FMO DATABASE

FMODB ID: YYRJ2

Calculation Name: 3LRU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LRU

Chain ID: A

ChEMBL ID:

UniProt ID: Q6P2Q9

Base Structure: X-ray

Registration Date: 2023-03-14

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	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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1430679.785029
FMO2-HF: Nuclear repulsion	1367371.165032
FMO2-HF: Total energy	-63308.619997
FMO2-MP2: Total energy	-63496.627438

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:1831:LYS)

Summations of interaction energy for fragment #1(A:1831: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.
-68.631	-63.233	4.825	-4.925	-5.298	-0.033

Interaction energy analysis for fragmet #1(A:1831:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.996 / q_NPA : 0.997

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	1833	LEU	0	-0.005	0.000	2.626	-13.966	-10.315	0.703	-2.104	-2.250	-0.011
4	A	1834	GLY	0	0.024	0.016	5.107	2.186	2.186	0.000	0.000	0.000	0.000
5	A	1835	GLN	0	-0.027	-0.021	6.356	2.575	2.575	0.000	0.000	0.000	0.000
6	A	1836	LEU	0	0.001	-0.004	9.784	-0.720	-0.720	0.000	0.000	0.000	0.000
7	A	1837	ALA	0	0.044	0.011	11.577	1.238	1.238	0.000	0.000	0.000	0.000
8	A	1838	LYS	1	0.944	0.971	13.082	17.633	17.633	0.000	0.000	0.000	0.000
9	A	1839	TRP	0	-0.015	0.008	13.280	1.950	1.950	0.000	0.000	0.000	0.000
10	A	1840	LYS	1	0.778	0.891	14.456	18.907	18.907	0.000	0.000	0.000	0.000
11	A	1841	THR	0	0.049	-0.003	13.832	0.550	0.550	0.000	0.000	0.000	0.000
12	A	1842	ALA	0	0.057	0.019	16.282	0.837	0.837	0.000	0.000	0.000	0.000
13	A	1843	GLU	-1	-0.755	-0.841	18.300	-13.144	-13.144	0.000	0.000	0.000	0.000
14	A	1844	GLU	-1	-0.800	-0.853	15.262	-19.751	-19.751	0.000	0.000	0.000	0.000
15	A	1845	VAL	0	0.005	0.002	19.461	0.666	0.666	0.000	0.000	0.000	0.000
16	A	1846	ALA	0	0.020	0.014	22.269	0.698	0.698	0.000	0.000	0.000	0.000
17	A	1847	ALA	0	-0.033	-0.021	22.069	0.621	0.621	0.000	0.000	0.000	0.000
18	A	1848	LEU	0	-0.005	0.004	23.428	0.449	0.449	0.000	0.000	0.000	0.000
19	A	1849	ILE	0	0.034	0.017	25.222	0.533	0.533	0.000	0.000	0.000	0.000
20	A	1850	ARG	1	0.786	0.847	23.419	13.077	13.077	0.000	0.000	0.000	0.000
21	A	1851	SER	0	-0.089	-0.045	27.783	0.305	0.305	0.000	0.000	0.000	0.000
22	A	1852	LEU	0	-0.014	0.009	29.653	0.285	0.285	0.000	0.000	0.000	0.000
23	A	1853	PRO	0	0.035	0.010	32.095	0.119	0.119	0.000	0.000	0.000	0.000
24	A	1854	VAL	0	0.034	0.008	35.530	-0.073	-0.073	0.000	0.000	0.000	0.000
25	A	1855	GLU	-1	-0.848	-0.910	36.773	-7.833	-7.833	0.000	0.000	0.000	0.000
26	A	1856	GLU	-1	-0.838	-0.922	34.441	-8.610	-8.610	0.000	0.000	0.000	0.000
27	A	1857	GLN	0	-0.072	-0.024	32.124	-0.251	-0.251	0.000	0.000	0.000	0.000
28	A	1858	PRO	0	-0.027	-0.013	32.863	-0.237	-0.237	0.000	0.000	0.000	0.000
29	A	1859	LYS	1	0.761	0.862	35.244	8.262	8.262	0.000	0.000	0.000	0.000
30	A	1860	GLN	0	-0.082	-0.033	29.753	-0.372	-0.372	0.000	0.000	0.000	0.000
31	A	1861	ILE	0	0.002	0.003	30.482	0.073	0.073	0.000	0.000	0.000	0.000
32	A	1862	ILE	0	-0.004	-0.007	23.356	-0.407	-0.407	0.000	0.000	0.000	0.000
33	A	1863	VAL	0	-0.005	-0.008	26.181	0.361	0.361	0.000	0.000	0.000	0.000
34	A	1864	THR	0	0.009	0.011	22.503	-0.465	-0.465	0.000	0.000	0.000	0.000
35	A	1865	ARG	1	0.893	0.948	22.048	13.526	13.526	0.000	0.000	0.000	0.000
36	A	1866	LYS	1	0.972	0.979	22.736	10.463	10.463	0.000	0.000	0.000	0.000
37	A	1867	GLY	0	0.018	0.002	20.807	-0.078	-0.078	0.000	0.000	0.000	0.000
38	A	1868	MET	0	-0.016	0.005	17.564	0.381	0.381	0.000	0.000	0.000	0.000
39	A	1869	LEU	0	-0.002	0.011	14.475	-0.239	-0.239	0.000	0.000	0.000	0.000
40	A	1870	ASP	-1	-0.811	-0.875	10.982	-23.446	-23.446	0.000	0.000	0.000	0.000
41	A	1871	PRO	0	0.037	-0.016	7.662	-0.337	-0.337	0.000	0.000	0.000	0.000
42	A	1872	LEU	0	-0.015	0.001	10.040	1.378	1.378	0.000	0.000	0.000	0.000
43	A	1873	GLU	-1	-0.844	-0.891	10.137	-18.440	-18.440	0.000	0.000	0.000	0.000
44	A	1874	VAL	0	0.017	-0.003	12.177	1.146	1.146	0.000	0.000	0.000	0.000
45	A	1875	HIS	0	-0.003	0.014	13.307	-0.593	-0.593	0.000	0.000	0.000	0.000
46	A	1876	LEU	0	0.041	0.010	15.971	0.493	0.493	0.000	0.000	0.000	0.000
47	A	1877	LEU	0	0.034	0.014	17.380	0.605	0.605	0.000	0.000	0.000	0.000
48	A	1878	ASP	-1	-0.828	-0.909	20.678	-11.295	-11.295	0.000	0.000	0.000	0.000
49	A	1879	PHE	0	0.009	0.024	22.417	0.279	0.279	0.000	0.000	0.000	0.000
50	A	1880	PRO	0	0.001	-0.008	24.275	0.314	0.314	0.000	0.000	0.000	0.000
51	A	1881	ASN	0	-0.084	-0.052	23.819	-0.089	-0.089	0.000	0.000	0.000	0.000
52	A	1882	ILE	0	0.005	0.005	18.044	-0.373	-0.373	0.000	0.000	0.000	0.000
53	A	1883	VAL	0	-0.014	0.004	18.607	0.178	0.178	0.000	0.000	0.000	0.000
54	A	1884	ILE	0	0.001	-0.011	15.754	-0.781	-0.781	0.000	0.000	0.000	0.000
55	A	1885	LYS	1	0.794	0.874	15.773	16.335	16.335	0.000	0.000	0.000	0.000
56	A	1886	GLY	0	0.017	0.003	14.838	-0.889	-0.889	0.000	0.000	0.000	0.000
57	A	1887	SER	0	-0.025	-0.025	12.766	0.784	0.784	0.000	0.000	0.000	0.000
58	A	1888	GLU	-1	-0.798	-0.906	14.775	-13.518	-13.518	0.000	0.000	0.000	0.000
59	A	1889	LEU	0	-0.022	-0.021	16.649	-0.946	-0.946	0.000	0.000	0.000	0.000
60	A	1890	GLN	0	-0.067	-0.063	18.036	0.002	0.002	0.000	0.000	0.000	0.000
61	A	1891	LEU	0	-0.032	0.009	14.048	0.181	0.181	0.000	0.000	0.000	0.000
62	A	1892	PRO	0	0.017	-0.008	13.667	-0.602	-0.602	0.000	0.000	0.000	0.000
63	A	1893	PHE	0	-0.027	-0.024	9.843	-1.266	-1.266	0.000	0.000	0.000	0.000
64	A	1894	GLN	0	0.035	0.052	10.597	-2.953	-2.953	0.000	0.000	0.000	0.000
65	A	1895	ALA	0	-0.022	-0.010	11.381	1.803	1.803	0.000	0.000	0.000	0.000
66	A	1896	CYS	0	-0.090	-0.048	13.148	-0.176	-0.176	0.000	0.000	0.000	0.000
67	A	1897	LEU	0	0.017	0.026	15.969	1.028	1.028	0.000	0.000	0.000	0.000
68	A	1898	LYS	1	0.802	0.881	18.578	12.886	12.886	0.000	0.000	0.000	0.000
69	A	1899	VAL	0	0.028	0.017	21.081	0.471	0.471	0.000	0.000	0.000	0.000
70	A	1900	GLU	-1	-0.846	-0.915	24.092	-13.273	-13.273	0.000	0.000	0.000	0.000
71	A	1901	LYS	1	0.944	0.965	26.838	10.375	10.375	0.000	0.000	0.000	0.000
72	A	1902	PHE	0	0.040	0.025	30.642	-0.081	-0.081	0.000	0.000	0.000	0.000
73	A	1903	GLY	0	0.022	0.004	32.964	0.216	0.216	0.000	0.000	0.000	0.000
74	A	1904	ASP	-1	-0.914	-0.947	33.611	-8.893	-8.893	0.000	0.000	0.000	0.000
75	A	1905	LEU	0	0.003	-0.001	28.289	-0.295	-0.295	0.000	0.000	0.000	0.000
76	A	1906	ILE	0	0.033	0.021	27.705	0.039	0.039	0.000	0.000	0.000	0.000
77	A	1907	LEU	0	-0.045	-0.024	25.399	-0.632	-0.632	0.000	0.000	0.000	0.000
78	A	1908	LYS	1	0.892	0.949	24.155	12.764	12.764	0.000	0.000	0.000	0.000
79	A	1909	ALA	0	0.043	0.024	24.757	-0.448	-0.448	0.000	0.000	0.000	0.000
80	A	1910	THR	0	-0.059	-0.049	20.452	-0.067	-0.067	0.000	0.000	0.000	0.000
81	A	1911	GLU	-1	-0.875	-0.925	20.380	-12.495	-12.495	0.000	0.000	0.000	0.000
82	A	1912	PRO	0	-0.016	-0.013	20.370	-0.527	-0.527	0.000	0.000	0.000	0.000
83	A	1913	GLN	0	-0.041	-0.028	14.187	-0.543	-0.543	0.000	0.000	0.000	0.000
84	A	1914	MET	0	0.003	0.004	15.112	1.048	1.048	0.000	0.000	0.000	0.000
85	A	1915	VAL	0	-0.018	-0.005	10.124	-1.255	-1.255	0.000	0.000	0.000	0.000
86	A	1916	LEU	0	0.019	0.015	10.358	1.087	1.087	0.000	0.000	0.000	0.000
87	A	1917	PHE	0	0.075	0.029	9.079	-2.540	-2.540	0.000	0.000	0.000	0.000
88	A	1918	ASN	0	-0.021	-0.026	9.758	1.963	1.963	0.000	0.000	0.000	0.000
89	A	1919	LEU	0	0.063	0.039	11.414	-0.189	-0.189	0.000	0.000	0.000	0.000
90	A	1920	TYR	0	0.003	0.004	13.097	0.705	0.705	0.000	0.000	0.000	0.000
91	A	1921	ASP	-1	-0.748	-0.877	8.578	-19.660	-19.660	0.000	0.000	0.000	0.000
92	A	1922	ASP	-1	-0.813	-0.896	6.477	-24.359	-24.359	0.000	0.000	0.000	0.000
93	A	1923	TRP	0	0.068	0.024	8.628	0.660	0.660	0.000	0.000	0.000	0.000
94	A	1924	LEU	0	-0.024	-0.011	12.096	0.649	0.649	0.000	0.000	0.000	0.000
95	A	1925	LYS	1	0.809	0.901	5.783	26.044	26.044	0.000	0.000	0.000	0.000
96	A	1926	THR	0	-0.035	-0.008	12.466	0.151	0.151	0.000	0.000	0.000	0.000
97	A	1927	ILE	0	0.000	0.014	15.597	0.908	0.908	0.000	0.000	0.000	0.000
98	A	1928	SER	0	0.042	0.023	16.847	-0.361	-0.361	0.000	0.000	0.000	0.000
99	A	1929	SER	0	0.069	0.010	17.794	0.049	0.049	0.000	0.000	0.000	0.000
100	A	1930	TYR	0	0.005	0.017	19.140	0.033	0.033	0.000	0.000	0.000	0.000
101	A	1931	THR	0	0.022	0.009	19.921	0.368	0.368	0.000	0.000	0.000	0.000
102	A	1932	ALA	0	0.015	0.010	16.186	0.015	0.015	0.000	0.000	0.000	0.000
103	A	1933	PHE	0	0.018	0.002	18.099	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	1934	SER	0	-0.017	-0.021	20.635	0.308	0.308	0.000	0.000	0.000	0.000
105	A	1935	ARG	1	0.824	0.925	16.333	13.708	13.708	0.000	0.000	0.000	0.000
106	A	1936	LEU	0	0.017	0.006	17.246	0.041	0.041	0.000	0.000	0.000	0.000
107	A	1937	ILE	0	-0.011	-0.008	19.526	0.204	0.204	0.000	0.000	0.000	0.000
108	A	1938	LEU	0	-0.047	-0.007	22.965	0.335	0.335	0.000	0.000	0.000	0.000
109	A	1939	ILE	0	0.012	0.012	17.755	0.237	0.237	0.000	0.000	0.000	0.000
110	A	1940	LEU	0	-0.011	-0.007	19.887	0.148	0.148	0.000	0.000	0.000	0.000
111	A	1941	ARG	1	0.963	0.986	23.134	9.019	9.019	0.000	0.000	0.000	0.000
112	A	1942	ALA	0	0.014	0.001	24.704	0.304	0.304	0.000	0.000	0.000	0.000
113	A	1943	LEU	0	-0.042	-0.024	20.512	0.158	0.158	0.000	0.000	0.000	0.000
114	A	1944	HIS	0	-0.023	-0.003	25.193	-0.053	-0.053	0.000	0.000	0.000	0.000
115	A	1945	VAL	0	-0.051	-0.015	28.069	0.193	0.193	0.000	0.000	0.000	0.000
116	A	1946	ASN	0	-0.025	-0.031	29.171	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	1947	ASN	0	0.012	0.005	24.709	-0.276	-0.276	0.000	0.000	0.000	0.000
118	A	1948	ASP	-1	-0.816	-0.924	25.918	-10.405	-10.405	0.000	0.000	0.000	0.000
119	A	1949	ARG	1	0.893	0.947	26.819	9.640	9.640	0.000	0.000	0.000	0.000
120	A	1950	ALA	0	0.054	0.020	24.196	-0.203	-0.203	0.000	0.000	0.000	0.000
121	A	1951	LYS	1	0.816	0.905	22.141	10.538	10.538	0.000	0.000	0.000	0.000
122	A	1952	VAL	0	-0.030	-0.015	22.019	-0.431	-0.431	0.000	0.000	0.000	0.000
123	A	1953	ILE	0	-0.089	-0.027	23.189	-0.093	-0.093	0.000	0.000	0.000	0.000
124	A	1954	LEU	0	-0.011	0.000	18.299	-0.279	-0.279	0.000	0.000	0.000	0.000
125	A	1955	LYS	1	0.860	0.917	16.297	14.782	14.782	0.000	0.000	0.000	0.000
126	A	1956	PRO	0	0.017	0.017	19.469	0.461	0.461	0.000	0.000	0.000	0.000
127	A	1957	ASP	-1	-0.766	-0.864	20.516	-13.139	-13.139	0.000	0.000	0.000	0.000
128	A	1958	LYS	1	0.912	0.960	20.181	11.141	11.141	0.000	0.000	0.000	0.000
129	A	1959	THR	0	-0.078	-0.053	16.882	-0.566	-0.566	0.000	0.000	0.000	0.000
130	A	1960	THR	0	-0.021	-0.007	15.716	-0.916	-0.916	0.000	0.000	0.000	0.000
131	A	1961	ILE	0	-0.004	0.003	9.719	0.476	0.476	0.000	0.000	0.000	0.000
132	A	1962	THR	0	0.025	-0.005	10.200	1.090	1.090	0.000	0.000	0.000	0.000
133	A	1963	GLU	-1	-0.856	-0.890	4.930	-29.577	-29.577	0.000	0.000	0.000	0.000
134	A	1964	PRO	0	0.012	-0.005	4.951	1.186	1.186	0.000	0.000	0.000	0.000
135	A	1965	HIS	0	-0.077	-0.049	2.433	-7.622	-5.875	4.122	-2.821	-3.048	-0.022
136	A	1966	HIS	0	-0.066	-0.019	5.543	-0.661	-0.661	0.000	0.000	0.000	0.000
137	A	1967	ILE	0	-0.041	-0.034	8.330	0.224	0.224	0.000	0.000	0.000	0.000
138	A	1968	TRP	0	-0.050	-0.024	11.800	1.418	1.418	0.000	0.000	0.000	0.000
139	A	1969	PRO	0	-0.030	0.008	12.072	-1.092	-1.092	0.000	0.000	0.000	0.000
140	A	1970	THR	0	-0.063	-0.075	9.383	0.520	0.520	0.000	0.000	0.000	0.000
141	A	1971	LEU	0	-0.029	-0.005	11.943	0.443	0.443	0.000	0.000	0.000	0.000
142	A	1972	THR	0	-0.031	-0.057	14.346	-0.163	-0.163	0.000	0.000	0.000	0.000
143	A	1973	ASP	-1	-0.837	-0.954	16.526	-14.242	-14.242	0.000	0.000	0.000	0.000
144	A	1974	GLU	-1	-0.919	-0.948	18.573	-11.081	-11.081	0.000	0.000	0.000	0.000
145	A	1975	GLU	-1	-0.845	-0.888	18.022	-14.525	-14.525	0.000	0.000	0.000	0.000
146	A	1976	TRP	0	0.021	0.005	14.059	0.847	0.847	0.000	0.000	0.000	0.000
147	A	1977	ILE	0	0.005	0.012	19.576	0.451	0.451	0.000	0.000	0.000	0.000
148	A	1978	LYS	1	0.907	0.952	23.122	10.909	10.909	0.000	0.000	0.000	0.000
149	A	1979	VAL	0	-0.001	-0.003	19.856	0.394	0.394	0.000	0.000	0.000	0.000
150	A	1980	GLU	-1	-0.802	-0.904	21.411	-11.167	-11.167	0.000	0.000	0.000	0.000
151	A	1981	VAL	0	-0.039	-0.015	23.865	0.336	0.336	0.000	0.000	0.000	0.000
152	A	1982	GLN	0	0.073	0.033	25.910	0.212	0.212	0.000	0.000	0.000	0.000
153	A	1983	LEU	0	-0.015	-0.010	21.731	0.200	0.200	0.000	0.000	0.000	0.000
154	A	1984	LYS	1	0.832	0.913	25.245	10.423	10.423	0.000	0.000	0.000	0.000
155	A	1985	ASP	-1	-0.877	-0.943	29.096	-8.638	-8.638	0.000	0.000	0.000	0.000
156	A	1986	LEU	0	-0.076	-0.025	27.329	0.215	0.215	0.000	0.000	0.000	0.000
157	A	1987	ILE	0	-0.048	-0.035	27.423	0.211	0.211	0.000	0.000	0.000	0.000
158	A	1988	LEU	0	-0.058	-0.024	31.580	0.230	0.230	0.000	0.000	0.000	0.000
159	A	1989	ALA	0	-0.051	-0.018	34.152	0.228	0.228	0.000	0.000	0.000	0.000
160	A	1990	ASP	-1	-0.939	-0.947	33.938	-7.891	-7.891	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1831:LYS)