FMO DATABASE

FMODB ID: YZ9V2

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	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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1565006.479701
FMO2-HF: Nuclear repulsion	1497361.779059
FMO2-HF: Total energy	-67644.700643
FMO2-MP2: Total energy	-67843.363943

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.
-121.156	-116.843	0.241	-1.519	-3.033	-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 : 1.024 / 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	-0.889	-0.938	2.946	-28.087	-25.349	0.007	-1.122	-1.622	-0.001
4	A	1439	LEU	0	-0.012	-0.007	2.876	2.457	3.670	0.233	-0.350	-1.096	-0.001
5	A	1440	ILE	0	0.048	0.026	3.788	2.811	3.173	0.001	-0.047	-0.315	0.000
6	A	1441	GLU	-1	-0.848	-0.892	6.258	-17.196	-17.196	0.000	0.000	0.000	0.000
7	A	1442	SER	0	0.000	-0.010	8.290	2.554	2.554	0.000	0.000	0.000	0.000
8	A	1443	ILE	0	0.009	-0.003	8.345	2.171	2.171	0.000	0.000	0.000	0.000
9	A	1444	SER	0	0.000	-0.016	9.901	1.832	1.832	0.000	0.000	0.000	0.000
10	A	1445	ARG	1	0.838	0.924	12.007	18.730	18.730	0.000	0.000	0.000	0.000
11	A	1446	LYS	1	0.957	0.974	13.643	18.066	18.066	0.000	0.000	0.000	0.000
12	A	1447	LEU	0	0.025	0.019	13.934	0.951	0.951	0.000	0.000	0.000	0.000
13	A	1448	GLN	0	0.023	-0.002	15.817	0.618	0.618	0.000	0.000	0.000	0.000
14	A	1449	VAL	0	-0.048	-0.012	18.052	0.758	0.758	0.000	0.000	0.000	0.000
15	A	1450	LEU	0	-0.005	-0.013	17.937	0.609	0.609	0.000	0.000	0.000	0.000
16	A	1451	ARG	1	0.820	0.913	20.119	13.038	13.038	0.000	0.000	0.000	0.000
17	A	1452	GLU	-1	-0.872	-0.951	21.879	-11.721	-11.721	0.000	0.000	0.000	0.000
18	A	1453	ALA	0	-0.032	-0.013	23.602	0.522	0.522	0.000	0.000	0.000	0.000
19	A	1454	ARG	1	0.819	0.901	24.261	11.844	11.844	0.000	0.000	0.000	0.000
20	A	1455	GLU	-1	-0.797	-0.888	25.985	-10.782	-10.782	0.000	0.000	0.000	0.000
21	A	1456	SER	0	-0.027	-0.007	28.123	0.386	0.386	0.000	0.000	0.000	0.000
22	A	1457	LEU	0	0.043	0.026	28.645	0.293	0.293	0.000	0.000	0.000	0.000
23	A	1458	LEU	0	-0.043	-0.019	29.995	0.285	0.285	0.000	0.000	0.000	0.000
24	A	1459	GLU	-1	-0.924	-0.964	32.051	-8.326	-8.326	0.000	0.000	0.000	0.000
25	A	1460	ASP	-1	-0.901	-0.952	33.733	-8.593	-8.593	0.000	0.000	0.000	0.000
26	A	1461	VAL	0	-0.069	-0.036	33.608	0.274	0.274	0.000	0.000	0.000	0.000
27	A	1462	GLN	0	0.007	0.026	36.110	0.198	0.198	0.000	0.000	0.000	0.000
28	A	1463	ALA	0	0.005	0.004	38.319	0.263	0.263	0.000	0.000	0.000	0.000
29	A	1464	ASN	0	0.003	-0.024	39.237	0.329	0.329	0.000	0.000	0.000	0.000
30	A	1465	THR	0	-0.057	-0.041	39.323	0.174	0.174	0.000	0.000	0.000	0.000
31	A	1466	VAL	0	-0.035	-0.020	41.886	0.180	0.180	0.000	0.000	0.000	0.000
32	A	1467	LEU	0	0.051	0.035	43.917	0.156	0.156	0.000	0.000	0.000	0.000
33	A	1468	GLY	0	0.019	0.000	44.565	0.165	0.165	0.000	0.000	0.000	0.000
34	A	1469	ALA	0	-0.047	-0.027	46.169	0.155	0.155	0.000	0.000	0.000	0.000
35	A	1470	GLU	-1	-0.931	-0.962	48.129	-6.247	-6.247	0.000	0.000	0.000	0.000
36	A	1471	VAL	0	0.016	0.003	48.763	0.168	0.168	0.000	0.000	0.000	0.000
37	A	1472	GLU	-1	-0.898	-0.943	49.526	-6.178	-6.178	0.000	0.000	0.000	0.000
38	A	1473	ALA	0	-0.045	-0.026	51.754	0.149	0.149	0.000	0.000	0.000	0.000
39	A	1474	ILE	0	0.025	0.009	53.394	0.151	0.151	0.000	0.000	0.000	0.000
40	A	1475	VAL	0	0.039	0.016	53.635	0.133	0.133	0.000	0.000	0.000	0.000
41	A	1476	LYS	1	0.895	0.957	55.790	5.587	5.587	0.000	0.000	0.000	0.000
42	A	1477	GLY	0	-0.060	-0.023	57.629	0.101	0.101	0.000	0.000	0.000	0.000
43	A	1478	VAL	0	-0.033	-0.023	58.878	0.110	0.110	0.000	0.000	0.000	0.000
44	A	1479	CYS	0	-0.081	-0.016	58.817	0.054	0.054	0.000	0.000	0.000	0.000
45	A	1480	LYS	1	0.862	0.924	60.890	4.974	4.974	0.000	0.000	0.000	0.000
46	A	1481	PRO	0	0.029	0.005	60.636	-0.085	-0.085	0.000	0.000	0.000	0.000
47	A	1482	SER	0	0.053	0.020	59.401	-0.101	-0.101	0.000	0.000	0.000	0.000
48	A	1483	GLU	-1	-0.788	-0.872	58.499	-5.202	-5.202	0.000	0.000	0.000	0.000
49	A	1484	PHE	0	0.028	0.026	53.910	-0.109	-0.109	0.000	0.000	0.000	0.000
50	A	1485	ASP	-1	-0.898	-0.954	54.760	-5.701	-5.701	0.000	0.000	0.000	0.000
51	A	1486	LYS	1	0.849	0.921	53.939	5.300	5.300	0.000	0.000	0.000	0.000
52	A	1487	PHE	0	0.077	0.035	49.826	-0.121	-0.121	0.000	0.000	0.000	0.000
53	A	1488	ARG	1	0.895	0.937	49.716	5.934	5.934	0.000	0.000	0.000	0.000
54	A	1489	MET	0	-0.050	-0.033	49.007	-0.138	-0.138	0.000	0.000	0.000	0.000
55	A	1490	PHE	0	0.002	0.015	46.401	-0.136	-0.136	0.000	0.000	0.000	0.000
56	A	1491	ILE	0	0.070	0.040	45.570	-0.184	-0.184	0.000	0.000	0.000	0.000
57	A	1492	GLY	0	-0.036	-0.018	44.271	-0.213	-0.213	0.000	0.000	0.000	0.000
58	A	1493	ASP	-1	-0.817	-0.898	43.576	-6.894	-6.894	0.000	0.000	0.000	0.000
59	A	1494	LEU	0	0.006	0.010	41.719	-0.184	-0.184	0.000	0.000	0.000	0.000
60	A	1495	ASP	-1	-0.871	-0.927	39.159	-8.358	-8.358	0.000	0.000	0.000	0.000
61	A	1496	LYS	1	0.915	0.959	38.884	7.241	7.241	0.000	0.000	0.000	0.000
62	A	1497	VAL	0	0.014	0.016	38.953	-0.227	-0.227	0.000	0.000	0.000	0.000
63	A	1498	VAL	0	0.009	0.004	36.125	-0.191	-0.191	0.000	0.000	0.000	0.000
64	A	1499	ASN	0	-0.015	-0.018	34.533	-0.556	-0.556	0.000	0.000	0.000	0.000
65	A	1500	LEU	0	-0.027	-0.019	34.311	-0.299	-0.299	0.000	0.000	0.000	0.000
66	A	1501	LEU	0	0.008	0.011	34.923	-0.228	-0.228	0.000	0.000	0.000	0.000
67	A	1502	LEU	0	0.045	0.031	29.843	-0.187	-0.187	0.000	0.000	0.000	0.000
68	A	1503	SER	0	-0.011	-0.005	30.360	-0.370	-0.370	0.000	0.000	0.000	0.000
69	A	1504	LEU	0	-0.063	-0.039	30.316	-0.375	-0.375	0.000	0.000	0.000	0.000
70	A	1505	SER	0	0.051	0.025	30.231	-0.117	-0.117	0.000	0.000	0.000	0.000
71	A	1506	GLY	0	0.037	0.032	27.221	-0.291	-0.291	0.000	0.000	0.000	0.000
72	A	1507	ARG	1	0.855	0.925	26.655	9.613	9.613	0.000	0.000	0.000	0.000
73	A	1508	LEU	0	0.003	0.006	27.575	-0.272	-0.272	0.000	0.000	0.000	0.000
74	A	1509	ALA	0	0.045	0.025	25.411	-0.147	-0.147	0.000	0.000	0.000	0.000
75	A	1510	ARG	1	0.951	0.974	22.151	12.512	12.512	0.000	0.000	0.000	0.000
76	A	1511	VAL	0	-0.051	-0.028	23.865	-0.410	-0.410	0.000	0.000	0.000	0.000
77	A	1512	GLU	-1	-0.832	-0.900	25.775	-11.000	-11.000	0.000	0.000	0.000	0.000
78	A	1513	ASN	0	-0.020	-0.013	20.234	-0.728	-0.728	0.000	0.000	0.000	0.000
79	A	1514	ALA	0	0.016	0.008	21.501	-0.547	-0.547	0.000	0.000	0.000	0.000
80	A	1515	LEU	0	-0.063	-0.042	22.589	-0.139	-0.139	0.000	0.000	0.000	0.000
81	A	1516	ASN	0	-0.071	-0.038	23.157	0.017	0.017	0.000	0.000	0.000	0.000
82	A	1517	ASN	0	0.015	0.022	16.756	-0.694	-0.694	0.000	0.000	0.000	0.000
83	A	1518	LEU	0	-0.080	-0.038	19.908	-0.366	-0.366	0.000	0.000	0.000	0.000
84	A	1519	ASP	-1	-0.992	-1.010	21.898	-12.626	-12.626	0.000	0.000	0.000	0.000
85	A	1520	ASP	-1	-0.905	-0.932	19.887	-14.686	-14.686	0.000	0.000	0.000	0.000
86	A	1521	GLY	0	-0.077	-0.025	20.136	-0.198	-0.198	0.000	0.000	0.000	0.000
87	A	1522	ALA	0	0.024	0.004	20.676	0.784	0.784	0.000	0.000	0.000	0.000
88	A	1523	SER	0	-0.036	-0.029	22.354	-0.615	-0.615	0.000	0.000	0.000	0.000
89	A	1524	PRO	0	-0.031	0.000	24.625	0.419	0.419	0.000	0.000	0.000	0.000
90	A	1525	GLY	0	0.014	-0.004	28.231	0.044	0.044	0.000	0.000	0.000	0.000
91	A	1526	ASP	-1	-0.872	-0.938	25.756	-11.895	-11.895	0.000	0.000	0.000	0.000
92	A	1527	ARG	1	0.997	0.993	28.112	10.636	10.636	0.000	0.000	0.000	0.000
93	A	1528	GLN	0	0.005	0.000	28.909	0.141	0.141	0.000	0.000	0.000	0.000
94	A	1529	SER	0	-0.004	-0.001	29.788	0.290	0.290	0.000	0.000	0.000	0.000
95	A	1530	LEU	0	0.040	0.015	25.054	0.205	0.205	0.000	0.000	0.000	0.000
96	A	1531	LEU	0	0.027	0.026	29.644	0.095	0.095	0.000	0.000	0.000	0.000
97	A	1532	GLU	-1	-0.843	-0.911	32.652	-8.536	-8.536	0.000	0.000	0.000	0.000
98	A	1533	LYS	1	0.899	0.933	31.075	9.575	9.575	0.000	0.000	0.000	0.000
99	A	1534	GLN	0	0.004	-0.011	31.236	0.308	0.308	0.000	0.000	0.000	0.000
100	A	1535	ARG	1	0.886	0.940	32.858	8.323	8.323	0.000	0.000	0.000	0.000
101	A	1536	VAL	0	-0.042	-0.024	35.303	0.167	0.167	0.000	0.000	0.000	0.000
102	A	1537	LEU	0	-0.013	-0.011	30.735	0.104	0.104	0.000	0.000	0.000	0.000
103	A	1538	ILE	0	0.039	0.021	34.497	0.075	0.075	0.000	0.000	0.000	0.000
104	A	1539	GLN	0	-0.091	-0.037	36.750	0.178	0.178	0.000	0.000	0.000	0.000
105	A	1540	GLN	0	-0.004	-0.016	36.407	-0.115	-0.115	0.000	0.000	0.000	0.000
106	A	1541	HIS	0	0.014	0.008	34.565	0.087	0.087	0.000	0.000	0.000	0.000
107	A	1542	GLU	-1	-0.801	-0.886	37.527	-7.985	-7.985	0.000	0.000	0.000	0.000
108	A	1543	ASP	-1	-0.860	-0.918	40.628	-7.296	-7.296	0.000	0.000	0.000	0.000
109	A	1544	ALA	0	-0.033	-0.022	38.631	0.135	0.135	0.000	0.000	0.000	0.000
110	A	1545	LYS	1	0.821	0.883	37.738	8.164	8.164	0.000	0.000	0.000	0.000
111	A	1546	GLU	-1	-0.798	-0.881	41.208	-6.569	-6.569	0.000	0.000	0.000	0.000
112	A	1547	LEU	0	-0.057	-0.031	43.290	0.159	0.159	0.000	0.000	0.000	0.000
113	A	1548	LYS	1	0.826	0.893	40.122	7.644	7.644	0.000	0.000	0.000	0.000
114	A	1549	GLU	-1	-0.867	-0.939	43.257	-6.756	-6.756	0.000	0.000	0.000	0.000
115	A	1550	ASN	0	-0.116	-0.064	45.994	0.299	0.299	0.000	0.000	0.000	0.000
116	A	1551	LEU	0	-0.035	-0.030	44.187	0.154	0.154	0.000	0.000	0.000	0.000
117	A	1552	ASP	-1	-0.786	-0.855	44.324	-7.211	-7.211	0.000	0.000	0.000	0.000
118	A	1553	ARG	1	0.861	0.922	47.366	6.564	6.564	0.000	0.000	0.000	0.000
119	A	1554	ARG	1	0.774	0.868	49.111	6.560	6.560	0.000	0.000	0.000	0.000
120	A	1555	GLU	-1	-0.772	-0.844	47.052	-6.325	-6.325	0.000	0.000	0.000	0.000
121	A	1556	ARG	1	0.807	0.874	49.791	6.285	6.285	0.000	0.000	0.000	0.000
122	A	1557	ILE	0	0.004	0.011	52.574	0.129	0.129	0.000	0.000	0.000	0.000
123	A	1558	VAL	0	-0.064	-0.038	51.666	0.118	0.118	0.000	0.000	0.000	0.000
124	A	1559	PHE	0	0.038	0.010	52.044	0.092	0.092	0.000	0.000	0.000	0.000
125	A	1560	ASP	-1	-0.879	-0.941	53.950	-5.512	-5.512	0.000	0.000	0.000	0.000
126	A	1561	ILE	0	-0.146	-0.080	56.262	0.121	0.121	0.000	0.000	0.000	0.000
127	A	1562	LEU	0	-0.003	-0.012	53.222	0.072	0.072	0.000	0.000	0.000	0.000
128	A	1563	ALA	0	0.003	0.017	57.310	0.053	0.053	0.000	0.000	0.000	0.000
129	A	1564	ASN	0	-0.084	-0.028	58.618	0.118	0.118	0.000	0.000	0.000	0.000
130	A	1565	TYR	0	-0.105	-0.073	60.004	0.121	0.121	0.000	0.000	0.000	0.000
131	A	1566	LEU	0	-0.036	-0.014	54.606	0.027	0.027	0.000	0.000	0.000	0.000
132	A	1567	SER	0	0.045	0.023	57.477	0.064	0.064	0.000	0.000	0.000	0.000
133	A	1568	GLU	-1	-0.892	-0.957	55.953	-5.484	-5.484	0.000	0.000	0.000	0.000
134	A	1569	GLU	-1	-0.945	-0.966	53.370	-5.740	-5.740	0.000	0.000	0.000	0.000
135	A	1570	SER	0	0.012	-0.001	52.214	-0.072	-0.072	0.000	0.000	0.000	0.000
136	A	1571	LEU	0	-0.013	-0.007	51.972	-0.122	-0.122	0.000	0.000	0.000	0.000
137	A	1572	ALA	0	0.001	0.010	49.727	-0.131	-0.131	0.000	0.000	0.000	0.000
138	A	1573	ASP	-1	-0.888	-0.948	47.822	-6.511	-6.511	0.000	0.000	0.000	0.000
139	A	1574	TYR	0	-0.109	-0.083	47.153	-0.163	-0.163	0.000	0.000	0.000	0.000
140	A	1575	GLU	-1	-0.831	-0.911	46.815	-6.483	-6.483	0.000	0.000	0.000	0.000
141	A	1576	HIS	0	-0.025	-0.012	41.896	-0.291	-0.291	0.000	0.000	0.000	0.000
142	A	1577	PHE	0	0.001	0.023	42.671	-0.209	-0.209	0.000	0.000	0.000	0.000
143	A	1578	VAL	0	0.022	0.011	42.231	-0.228	-0.228	0.000	0.000	0.000	0.000
144	A	1579	LYS	1	0.945	0.977	39.902	7.450	7.450	0.000	0.000	0.000	0.000
145	A	1580	MET	0	0.029	0.007	36.435	-0.259	-0.259	0.000	0.000	0.000	0.000
146	A	1581	LYS	1	0.907	0.961	37.402	7.560	7.560	0.000	0.000	0.000	0.000
147	A	1582	SER	0	-0.091	-0.047	36.876	-0.239	-0.239	0.000	0.000	0.000	0.000
148	A	1583	ALA	0	0.018	0.000	34.880	-0.261	-0.261	0.000	0.000	0.000	0.000
149	A	1584	LEU	0	0.030	0.025	33.113	-0.330	-0.330	0.000	0.000	0.000	0.000
150	A	1585	ILE	0	-0.033	-0.017	31.998	-0.348	-0.348	0.000	0.000	0.000	0.000
151	A	1586	ILE	0	-0.020	-0.024	30.678	-0.326	-0.326	0.000	0.000	0.000	0.000
152	A	1587	GLU	-1	-0.893	-0.945	28.501	-10.875	-10.875	0.000	0.000	0.000	0.000
153	A	1588	GLN	0	-0.014	-0.003	27.225	-0.434	-0.434	0.000	0.000	0.000	0.000
154	A	1589	ARG	1	0.835	0.898	26.500	9.884	9.884	0.000	0.000	0.000	0.000
155	A	1590	GLU	-1	-0.808	-0.877	24.015	-12.527	-12.527	0.000	0.000	0.000	0.000
156	A	1591	LEU	0	-0.006	-0.016	22.735	-0.808	-0.808	0.000	0.000	0.000	0.000
157	A	1592	GLU	-1	-0.829	-0.899	21.566	-12.115	-12.115	0.000	0.000	0.000	0.000
158	A	1593	ASP	-1	-0.889	-0.939	21.254	-13.727	-13.727	0.000	0.000	0.000	0.000
159	A	1594	LYS	1	0.782	0.880	18.554	12.204	12.204	0.000	0.000	0.000	0.000
160	A	1595	ILE	0	-0.028	-0.015	16.933	-1.167	-1.167	0.000	0.000	0.000	0.000
161	A	1596	HIS	0	-0.034	-0.010	16.549	-0.623	-0.623	0.000	0.000	0.000	0.000
162	A	1597	LEU	0	-0.002	0.004	13.960	-1.041	-1.041	0.000	0.000	0.000	0.000
163	A	1598	GLY	0	0.007	-0.006	12.573	-1.683	-1.683	0.000	0.000	0.000	0.000
164	A	1599	GLU	-1	-0.903	-0.946	11.751	-20.511	-20.511	0.000	0.000	0.000	0.000
165	A	1600	GLU	-1	-0.922	-0.961	11.945	-20.971	-20.971	0.000	0.000	0.000	0.000
166	A	1601	GLN	0	-0.007	-0.004	8.420	-0.510	-0.510	0.000	0.000	0.000	0.000
167	A	1602	LEU	0	-0.043	-0.035	6.711	-4.715	-4.715	0.000	0.000	0.000	0.000
168	A	1603	LYS	1	0.813	0.916	7.629	17.443	17.443	0.000	0.000	0.000	0.000
169	A	1604	CYS	0	-0.115	-0.039	5.519	-8.941	-8.941	0.000	0.000	0.000	0.000

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