FMO DATABASE

FMODB ID: KR123

Calculation Name: 3LRU-A-Xray313

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	160
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1424962.439997
FMO2-HF: Nuclear repulsion	1361656.264686
FMO2-HF: Total energy	-63306.175311
FMO2-MP2: Total energy	-63494.249631

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.
-68.919	-65.089	1.607	-2.293	-3.145	-0.017

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 : 0.982 / q_NPA : 0.980

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	-0.028	-0.012	2.560	-11.966	-9.635	1.442	-1.587	-2.186	-0.011
4	A	1834	GLY	0	0.037	0.023	4.609	3.315	3.455	0.000	-0.008	-0.133	0.000
5	A	1835	GLN	0	0.013	0.010	6.113	4.036	4.036	0.000	0.000	0.000	0.000
6	A	1836	LEU	0	0.001	-0.018	9.395	-0.840	-0.840	0.000	0.000	0.000	0.000
7	A	1837	ALA	0	0.067	0.028	11.767	0.580	0.580	0.000	0.000	0.000	0.000
8	A	1838	LYS	1	0.888	0.943	13.271	18.009	18.009	0.000	0.000	0.000	0.000
9	A	1839	TRP	0	-0.051	-0.012	13.085	1.909	1.909	0.000	0.000	0.000	0.000
10	A	1840	LYS	1	0.964	0.997	13.899	17.119	17.119	0.000	0.000	0.000	0.000
11	A	1841	THR	0	0.054	0.017	13.195	0.568	0.568	0.000	0.000	0.000	0.000
12	A	1842	ALA	0	0.053	0.014	15.844	0.866	0.866	0.000	0.000	0.000	0.000
13	A	1843	GLU	-1	-0.905	-0.948	17.726	-14.004	-14.004	0.000	0.000	0.000	0.000
14	A	1844	GLU	-1	-0.888	-0.949	15.397	-19.705	-19.705	0.000	0.000	0.000	0.000
15	A	1845	VAL	0	-0.011	-0.006	19.254	0.716	0.716	0.000	0.000	0.000	0.000
16	A	1846	ALA	0	0.030	0.012	21.756	0.776	0.776	0.000	0.000	0.000	0.000
17	A	1847	ALA	0	-0.033	-0.018	22.218	0.687	0.687	0.000	0.000	0.000	0.000
18	A	1848	LEU	0	-0.008	0.000	23.423	0.455	0.455	0.000	0.000	0.000	0.000
19	A	1849	ILE	0	0.023	0.011	25.156	0.570	0.570	0.000	0.000	0.000	0.000
20	A	1850	ARG	1	0.941	0.963	24.322	12.616	12.616	0.000	0.000	0.000	0.000
21	A	1851	SER	0	-0.091	-0.028	28.023	0.302	0.302	0.000	0.000	0.000	0.000
22	A	1852	LEU	0	-0.013	0.002	29.673	0.274	0.274	0.000	0.000	0.000	0.000
23	A	1853	PRO	0	0.040	0.011	32.250	0.118	0.118	0.000	0.000	0.000	0.000
24	A	1854	VAL	0	0.038	0.014	35.470	-0.069	-0.069	0.000	0.000	0.000	0.000
25	A	1855	GLU	-1	-0.905	-0.958	36.517	-7.783	-7.783	0.000	0.000	0.000	0.000
26	A	1856	GLU	-1	-0.845	-0.922	34.296	-8.632	-8.632	0.000	0.000	0.000	0.000
27	A	1857	GLN	0	-0.066	-0.017	31.706	-0.306	-0.306	0.000	0.000	0.000	0.000
28	A	1858	PRO	0	-0.018	-0.006	32.354	-0.250	-0.250	0.000	0.000	0.000	0.000
29	A	1859	LYS	1	0.812	0.903	34.685	8.353	8.353	0.000	0.000	0.000	0.000
30	A	1860	GLN	0	-0.096	-0.047	29.094	-0.343	-0.343	0.000	0.000	0.000	0.000
31	A	1861	ILE	0	0.019	0.014	30.189	0.016	0.016	0.000	0.000	0.000	0.000
32	A	1862	ILE	0	0.004	0.002	22.755	-0.343	-0.343	0.000	0.000	0.000	0.000
33	A	1863	VAL	0	-0.013	-0.005	26.207	0.314	0.314	0.000	0.000	0.000	0.000
34	A	1864	THR	0	0.019	0.007	22.633	-0.705	-0.705	0.000	0.000	0.000	0.000
35	A	1865	ARG	1	0.915	0.951	21.757	13.420	13.420	0.000	0.000	0.000	0.000
36	A	1866	LYS	1	1.007	0.996	22.364	10.266	10.266	0.000	0.000	0.000	0.000
37	A	1867	GLY	0	-0.001	0.001	21.086	-0.154	-0.154	0.000	0.000	0.000	0.000
38	A	1868	MET	0	-0.029	-0.008	17.410	0.227	0.227	0.000	0.000	0.000	0.000
39	A	1869	LEU	0	0.021	0.019	14.667	-0.215	-0.215	0.000	0.000	0.000	0.000
40	A	1870	ASP	-1	-0.884	-0.917	10.576	-22.715	-22.715	0.000	0.000	0.000	0.000
41	A	1871	PRO	0	0.006	-0.032	7.441	-0.612	-0.612	0.000	0.000	0.000	0.000
42	A	1872	LEU	0	-0.019	-0.008	9.634	1.300	1.300	0.000	0.000	0.000	0.000
43	A	1873	GLU	-1	-0.893	-0.944	10.305	-18.569	-18.569	0.000	0.000	0.000	0.000
44	A	1874	VAL	0	-0.011	-0.012	12.139	1.269	1.269	0.000	0.000	0.000	0.000
45	A	1875	HIS	0	0.023	0.029	13.544	-0.330	-0.330	0.000	0.000	0.000	0.000
46	A	1876	LEU	0	0.051	0.009	16.132	0.483	0.483	0.000	0.000	0.000	0.000
47	A	1877	LEU	0	0.022	0.000	17.672	0.590	0.590	0.000	0.000	0.000	0.000
48	A	1878	ASP	-1	-0.911	-0.942	20.881	-11.256	-11.256	0.000	0.000	0.000	0.000
49	A	1879	PHE	0	0.000	0.020	23.205	0.292	0.292	0.000	0.000	0.000	0.000
50	A	1880	PRO	0	-0.001	-0.008	24.515	0.272	0.272	0.000	0.000	0.000	0.000
51	A	1881	ASN	0	-0.028	-0.023	23.753	0.024	0.024	0.000	0.000	0.000	0.000
52	A	1882	ILE	0	-0.003	-0.002	18.350	-0.365	-0.365	0.000	0.000	0.000	0.000
53	A	1883	VAL	0	-0.036	-0.012	18.616	0.230	0.230	0.000	0.000	0.000	0.000
54	A	1884	ILE	0	0.007	-0.007	15.611	-0.716	-0.716	0.000	0.000	0.000	0.000
55	A	1885	LYS	1	0.900	0.956	15.809	15.608	15.608	0.000	0.000	0.000	0.000
56	A	1886	GLY	0	0.003	-0.003	14.887	-0.941	-0.941	0.000	0.000	0.000	0.000
57	A	1887	SER	0	-0.013	-0.017	12.528	0.459	0.459	0.000	0.000	0.000	0.000
58	A	1888	GLU	-1	-0.876	-0.963	14.561	-13.189	-13.189	0.000	0.000	0.000	0.000
59	A	1889	LEU	0	-0.018	-0.014	16.153	-1.000	-1.000	0.000	0.000	0.000	0.000
60	A	1890	GLN	0	-0.017	-0.028	17.663	-0.540	-0.540	0.000	0.000	0.000	0.000
61	A	1891	LEU	0	-0.016	0.017	13.842	0.085	0.085	0.000	0.000	0.000	0.000
62	A	1892	PRO	0	0.037	0.008	13.771	-0.765	-0.765	0.000	0.000	0.000	0.000
63	A	1893	PHE	0	-0.050	-0.032	10.191	-1.281	-1.281	0.000	0.000	0.000	0.000
64	A	1894	GLN	0	0.068	0.068	10.363	-2.974	-2.974	0.000	0.000	0.000	0.000
65	A	1895	ALA	0	-0.024	-0.021	10.806	1.662	1.662	0.000	0.000	0.000	0.000
66	A	1896	CYS	0	-0.079	-0.035	12.639	-0.064	-0.064	0.000	0.000	0.000	0.000
67	A	1897	LEU	0	0.016	0.014	15.553	1.149	1.149	0.000	0.000	0.000	0.000
68	A	1898	LYS	1	0.879	0.953	18.131	13.539	13.539	0.000	0.000	0.000	0.000
69	A	1899	VAL	0	0.031	0.016	20.366	0.484	0.484	0.000	0.000	0.000	0.000
70	A	1900	GLU	-1	-0.934	-0.978	23.587	-12.965	-12.965	0.000	0.000	0.000	0.000
71	A	1901	LYS	1	0.933	0.962	26.338	10.647	10.647	0.000	0.000	0.000	0.000
72	A	1902	PHE	0	0.051	0.029	30.051	-0.068	-0.068	0.000	0.000	0.000	0.000
73	A	1903	GLY	0	0.008	-0.005	32.474	0.156	0.156	0.000	0.000	0.000	0.000
74	A	1904	ASP	-1	-0.911	-0.935	33.828	-8.702	-8.702	0.000	0.000	0.000	0.000
75	A	1905	LEU	0	-0.020	-0.018	28.103	-0.311	-0.311	0.000	0.000	0.000	0.000
76	A	1906	ILE	0	0.015	0.016	27.692	0.169	0.169	0.000	0.000	0.000	0.000
77	A	1907	LEU	0	-0.067	-0.038	25.383	-0.662	-0.662	0.000	0.000	0.000	0.000
78	A	1908	LYS	1	0.949	0.971	23.955	12.695	12.695	0.000	0.000	0.000	0.000
79	A	1909	ALA	0	0.004	0.004	24.111	-0.463	-0.463	0.000	0.000	0.000	0.000
80	A	1910	THR	0	-0.053	-0.037	20.206	0.053	0.053	0.000	0.000	0.000	0.000
81	A	1911	GLU	-1	-0.905	-0.944	20.100	-12.324	-12.324	0.000	0.000	0.000	0.000
82	A	1912	PRO	0	-0.019	-0.010	20.207	-0.510	-0.510	0.000	0.000	0.000	0.000
83	A	1913	GLN	0	-0.014	-0.008	14.036	-0.991	-0.991	0.000	0.000	0.000	0.000
84	A	1914	MET	0	0.006	0.009	15.538	0.983	0.983	0.000	0.000	0.000	0.000
85	A	1915	VAL	0	-0.008	0.004	10.242	-1.181	-1.181	0.000	0.000	0.000	0.000
86	A	1916	LEU	0	0.010	0.005	11.080	1.052	1.052	0.000	0.000	0.000	0.000
87	A	1917	PHE	0	0.035	0.016	9.473	-1.800	-1.800	0.000	0.000	0.000	0.000
88	A	1918	ASN	0	0.008	-0.006	10.905	1.429	1.429	0.000	0.000	0.000	0.000
89	A	1919	LEU	0	0.058	0.032	12.532	-0.253	-0.253	0.000	0.000	0.000	0.000
90	A	1920	TYR	0	0.024	0.006	14.036	0.682	0.682	0.000	0.000	0.000	0.000
91	A	1921	ASP	-1	-0.734	-0.852	9.902	-19.034	-19.034	0.000	0.000	0.000	0.000
92	A	1922	ASP	-1	-0.939	-0.990	7.477	-22.293	-22.293	0.000	0.000	0.000	0.000
93	A	1923	TRP	0	0.056	0.016	9.600	0.753	0.753	0.000	0.000	0.000	0.000
94	A	1924	LEU	0	-0.038	-0.018	13.116	0.433	0.433	0.000	0.000	0.000	0.000
95	A	1925	LYS	1	0.900	0.961	6.359	26.173	26.173	0.000	0.000	0.000	0.000
96	A	1926	THR	0	0.007	0.005	12.760	0.221	0.221	0.000	0.000	0.000	0.000
97	A	1927	ILE	0	-0.004	0.025	15.657	0.919	0.919	0.000	0.000	0.000	0.000
98	A	1928	SER	0	0.027	0.018	17.514	-0.291	-0.291	0.000	0.000	0.000	0.000
99	A	1929	SER	0	0.086	0.006	19.414	-0.277	-0.277	0.000	0.000	0.000	0.000
100	A	1930	TYR	0	-0.020	0.014	20.333	0.087	0.087	0.000	0.000	0.000	0.000
101	A	1931	THR	0	0.015	-0.017	20.940	0.355	0.355	0.000	0.000	0.000	0.000
102	A	1932	ALA	0	0.032	0.016	17.552	0.008	0.008	0.000	0.000	0.000	0.000
103	A	1933	PHE	0	0.008	0.005	19.348	0.037	0.037	0.000	0.000	0.000	0.000
104	A	1934	SER	0	-0.018	-0.013	21.891	0.294	0.294	0.000	0.000	0.000	0.000
105	A	1935	ARG	1	0.893	0.964	16.172	13.981	13.981	0.000	0.000	0.000	0.000
106	A	1936	LEU	0	-0.002	-0.002	18.413	0.038	0.038	0.000	0.000	0.000	0.000
107	A	1937	ILE	0	-0.018	-0.013	20.841	0.185	0.185	0.000	0.000	0.000	0.000
108	A	1938	LEU	0	-0.041	-0.004	24.337	0.360	0.360	0.000	0.000	0.000	0.000
109	A	1939	ILE	0	0.008	0.004	18.912	0.194	0.194	0.000	0.000	0.000	0.000
110	A	1940	LEU	0	-0.024	-0.018	21.065	0.151	0.151	0.000	0.000	0.000	0.000
111	A	1941	ARG	1	0.953	0.986	24.249	8.890	8.890	0.000	0.000	0.000	0.000
112	A	1942	ALA	0	0.035	0.013	25.687	0.265	0.265	0.000	0.000	0.000	0.000
113	A	1943	LEU	0	-0.050	-0.024	21.272	0.118	0.118	0.000	0.000	0.000	0.000
114	A	1944	HIS	0	-0.046	-0.025	25.988	0.019	0.019	0.000	0.000	0.000	0.000
115	A	1945	VAL	0	-0.023	0.005	28.917	0.132	0.132	0.000	0.000	0.000	0.000
116	A	1946	ASN	0	0.030	0.006	29.695	0.047	0.047	0.000	0.000	0.000	0.000
117	A	1947	ASN	0	0.005	-0.011	24.810	-0.319	-0.319	0.000	0.000	0.000	0.000
118	A	1948	ASP	-1	-0.873	-0.936	26.315	-9.958	-9.958	0.000	0.000	0.000	0.000
119	A	1949	ARG	1	0.906	0.953	27.184	9.522	9.522	0.000	0.000	0.000	0.000
120	A	1950	ALA	0	0.035	0.012	24.604	-0.259	-0.259	0.000	0.000	0.000	0.000
121	A	1951	LYS	1	0.950	0.971	22.319	10.666	10.666	0.000	0.000	0.000	0.000
122	A	1952	VAL	0	-0.066	-0.026	22.313	-0.417	-0.417	0.000	0.000	0.000	0.000
123	A	1953	ILE	0	-0.062	-0.022	23.750	-0.218	-0.218	0.000	0.000	0.000	0.000
124	A	1954	LEU	0	0.001	0.001	18.895	-0.329	-0.329	0.000	0.000	0.000	0.000
125	A	1955	LYS	1	0.917	0.959	17.920	13.818	13.818	0.000	0.000	0.000	0.000
126	A	1956	PRO	0	0.028	0.020	19.592	0.538	0.538	0.000	0.000	0.000	0.000
127	A	1957	ASP	-1	-0.784	-0.859	20.199	-13.696	-13.696	0.000	0.000	0.000	0.000
128	A	1958	LYS	1	0.905	0.940	20.552	11.455	11.455	0.000	0.000	0.000	0.000
129	A	1959	THR	0	-0.113	-0.083	17.236	-0.589	-0.589	0.000	0.000	0.000	0.000
130	A	1960	THR	0	-0.003	0.018	16.226	-0.736	-0.736	0.000	0.000	0.000	0.000
131	A	1961	ILE	0	-0.034	-0.019	10.128	0.333	0.333	0.000	0.000	0.000	0.000
132	A	1962	THR	0	0.016	0.014	10.797	0.551	0.551	0.000	0.000	0.000	0.000
133	A	1963	GLU	-1	-0.898	-0.947	5.606	-31.654	-31.654	0.000	0.000	0.000	0.000
134	A	1964	PRO	0	0.017	0.009	5.056	1.468	1.468	0.000	0.000	0.000	0.000
135	A	1965	HIS	0	-0.101	-0.056	3.402	-1.024	0.335	0.165	-0.698	-0.826	-0.006
136	A	1966	HIS	0	-0.033	-0.007	6.193	0.856	0.856	0.000	0.000	0.000	0.000
137	A	1967	ILE	0	-0.040	-0.036	8.857	0.357	0.357	0.000	0.000	0.000	0.000
138	A	1968	TRP	0	-0.084	-0.044	12.363	1.274	1.274	0.000	0.000	0.000	0.000
139	A	1969	PRO	0	-0.045	-0.018	12.242	-1.109	-1.109	0.000	0.000	0.000	0.000
140	A	1970	THR	0	-0.036	-0.028	9.740	0.348	0.348	0.000	0.000	0.000	0.000
141	A	1971	LEU	0	-0.035	-0.013	12.332	0.488	0.488	0.000	0.000	0.000	0.000
142	A	1972	THR	0	-0.010	-0.013	14.869	-0.010	-0.010	0.000	0.000	0.000	0.000
143	A	1973	ASP	-1	-0.896	-0.961	16.729	-14.455	-14.455	0.000	0.000	0.000	0.000
144	A	1974	GLU	-1	-0.924	-0.962	18.897	-11.353	-11.353	0.000	0.000	0.000	0.000
145	A	1975	GLU	-1	-0.908	-0.956	17.737	-14.659	-14.659	0.000	0.000	0.000	0.000
146	A	1976	TRP	0	0.023	0.000	14.739	0.819	0.819	0.000	0.000	0.000	0.000
147	A	1977	ILE	0	0.022	0.030	20.159	0.529	0.529	0.000	0.000	0.000	0.000
148	A	1978	LYS	1	0.926	0.966	23.662	10.943	10.943	0.000	0.000	0.000	0.000
149	A	1979	VAL	0	0.034	0.017	20.815	0.393	0.393	0.000	0.000	0.000	0.000
150	A	1980	GLU	-1	-0.878	-0.951	21.805	-11.443	-11.443	0.000	0.000	0.000	0.000
151	A	1981	VAL	0	-0.029	-0.016	24.951	0.389	0.389	0.000	0.000	0.000	0.000
152	A	1982	GLN	0	0.009	-0.005	25.936	-0.053	-0.053	0.000	0.000	0.000	0.000
153	A	1983	LEU	0	-0.009	-0.006	22.870	0.229	0.229	0.000	0.000	0.000	0.000
154	A	1984	LYS	1	0.916	0.956	27.544	9.755	9.755	0.000	0.000	0.000	0.000
155	A	1985	ASP	-1	-0.891	-0.943	30.277	-8.428	-8.428	0.000	0.000	0.000	0.000
156	A	1986	LEU	0	-0.102	-0.041	28.026	0.176	0.176	0.000	0.000	0.000	0.000
157	A	1987	ILE	0	-0.069	-0.049	28.863	0.153	0.153	0.000	0.000	0.000	0.000
158	A	1988	LEU	0	-0.041	-0.010	32.720	0.206	0.206	0.000	0.000	0.000	0.000
159	A	1989	ALA	0	-0.095	-0.043	35.181	0.222	0.222	0.000	0.000	0.000	0.000
160	A	1990	ASP	-2	-1.907	-1.934	35.323	-15.425	-15.425	0.000	0.000	0.000	0.000

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