FMO DATABASE

FMODB ID: JQRM9

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:

Apendix: None

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	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1435474.189831
FMO2-HF: Nuclear repulsion	1373844.316424
FMO2-HF: Total energy	-61629.873407
FMO2-MP2: Total energy	-61807.907955

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.
-9.354	-6.235	6.184	-3.352	-5.95	-0.019

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 : -0.048 / q_NPA : -0.041

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	0.048	0.021	3.801	-2.046	-0.515	-0.012	-0.707	-0.812	0.002
4	A	1371	ARG	1	0.781	0.885	5.203	2.074	2.074	0.000	0.000	0.000	0.000
5	A	1372	LYS	1	0.965	0.985	7.015	0.838	0.838	0.000	0.000	0.000	0.000
6	A	1373	GLU	-1	-0.900	-0.920	9.298	-0.647	-0.647	0.000	0.000	0.000	0.000
7	A	1374	LEU	0	0.034	0.028	12.361	-0.063	-0.063	0.000	0.000	0.000	0.000
8	A	1375	VAL	0	-0.007	-0.009	12.469	0.068	0.068	0.000	0.000	0.000	0.000
9	A	1376	GLY	0	-0.027	-0.018	15.568	0.007	0.007	0.000	0.000	0.000	0.000
10	A	1377	ASN	0	0.046	0.026	19.278	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	1378	LYS	1	0.909	0.944	15.608	0.421	0.421	0.000	0.000	0.000	0.000
12	A	1379	TRP	0	0.044	0.020	14.209	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	1380	PHE	0	-0.063	-0.026	9.245	0.020	0.020	0.000	0.000	0.000	0.000
14	A	1381	ILE	0	0.000	-0.007	9.907	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	1382	GLU	-1	-0.864	-0.963	5.424	-2.630	-2.630	0.000	0.000	0.000	0.000
16	A	1383	ASN	0	-0.024	-0.014	2.488	-4.373	-2.776	3.879	-2.152	-3.324	-0.024
17	A	1384	TYR	0	0.003	0.004	4.967	0.258	0.277	-0.001	-0.010	-0.008	0.000
18	A	1385	GLU	-1	-0.896	-0.969	7.277	-2.562	-2.562	0.000	0.000	0.000	0.000
19	A	1386	ASN	0	-0.077	-0.042	10.388	0.201	0.201	0.000	0.000	0.000	0.000
20	A	1387	GLU	-1	-0.893	-0.943	12.422	-0.948	-0.948	0.000	0.000	0.000	0.000
21	A	1388	THR	0	-0.067	-0.037	15.307	0.072	0.072	0.000	0.000	0.000	0.000
22	A	1389	GLU	-1	-0.938	-0.973	18.058	-0.354	-0.354	0.000	0.000	0.000	0.000
23	A	1390	SER	0	-0.016	0.009	17.646	-0.080	-0.080	0.000	0.000	0.000	0.000
24	A	1391	LEU	0	-0.016	-0.003	12.561	0.023	0.023	0.000	0.000	0.000	0.000
25	A	1392	VAL	0	-0.029	-0.024	16.860	0.000	0.000	0.000	0.000	0.000	0.000
26	A	1393	ILE	0	-0.037	-0.021	15.122	-0.038	-0.038	0.000	0.000	0.000	0.000
27	A	1394	ASP	-1	-0.948	-0.970	19.118	-0.352	-0.352	0.000	0.000	0.000	0.000
28	A	1395	ALA	0	-0.015	0.002	20.643	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	1396	ASN	0	-0.046	-0.027	22.336	0.052	0.052	0.000	0.000	0.000	0.000
30	A	1397	LYS	1	0.958	0.961	24.097	0.209	0.209	0.000	0.000	0.000	0.000
31	A	1398	ASP	-1	-0.975	-0.996	24.925	-0.291	-0.291	0.000	0.000	0.000	0.000
32	A	1399	GLU	-1	-0.817	-0.890	20.080	-0.412	-0.412	0.000	0.000	0.000	0.000
33	A	1400	SER	0	-0.069	-0.038	18.892	0.021	0.021	0.000	0.000	0.000	0.000
34	A	1401	ILE	0	-0.004	-0.003	15.762	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	1402	PHE	0	-0.014	0.007	8.703	0.075	0.075	0.000	0.000	0.000	0.000
36	A	1403	ILE	0	0.019	0.007	11.453	-0.114	-0.114	0.000	0.000	0.000	0.000
37	A	1404	GLY	0	0.062	0.025	8.384	0.191	0.191	0.000	0.000	0.000	0.000
38	A	1405	LYS	1	0.894	0.962	2.192	4.829	4.801	2.318	-0.483	-1.806	0.003
39	A	1406	CYS	0	-0.019	0.009	6.215	-0.612	-0.612	0.000	0.000	0.000	0.000
40	A	1407	SER	0	0.033	-0.005	8.947	0.312	0.312	0.000	0.000	0.000	0.000
41	A	1408	GLN	0	-0.037	-0.008	11.573	0.006	0.006	0.000	0.000	0.000	0.000
42	A	1409	VAL	0	0.062	0.024	11.692	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	1410	LEU	0	0.009	0.017	14.929	0.033	0.033	0.000	0.000	0.000	0.000
44	A	1411	VAL	0	0.000	-0.004	14.317	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	1412	GLN	0	0.015	0.000	17.262	0.045	0.045	0.000	0.000	0.000	0.000
46	A	1413	ILE	0	-0.025	-0.026	18.649	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	1414	LYS	1	0.939	0.975	21.439	0.386	0.386	0.000	0.000	0.000	0.000
48	A	1415	GLY	0	0.037	0.019	24.292	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	1416	LYS	1	0.850	0.923	25.332	0.243	0.243	0.000	0.000	0.000	0.000
50	A	1417	VAL	0	0.037	0.039	21.484	0.000	0.000	0.000	0.000	0.000	0.000
51	A	1418	ASN	0	-0.012	-0.015	23.114	0.046	0.046	0.000	0.000	0.000	0.000
52	A	1419	ALA	0	0.006	0.020	20.910	0.024	0.024	0.000	0.000	0.000	0.000
53	A	1420	ILE	0	0.028	0.017	18.108	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	1421	SER	0	0.008	0.006	14.944	0.051	0.051	0.000	0.000	0.000	0.000
55	A	1422	LEU	0	-0.028	0.001	13.335	-0.093	-0.093	0.000	0.000	0.000	0.000
56	A	1423	SER	0	0.013	-0.021	10.090	0.178	0.178	0.000	0.000	0.000	0.000
57	A	1424	GLU	-1	-1.034	-1.010	7.676	-1.870	-1.870	0.000	0.000	0.000	0.000
58	A	1425	THR	0	-0.034	-0.023	8.816	-0.299	-0.299	0.000	0.000	0.000	0.000
59	A	1426	GLU	-1	-0.812	-0.901	11.257	-0.606	-0.606	0.000	0.000	0.000	0.000
60	A	1427	SER	0	-0.042	-0.034	13.515	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	1428	CYS	0	-0.027	0.019	13.025	-0.069	-0.069	0.000	0.000	0.000	0.000
62	A	1429	SER	0	-0.022	-0.018	15.769	0.097	0.097	0.000	0.000	0.000	0.000
63	A	1430	VAL	0	-0.010	-0.007	17.171	-0.053	-0.053	0.000	0.000	0.000	0.000
64	A	1431	VAL	0	0.006	0.013	19.698	0.053	0.053	0.000	0.000	0.000	0.000
65	A	1432	LEU	0	0.002	0.008	22.326	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	1433	ASP	-1	-0.790	-0.875	24.281	-0.301	-0.301	0.000	0.000	0.000	0.000
67	A	1434	SER	0	0.029	-0.013	26.944	0.022	0.022	0.000	0.000	0.000	0.000
68	A	1435	SER	0	-0.042	-0.039	23.691	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	1436	ILE	0	-0.060	-0.041	26.154	0.021	0.021	0.000	0.000	0.000	0.000
70	A	1437	SER	0	-0.059	-0.068	24.531	0.011	0.011	0.000	0.000	0.000	0.000
71	A	1438	GLY	0	0.015	0.021	25.125	0.011	0.011	0.000	0.000	0.000	0.000
72	A	1439	MET	0	-0.024	0.007	18.447	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	1440	ASP	-1	-0.910	-0.930	17.227	-0.572	-0.572	0.000	0.000	0.000	0.000
74	A	1441	VAL	0	0.023	0.010	16.916	-0.068	-0.068	0.000	0.000	0.000	0.000
75	A	1442	ILE	0	0.029	0.007	13.469	0.075	0.075	0.000	0.000	0.000	0.000
76	A	1443	LYS	1	0.923	0.960	12.236	0.543	0.543	0.000	0.000	0.000	0.000
77	A	1444	SER	0	0.004	0.016	12.955	-0.177	-0.177	0.000	0.000	0.000	0.000
78	A	1445	ASN	0	0.007	-0.007	14.707	0.147	0.147	0.000	0.000	0.000	0.000
79	A	1446	LYS	1	0.874	0.936	16.610	0.386	0.386	0.000	0.000	0.000	0.000
80	A	1447	PHE	0	0.039	0.034	17.280	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	1448	GLY	0	0.031	0.014	18.758	0.066	0.066	0.000	0.000	0.000	0.000
82	A	1449	ILE	0	-0.028	-0.015	20.456	-0.048	-0.048	0.000	0.000	0.000	0.000
83	A	1450	GLN	0	0.003	-0.005	22.798	0.032	0.032	0.000	0.000	0.000	0.000
84	A	1451	VAL	0	-0.018	0.001	25.391	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	1452	ASN	0	-0.009	-0.007	27.561	0.028	0.028	0.000	0.000	0.000	0.000
86	A	1453	HIS	0	-0.059	-0.022	29.731	0.013	0.013	0.000	0.000	0.000	0.000
87	A	1454	SER	0	-0.003	-0.027	30.311	0.006	0.006	0.000	0.000	0.000	0.000
88	A	1455	LEU	0	0.052	0.023	24.774	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	1456	PRO	0	-0.038	0.003	28.124	0.010	0.010	0.000	0.000	0.000	0.000
90	A	1457	GLN	0	0.001	-0.012	26.306	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	1458	ILE	0	0.020	0.014	22.650	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	1459	SER	0	-0.023	-0.003	22.063	0.036	0.036	0.000	0.000	0.000	0.000
93	A	1460	ILE	0	0.013	0.007	20.812	-0.042	-0.042	0.000	0.000	0.000	0.000
94	A	1461	ASP	-1	-0.843	-0.950	19.153	-0.342	-0.342	0.000	0.000	0.000	0.000
95	A	1462	LYS	1	0.858	0.926	17.183	0.321	0.321	0.000	0.000	0.000	0.000
96	A	1463	SER	0	0.006	0.000	17.373	-0.081	-0.081	0.000	0.000	0.000	0.000
97	A	1464	ASP	-1	-0.831	-0.869	18.701	-0.330	-0.330	0.000	0.000	0.000	0.000
98	A	1465	GLY	0	-0.022	-0.022	19.932	-0.036	-0.036	0.000	0.000	0.000	0.000
99	A	1466	GLY	0	0.002	-0.010	20.595	-0.056	-0.056	0.000	0.000	0.000	0.000
100	A	1467	ASN	0	-0.047	-0.018	22.591	0.060	0.060	0.000	0.000	0.000	0.000
101	A	1468	ILE	0	0.037	0.019	24.233	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	1469	TYR	0	0.000	0.007	26.275	0.022	0.022	0.000	0.000	0.000	0.000
103	A	1470	LEU	0	-0.008	-0.003	28.524	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	1471	SER	0	0.036	0.018	30.873	0.017	0.017	0.000	0.000	0.000	0.000
105	A	1472	LYS	1	0.870	0.893	33.322	0.168	0.168	0.000	0.000	0.000	0.000
106	A	1473	GLU	-1	-0.951	-0.968	34.496	-0.215	-0.215	0.000	0.000	0.000	0.000
107	A	1474	SER	0	-0.033	-0.041	30.806	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	1475	LEU	0	-0.007	0.009	32.791	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	1476	ASN	0	-0.050	-0.036	35.093	0.005	0.005	0.000	0.000	0.000	0.000
110	A	1477	THR	0	-0.012	0.021	28.530	0.003	0.003	0.000	0.000	0.000	0.000
111	A	1478	GLU	-1	-0.891	-0.910	30.721	-0.208	-0.208	0.000	0.000	0.000	0.000
112	A	1479	ILE	0	0.010	-0.007	26.567	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	1480	TYR	0	-0.092	-0.057	26.354	0.023	0.023	0.000	0.000	0.000	0.000
114	A	1481	THR	0	0.017	0.002	25.063	-0.022	-0.022	0.000	0.000	0.000	0.000
115	A	1482	SER	0	-0.034	-0.010	23.332	0.038	0.038	0.000	0.000	0.000	0.000
116	A	1483	CYS	0	-0.066	-0.038	21.656	-0.023	-0.023	0.000	0.000	0.000	0.000
117	A	1484	SER	0	0.023	0.015	21.880	-0.042	-0.042	0.000	0.000	0.000	0.000
118	A	1485	THR	0	-0.021	-0.033	22.814	0.028	0.028	0.000	0.000	0.000	0.000
119	A	1486	ALA	0	-0.031	-0.001	24.001	-0.028	-0.028	0.000	0.000	0.000	0.000
120	A	1487	ILE	0	0.001	0.013	22.580	-0.025	-0.025	0.000	0.000	0.000	0.000
121	A	1488	ASN	0	0.019	0.007	26.173	0.041	0.041	0.000	0.000	0.000	0.000
122	A	1489	VAL	0	-0.001	-0.001	27.645	-0.024	-0.024	0.000	0.000	0.000	0.000
123	A	1490	ASN	0	-0.015	-0.009	29.280	0.033	0.033	0.000	0.000	0.000	0.000
124	A	1491	LEU	0	0.021	0.007	32.087	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	1492	PRO	0	-0.011	0.012	34.441	0.008	0.008	0.000	0.000	0.000	0.000
126	A	1493	ILE	0	-0.061	-0.057	36.979	0.007	0.007	0.000	0.000	0.000	0.000
127	A	1494	GLY	0	0.020	0.010	39.794	0.008	0.008	0.000	0.000	0.000	0.000
128	A	1495	GLU	-1	-0.971	-0.978	41.449	-0.120	-0.120	0.000	0.000	0.000	0.000
129	A	1496	ASP	-1	-0.924	-0.975	42.890	-0.142	-0.142	0.000	0.000	0.000	0.000
130	A	1497	ASP	-1	-0.910	-0.936	39.473	-0.166	-0.166	0.000	0.000	0.000	0.000
131	A	1498	ASP	-1	-0.912	-0.942	38.458	-0.173	-0.173	0.000	0.000	0.000	0.000
132	A	1499	TYR	0	-0.079	-0.055	31.966	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	1500	VAL	0	-0.026	-0.001	36.065	0.008	0.008	0.000	0.000	0.000	0.000
134	A	1501	GLU	-1	-0.935	-0.975	31.281	-0.236	-0.236	0.000	0.000	0.000	0.000
135	A	1502	PHE	0	-0.058	-0.024	32.999	0.017	0.017	0.000	0.000	0.000	0.000
136	A	1503	PRO	0	0.015	0.013	31.261	-0.014	-0.014	0.000	0.000	0.000	0.000
137	A	1504	ILE	0	-0.030	-0.019	28.559	0.013	0.013	0.000	0.000	0.000	0.000
138	A	1505	PRO	0	-0.046	-0.017	30.472	0.001	0.001	0.000	0.000	0.000	0.000
139	A	1506	GLU	-1	-0.805	-0.920	28.025	-0.244	-0.244	0.000	0.000	0.000	0.000
140	A	1507	GLN	0	-0.055	-0.017	30.359	0.009	0.009	0.000	0.000	0.000	0.000
141	A	1508	MET	0	0.021	0.011	31.075	0.005	0.005	0.000	0.000	0.000	0.000
142	A	1509	LYS	1	0.910	0.958	35.286	0.115	0.115	0.000	0.000	0.000	0.000
143	A	1510	HIS	0	0.074	0.036	34.663	0.004	0.004	0.000	0.000	0.000	0.000
144	A	1511	SER	0	-0.047	-0.013	40.106	0.005	0.005	0.000	0.000	0.000	0.000
145	A	1512	PHE	0	0.004	0.002	43.672	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	1513	ALA	0	0.012	-0.004	46.743	0.002	0.002	0.000	0.000	0.000	0.000
147	A	1514	ASP	-1	-0.842	-0.919	49.417	-0.074	-0.074	0.000	0.000	0.000	0.000
148	A	1515	GLY	0	-0.005	0.000	52.122	0.000	0.000	0.000	0.000	0.000	0.000
149	A	1516	LYS	1	0.936	0.964	44.017	0.090	0.090	0.000	0.000	0.000	0.000
150	A	1517	PHE	0	0.023	0.018	39.694	0.000	0.000	0.000	0.000	0.000	0.000
151	A	1518	LYS	1	0.818	0.907	42.548	0.081	0.081	0.000	0.000	0.000	0.000
152	A	1519	SER	0	0.028	-0.006	37.480	0.003	0.003	0.000	0.000	0.000	0.000
153	A	1520	ALA	0	-0.026	-0.013	38.772	0.001	0.001	0.000	0.000	0.000	0.000
154	A	1521	VAL	0	0.078	0.053	34.912	0.000	0.000	0.000	0.000	0.000	0.000
155	A	1522	PHE	0	-0.094	-0.057	36.183	0.010	0.010	0.000	0.000	0.000	0.000
156	A	1523	GLH	0	0.021	-0.030	37.035	-0.007	-0.007	0.000	0.000	0.000	0.000
157	A	1524	HIS	0	0.015	0.053	39.565	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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