FMO DATABASE

FMODB ID: LN6L9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1434998.621696
FMO2-HF: Nuclear repulsion	1373367.578359
FMO2-HF: Total energy	-61631.043337
FMO2-MP2: Total energy	-61809.057794

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.
-11.445	-7.432	3.316	-2.639	-4.691	-0.018

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 : -0.033 / q_NPA : -0.029

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	3.529	-2.717	-1.162	0.013	-0.756	-0.812	0.001
4	A	1371	ARG	1	0.730	0.856	5.092	2.485	2.485	0.000	0.000	0.000	0.000
5	A	1372	LYS	1	0.922	0.955	6.973	0.973	0.973	0.000	0.000	0.000	0.000
6	A	1373	GLU	-1	-0.868	-0.905	9.644	-0.853	-0.853	0.000	0.000	0.000	0.000
7	A	1374	LEU	0	0.026	0.019	12.489	-0.052	-0.052	0.000	0.000	0.000	0.000
8	A	1375	VAL	0	0.019	0.011	12.608	0.089	0.089	0.000	0.000	0.000	0.000
9	A	1376	GLY	0	-0.023	-0.012	15.620	0.028	0.028	0.000	0.000	0.000	0.000
10	A	1377	ASN	0	0.016	0.001	19.272	0.005	0.005	0.000	0.000	0.000	0.000
11	A	1378	LYS	1	0.864	0.924	15.382	0.439	0.439	0.000	0.000	0.000	0.000
12	A	1379	TRP	0	0.033	0.007	14.343	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	1380	PHE	0	-0.050	-0.022	9.437	0.043	0.043	0.000	0.000	0.000	0.000
14	A	1381	ILE	0	0.001	-0.004	10.146	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	1382	GLU	-1	-0.796	-0.891	5.393	-3.013	-3.013	0.000	0.000	0.000	0.000
16	A	1383	ASN	0	-0.032	-0.030	2.734	-4.021	-2.202	3.132	-1.766	-3.185	-0.019
17	A	1384	TYR	0	-0.009	-0.014	4.819	0.294	0.322	-0.001	-0.013	-0.015	0.000
18	A	1385	GLU	-1	-0.864	-0.931	7.184	-2.530	-2.530	0.000	0.000	0.000	0.000
19	A	1386	ASN	0	-0.084	-0.054	10.106	0.294	0.294	0.000	0.000	0.000	0.000
20	A	1387	GLU	-1	-0.884	-0.941	12.645	-0.972	-0.972	0.000	0.000	0.000	0.000
21	A	1388	THR	0	-0.071	-0.036	15.051	0.095	0.095	0.000	0.000	0.000	0.000
22	A	1389	GLU	-1	-0.894	-0.934	17.788	-0.420	-0.420	0.000	0.000	0.000	0.000
23	A	1390	SER	0	-0.030	-0.017	17.676	-0.093	-0.093	0.000	0.000	0.000	0.000
24	A	1391	LEU	0	0.001	0.008	12.194	0.029	0.029	0.000	0.000	0.000	0.000
25	A	1392	VAL	0	-0.031	-0.030	16.688	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	1393	ILE	0	-0.050	-0.025	15.242	-0.064	-0.064	0.000	0.000	0.000	0.000
27	A	1394	ASP	-1	-0.814	-0.890	19.212	-0.396	-0.396	0.000	0.000	0.000	0.000
28	A	1395	ALA	0	-0.004	0.013	20.853	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	1396	ASN	0	-0.059	-0.046	22.511	0.067	0.067	0.000	0.000	0.000	0.000
30	A	1397	LYS	1	0.902	0.922	24.438	0.236	0.236	0.000	0.000	0.000	0.000
31	A	1398	ASP	-1	-0.900	-0.931	25.557	-0.292	-0.292	0.000	0.000	0.000	0.000
32	A	1399	GLU	-1	-0.768	-0.856	20.312	-0.476	-0.476	0.000	0.000	0.000	0.000
33	A	1400	SER	0	-0.074	-0.049	19.316	0.042	0.042	0.000	0.000	0.000	0.000
34	A	1401	ILE	0	-0.006	-0.001	15.750	-0.037	-0.037	0.000	0.000	0.000	0.000
35	A	1402	PHE	0	0.005	0.015	8.318	0.077	0.077	0.000	0.000	0.000	0.000
36	A	1403	ILE	0	0.034	0.007	11.235	-0.137	-0.137	0.000	0.000	0.000	0.000
37	A	1404	GLY	0	0.053	0.013	8.533	0.258	0.258	0.000	0.000	0.000	0.000
38	A	1405	LYS	1	0.840	0.907	2.763	2.836	3.447	0.172	-0.104	-0.679	0.000
39	A	1406	CYS	0	-0.036	0.016	5.817	-0.907	-0.907	0.000	0.000	0.000	0.000
40	A	1407	SER	0	0.032	-0.021	8.427	0.425	0.425	0.000	0.000	0.000	0.000
41	A	1408	GLN	0	-0.049	-0.012	11.025	0.000	0.000	0.000	0.000	0.000	0.000
42	A	1409	VAL	0	0.040	0.013	11.363	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	1410	LEU	0	0.021	0.019	14.655	0.050	0.050	0.000	0.000	0.000	0.000
44	A	1411	VAL	0	0.013	0.004	14.469	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	1412	GLN	0	0.001	-0.004	17.339	0.071	0.071	0.000	0.000	0.000	0.000
46	A	1413	ILE	0	-0.020	-0.013	18.284	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	1414	LYS	1	0.830	0.908	21.513	0.468	0.468	0.000	0.000	0.000	0.000
48	A	1415	GLY	0	0.014	-0.005	24.238	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	1416	LYS	1	0.865	0.925	25.761	0.267	0.267	0.000	0.000	0.000	0.000
50	A	1417	VAL	0	0.011	0.014	21.776	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	1418	ASN	0	-0.015	-0.017	22.761	0.051	0.051	0.000	0.000	0.000	0.000
52	A	1419	ALA	0	0.014	0.023	20.733	0.025	0.025	0.000	0.000	0.000	0.000
53	A	1420	ILE	0	0.020	0.006	18.014	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	1421	SER	0	-0.017	-0.030	14.785	0.057	0.057	0.000	0.000	0.000	0.000
55	A	1422	LEU	0	-0.024	-0.003	13.089	-0.113	-0.113	0.000	0.000	0.000	0.000
56	A	1423	SER	0	0.029	0.009	9.895	0.200	0.200	0.000	0.000	0.000	0.000
57	A	1424	GLU	-1	-0.947	-0.963	7.592	-1.546	-1.546	0.000	0.000	0.000	0.000
58	A	1425	THR	0	-0.020	-0.014	8.747	-0.374	-0.374	0.000	0.000	0.000	0.000
59	A	1426	GLU	-1	-0.749	-0.880	11.231	-0.466	-0.466	0.000	0.000	0.000	0.000
60	A	1427	SER	0	-0.023	-0.004	13.348	-0.038	-0.038	0.000	0.000	0.000	0.000
61	A	1428	CYS	0	-0.038	0.013	12.986	-0.071	-0.071	0.000	0.000	0.000	0.000
62	A	1429	SER	0	-0.011	-0.016	15.676	0.111	0.111	0.000	0.000	0.000	0.000
63	A	1430	VAL	0	-0.025	-0.012	16.789	-0.072	-0.072	0.000	0.000	0.000	0.000
64	A	1431	VAL	0	0.020	0.020	19.429	0.062	0.062	0.000	0.000	0.000	0.000
65	A	1432	LEU	0	-0.018	-0.006	21.942	-0.040	-0.040	0.000	0.000	0.000	0.000
66	A	1433	ASP	-1	-0.771	-0.855	23.910	-0.325	-0.325	0.000	0.000	0.000	0.000
67	A	1434	SER	0	0.000	-0.012	26.437	0.031	0.031	0.000	0.000	0.000	0.000
68	A	1435	SER	0	-0.048	-0.029	23.408	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	1436	ILE	0	-0.046	-0.029	25.748	0.023	0.023	0.000	0.000	0.000	0.000
70	A	1437	SER	0	-0.047	-0.053	24.246	0.013	0.013	0.000	0.000	0.000	0.000
71	A	1438	GLY	0	0.021	0.012	25.073	0.020	0.020	0.000	0.000	0.000	0.000
72	A	1439	MET	0	-0.038	0.005	18.022	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	1440	ASP	-1	-0.875	-0.902	16.755	-0.596	-0.596	0.000	0.000	0.000	0.000
74	A	1441	VAL	0	0.036	0.013	16.730	-0.071	-0.071	0.000	0.000	0.000	0.000
75	A	1442	ILE	0	0.000	-0.003	13.556	0.081	0.081	0.000	0.000	0.000	0.000
76	A	1443	LYS	1	0.836	0.918	10.946	0.476	0.476	0.000	0.000	0.000	0.000
77	A	1444	SER	0	-0.010	0.002	12.736	-0.193	-0.193	0.000	0.000	0.000	0.000
78	A	1445	ASN	0	0.029	0.020	14.691	0.114	0.114	0.000	0.000	0.000	0.000
79	A	1446	LYS	1	0.777	0.867	16.493	0.499	0.499	0.000	0.000	0.000	0.000
80	A	1447	PHE	0	0.036	0.035	17.338	-0.013	-0.013	0.000	0.000	0.000	0.000
81	A	1448	GLY	0	0.028	0.014	18.926	0.071	0.071	0.000	0.000	0.000	0.000
82	A	1449	ILE	0	-0.033	-0.026	20.270	-0.057	-0.057	0.000	0.000	0.000	0.000
83	A	1450	GLN	0	0.005	0.000	22.708	0.031	0.031	0.000	0.000	0.000	0.000
84	A	1451	VAL	0	-0.006	0.004	25.011	-0.026	-0.026	0.000	0.000	0.000	0.000
85	A	1452	ASN	0	-0.025	-0.025	27.401	0.027	0.027	0.000	0.000	0.000	0.000
86	A	1453	HIS	0	-0.037	-0.011	29.704	0.015	0.015	0.000	0.000	0.000	0.000
87	A	1454	SER	0	-0.010	-0.057	30.220	0.007	0.007	0.000	0.000	0.000	0.000
88	A	1455	LEU	0	0.022	0.010	24.469	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	1456	PRO	0	-0.037	0.017	27.751	0.011	0.011	0.000	0.000	0.000	0.000
90	A	1457	GLN	0	-0.012	-0.019	26.295	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	1458	ILE	0	0.018	0.008	22.461	-0.026	-0.026	0.000	0.000	0.000	0.000
92	A	1459	SER	0	-0.017	-0.003	22.629	0.037	0.037	0.000	0.000	0.000	0.000
93	A	1460	ILE	0	0.009	0.003	20.589	-0.046	-0.046	0.000	0.000	0.000	0.000
94	A	1461	ASP	-1	-0.754	-0.861	19.111	-0.285	-0.285	0.000	0.000	0.000	0.000
95	A	1462	LYS	1	0.754	0.868	17.553	0.242	0.242	0.000	0.000	0.000	0.000
96	A	1463	SER	0	0.022	0.005	17.006	-0.085	-0.085	0.000	0.000	0.000	0.000
97	A	1464	ASP	-1	-0.824	-0.889	18.323	-0.301	-0.301	0.000	0.000	0.000	0.000
98	A	1465	GLY	0	-0.014	-0.008	19.615	-0.040	-0.040	0.000	0.000	0.000	0.000
99	A	1466	GLY	0	-0.001	-0.008	20.522	-0.060	-0.060	0.000	0.000	0.000	0.000
100	A	1467	ASN	0	-0.049	-0.010	22.585	0.067	0.067	0.000	0.000	0.000	0.000
101	A	1468	ILE	0	0.007	0.002	23.798	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	1469	TYR	0	0.025	0.017	26.112	0.024	0.024	0.000	0.000	0.000	0.000
103	A	1470	LEU	0	0.006	0.003	28.124	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	1471	SER	0	0.041	0.033	30.630	0.020	0.020	0.000	0.000	0.000	0.000
105	A	1472	LYS	1	0.834	0.872	33.275	0.179	0.179	0.000	0.000	0.000	0.000
106	A	1473	GLU	-1	-0.921	-0.916	33.886	-0.236	-0.236	0.000	0.000	0.000	0.000
107	A	1474	SER	0	-0.008	-0.039	30.302	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	1475	LEU	0	-0.020	0.009	32.523	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	1476	ASN	0	-0.047	-0.029	34.925	0.012	0.012	0.000	0.000	0.000	0.000
110	A	1477	THR	0	-0.033	0.007	28.278	0.004	0.004	0.000	0.000	0.000	0.000
111	A	1478	GLU	-1	-0.840	-0.899	30.094	-0.219	-0.219	0.000	0.000	0.000	0.000
112	A	1479	ILE	0	0.004	-0.013	26.370	-0.023	-0.023	0.000	0.000	0.000	0.000
113	A	1480	TYR	0	-0.101	-0.054	26.136	0.027	0.027	0.000	0.000	0.000	0.000
114	A	1481	THR	0	0.023	0.004	24.845	-0.023	-0.023	0.000	0.000	0.000	0.000
115	A	1482	SER	0	-0.055	-0.038	22.820	0.040	0.040	0.000	0.000	0.000	0.000
116	A	1483	CYS	0	-0.079	-0.045	21.929	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	1484	SER	0	0.022	0.008	21.812	-0.035	-0.035	0.000	0.000	0.000	0.000
118	A	1485	THR	0	-0.056	-0.042	22.865	0.025	0.025	0.000	0.000	0.000	0.000
119	A	1486	ALA	0	-0.002	-0.014	23.764	-0.033	-0.033	0.000	0.000	0.000	0.000
120	A	1487	ILE	0	-0.014	0.014	22.312	-0.026	-0.026	0.000	0.000	0.000	0.000
121	A	1488	ASN	0	-0.005	-0.008	25.963	0.031	0.031	0.000	0.000	0.000	0.000
122	A	1489	VAL	0	-0.009	-0.006	27.378	-0.027	-0.027	0.000	0.000	0.000	0.000
123	A	1490	ASN	0	-0.038	-0.031	29.687	0.033	0.033	0.000	0.000	0.000	0.000
124	A	1491	LEU	0	0.004	-0.005	31.839	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	1492	PRO	0	0.002	0.023	34.271	0.009	0.009	0.000	0.000	0.000	0.000
126	A	1493	ILE	0	-0.067	-0.052	36.914	0.008	0.008	0.000	0.000	0.000	0.000
127	A	1494	GLY	0	0.016	0.016	39.949	0.008	0.008	0.000	0.000	0.000	0.000
128	A	1495	GLU	-1	-0.952	-0.980	41.663	-0.127	-0.127	0.000	0.000	0.000	0.000
129	A	1496	ASP	-1	-0.973	-0.998	42.896	-0.155	-0.155	0.000	0.000	0.000	0.000
130	A	1497	ASP	-1	-0.850	-0.910	39.690	-0.180	-0.180	0.000	0.000	0.000	0.000
131	A	1498	ASP	-1	-0.895	-0.920	37.825	-0.204	-0.204	0.000	0.000	0.000	0.000
132	A	1499	TYR	0	-0.112	-0.085	32.189	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	1500	VAL	0	-0.033	-0.009	36.200	0.007	0.007	0.000	0.000	0.000	0.000
134	A	1501	GLU	-1	-0.842	-0.917	31.006	-0.262	-0.262	0.000	0.000	0.000	0.000
135	A	1502	PHE	0	-0.044	-0.032	33.047	0.019	0.019	0.000	0.000	0.000	0.000
136	A	1503	PRO	0	0.005	0.005	30.942	-0.015	-0.015	0.000	0.000	0.000	0.000
137	A	1504	ILE	0	-0.016	-0.002	28.727	0.017	0.017	0.000	0.000	0.000	0.000
138	A	1505	PRO	0	-0.053	-0.024	30.214	0.001	0.001	0.000	0.000	0.000	0.000
139	A	1506	GLU	-1	-0.804	-0.906	27.980	-0.231	-0.231	0.000	0.000	0.000	0.000
140	A	1507	GLN	0	-0.045	-0.021	29.985	0.015	0.015	0.000	0.000	0.000	0.000
141	A	1508	MET	0	-0.004	-0.009	31.462	0.002	0.002	0.000	0.000	0.000	0.000
142	A	1509	LYS	1	0.914	0.966	35.497	0.108	0.108	0.000	0.000	0.000	0.000
143	A	1510	HIS	0	0.075	0.039	34.768	0.003	0.003	0.000	0.000	0.000	0.000
144	A	1511	SER	0	-0.008	0.001	40.253	0.004	0.004	0.000	0.000	0.000	0.000
145	A	1512	PHE	0	-0.015	-0.008	43.909	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	1513	ALA	0	0.047	0.021	47.080	0.002	0.002	0.000	0.000	0.000	0.000
147	A	1514	ASP	-1	-0.858	-0.913	49.765	-0.068	-0.068	0.000	0.000	0.000	0.000
148	A	1515	GLY	0	0.013	0.017	52.419	0.000	0.000	0.000	0.000	0.000	0.000
149	A	1516	LYS	1	0.898	0.936	44.091	0.080	0.080	0.000	0.000	0.000	0.000
150	A	1517	PHE	0	0.034	0.021	40.111	0.000	0.000	0.000	0.000	0.000	0.000
151	A	1518	LYS	1	0.774	0.871	42.743	0.071	0.071	0.000	0.000	0.000	0.000
152	A	1519	SER	0	0.038	-0.003	37.916	0.004	0.004	0.000	0.000	0.000	0.000
153	A	1520	ALA	0	-0.010	0.000	39.201	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	1521	VAL	0	0.080	0.041	35.104	0.002	0.002	0.000	0.000	0.000	0.000
155	A	1522	PHE	0	-0.093	-0.042	35.985	0.011	0.011	0.000	0.000	0.000	0.000
156	A	1523	GLH	0	0.032	0.006	36.826	-0.007	-0.007	0.000	0.000	0.000	0.000
157	A	1524	HIS	0	0.004	0.018	39.389	0.006	0.006	0.000	0.000	0.000	0.000

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