FMO DATABASE

FMODB ID: 52RNZ

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	OptH
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	-1564050.025332
FMO2-HF: Nuclear repulsion	1496406.564994
FMO2-HF: Total energy	-67643.460338
FMO2-MP2: Total energy	-67842.13186

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.
-113.802	-109.685	0.253	-1.502	-2.868	-0.001

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 : 1.022 / q_NPA : 0.990

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	-0.884	-0.933	2.974	-27.333	-24.611	0.004	-1.130	-1.596	-0.001
4	A	1439	LEU	0	-0.018	-0.008	2.720	2.764	3.788	0.247	-0.322	-0.948	0.000
5	A	1440	ILE	0	0.039	0.024	3.725	2.731	3.102	0.002	-0.050	-0.324	0.000
6	A	1441	GLU	-1	-0.918	-0.951	6.222	-18.429	-18.429	0.000	0.000	0.000	0.000
7	A	1442	SER	0	-0.015	-0.017	8.179	2.617	2.617	0.000	0.000	0.000	0.000
8	A	1443	ILE	0	0.004	-0.004	8.175	2.199	2.199	0.000	0.000	0.000	0.000
9	A	1444	SER	0	0.019	0.004	10.021	2.016	2.016	0.000	0.000	0.000	0.000
10	A	1445	ARG	1	0.921	0.977	12.006	18.251	18.251	0.000	0.000	0.000	0.000
11	A	1446	LYS	1	0.962	0.976	13.636	17.503	17.503	0.000	0.000	0.000	0.000
12	A	1447	LEU	0	0.037	0.024	13.959	0.963	0.963	0.000	0.000	0.000	0.000
13	A	1448	GLN	0	0.034	0.002	15.885	0.639	0.639	0.000	0.000	0.000	0.000
14	A	1449	VAL	0	-0.046	-0.010	18.102	0.740	0.740	0.000	0.000	0.000	0.000
15	A	1450	LEU	0	-0.005	-0.012	17.780	0.578	0.578	0.000	0.000	0.000	0.000
16	A	1451	ARG	1	0.937	0.984	20.177	13.102	13.102	0.000	0.000	0.000	0.000
17	A	1452	GLU	-1	-0.882	-0.948	21.932	-11.525	-11.525	0.000	0.000	0.000	0.000
18	A	1453	ALA	0	-0.046	-0.019	23.676	0.505	0.505	0.000	0.000	0.000	0.000
19	A	1454	ARG	1	0.893	0.950	24.491	11.730	11.730	0.000	0.000	0.000	0.000
20	A	1455	GLU	-1	-0.920	-0.963	26.200	-10.288	-10.288	0.000	0.000	0.000	0.000
21	A	1456	SER	0	-0.063	-0.025	28.291	0.407	0.407	0.000	0.000	0.000	0.000
22	A	1457	LEU	0	0.042	0.034	28.707	0.271	0.271	0.000	0.000	0.000	0.000
23	A	1458	LEU	0	-0.034	-0.016	30.065	0.267	0.267	0.000	0.000	0.000	0.000
24	A	1459	GLU	-1	-0.933	-0.968	32.123	-8.338	-8.338	0.000	0.000	0.000	0.000
25	A	1460	ASP	-1	-0.906	-0.956	33.959	-8.560	-8.560	0.000	0.000	0.000	0.000
26	A	1461	VAL	0	-0.043	-0.022	33.411	0.273	0.273	0.000	0.000	0.000	0.000
27	A	1462	GLN	0	0.015	0.055	36.200	0.193	0.193	0.000	0.000	0.000	0.000
28	A	1463	ALA	0	-0.002	0.000	38.394	0.265	0.265	0.000	0.000	0.000	0.000
29	A	1464	ASN	0	-0.010	-0.032	39.223	0.270	0.270	0.000	0.000	0.000	0.000
30	A	1465	THR	0	-0.081	-0.078	39.343	0.161	0.161	0.000	0.000	0.000	0.000
31	A	1466	VAL	0	-0.037	-0.018	41.974	0.181	0.181	0.000	0.000	0.000	0.000
32	A	1467	LEU	0	0.043	0.032	43.964	0.152	0.152	0.000	0.000	0.000	0.000
33	A	1468	GLY	0	0.020	-0.004	44.668	0.162	0.162	0.000	0.000	0.000	0.000
34	A	1469	ALA	0	-0.031	-0.019	46.273	0.151	0.151	0.000	0.000	0.000	0.000
35	A	1470	GLU	-1	-0.935	-0.964	48.215	-6.209	-6.209	0.000	0.000	0.000	0.000
36	A	1471	VAL	0	0.017	0.003	48.660	0.169	0.169	0.000	0.000	0.000	0.000
37	A	1472	GLU	-1	-0.952	-0.978	49.478	-6.165	-6.165	0.000	0.000	0.000	0.000
38	A	1473	ALA	0	-0.057	-0.032	51.858	0.148	0.148	0.000	0.000	0.000	0.000
39	A	1474	ILE	0	0.015	0.006	53.616	0.150	0.150	0.000	0.000	0.000	0.000
40	A	1475	VAL	0	0.042	0.016	53.644	0.132	0.132	0.000	0.000	0.000	0.000
41	A	1476	LYS	1	0.902	0.958	55.899	5.577	5.577	0.000	0.000	0.000	0.000
42	A	1477	GLY	0	-0.066	-0.025	57.732	0.099	0.099	0.000	0.000	0.000	0.000
43	A	1478	VAL	0	-0.036	-0.021	59.004	0.110	0.110	0.000	0.000	0.000	0.000
44	A	1479	CYS	0	-0.057	-0.007	58.942	0.052	0.052	0.000	0.000	0.000	0.000
45	A	1480	LYS	1	0.932	0.971	61.013	4.909	4.909	0.000	0.000	0.000	0.000
46	A	1481	PRO	0	0.025	0.006	60.770	-0.085	-0.085	0.000	0.000	0.000	0.000
47	A	1482	SER	0	0.025	0.000	59.519	-0.099	-0.099	0.000	0.000	0.000	0.000
48	A	1483	GLU	-1	-0.857	-0.936	58.629	-5.213	-5.213	0.000	0.000	0.000	0.000
49	A	1484	PHE	0	0.038	0.029	53.938	-0.111	-0.111	0.000	0.000	0.000	0.000
50	A	1485	ASP	-1	-0.905	-0.955	54.881	-5.673	-5.673	0.000	0.000	0.000	0.000
51	A	1486	LYS	1	0.863	0.926	54.066	5.255	5.255	0.000	0.000	0.000	0.000
52	A	1487	PHE	0	0.088	0.043	49.946	-0.119	-0.119	0.000	0.000	0.000	0.000
53	A	1488	ARG	1	0.944	0.974	49.892	5.871	5.871	0.000	0.000	0.000	0.000
54	A	1489	MET	0	-0.044	-0.040	49.131	-0.150	-0.150	0.000	0.000	0.000	0.000
55	A	1490	PHE	0	-0.022	0.020	46.743	-0.125	-0.125	0.000	0.000	0.000	0.000
56	A	1491	ILE	0	0.049	0.032	45.783	-0.181	-0.181	0.000	0.000	0.000	0.000
57	A	1492	GLY	0	-0.034	-0.018	44.404	-0.206	-0.206	0.000	0.000	0.000	0.000
58	A	1493	ASP	-1	-0.830	-0.904	43.708	-6.841	-6.841	0.000	0.000	0.000	0.000
59	A	1494	LEU	0	0.013	0.009	41.886	-0.178	-0.178	0.000	0.000	0.000	0.000
60	A	1495	ASP	-1	-0.908	-0.962	38.817	-8.279	-8.279	0.000	0.000	0.000	0.000
61	A	1496	LYS	1	0.884	0.940	39.025	7.162	7.162	0.000	0.000	0.000	0.000
62	A	1497	VAL	0	0.007	0.013	39.188	-0.219	-0.219	0.000	0.000	0.000	0.000
63	A	1498	VAL	0	-0.002	-0.003	36.219	-0.181	-0.181	0.000	0.000	0.000	0.000
64	A	1499	ASN	0	0.014	0.007	34.618	-0.528	-0.528	0.000	0.000	0.000	0.000
65	A	1500	LEU	0	-0.045	-0.026	34.480	-0.291	-0.291	0.000	0.000	0.000	0.000
66	A	1501	LEU	0	0.023	0.019	34.842	-0.218	-0.218	0.000	0.000	0.000	0.000
67	A	1502	LEU	0	0.030	0.023	29.552	-0.178	-0.178	0.000	0.000	0.000	0.000
68	A	1503	SER	0	-0.019	-0.010	30.577	-0.353	-0.353	0.000	0.000	0.000	0.000
69	A	1504	LEU	0	-0.067	-0.036	30.509	-0.366	-0.366	0.000	0.000	0.000	0.000
70	A	1505	SER	0	0.027	0.018	30.893	-0.218	-0.218	0.000	0.000	0.000	0.000
71	A	1506	GLY	0	0.074	0.046	27.287	-0.281	-0.281	0.000	0.000	0.000	0.000
72	A	1507	ARG	1	0.866	0.922	26.714	9.584	9.584	0.000	0.000	0.000	0.000
73	A	1508	LEU	0	0.022	0.015	27.729	-0.265	-0.265	0.000	0.000	0.000	0.000
74	A	1509	ALA	0	0.043	0.023	25.472	-0.145	-0.145	0.000	0.000	0.000	0.000
75	A	1510	ARG	1	0.941	0.972	22.497	12.160	12.160	0.000	0.000	0.000	0.000
76	A	1511	VAL	0	-0.054	-0.030	23.934	-0.394	-0.394	0.000	0.000	0.000	0.000
77	A	1512	GLU	-1	-0.844	-0.909	25.907	-10.746	-10.746	0.000	0.000	0.000	0.000
78	A	1513	ASN	0	-0.018	-0.024	20.626	-0.686	-0.686	0.000	0.000	0.000	0.000
79	A	1514	ALA	0	-0.005	0.003	21.636	-0.532	-0.532	0.000	0.000	0.000	0.000
80	A	1515	LEU	0	-0.074	-0.054	22.724	-0.109	-0.109	0.000	0.000	0.000	0.000
81	A	1516	ASN	0	-0.069	-0.031	23.009	-0.049	-0.049	0.000	0.000	0.000	0.000
82	A	1517	ASN	0	0.035	0.038	16.527	-0.385	-0.385	0.000	0.000	0.000	0.000
83	A	1518	LEU	0	-0.089	-0.038	20.116	-0.327	-0.327	0.000	0.000	0.000	0.000
84	A	1519	ASP	-1	-0.954	-0.974	22.077	-12.743	-12.743	0.000	0.000	0.000	0.000
85	A	1520	ASP	-1	-0.923	-0.957	20.278	-14.256	-14.256	0.000	0.000	0.000	0.000
86	A	1521	GLY	0	-0.070	-0.023	20.326	-0.215	-0.215	0.000	0.000	0.000	0.000
87	A	1522	ALA	0	0.025	0.004	20.879	0.756	0.756	0.000	0.000	0.000	0.000
88	A	1523	SER	0	-0.031	-0.028	22.786	-0.558	-0.558	0.000	0.000	0.000	0.000
89	A	1524	PRO	0	-0.023	-0.003	25.080	0.414	0.414	0.000	0.000	0.000	0.000
90	A	1525	GLY	0	0.000	-0.009	28.771	0.034	0.034	0.000	0.000	0.000	0.000
91	A	1526	ASP	-1	-0.862	-0.933	26.260	-11.624	-11.624	0.000	0.000	0.000	0.000
92	A	1527	ARG	1	0.988	0.993	28.365	10.317	10.317	0.000	0.000	0.000	0.000
93	A	1528	GLN	0	0.000	0.000	29.263	0.170	0.170	0.000	0.000	0.000	0.000
94	A	1529	SER	0	-0.009	-0.005	30.469	0.278	0.278	0.000	0.000	0.000	0.000
95	A	1530	LEU	0	0.039	0.014	25.621	0.193	0.193	0.000	0.000	0.000	0.000
96	A	1531	LEU	0	0.031	0.022	30.057	0.089	0.089	0.000	0.000	0.000	0.000
97	A	1532	GLU	-1	-0.927	-0.960	32.908	-8.469	-8.469	0.000	0.000	0.000	0.000
98	A	1533	LYS	1	0.969	0.964	31.546	9.527	9.527	0.000	0.000	0.000	0.000
99	A	1534	GLN	0	-0.004	-0.011	31.328	0.320	0.320	0.000	0.000	0.000	0.000
100	A	1535	ARG	1	0.925	0.970	33.087	8.242	8.242	0.000	0.000	0.000	0.000
101	A	1536	VAL	0	-0.045	-0.025	35.775	0.171	0.171	0.000	0.000	0.000	0.000
102	A	1537	LEU	0	-0.019	-0.013	31.050	0.094	0.094	0.000	0.000	0.000	0.000
103	A	1538	ILE	0	0.035	0.021	34.799	0.067	0.067	0.000	0.000	0.000	0.000
104	A	1539	GLN	0	-0.017	0.006	36.829	0.110	0.110	0.000	0.000	0.000	0.000
105	A	1540	GLN	0	-0.036	-0.027	36.840	-0.090	-0.090	0.000	0.000	0.000	0.000
106	A	1541	HIS	0	0.025	0.005	34.881	0.051	0.051	0.000	0.000	0.000	0.000
107	A	1542	GLU	-1	-0.858	-0.938	37.594	-7.828	-7.828	0.000	0.000	0.000	0.000
108	A	1543	ASP	-1	-0.913	-0.947	40.711	-7.224	-7.224	0.000	0.000	0.000	0.000
109	A	1544	ALA	0	-0.043	-0.030	38.701	0.128	0.128	0.000	0.000	0.000	0.000
110	A	1545	LYS	1	0.875	0.929	37.871	8.126	8.126	0.000	0.000	0.000	0.000
111	A	1546	GLU	-1	-0.891	-0.924	41.290	-6.538	-6.538	0.000	0.000	0.000	0.000
112	A	1547	LEU	0	-0.081	-0.050	43.247	0.147	0.147	0.000	0.000	0.000	0.000
113	A	1548	LYS	1	0.918	0.958	39.636	7.685	7.685	0.000	0.000	0.000	0.000
114	A	1549	GLU	-1	-0.855	-0.920	43.328	-6.894	-6.894	0.000	0.000	0.000	0.000
115	A	1550	ASN	0	-0.073	-0.047	46.083	0.231	0.231	0.000	0.000	0.000	0.000
116	A	1551	LEU	0	-0.047	-0.043	44.034	0.158	0.158	0.000	0.000	0.000	0.000
117	A	1552	ASP	-1	-0.837	-0.897	44.740	-7.068	-7.068	0.000	0.000	0.000	0.000
118	A	1553	ARG	1	0.928	0.958	47.449	6.395	6.395	0.000	0.000	0.000	0.000
119	A	1554	ARG	1	0.787	0.876	49.259	6.474	6.474	0.000	0.000	0.000	0.000
120	A	1555	GLU	-1	-0.828	-0.914	47.196	-6.289	-6.289	0.000	0.000	0.000	0.000
121	A	1556	ARG	1	0.921	0.954	49.926	6.202	6.202	0.000	0.000	0.000	0.000
122	A	1557	ILE	0	-0.017	0.008	52.677	0.123	0.123	0.000	0.000	0.000	0.000
123	A	1558	VAL	0	-0.061	-0.036	51.731	0.117	0.117	0.000	0.000	0.000	0.000
124	A	1559	PHE	0	0.039	0.007	52.241	0.082	0.082	0.000	0.000	0.000	0.000
125	A	1560	ASP	-1	-0.884	-0.944	54.113	-5.491	-5.491	0.000	0.000	0.000	0.000
126	A	1561	ILE	0	-0.150	-0.079	56.471	0.113	0.113	0.000	0.000	0.000	0.000
127	A	1562	LEU	0	-0.017	-0.017	53.286	0.068	0.068	0.000	0.000	0.000	0.000
128	A	1563	ALA	0	0.001	0.020	57.457	0.052	0.052	0.000	0.000	0.000	0.000
129	A	1564	ASN	0	-0.059	-0.023	58.775	0.073	0.073	0.000	0.000	0.000	0.000
130	A	1565	TYR	0	-0.109	-0.055	60.146	0.122	0.122	0.000	0.000	0.000	0.000
131	A	1566	LEU	0	-0.028	-0.013	54.691	0.026	0.026	0.000	0.000	0.000	0.000
132	A	1567	SER	0	0.040	0.018	57.727	0.053	0.053	0.000	0.000	0.000	0.000
133	A	1568	GLU	-1	-0.890	-0.957	55.888	-5.439	-5.439	0.000	0.000	0.000	0.000
134	A	1569	GLU	-1	-0.946	-0.969	53.355	-5.769	-5.769	0.000	0.000	0.000	0.000
135	A	1570	SER	0	-0.005	0.000	52.265	-0.067	-0.067	0.000	0.000	0.000	0.000
136	A	1571	LEU	0	-0.023	-0.012	52.106	-0.119	-0.119	0.000	0.000	0.000	0.000
137	A	1572	ALA	0	0.012	0.019	49.717	-0.126	-0.126	0.000	0.000	0.000	0.000
138	A	1573	ASP	-1	-0.885	-0.950	47.936	-6.449	-6.449	0.000	0.000	0.000	0.000
139	A	1574	TYR	0	-0.061	-0.033	47.283	-0.166	-0.166	0.000	0.000	0.000	0.000
140	A	1575	GLU	-1	-0.897	-0.962	46.959	-6.434	-6.434	0.000	0.000	0.000	0.000
141	A	1576	HIS	0	-0.019	-0.012	41.865	-0.297	-0.297	0.000	0.000	0.000	0.000
142	A	1577	PHE	0	0.001	0.026	42.815	-0.214	-0.214	0.000	0.000	0.000	0.000
143	A	1578	VAL	0	0.022	0.010	42.368	-0.228	-0.228	0.000	0.000	0.000	0.000
144	A	1579	LYS	1	0.949	0.977	39.808	7.328	7.328	0.000	0.000	0.000	0.000
145	A	1580	MET	0	0.046	0.014	36.390	-0.261	-0.261	0.000	0.000	0.000	0.000
146	A	1581	LYS	1	0.967	1.006	37.542	7.317	7.317	0.000	0.000	0.000	0.000
147	A	1582	SER	0	-0.105	-0.056	37.019	-0.250	-0.250	0.000	0.000	0.000	0.000
148	A	1583	ALA	0	0.029	0.004	35.050	-0.248	-0.248	0.000	0.000	0.000	0.000
149	A	1584	LEU	0	0.029	0.025	33.271	-0.326	-0.326	0.000	0.000	0.000	0.000
150	A	1585	ILE	0	-0.027	-0.013	32.134	-0.348	-0.348	0.000	0.000	0.000	0.000
151	A	1586	ILE	0	-0.025	-0.025	30.746	-0.312	-0.312	0.000	0.000	0.000	0.000
152	A	1587	GLU	-1	-0.869	-0.934	28.743	-10.641	-10.641	0.000	0.000	0.000	0.000
153	A	1588	GLN	0	-0.046	-0.028	27.373	-0.356	-0.356	0.000	0.000	0.000	0.000
154	A	1589	ARG	1	0.898	0.947	26.628	9.808	9.808	0.000	0.000	0.000	0.000
155	A	1590	GLU	-1	-0.875	-0.915	24.430	-12.154	-12.154	0.000	0.000	0.000	0.000
156	A	1591	LEU	0	-0.026	-0.030	22.881	-0.800	-0.800	0.000	0.000	0.000	0.000
157	A	1592	GLU	-1	-0.910	-0.979	21.697	-12.048	-12.048	0.000	0.000	0.000	0.000
158	A	1593	ASP	-1	-0.889	-0.939	21.374	-13.398	-13.398	0.000	0.000	0.000	0.000
159	A	1594	LYS	1	0.868	0.931	18.720	12.372	12.372	0.000	0.000	0.000	0.000
160	A	1595	ILE	0	-0.057	-0.023	17.077	-1.126	-1.126	0.000	0.000	0.000	0.000
161	A	1596	HIS	0	0.026	0.022	16.644	-0.919	-0.919	0.000	0.000	0.000	0.000
162	A	1597	LEU	0	0.008	0.013	14.225	-0.951	-0.951	0.000	0.000	0.000	0.000
163	A	1598	GLY	0	-0.009	-0.014	12.713	-1.590	-1.590	0.000	0.000	0.000	0.000
164	A	1599	GLU	-1	-0.967	-0.986	11.848	-19.309	-19.309	0.000	0.000	0.000	0.000
165	A	1600	GLU	-1	-0.978	-0.995	12.201	-21.006	-21.006	0.000	0.000	0.000	0.000
166	A	1601	GLN	0	-0.050	-0.017	8.893	-0.665	-0.665	0.000	0.000	0.000	0.000
167	A	1602	LEU	0	-0.073	-0.049	6.884	-4.246	-4.246	0.000	0.000	0.000	0.000
168	A	1603	LYS	1	0.915	0.974	7.761	18.137	18.137	0.000	0.000	0.000	0.000
169	A	1604	CYS	0	-0.064	-0.020	5.200	-4.314	-4.314	0.000	0.000	0.000	0.000

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