FMO DATABASE

FMODB ID: 3J4NL

Calculation Name: 1K4Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K4Z

Chain ID: A

ChEMBL ID:

UniProt ID: P17555

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1436211.032113
FMO2-HF: Nuclear repulsion	1374580.149001
FMO2-HF: Total energy	-61630.883112
FMO2-MP2: Total energy	-61808.907741

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:1368:MET)

Summations of interaction energy for fragment #1(A:1368:MET)

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.
-10.009	-6.267	3.651	-2.626	-4.768	-0.017

Interaction energy analysis for fragmet #1(A:1368:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.035

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	1370	PRO	0	0.043	0.023	3.762	-2.393	-0.769	-0.011	-0.764	-0.850	0.002
4	A	1371	ARG	1	0.739	0.865	5.104	2.222	2.222	0.000	0.000	0.000	0.000
5	A	1372	LYS	1	0.941	0.960	6.985	0.849	0.849	0.000	0.000	0.000	0.000
6	A	1373	GLU	-1	-0.883	-0.911	9.525	-0.700	-0.700	0.000	0.000	0.000	0.000
7	A	1374	LEU	0	0.020	0.023	12.345	-0.059	-0.059	0.000	0.000	0.000	0.000
8	A	1375	VAL	0	0.003	-0.005	12.421	0.071	0.071	0.000	0.000	0.000	0.000
9	A	1376	GLY	0	-0.020	-0.011	15.569	0.013	0.013	0.000	0.000	0.000	0.000
10	A	1377	ASN	0	0.021	0.007	19.280	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	1378	LYS	1	0.875	0.926	15.585	0.407	0.407	0.000	0.000	0.000	0.000
12	A	1379	TRP	0	0.039	0.015	14.280	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	1380	PHE	0	-0.050	-0.022	9.238	0.028	0.028	0.000	0.000	0.000	0.000
14	A	1381	ILE	0	-0.008	-0.011	9.883	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	1382	GLU	-1	-0.807	-0.903	5.464	-2.900	-2.900	0.000	0.000	0.000	0.000
16	A	1383	ASN	0	-0.036	-0.032	2.543	-3.663	-2.098	2.999	-1.666	-2.898	-0.019
17	A	1384	TYR	0	0.000	-0.002	5.014	0.271	0.287	-0.001	-0.009	-0.006	0.000
18	A	1385	GLU	-1	-0.859	-0.929	7.207	-2.628	-2.628	0.000	0.000	0.000	0.000
19	A	1386	ASN	0	-0.074	-0.042	10.410	0.250	0.250	0.000	0.000	0.000	0.000
20	A	1387	GLU	-1	-0.884	-0.938	12.722	-0.954	-0.954	0.000	0.000	0.000	0.000
21	A	1388	THR	0	-0.068	-0.035	15.363	0.077	0.077	0.000	0.000	0.000	0.000
22	A	1389	GLU	-1	-0.919	-0.954	18.127	-0.398	-0.398	0.000	0.000	0.000	0.000
23	A	1390	SER	0	-0.020	-0.002	17.702	-0.085	-0.085	0.000	0.000	0.000	0.000
24	A	1391	LEU	0	-0.012	-0.003	12.457	0.030	0.030	0.000	0.000	0.000	0.000
25	A	1392	VAL	0	-0.007	-0.010	16.887	0.002	0.002	0.000	0.000	0.000	0.000
26	A	1393	ILE	0	-0.035	-0.019	15.068	-0.043	-0.043	0.000	0.000	0.000	0.000
27	A	1394	ASP	-1	-0.827	-0.904	19.088	-0.367	-0.367	0.000	0.000	0.000	0.000
28	A	1395	ALA	0	-0.004	0.007	20.623	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	1396	ASN	0	-0.046	-0.033	22.314	0.059	0.059	0.000	0.000	0.000	0.000
30	A	1397	LYS	1	0.916	0.935	24.083	0.221	0.221	0.000	0.000	0.000	0.000
31	A	1398	ASP	-1	-0.922	-0.951	25.468	-0.272	-0.272	0.000	0.000	0.000	0.000
32	A	1399	GLU	-1	-0.792	-0.877	20.075	-0.426	-0.426	0.000	0.000	0.000	0.000
33	A	1400	SER	0	-0.061	-0.033	18.770	0.027	0.027	0.000	0.000	0.000	0.000
34	A	1401	ILE	0	0.000	-0.003	15.890	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	1402	PHE	0	0.006	0.018	8.535	0.065	0.065	0.000	0.000	0.000	0.000
36	A	1403	ILE	0	0.022	0.006	11.520	-0.133	-0.133	0.000	0.000	0.000	0.000
37	A	1404	GLY	0	0.056	0.023	8.326	0.216	0.216	0.000	0.000	0.000	0.000
38	A	1405	LYS	1	0.837	0.914	2.345	3.756	4.293	0.664	-0.187	-1.014	0.000
39	A	1406	CYS	0	-0.029	0.011	6.320	-0.715	-0.715	0.000	0.000	0.000	0.000
40	A	1407	SER	0	0.011	-0.040	9.009	0.308	0.308	0.000	0.000	0.000	0.000
41	A	1408	GLN	0	-0.054	-0.019	11.407	0.025	0.025	0.000	0.000	0.000	0.000
42	A	1409	VAL	0	0.059	0.025	11.535	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	1410	LEU	0	0.009	0.016	14.974	0.038	0.038	0.000	0.000	0.000	0.000
44	A	1411	VAL	0	-0.002	-0.006	14.297	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	1412	GLN	0	0.016	0.002	17.302	0.055	0.055	0.000	0.000	0.000	0.000
46	A	1413	ILE	0	-0.036	-0.031	18.706	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	1414	LYS	1	0.826	0.917	21.410	0.423	0.423	0.000	0.000	0.000	0.000
48	A	1415	GLY	0	0.022	0.006	24.265	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	1416	LYS	1	0.858	0.920	25.309	0.249	0.249	0.000	0.000	0.000	0.000
50	A	1417	VAL	0	0.030	0.031	21.448	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	1418	ASN	0	-0.023	-0.023	22.746	0.047	0.047	0.000	0.000	0.000	0.000
52	A	1419	ALA	0	0.012	0.020	20.753	0.025	0.025	0.000	0.000	0.000	0.000
53	A	1420	ILE	0	0.022	0.007	18.164	-0.032	-0.032	0.000	0.000	0.000	0.000
54	A	1421	SER	0	-0.005	-0.014	14.876	0.050	0.050	0.000	0.000	0.000	0.000
55	A	1422	LEU	0	-0.030	0.002	13.422	-0.101	-0.101	0.000	0.000	0.000	0.000
56	A	1423	SER	0	0.017	-0.015	10.017	0.193	0.193	0.000	0.000	0.000	0.000
57	A	1424	GLU	-1	-0.934	-0.957	7.777	-1.597	-1.597	0.000	0.000	0.000	0.000
58	A	1425	THR	0	-0.026	-0.017	9.031	-0.339	-0.339	0.000	0.000	0.000	0.000
59	A	1426	GLU	-1	-0.764	-0.882	11.564	-0.530	-0.530	0.000	0.000	0.000	0.000
60	A	1427	SER	0	-0.031	-0.017	13.598	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	1428	CYS	0	-0.034	0.017	13.229	-0.081	-0.081	0.000	0.000	0.000	0.000
62	A	1429	SER	0	-0.011	-0.014	15.895	0.105	0.105	0.000	0.000	0.000	0.000
63	A	1430	VAL	0	-0.024	-0.017	17.320	-0.058	-0.058	0.000	0.000	0.000	0.000
64	A	1431	VAL	0	0.012	0.017	19.927	0.055	0.055	0.000	0.000	0.000	0.000
65	A	1432	LEU	0	0.001	0.004	22.360	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	1433	ASP	-1	-0.773	-0.856	24.310	-0.313	-0.313	0.000	0.000	0.000	0.000
67	A	1434	SER	0	0.040	0.002	26.947	0.024	0.024	0.000	0.000	0.000	0.000
68	A	1435	SER	0	-0.068	-0.039	23.544	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	1436	ILE	0	-0.058	-0.039	26.083	0.022	0.022	0.000	0.000	0.000	0.000
70	A	1437	SER	0	-0.054	-0.054	24.366	0.013	0.013	0.000	0.000	0.000	0.000
71	A	1438	GLY	0	0.013	0.019	24.985	0.012	0.012	0.000	0.000	0.000	0.000
72	A	1439	MET	0	-0.023	-0.001	18.264	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	1440	ASP	-1	-0.896	-0.909	17.117	-0.558	-0.558	0.000	0.000	0.000	0.000
74	A	1441	VAL	0	0.024	0.007	16.957	-0.073	-0.073	0.000	0.000	0.000	0.000
75	A	1442	ILE	0	0.014	0.003	13.498	0.076	0.076	0.000	0.000	0.000	0.000
76	A	1443	LYS	1	0.850	0.919	11.173	0.562	0.562	0.000	0.000	0.000	0.000
77	A	1444	SER	0	-0.011	0.003	13.043	-0.197	-0.197	0.000	0.000	0.000	0.000
78	A	1445	ASN	0	0.006	-0.003	15.117	0.132	0.132	0.000	0.000	0.000	0.000
79	A	1446	LYS	1	0.810	0.900	16.801	0.517	0.517	0.000	0.000	0.000	0.000
80	A	1447	PHE	0	0.028	0.025	17.482	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	1448	GLY	0	0.037	0.021	19.047	0.069	0.069	0.000	0.000	0.000	0.000
82	A	1449	ILE	0	-0.031	-0.020	20.476	-0.051	-0.051	0.000	0.000	0.000	0.000
83	A	1450	GLN	0	0.012	0.004	23.042	0.031	0.031	0.000	0.000	0.000	0.000
84	A	1451	VAL	0	-0.020	-0.001	25.613	-0.021	-0.021	0.000	0.000	0.000	0.000
85	A	1452	ASN	0	-0.021	-0.024	27.371	0.026	0.026	0.000	0.000	0.000	0.000
86	A	1453	HIS	0	-0.057	-0.027	29.850	0.012	0.012	0.000	0.000	0.000	0.000
87	A	1454	SER	0	-0.016	-0.056	30.402	0.007	0.007	0.000	0.000	0.000	0.000
88	A	1455	LEU	0	0.023	0.006	24.840	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	1456	PRO	0	-0.027	0.012	27.945	0.010	0.010	0.000	0.000	0.000	0.000
90	A	1457	GLN	0	-0.010	-0.013	26.348	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1458	ILE	0	0.019	0.011	22.639	-0.024	-0.024	0.000	0.000	0.000	0.000
92	A	1459	SER	0	-0.016	0.003	22.124	0.036	0.036	0.000	0.000	0.000	0.000
93	A	1460	ILE	0	0.007	0.004	20.757	-0.043	-0.043	0.000	0.000	0.000	0.000
94	A	1461	ASP	-1	-0.748	-0.869	19.136	-0.315	-0.315	0.000	0.000	0.000	0.000
95	A	1462	LYS	1	0.763	0.865	17.654	0.279	0.279	0.000	0.000	0.000	0.000
96	A	1463	SER	0	0.009	0.004	17.542	-0.082	-0.082	0.000	0.000	0.000	0.000
97	A	1464	ASP	-1	-0.828	-0.870	18.787	-0.319	-0.319	0.000	0.000	0.000	0.000
98	A	1465	GLY	0	-0.007	-0.012	20.033	-0.042	-0.042	0.000	0.000	0.000	0.000
99	A	1466	GLY	0	-0.006	-0.012	20.870	-0.058	-0.058	0.000	0.000	0.000	0.000
100	A	1467	ASN	0	-0.055	-0.020	22.857	0.062	0.062	0.000	0.000	0.000	0.000
101	A	1468	ILE	0	0.020	0.007	24.115	-0.029	-0.029	0.000	0.000	0.000	0.000
102	A	1469	TYR	0	0.021	0.019	26.504	0.021	0.021	0.000	0.000	0.000	0.000
103	A	1470	LEU	0	0.003	0.001	28.567	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	1471	SER	0	0.053	0.033	31.055	0.019	0.019	0.000	0.000	0.000	0.000
105	A	1472	LYS	1	0.836	0.866	33.510	0.173	0.173	0.000	0.000	0.000	0.000
106	A	1473	GLU	-1	-0.910	-0.922	34.058	-0.228	-0.228	0.000	0.000	0.000	0.000
107	A	1474	SER	0	-0.014	-0.023	30.871	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	1475	LEU	0	-0.020	0.001	32.855	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	1476	ASN	0	-0.064	-0.042	35.154	0.006	0.006	0.000	0.000	0.000	0.000
110	A	1477	THR	0	-0.011	0.016	28.552	0.003	0.003	0.000	0.000	0.000	0.000
111	A	1478	GLU	-1	-0.865	-0.901	30.417	-0.209	-0.209	0.000	0.000	0.000	0.000
112	A	1479	ILE	0	0.001	-0.014	26.488	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	1480	TYR	0	-0.101	-0.059	26.218	0.024	0.024	0.000	0.000	0.000	0.000
114	A	1481	THR	0	0.017	0.000	24.981	-0.022	-0.022	0.000	0.000	0.000	0.000
115	A	1482	SER	0	-0.050	-0.032	22.812	0.039	0.039	0.000	0.000	0.000	0.000
116	A	1483	CYS	0	-0.057	-0.034	22.055	-0.022	-0.022	0.000	0.000	0.000	0.000
117	A	1484	SER	0	0.007	0.001	22.067	-0.041	-0.041	0.000	0.000	0.000	0.000
118	A	1485	THR	0	-0.037	-0.044	23.110	0.030	0.030	0.000	0.000	0.000	0.000
119	A	1486	ALA	0	-0.013	0.002	24.120	-0.031	-0.031	0.000	0.000	0.000	0.000
120	A	1487	ILE	0	-0.007	0.008	22.630	-0.027	-0.027	0.000	0.000	0.000	0.000
121	A	1488	ASN	0	-0.014	-0.012	26.364	0.030	0.030	0.000	0.000	0.000	0.000
122	A	1489	VAL	0	-0.005	-0.007	27.870	-0.025	-0.025	0.000	0.000	0.000	0.000
123	A	1490	ASN	0	-0.018	-0.009	29.795	0.033	0.033	0.000	0.000	0.000	0.000
124	A	1491	LEU	0	0.019	0.007	32.314	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	1492	PRO	0	0.004	0.022	34.786	0.007	0.007	0.000	0.000	0.000	0.000
126	A	1493	ILE	0	-0.078	-0.067	37.226	0.008	0.008	0.000	0.000	0.000	0.000
127	A	1494	GLY	0	0.033	0.020	40.050	0.008	0.008	0.000	0.000	0.000	0.000
128	A	1495	GLU	-1	-0.972	-0.987	41.735	-0.124	-0.124	0.000	0.000	0.000	0.000
129	A	1496	ASP	-1	-0.945	-0.981	43.130	-0.148	-0.148	0.000	0.000	0.000	0.000
130	A	1497	ASP	-1	-0.868	-0.918	39.762	-0.174	-0.174	0.000	0.000	0.000	0.000
131	A	1498	ASP	-1	-0.901	-0.936	38.236	-0.196	-0.196	0.000	0.000	0.000	0.000
132	A	1499	TYR	0	-0.098	-0.056	32.469	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	1500	VAL	0	-0.027	-0.001	36.324	0.009	0.009	0.000	0.000	0.000	0.000
134	A	1501	GLU	-1	-0.884	-0.942	31.234	-0.254	-0.254	0.000	0.000	0.000	0.000
135	A	1502	PHE	0	-0.046	-0.024	33.230	0.018	0.018	0.000	0.000	0.000	0.000
136	A	1503	PRO	0	0.003	0.005	31.471	-0.014	-0.014	0.000	0.000	0.000	0.000
137	A	1504	ILE	0	-0.016	-0.010	28.767	0.014	0.014	0.000	0.000	0.000	0.000
138	A	1505	PRO	0	-0.047	-0.019	30.585	0.001	0.001	0.000	0.000	0.000	0.000
139	A	1506	GLU	-1	-0.804	-0.911	28.199	-0.244	-0.244	0.000	0.000	0.000	0.000
140	A	1507	GLN	0	-0.050	-0.016	30.540	0.012	0.012	0.000	0.000	0.000	0.000
141	A	1508	MET	0	0.014	0.005	31.267	0.003	0.003	0.000	0.000	0.000	0.000
142	A	1509	LYS	1	0.909	0.961	35.496	0.111	0.111	0.000	0.000	0.000	0.000
143	A	1510	HIS	0	0.073	0.030	34.896	0.004	0.004	0.000	0.000	0.000	0.000
144	A	1511	SER	0	-0.006	0.005	40.353	0.003	0.003	0.000	0.000	0.000	0.000
145	A	1512	PHE	0	-0.022	-0.008	43.925	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	1513	ALA	0	0.023	0.001	47.010	0.002	0.002	0.000	0.000	0.000	0.000
147	A	1514	ASP	-1	-0.844	-0.903	49.636	-0.071	-0.071	0.000	0.000	0.000	0.000
148	A	1515	GLY	0	-0.001	0.006	52.232	0.000	0.000	0.000	0.000	0.000	0.000
149	A	1516	LYS	1	0.922	0.956	43.754	0.084	0.084	0.000	0.000	0.000	0.000
150	A	1517	PHE	0	0.024	0.021	39.923	0.000	0.000	0.000	0.000	0.000	0.000
151	A	1518	LYS	1	0.791	0.871	42.611	0.075	0.075	0.000	0.000	0.000	0.000
152	A	1519	SER	0	0.044	0.009	37.568	0.003	0.003	0.000	0.000	0.000	0.000
153	A	1520	ALA	0	-0.019	-0.011	38.886	0.000	0.000	0.000	0.000	0.000	0.000
154	A	1521	VAL	0	0.075	0.049	34.906	0.000	0.000	0.000	0.000	0.000	0.000
155	A	1522	PHE	0	-0.096	-0.057	36.349	0.010	0.010	0.000	0.000	0.000	0.000
156	A	1523	GLH	0	0.031	-0.001	37.188	-0.007	-0.007	0.000	0.000	0.000	0.000
157	A	1524	HIS	0	0.011	0.028	39.661	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1368:MET)