FMO DATABASE

FMODB ID: 5354Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1425777.686019
FMO2-HF: Nuclear repulsion	1362469.533095
FMO2-HF: Total energy	-63308.152924
FMO2-MP2: Total energy	-63496.209097

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.
-62.96	-57.167	1.541	-3.445	-3.888	-0.024

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 : 0.993 / q_NPA : 1.002

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	-0.021	-0.010	2.584	-12.305	-8.734	0.826	-2.055	-2.342	-0.009
4	A	1834	GLY	0	0.035	0.022	4.790	3.122	3.238	-0.001	-0.005	-0.110	0.000
5	A	1835	GLN	0	0.013	0.010	6.097	3.233	3.233	0.000	0.000	0.000	0.000
6	A	1836	LEU	0	0.001	-0.012	9.752	-0.872	-0.872	0.000	0.000	0.000	0.000
7	A	1837	ALA	0	0.051	0.018	11.850	0.457	0.457	0.000	0.000	0.000	0.000
8	A	1838	LYS	1	0.921	0.956	13.563	17.478	17.478	0.000	0.000	0.000	0.000
9	A	1839	TRP	0	-0.046	-0.002	13.415	1.829	1.829	0.000	0.000	0.000	0.000
10	A	1840	LYS	1	0.816	0.912	14.287	18.794	18.794	0.000	0.000	0.000	0.000
11	A	1841	THR	0	0.045	-0.014	13.280	0.495	0.495	0.000	0.000	0.000	0.000
12	A	1842	ALA	0	0.058	0.017	15.935	0.841	0.841	0.000	0.000	0.000	0.000
13	A	1843	GLU	-1	-0.777	-0.864	17.856	-13.300	-13.300	0.000	0.000	0.000	0.000
14	A	1844	GLU	-1	-0.783	-0.849	15.158	-19.751	-19.751	0.000	0.000	0.000	0.000
15	A	1845	VAL	0	-0.004	-0.005	19.287	0.677	0.677	0.000	0.000	0.000	0.000
16	A	1846	ALA	0	0.023	0.012	21.905	0.738	0.738	0.000	0.000	0.000	0.000
17	A	1847	ALA	0	-0.027	-0.020	21.989	0.653	0.653	0.000	0.000	0.000	0.000
18	A	1848	LEU	0	-0.008	0.004	23.293	0.446	0.446	0.000	0.000	0.000	0.000
19	A	1849	ILE	0	0.034	0.018	25.073	0.550	0.550	0.000	0.000	0.000	0.000
20	A	1850	ARG	1	0.793	0.863	23.240	13.154	13.154	0.000	0.000	0.000	0.000
21	A	1851	SER	0	-0.087	-0.034	27.723	0.268	0.268	0.000	0.000	0.000	0.000
22	A	1852	LEU	0	-0.020	0.004	29.632	0.267	0.267	0.000	0.000	0.000	0.000
23	A	1853	PRO	0	0.041	0.013	32.133	0.105	0.105	0.000	0.000	0.000	0.000
24	A	1854	VAL	0	0.041	0.010	35.516	-0.067	-0.067	0.000	0.000	0.000	0.000
25	A	1855	GLU	-1	-0.861	-0.918	36.549	-7.864	-7.864	0.000	0.000	0.000	0.000
26	A	1856	GLU	-1	-0.822	-0.914	34.481	-8.596	-8.596	0.000	0.000	0.000	0.000
27	A	1857	GLN	0	-0.071	-0.029	32.042	-0.275	-0.275	0.000	0.000	0.000	0.000
28	A	1858	PRO	0	-0.023	-0.010	32.453	-0.249	-0.249	0.000	0.000	0.000	0.000
29	A	1859	LYS	1	0.746	0.858	34.855	8.294	8.294	0.000	0.000	0.000	0.000
30	A	1860	GLN	0	-0.091	-0.034	29.295	-0.334	-0.334	0.000	0.000	0.000	0.000
31	A	1861	ILE	0	0.014	0.009	30.402	0.023	0.023	0.000	0.000	0.000	0.000
32	A	1862	ILE	0	0.000	-0.001	22.933	-0.338	-0.338	0.000	0.000	0.000	0.000
33	A	1863	VAL	0	-0.013	-0.002	26.466	0.306	0.306	0.000	0.000	0.000	0.000
34	A	1864	THR	0	0.021	0.006	22.896	-0.580	-0.580	0.000	0.000	0.000	0.000
35	A	1865	ARG	1	0.917	0.957	21.825	13.540	13.540	0.000	0.000	0.000	0.000
36	A	1866	LYS	1	0.997	0.993	22.603	10.338	10.338	0.000	0.000	0.000	0.000
37	A	1867	GLY	0	0.007	0.001	21.370	-0.148	-0.148	0.000	0.000	0.000	0.000
38	A	1868	MET	0	-0.033	-0.010	17.507	0.193	0.193	0.000	0.000	0.000	0.000
39	A	1869	LEU	0	0.018	0.020	14.545	-0.210	-0.210	0.000	0.000	0.000	0.000
40	A	1870	ASP	-1	-0.845	-0.891	10.866	-22.823	-22.823	0.000	0.000	0.000	0.000
41	A	1871	PRO	0	0.035	-0.022	7.657	-0.378	-0.378	0.000	0.000	0.000	0.000
42	A	1872	LEU	0	-0.020	-0.001	9.896	1.248	1.248	0.000	0.000	0.000	0.000
43	A	1873	GLU	-1	-0.810	-0.877	10.327	-18.356	-18.356	0.000	0.000	0.000	0.000
44	A	1874	VAL	0	0.001	-0.006	12.141	1.242	1.242	0.000	0.000	0.000	0.000
45	A	1875	HIS	0	0.014	0.026	13.554	-0.434	-0.434	0.000	0.000	0.000	0.000
46	A	1876	LEU	0	0.048	0.009	16.142	0.477	0.477	0.000	0.000	0.000	0.000
47	A	1877	LEU	0	0.035	0.009	17.769	0.626	0.626	0.000	0.000	0.000	0.000
48	A	1878	ASP	-1	-0.836	-0.906	20.884	-11.388	-11.388	0.000	0.000	0.000	0.000
49	A	1879	PHE	0	0.015	0.031	22.961	0.302	0.302	0.000	0.000	0.000	0.000
50	A	1880	PRO	0	-0.010	-0.013	24.522	0.279	0.279	0.000	0.000	0.000	0.000
51	A	1881	ASN	0	-0.067	-0.046	24.011	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	1882	ILE	0	-0.001	0.000	18.317	-0.355	-0.355	0.000	0.000	0.000	0.000
53	A	1883	VAL	0	-0.034	-0.007	18.994	0.270	0.270	0.000	0.000	0.000	0.000
54	A	1884	ILE	0	0.009	-0.006	15.597	-0.746	-0.746	0.000	0.000	0.000	0.000
55	A	1885	LYS	1	0.799	0.879	15.832	16.343	16.343	0.000	0.000	0.000	0.000
56	A	1886	GLY	0	0.012	0.000	14.909	-0.992	-0.992	0.000	0.000	0.000	0.000
57	A	1887	SER	0	-0.026	-0.028	12.680	0.575	0.575	0.000	0.000	0.000	0.000
58	A	1888	GLU	-1	-0.808	-0.921	14.700	-13.429	-13.429	0.000	0.000	0.000	0.000
59	A	1889	LEU	0	-0.025	-0.023	16.321	-0.992	-0.992	0.000	0.000	0.000	0.000
60	A	1890	GLN	0	-0.058	-0.052	17.618	-0.168	-0.168	0.000	0.000	0.000	0.000
61	A	1891	LEU	0	-0.039	0.010	13.877	0.125	0.125	0.000	0.000	0.000	0.000
62	A	1892	PRO	0	0.038	0.004	13.603	-0.676	-0.676	0.000	0.000	0.000	0.000
63	A	1893	PHE	0	-0.053	-0.033	9.936	-1.225	-1.225	0.000	0.000	0.000	0.000
64	A	1894	GLN	0	0.048	0.062	10.277	-3.204	-3.204	0.000	0.000	0.000	0.000
65	A	1895	ALA	0	-0.033	-0.023	11.061	1.640	1.640	0.000	0.000	0.000	0.000
66	A	1896	CYS	0	-0.074	-0.038	12.843	-0.081	-0.081	0.000	0.000	0.000	0.000
67	A	1897	LEU	0	0.019	0.020	15.820	1.090	1.090	0.000	0.000	0.000	0.000
68	A	1898	LYS	1	0.799	0.893	18.498	12.988	12.988	0.000	0.000	0.000	0.000
69	A	1899	VAL	0	0.042	0.021	20.802	0.462	0.462	0.000	0.000	0.000	0.000
70	A	1900	GLU	-1	-0.845	-0.916	24.010	-13.070	-13.070	0.000	0.000	0.000	0.000
71	A	1901	LYS	1	0.941	0.964	26.838	10.477	10.477	0.000	0.000	0.000	0.000
72	A	1902	PHE	0	0.048	0.026	30.522	-0.080	-0.080	0.000	0.000	0.000	0.000
73	A	1903	GLY	0	0.009	-0.003	32.930	0.150	0.150	0.000	0.000	0.000	0.000
74	A	1904	ASP	-1	-0.913	-0.933	34.073	-8.710	-8.710	0.000	0.000	0.000	0.000
75	A	1905	LEU	0	-0.014	-0.020	28.091	-0.307	-0.307	0.000	0.000	0.000	0.000
76	A	1906	ILE	0	0.010	0.013	27.905	0.141	0.141	0.000	0.000	0.000	0.000
77	A	1907	LEU	0	-0.049	-0.029	24.990	-0.632	-0.632	0.000	0.000	0.000	0.000
78	A	1908	LYS	1	0.946	0.973	24.152	12.701	12.701	0.000	0.000	0.000	0.000
79	A	1909	ALA	0	0.008	0.004	24.169	-0.478	-0.478	0.000	0.000	0.000	0.000
80	A	1910	THR	0	-0.052	-0.042	20.292	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	1911	GLU	-1	-0.898	-0.938	20.201	-12.451	-12.451	0.000	0.000	0.000	0.000
82	A	1912	PRO	0	-0.021	-0.011	20.264	-0.505	-0.505	0.000	0.000	0.000	0.000
83	A	1913	GLN	0	-0.027	-0.027	14.179	-0.604	-0.604	0.000	0.000	0.000	0.000
84	A	1914	MET	0	-0.008	0.004	15.244	0.993	0.993	0.000	0.000	0.000	0.000
85	A	1915	VAL	0	-0.005	0.003	10.213	-1.217	-1.217	0.000	0.000	0.000	0.000
86	A	1916	LEU	0	0.022	0.015	10.647	1.134	1.134	0.000	0.000	0.000	0.000
87	A	1917	PHE	0	0.057	0.020	9.317	-2.334	-2.334	0.000	0.000	0.000	0.000
88	A	1918	ASN	0	-0.006	-0.020	9.841	1.735	1.735	0.000	0.000	0.000	0.000
89	A	1919	LEU	0	0.051	0.033	11.525	-0.268	-0.268	0.000	0.000	0.000	0.000
90	A	1920	TYR	0	0.018	0.009	13.163	0.704	0.704	0.000	0.000	0.000	0.000
91	A	1921	ASP	-1	-0.720	-0.842	9.148	-19.743	-19.743	0.000	0.000	0.000	0.000
92	A	1922	ASP	-1	-0.819	-0.912	6.821	-23.660	-23.660	0.000	0.000	0.000	0.000
93	A	1923	TRP	0	0.050	0.014	8.947	0.826	0.826	0.000	0.000	0.000	0.000
94	A	1924	LEU	0	-0.028	-0.018	12.378	0.520	0.520	0.000	0.000	0.000	0.000
95	A	1925	LYS	1	0.804	0.904	5.871	25.713	25.713	0.000	0.000	0.000	0.000
96	A	1926	THR	0	-0.001	0.001	12.561	0.230	0.230	0.000	0.000	0.000	0.000
97	A	1927	ILE	0	0.001	0.022	15.629	0.893	0.893	0.000	0.000	0.000	0.000
98	A	1928	SER	0	0.035	0.018	17.012	-0.319	-0.319	0.000	0.000	0.000	0.000
99	A	1929	SER	0	0.073	0.012	18.127	-0.075	-0.075	0.000	0.000	0.000	0.000
100	A	1930	TYR	0	0.004	0.018	19.539	0.037	0.037	0.000	0.000	0.000	0.000
101	A	1931	THR	0	0.012	-0.010	20.295	0.330	0.330	0.000	0.000	0.000	0.000
102	A	1932	ALA	0	0.028	0.016	16.678	0.012	0.012	0.000	0.000	0.000	0.000
103	A	1933	PHE	0	0.009	0.004	18.558	0.002	0.002	0.000	0.000	0.000	0.000
104	A	1934	SER	0	-0.021	-0.020	20.998	0.285	0.285	0.000	0.000	0.000	0.000
105	A	1935	ARG	1	0.860	0.944	16.572	13.746	13.746	0.000	0.000	0.000	0.000
106	A	1936	LEU	0	0.001	-0.002	17.519	0.058	0.058	0.000	0.000	0.000	0.000
107	A	1937	ILE	0	-0.003	-0.006	19.969	0.174	0.174	0.000	0.000	0.000	0.000
108	A	1938	LEU	0	-0.046	-0.006	23.516	0.371	0.371	0.000	0.000	0.000	0.000
109	A	1939	ILE	0	0.005	0.001	18.366	0.225	0.225	0.000	0.000	0.000	0.000
110	A	1940	LEU	0	-0.008	-0.009	20.461	0.159	0.159	0.000	0.000	0.000	0.000
111	A	1941	ARG	1	0.962	0.989	23.691	8.996	8.996	0.000	0.000	0.000	0.000
112	A	1942	ALA	0	0.017	0.003	25.284	0.290	0.290	0.000	0.000	0.000	0.000
113	A	1943	LEU	0	-0.030	-0.015	21.157	0.149	0.149	0.000	0.000	0.000	0.000
114	A	1944	HIS	0	-0.034	-0.013	25.851	-0.022	-0.022	0.000	0.000	0.000	0.000
115	A	1945	VAL	0	-0.041	-0.012	28.687	0.187	0.187	0.000	0.000	0.000	0.000
116	A	1946	ASN	0	0.025	0.004	29.569	0.027	0.027	0.000	0.000	0.000	0.000
117	A	1947	ASN	0	0.031	0.017	24.860	-0.323	-0.323	0.000	0.000	0.000	0.000
118	A	1948	ASP	-1	-0.860	-0.930	26.312	-10.069	-10.069	0.000	0.000	0.000	0.000
119	A	1949	ARG	1	0.892	0.946	27.178	9.658	9.658	0.000	0.000	0.000	0.000
120	A	1950	ALA	0	0.039	0.007	24.605	-0.246	-0.246	0.000	0.000	0.000	0.000
121	A	1951	LYS	1	0.878	0.922	22.292	10.763	10.763	0.000	0.000	0.000	0.000
122	A	1952	VAL	0	-0.047	-0.021	22.303	-0.418	-0.418	0.000	0.000	0.000	0.000
123	A	1953	ILE	0	-0.090	-0.033	23.667	-0.182	-0.182	0.000	0.000	0.000	0.000
124	A	1954	LEU	0	0.004	0.006	18.803	-0.272	-0.272	0.000	0.000	0.000	0.000
125	A	1955	LYS	1	0.862	0.926	16.659	14.882	14.882	0.000	0.000	0.000	0.000
126	A	1956	PRO	0	0.013	0.013	19.648	0.489	0.489	0.000	0.000	0.000	0.000
127	A	1957	ASP	-1	-0.770	-0.863	20.358	-13.431	-13.431	0.000	0.000	0.000	0.000
128	A	1958	LYS	1	0.906	0.946	20.531	11.336	11.336	0.000	0.000	0.000	0.000
129	A	1959	THR	0	-0.094	-0.066	16.985	-0.572	-0.572	0.000	0.000	0.000	0.000
130	A	1960	THR	0	0.010	0.026	16.307	-0.750	-0.750	0.000	0.000	0.000	0.000
131	A	1961	ILE	0	-0.015	-0.013	10.396	0.454	0.454	0.000	0.000	0.000	0.000
132	A	1962	THR	0	0.024	0.020	10.819	0.647	0.647	0.000	0.000	0.000	0.000
133	A	1963	GLU	-1	-0.869	-0.910	5.584	-29.582	-29.582	0.000	0.000	0.000	0.000
134	A	1964	PRO	0	0.012	0.002	5.205	1.222	1.222	0.000	0.000	0.000	0.000
135	A	1965	HIS	0	-0.092	-0.051	3.019	-4.543	-2.437	0.716	-1.385	-1.436	-0.015
136	A	1966	HIS	0	-0.047	-0.024	6.019	-0.431	-0.431	0.000	0.000	0.000	0.000
137	A	1967	ILE	0	-0.046	-0.036	8.858	0.431	0.431	0.000	0.000	0.000	0.000
138	A	1968	TRP	0	-0.082	-0.044	12.149	1.375	1.375	0.000	0.000	0.000	0.000
139	A	1969	PRO	0	-0.053	-0.021	12.208	-1.142	-1.142	0.000	0.000	0.000	0.000
140	A	1970	THR	0	-0.052	-0.060	9.812	0.446	0.446	0.000	0.000	0.000	0.000
141	A	1971	LEU	0	-0.046	-0.016	12.534	0.500	0.500	0.000	0.000	0.000	0.000
142	A	1972	THR	0	-0.009	-0.049	15.189	-0.034	-0.034	0.000	0.000	0.000	0.000
143	A	1973	ASP	-1	-0.918	-0.974	17.253	-14.425	-14.425	0.000	0.000	0.000	0.000
144	A	1974	GLU	-1	-0.919	-0.956	19.233	-11.198	-11.198	0.000	0.000	0.000	0.000
145	A	1975	GLU	-1	-0.855	-0.895	18.476	-14.642	-14.642	0.000	0.000	0.000	0.000
146	A	1976	TRP	0	0.009	-0.007	14.568	0.824	0.824	0.000	0.000	0.000	0.000
147	A	1977	ILE	0	0.011	0.014	20.179	0.488	0.488	0.000	0.000	0.000	0.000
148	A	1978	LYS	1	0.913	0.956	23.705	10.983	10.983	0.000	0.000	0.000	0.000
149	A	1979	VAL	0	0.028	0.015	20.669	0.394	0.394	0.000	0.000	0.000	0.000
150	A	1980	GLU	-1	-0.841	-0.929	21.671	-11.268	-11.268	0.000	0.000	0.000	0.000
151	A	1981	VAL	0	-0.036	-0.019	24.671	0.354	0.354	0.000	0.000	0.000	0.000
152	A	1982	GLN	0	0.055	0.026	26.451	0.095	0.095	0.000	0.000	0.000	0.000
153	A	1983	LEU	0	-0.006	-0.006	22.413	0.226	0.226	0.000	0.000	0.000	0.000
154	A	1984	LYS	1	0.876	0.947	26.269	10.267	10.267	0.000	0.000	0.000	0.000
155	A	1985	ASP	-1	-0.878	-0.935	29.817	-8.535	-8.535	0.000	0.000	0.000	0.000
156	A	1986	LEU	0	-0.087	-0.035	27.789	0.201	0.201	0.000	0.000	0.000	0.000
157	A	1987	ILE	0	-0.062	-0.043	28.148	0.190	0.190	0.000	0.000	0.000	0.000
158	A	1988	LEU	0	-0.051	-0.023	32.246	0.220	0.220	0.000	0.000	0.000	0.000
159	A	1989	ALA	0	-0.061	-0.021	34.815	0.229	0.229	0.000	0.000	0.000	0.000
160	A	1990	ASP	-1	-0.994	-0.976	35.142	-7.647	-7.647	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:1831:LYS)