FMO DATABASE

FMODB ID: QYKNY

Calculation Name: 5F4Y-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F4Y

Chain ID: B

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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1299174.787205
FMO2-HF: Nuclear repulsion	1238483.443799
FMO2-HF: Total energy	-60691.343405
FMO2-MP2: Total energy	-60869.219444

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(B:1426:SER)

Summations of interaction energy for fragment #1(B:1426:SER)

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.
-7.659	-3.372	3.347	-3.523	-4.111	-0.024

Interaction energy analysis for fragmet #1(B:1426:SER)

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	B	1428	LEU	0	0.056	0.015	3.808	-2.092	-0.370	-0.020	-0.786	-0.917	0.002
4	B	1429	ASP	-1	-0.884	-0.943	2.065	-9.211	-6.822	3.368	-2.691	-3.065	-0.026
5	B	1430	HIS	0	-0.027	-0.010	4.130	1.462	1.638	-0.001	-0.046	-0.129	0.000
6	B	1431	ASP	-1	-0.870	-0.952	5.731	-0.103	-0.103	0.000	0.000	0.000	0.000
7	B	1432	LEU	0	-0.020	-0.011	7.041	0.632	0.632	0.000	0.000	0.000	0.000
8	B	1433	SER	0	-0.047	-0.020	7.958	0.575	0.575	0.000	0.000	0.000	0.000
9	B	1434	VAL	0	0.017	0.014	9.747	0.334	0.334	0.000	0.000	0.000	0.000
10	B	1435	LYS	1	0.942	0.976	11.926	0.998	0.998	0.000	0.000	0.000	0.000
11	B	1436	LYS	1	0.930	0.971	10.813	1.296	1.296	0.000	0.000	0.000	0.000
12	B	1437	GLN	0	0.020	0.017	13.837	0.088	0.088	0.000	0.000	0.000	0.000
13	B	1438	GLU	-1	-0.920	-0.961	15.734	-0.529	-0.529	0.000	0.000	0.000	0.000
14	B	1439	LEU	0	-0.051	-0.026	17.425	0.087	0.087	0.000	0.000	0.000	0.000
15	B	1440	ILE	0	0.023	0.013	16.298	0.073	0.073	0.000	0.000	0.000	0.000
16	B	1441	GLU	-1	-0.910	-0.957	19.274	-0.416	-0.416	0.000	0.000	0.000	0.000
17	B	1442	SER	0	-0.094	-0.048	21.842	0.059	0.059	0.000	0.000	0.000	0.000
18	B	1443	ILE	0	0.024	0.009	22.396	0.039	0.039	0.000	0.000	0.000	0.000
19	B	1444	SER	0	0.013	0.008	24.061	0.040	0.040	0.000	0.000	0.000	0.000
20	B	1445	ARG	1	0.969	0.975	25.919	0.288	0.288	0.000	0.000	0.000	0.000
21	B	1446	LYS	1	0.940	0.981	27.595	0.214	0.214	0.000	0.000	0.000	0.000
22	B	1447	LEU	0	0.008	-0.006	27.108	0.019	0.019	0.000	0.000	0.000	0.000
23	B	1448	GLN	0	-0.023	-0.007	30.152	0.024	0.024	0.000	0.000	0.000	0.000
24	B	1449	VAL	0	-0.003	0.005	32.145	0.011	0.011	0.000	0.000	0.000	0.000
25	B	1450	LEU	0	-0.049	-0.019	31.544	0.010	0.010	0.000	0.000	0.000	0.000
26	B	1451	ARG	1	0.925	0.965	30.180	0.197	0.197	0.000	0.000	0.000	0.000
27	B	1452	GLU	-1	-0.896	-0.940	35.988	-0.141	-0.141	0.000	0.000	0.000	0.000
28	B	1453	ALA	0	-0.032	-0.017	37.826	0.008	0.008	0.000	0.000	0.000	0.000
29	B	1454	ARG	1	0.963	0.980	36.220	0.145	0.145	0.000	0.000	0.000	0.000
30	B	1455	GLU	-1	-0.961	-0.993	38.688	-0.126	-0.126	0.000	0.000	0.000	0.000
31	B	1456	SER	0	-0.015	-0.018	42.182	0.006	0.006	0.000	0.000	0.000	0.000
32	B	1457	LEU	0	0.013	0.028	43.396	0.004	0.004	0.000	0.000	0.000	0.000
33	B	1458	LEU	0	-0.041	-0.030	43.900	0.005	0.005	0.000	0.000	0.000	0.000
34	B	1459	GLU	-1	-0.950	-0.957	47.005	-0.074	-0.074	0.000	0.000	0.000	0.000
35	B	1460	ASP	-1	-0.865	-0.941	47.493	-0.084	-0.084	0.000	0.000	0.000	0.000
36	B	1461	VAL	0	-0.036	-0.016	48.093	0.004	0.004	0.000	0.000	0.000	0.000
37	B	1462	GLN	0	0.011	0.054	50.947	0.003	0.003	0.000	0.000	0.000	0.000
38	B	1463	ALA	0	0.010	0.005	53.146	0.004	0.004	0.000	0.000	0.000	0.000
39	B	1464	ASN	0	0.014	-0.012	53.869	0.004	0.004	0.000	0.000	0.000	0.000
40	B	1465	THR	0	-0.087	-0.089	54.332	0.002	0.002	0.000	0.000	0.000	0.000
41	B	1466	VAL	0	-0.064	-0.033	56.889	0.003	0.003	0.000	0.000	0.000	0.000
42	B	1467	LEU	0	0.035	0.035	58.272	0.002	0.002	0.000	0.000	0.000	0.000
43	B	1468	GLY	0	0.036	0.001	59.307	0.002	0.002	0.000	0.000	0.000	0.000
44	B	1469	ALA	0	-0.036	-0.024	60.835	0.002	0.002	0.000	0.000	0.000	0.000
45	B	1470	GLU	-1	-0.939	-0.959	63.179	-0.047	-0.047	0.000	0.000	0.000	0.000
46	B	1471	VAL	0	0.023	0.002	63.175	0.002	0.002	0.000	0.000	0.000	0.000
47	B	1472	GLU	-1	-0.987	-0.988	64.328	-0.046	-0.046	0.000	0.000	0.000	0.000
48	B	1473	ALA	0	-0.065	-0.046	66.510	0.002	0.002	0.000	0.000	0.000	0.000
49	B	1474	ILE	0	0.034	0.019	67.996	0.002	0.002	0.000	0.000	0.000	0.000
50	B	1475	VAL	0	0.032	0.009	68.053	0.002	0.002	0.000	0.000	0.000	0.000
51	B	1476	LYS	1	0.887	0.949	69.010	0.043	0.043	0.000	0.000	0.000	0.000
52	B	1477	GLY	0	-0.062	-0.022	72.306	0.001	0.001	0.000	0.000	0.000	0.000
53	B	1478	VAL	0	-0.038	-0.010	73.536	0.001	0.001	0.000	0.000	0.000	0.000
54	B	1479	CYS	0	-0.023	0.000	73.427	0.001	0.001	0.000	0.000	0.000	0.000
55	B	1480	LYS	1	0.931	0.965	75.501	0.032	0.032	0.000	0.000	0.000	0.000
56	B	1481	PRO	0	0.043	0.005	75.148	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	1482	SER	0	-0.008	0.001	74.208	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	1483	GLU	-1	-0.863	-0.949	73.058	-0.036	-0.036	0.000	0.000	0.000	0.000
59	B	1484	PHE	0	0.029	0.028	69.048	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	1485	ASP	-1	-0.882	-0.949	69.552	-0.041	-0.041	0.000	0.000	0.000	0.000
61	B	1486	LYS	1	0.915	0.954	68.652	0.035	0.035	0.000	0.000	0.000	0.000
62	B	1487	PHE	0	0.058	0.036	64.565	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	1488	ARG	1	0.939	0.964	65.020	0.042	0.042	0.000	0.000	0.000	0.000
64	B	1489	MET	0	-0.065	-0.036	63.872	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	1490	PHE	0	-0.031	0.011	60.218	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	1491	ILE	0	0.016	0.008	59.819	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	1492	GLY	0	-0.044	-0.018	59.076	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	1493	ASP	-1	-0.855	-0.946	58.396	-0.053	-0.053	0.000	0.000	0.000	0.000
69	B	1494	LEU	0	0.009	0.012	55.219	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	1495	ASP	-1	-0.880	-0.954	53.522	-0.066	-0.066	0.000	0.000	0.000	0.000
71	B	1496	LYS	1	0.895	0.965	52.668	0.057	0.057	0.000	0.000	0.000	0.000
72	B	1497	VAL	0	0.014	0.009	52.827	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	1498	VAL	0	0.001	-0.001	49.262	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	1499	ASN	0	0.025	0.002	48.627	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	1500	LEU	0	-0.037	-0.018	47.985	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	1501	LEU	0	0.002	0.002	46.981	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	1502	LEU	0	-0.004	-0.007	44.430	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	1503	SER	0	-0.078	-0.027	43.701	-0.006	-0.006	0.000	0.000	0.000	0.000
79	B	1504	LEU	0	-0.083	-0.025	43.849	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	1505	SER	0	-0.040	-0.015	41.076	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	1538	ILE	0	0.021	-0.010	46.660	0.000	0.000	0.000	0.000	0.000	0.000
82	B	1539	GLN	0	0.042	0.021	48.671	0.000	0.000	0.000	0.000	0.000	0.000
83	B	1540	GLN	0	0.031	0.032	49.175	0.000	0.000	0.000	0.000	0.000	0.000
84	B	1541	HIS	0	0.034	0.012	46.526	0.003	0.003	0.000	0.000	0.000	0.000
85	B	1542	GLU	-1	-0.955	-0.997	49.533	-0.057	-0.057	0.000	0.000	0.000	0.000
86	B	1543	ASP	-1	-0.868	-0.930	52.339	-0.055	-0.055	0.000	0.000	0.000	0.000
87	B	1544	ALA	0	-0.030	-0.022	50.888	0.001	0.001	0.000	0.000	0.000	0.000
88	B	1545	LYS	1	0.896	0.953	49.797	0.063	0.063	0.000	0.000	0.000	0.000
89	B	1546	GLU	-1	-0.925	-0.949	53.326	-0.048	-0.048	0.000	0.000	0.000	0.000
90	B	1547	LEU	0	-0.037	-0.032	55.970	0.002	0.002	0.000	0.000	0.000	0.000
91	B	1548	LYS	1	0.864	0.933	52.379	0.066	0.066	0.000	0.000	0.000	0.000
92	B	1549	GLU	-1	-0.887	-0.939	55.774	-0.055	-0.055	0.000	0.000	0.000	0.000
93	B	1550	ASN	0	-0.048	-0.037	58.104	0.002	0.002	0.000	0.000	0.000	0.000
94	B	1551	LEU	0	-0.050	-0.012	56.400	0.002	0.002	0.000	0.000	0.000	0.000
95	B	1552	ASP	-1	-0.757	-0.874	56.803	-0.059	-0.059	0.000	0.000	0.000	0.000
96	B	1553	ARG	1	0.925	0.951	59.840	0.046	0.046	0.000	0.000	0.000	0.000
97	B	1554	ARG	1	0.845	0.921	62.589	0.050	0.050	0.000	0.000	0.000	0.000
98	B	1555	GLU	-1	-0.855	-0.932	60.081	-0.050	-0.050	0.000	0.000	0.000	0.000
99	B	1556	ARG	1	0.959	0.974	62.754	0.048	0.048	0.000	0.000	0.000	0.000
100	B	1557	ILE	0	-0.040	-0.008	65.228	0.002	0.002	0.000	0.000	0.000	0.000
101	B	1558	VAL	0	-0.038	-0.025	65.402	0.001	0.001	0.000	0.000	0.000	0.000
102	B	1559	PHE	0	0.011	0.003	65.043	0.001	0.001	0.000	0.000	0.000	0.000
103	B	1560	ASP	-1	-0.897	-0.955	67.072	-0.039	-0.039	0.000	0.000	0.000	0.000
104	B	1561	ILE	0	-0.158	-0.081	70.343	0.001	0.001	0.000	0.000	0.000	0.000
105	B	1562	LEU	0	-0.018	-0.008	66.922	0.001	0.001	0.000	0.000	0.000	0.000
106	B	1563	ALA	0	0.027	0.019	70.093	0.000	0.000	0.000	0.000	0.000	0.000
107	B	1564	ASN	0	-0.075	-0.023	71.409	0.000	0.000	0.000	0.000	0.000	0.000
108	B	1565	TYR	0	-0.090	-0.050	73.955	0.001	0.001	0.000	0.000	0.000	0.000
109	B	1566	LEU	0	-0.033	-0.013	68.800	0.000	0.000	0.000	0.000	0.000	0.000
110	B	1567	SER	0	0.000	0.003	71.737	0.000	0.000	0.000	0.000	0.000	0.000
111	B	1568	GLU	-1	-0.940	-0.985	67.588	-0.044	-0.044	0.000	0.000	0.000	0.000
112	B	1569	GLU	-1	-0.870	-0.935	66.239	-0.046	-0.046	0.000	0.000	0.000	0.000
113	B	1570	SER	0	0.006	0.002	66.155	-0.001	-0.001	0.000	0.000	0.000	0.000
114	B	1571	LEU	0	-0.026	0.004	66.232	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	1572	ALA	0	0.027	0.016	63.320	-0.002	-0.002	0.000	0.000	0.000	0.000
116	B	1573	ASP	-1	-0.876	-0.939	62.045	-0.052	-0.052	0.000	0.000	0.000	0.000
117	B	1574	TYR	0	-0.066	-0.041	61.558	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	1575	GLU	-1	-0.912	-0.970	60.899	-0.052	-0.052	0.000	0.000	0.000	0.000
119	B	1576	HIS	0	-0.042	-0.015	55.779	-0.005	-0.005	0.000	0.000	0.000	0.000
120	B	1577	PHE	0	0.016	0.028	56.826	-0.003	-0.003	0.000	0.000	0.000	0.000
121	B	1578	VAL	0	0.030	0.004	56.786	-0.003	-0.003	0.000	0.000	0.000	0.000
122	B	1579	LYS	1	0.946	0.976	52.603	0.066	0.066	0.000	0.000	0.000	0.000
123	B	1580	MET	0	0.003	-0.008	51.570	-0.004	-0.004	0.000	0.000	0.000	0.000
124	B	1581	LYS	1	0.939	0.992	51.883	0.060	0.060	0.000	0.000	0.000	0.000
125	B	1582	SER	0	-0.022	-0.019	51.744	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	1583	ALA	0	-0.044	-0.024	48.946	-0.003	-0.003	0.000	0.000	0.000	0.000
127	B	1584	LEU	0	0.061	0.038	47.290	-0.004	-0.004	0.000	0.000	0.000	0.000
128	B	1585	ILE	0	-0.016	0.001	46.390	-0.004	-0.004	0.000	0.000	0.000	0.000
129	B	1586	ILE	0	-0.026	-0.022	44.408	-0.004	-0.004	0.000	0.000	0.000	0.000
130	B	1587	GLU	-1	-0.896	-0.942	42.469	-0.109	-0.109	0.000	0.000	0.000	0.000
131	B	1588	GLN	0	0.007	-0.004	41.561	-0.006	-0.006	0.000	0.000	0.000	0.000
132	B	1589	ARG	1	0.944	0.976	40.917	0.105	0.105	0.000	0.000	0.000	0.000
133	B	1590	GLU	-1	-0.921	-0.967	38.955	-0.121	-0.121	0.000	0.000	0.000	0.000
134	B	1591	LEU	0	-0.058	-0.025	37.156	-0.012	-0.012	0.000	0.000	0.000	0.000
135	B	1592	GLU	-1	-0.985	-1.000	36.018	-0.127	-0.127	0.000	0.000	0.000	0.000
136	B	1593	ASP	-1	-0.890	-0.931	35.309	-0.142	-0.142	0.000	0.000	0.000	0.000
137	B	1594	LYS	1	0.875	0.928	32.598	0.137	0.137	0.000	0.000	0.000	0.000
138	B	1595	ILE	0	-0.043	-0.026	31.182	-0.016	-0.016	0.000	0.000	0.000	0.000
139	B	1596	HIS	0	0.015	0.026	30.705	-0.012	-0.012	0.000	0.000	0.000	0.000
140	B	1597	LEU	0	0.012	0.007	27.471	-0.015	-0.015	0.000	0.000	0.000	0.000
141	B	1598	GLY	0	0.015	-0.006	26.668	-0.020	-0.020	0.000	0.000	0.000	0.000
142	B	1599	GLU	-1	-0.942	-0.986	25.702	-0.218	-0.218	0.000	0.000	0.000	0.000
143	B	1600	GLU	-1	-0.882	-0.944	25.494	-0.245	-0.245	0.000	0.000	0.000	0.000
144	B	1601	GLN	0	-0.085	-0.046	22.724	-0.019	-0.019	0.000	0.000	0.000	0.000
145	B	1602	LEU	0	-0.019	-0.012	21.186	-0.045	-0.045	0.000	0.000	0.000	0.000
146	B	1603	LYS	1	0.940	0.983	20.802	0.230	0.230	0.000	0.000	0.000	0.000
147	B	1604	CYS	0	-0.046	-0.017	19.617	-0.023	-0.023	0.000	0.000	0.000	0.000
148	B	1605	LEU	0	-0.075	-0.045	16.534	-0.057	-0.057	0.000	0.000	0.000	0.000
149	B	1606	LEU	0	-0.056	-0.031	15.863	-0.075	-0.075	0.000	0.000	0.000	0.000
150	B	1607	ASP	-1	-0.982	-0.973	14.661	-0.446	-0.446	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1426:SER)