	A	1592	GLU	-1	-0.830	-0.889	21.305	-12.147	-12.147	0.000	0.000	0.000	0.000
158	A	1593	ASP	-1	-0.898	-0.948	20.882	-13.996	-13.996	0.000	0.000	0.000	0.000
159	A	1594	LYS	1	0.792	0.886	18.319	12.251	12.251	0.000	0.000	0.000	0.000
160	A	1595	ILE	0	-0.038	-0.024	16.689	-1.194	-1.194	0.000	0.000	0.000	0.000
161	A	1596	HIS	0	-0.058	-0.025	16.294	-0.539	-0.539	0.000	0.000	0.000	0.000
162	A	1597	LEU	0	0.004	0.005	13.328	-1.134	-1.134	0.000	0.000	0.000	0.000
163	A	1598	GLY	0	0.005	-0.003	12.256	-1.825	-1.825	0.000	0.000	0.000	0.000
164	A	1599	GLU	-1	-0.841	-0.910	11.368	-21.740	-21.740	0.000	0.000	0.000	0.000
165	A	1600	GLU	-1	-0.861	-0.925	11.657	-21.178	-21.178	0.000	0.000	0.000	0.000
166	A	1601	GLN	0	0.008	0.002	7.606	-0.479	-0.479	0.000	0.000	0.000	0.000
167	A	1602	LEU	0	-0.056	-0.023	6.791	-5.473	-5.473	0.000	0.000	0.000	0.000
168	A	1603	LYS	1	0.775	0.883	7.692	17.917	17.917	0.000	0.000	0.000	0.000
169	A	1604	CYS	0	-0.161	-0.072	4.565	-10.936	-10.830	-0.001	-0.008	-0.098	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1436:LYS)