FMO DATABASE

FMODB ID: 43Y5N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1425171.404682
FMO2-HF: Nuclear repulsion	1361864.40669
FMO2-HF: Total energy	-63306.997992
FMO2-MP2: Total energy	-63495.081275

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.
-60.587	-56.783	1.604	-2.26	-3.147	-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 : 0.984 / 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	-11.806	-9.487	1.442	-1.573	-2.188	-0.011
4	A	1834	GLY	0	0.035	0.022	4.609	3.246	3.387	-0.001	-0.007	-0.132	0.000
5	A	1835	GLN	0	0.014	0.010	6.113	3.857	3.857	0.000	0.000	0.000	0.000
6	A	1836	LEU	0	0.002	-0.017	9.395	-0.873	-0.873	0.000	0.000	0.000	0.000
7	A	1837	ALA	0	0.067	0.027	11.767	0.540	0.540	0.000	0.000	0.000	0.000
8	A	1838	LYS	1	0.889	0.944	13.271	17.958	17.958	0.000	0.000	0.000	0.000
9	A	1839	TRP	0	-0.053	-0.013	13.085	1.911	1.911	0.000	0.000	0.000	0.000
10	A	1840	LYS	1	0.967	1.000	13.899	17.125	17.125	0.000	0.000	0.000	0.000
11	A	1841	THR	0	0.049	0.016	13.195	0.562	0.562	0.000	0.000	0.000	0.000
12	A	1842	ALA	0	0.055	0.015	15.844	0.820	0.820	0.000	0.000	0.000	0.000
13	A	1843	GLU	-1	-0.905	-0.949	17.726	-14.012	-14.012	0.000	0.000	0.000	0.000
14	A	1844	GLU	-1	-0.891	-0.950	15.397	-19.711	-19.711	0.000	0.000	0.000	0.000
15	A	1845	VAL	0	-0.006	-0.004	19.254	0.685	0.685	0.000	0.000	0.000	0.000
16	A	1846	ALA	0	0.026	0.010	21.756	0.752	0.752	0.000	0.000	0.000	0.000
17	A	1847	ALA	0	-0.037	-0.020	22.218	0.679	0.679	0.000	0.000	0.000	0.000
18	A	1848	LEU	0	-0.005	0.001	23.423	0.443	0.443	0.000	0.000	0.000	0.000
19	A	1849	ILE	0	0.025	0.011	25.156	0.547	0.547	0.000	0.000	0.000	0.000
20	A	1850	ARG	1	0.939	0.962	24.322	12.602	12.602	0.000	0.000	0.000	0.000
21	A	1851	SER	0	-0.092	-0.028	28.023	0.295	0.295	0.000	0.000	0.000	0.000
22	A	1852	LEU	0	-0.011	0.003	29.673	0.259	0.259	0.000	0.000	0.000	0.000
23	A	1853	PRO	0	0.040	0.012	32.250	0.102	0.102	0.000	0.000	0.000	0.000
24	A	1854	VAL	0	0.039	0.014	35.470	-0.071	-0.071	0.000	0.000	0.000	0.000
25	A	1855	GLU	-1	-0.906	-0.959	36.517	-7.789	-7.789	0.000	0.000	0.000	0.000
26	A	1856	GLU	-1	-0.844	-0.921	34.296	-8.626	-8.626	0.000	0.000	0.000	0.000
27	A	1857	GLN	0	-0.065	-0.017	31.706	-0.298	-0.298	0.000	0.000	0.000	0.000
28	A	1858	PRO	0	-0.019	-0.006	32.354	-0.254	-0.254	0.000	0.000	0.000	0.000
29	A	1859	LYS	1	0.813	0.903	34.685	8.353	8.353	0.000	0.000	0.000	0.000
30	A	1860	GLN	0	-0.097	-0.048	29.094	-0.331	-0.331	0.000	0.000	0.000	0.000
31	A	1861	ILE	0	0.020	0.014	30.189	0.021	0.021	0.000	0.000	0.000	0.000
32	A	1862	ILE	0	0.004	0.002	22.755	-0.329	-0.329	0.000	0.000	0.000	0.000
33	A	1863	VAL	0	-0.011	-0.004	26.209	0.310	0.310	0.000	0.000	0.000	0.000
34	A	1864	THR	0	0.015	0.005	22.633	-0.681	-0.681	0.000	0.000	0.000	0.000
35	A	1865	ARG	1	0.917	0.953	21.757	13.420	13.420	0.000	0.000	0.000	0.000
36	A	1866	LYS	1	1.008	0.996	22.364	10.268	10.268	0.000	0.000	0.000	0.000
37	A	1867	GLY	0	-0.001	0.000	21.086	-0.139	-0.139	0.000	0.000	0.000	0.000
38	A	1868	MET	0	-0.029	-0.009	17.410	0.247	0.247	0.000	0.000	0.000	0.000
39	A	1869	LEU	0	0.025	0.021	14.667	-0.185	-0.185	0.000	0.000	0.000	0.000
40	A	1870	ASP	-1	-0.890	-0.920	10.576	-22.680	-22.680	0.000	0.000	0.000	0.000
41	A	1871	PRO	0	0.011	-0.030	7.441	-0.558	-0.558	0.000	0.000	0.000	0.000
42	A	1872	LEU	0	-0.023	-0.009	9.634	1.250	1.250	0.000	0.000	0.000	0.000
43	A	1873	GLU	-1	-0.892	-0.944	10.305	-18.549	-18.549	0.000	0.000	0.000	0.000
44	A	1874	VAL	0	-0.009	-0.012	12.139	1.236	1.236	0.000	0.000	0.000	0.000
45	A	1875	HIS	0	0.024	0.029	13.543	-0.333	-0.333	0.000	0.000	0.000	0.000
46	A	1876	LEU	0	0.049	0.009	16.132	0.461	0.461	0.000	0.000	0.000	0.000
47	A	1877	LEU	0	0.021	0.000	17.671	0.590	0.590	0.000	0.000	0.000	0.000
48	A	1878	ASP	-1	-0.908	-0.941	20.881	-11.265	-11.265	0.000	0.000	0.000	0.000
49	A	1879	PHE	0	-0.002	0.018	23.204	0.297	0.297	0.000	0.000	0.000	0.000
50	A	1880	PRO	0	-0.008	-0.011	24.514	0.261	0.261	0.000	0.000	0.000	0.000
51	A	1881	ASN	0	-0.023	-0.020	23.752	0.036	0.036	0.000	0.000	0.000	0.000
52	A	1882	ILE	0	-0.005	-0.003	18.349	-0.341	-0.341	0.000	0.000	0.000	0.000
53	A	1883	VAL	0	-0.033	-0.011	18.615	0.239	0.239	0.000	0.000	0.000	0.000
54	A	1884	ILE	0	0.006	-0.007	15.611	-0.686	-0.686	0.000	0.000	0.000	0.000
55	A	1885	LYS	1	0.900	0.957	15.809	15.610	15.610	0.000	0.000	0.000	0.000
56	A	1886	GLY	0	0.002	-0.002	14.886	-0.915	-0.915	0.000	0.000	0.000	0.000
57	A	1887	SER	0	-0.008	-0.016	12.528	0.475	0.475	0.000	0.000	0.000	0.000
58	A	1888	GLU	-1	-0.880	-0.964	14.561	-13.226	-13.226	0.000	0.000	0.000	0.000
59	A	1889	LEU	0	-0.015	-0.013	16.153	-0.998	-0.998	0.000	0.000	0.000	0.000
60	A	1890	GLN	0	-0.020	-0.029	17.663	-0.536	-0.536	0.000	0.000	0.000	0.000
61	A	1891	LEU	0	-0.013	0.019	13.842	0.105	0.105	0.000	0.000	0.000	0.000
62	A	1892	PRO	0	0.036	0.007	13.771	-0.734	-0.734	0.000	0.000	0.000	0.000
63	A	1893	PHE	0	-0.050	-0.032	10.191	-1.227	-1.227	0.000	0.000	0.000	0.000
64	A	1894	GLN	0	0.068	0.068	10.363	-2.958	-2.958	0.000	0.000	0.000	0.000
65	A	1895	ALA	0	-0.028	-0.022	10.807	1.641	1.641	0.000	0.000	0.000	0.000
66	A	1896	CYS	0	-0.076	-0.035	12.639	-0.113	-0.113	0.000	0.000	0.000	0.000
67	A	1897	LEU	0	0.017	0.016	15.553	1.102	1.102	0.000	0.000	0.000	0.000
68	A	1898	LYS	1	0.880	0.953	18.131	13.536	13.536	0.000	0.000	0.000	0.000
69	A	1899	VAL	0	0.031	0.015	20.366	0.454	0.454	0.000	0.000	0.000	0.000
70	A	1900	GLU	-1	-0.933	-0.978	23.587	-12.986	-12.986	0.000	0.000	0.000	0.000
71	A	1901	LYS	1	0.934	0.962	26.338	10.628	10.628	0.000	0.000	0.000	0.000
72	A	1902	PHE	0	0.051	0.028	30.051	-0.078	-0.078	0.000	0.000	0.000	0.000
73	A	1903	GLY	0	0.007	-0.005	32.474	0.148	0.148	0.000	0.000	0.000	0.000
74	A	1904	ASP	-1	-0.911	-0.934	33.828	-8.703	-8.703	0.000	0.000	0.000	0.000
75	A	1905	LEU	0	-0.022	-0.019	28.103	-0.301	-0.301	0.000	0.000	0.000	0.000
76	A	1906	ILE	0	0.018	0.016	27.696	0.174	0.174	0.000	0.000	0.000	0.000
77	A	1907	LEU	0	-0.068	-0.038	25.383	-0.649	-0.649	0.000	0.000	0.000	0.000
78	A	1908	LYS	1	0.950	0.972	23.954	12.701	12.701	0.000	0.000	0.000	0.000
79	A	1909	ALA	0	0.004	0.004	24.111	-0.461	-0.461	0.000	0.000	0.000	0.000
80	A	1910	THR	0	-0.053	-0.038	20.207	0.060	0.060	0.000	0.000	0.000	0.000
81	A	1911	GLU	-1	-0.904	-0.942	20.100	-12.330	-12.330	0.000	0.000	0.000	0.000
82	A	1912	PRO	0	-0.020	-0.010	20.207	-0.502	-0.502	0.000	0.000	0.000	0.000
83	A	1913	GLN	0	-0.014	-0.009	14.036	-0.969	-0.969	0.000	0.000	0.000	0.000
84	A	1914	MET	0	0.005	0.009	15.538	0.987	0.987	0.000	0.000	0.000	0.000
85	A	1915	VAL	0	-0.008	0.004	10.242	-1.146	-1.146	0.000	0.000	0.000	0.000
86	A	1916	LEU	0	0.011	0.006	11.079	1.047	1.047	0.000	0.000	0.000	0.000
87	A	1917	PHE	0	0.033	0.015	9.472	-1.792	-1.792	0.000	0.000	0.000	0.000
88	A	1918	ASN	0	0.008	-0.006	10.905	1.408	1.408	0.000	0.000	0.000	0.000
89	A	1919	LEU	0	0.057	0.031	12.532	-0.262	-0.262	0.000	0.000	0.000	0.000
90	A	1920	TYR	0	0.026	0.006	14.036	0.701	0.701	0.000	0.000	0.000	0.000
91	A	1921	ASP	-1	-0.737	-0.854	9.918	-18.963	-18.963	0.000	0.000	0.000	0.000
92	A	1922	ASP	-1	-0.937	-0.988	7.503	-22.221	-22.221	0.000	0.000	0.000	0.000
93	A	1923	TRP	0	0.059	0.016	9.626	0.730	0.730	0.000	0.000	0.000	0.000
94	A	1924	LEU	0	-0.040	-0.020	13.137	0.424	0.424	0.000	0.000	0.000	0.000
95	A	1925	LYS	1	0.901	0.962	6.356	26.166	26.166	0.000	0.000	0.000	0.000
96	A	1926	THR	0	0.007	0.006	12.770	0.190	0.190	0.000	0.000	0.000	0.000
97	A	1927	ILE	0	-0.004	0.025	15.671	0.887	0.887	0.000	0.000	0.000	0.000
98	A	1928	SER	0	0.031	0.019	17.531	-0.303	-0.303	0.000	0.000	0.000	0.000
99	A	1929	SER	0	0.085	0.006	19.394	-0.277	-0.277	0.000	0.000	0.000	0.000
100	A	1930	TYR	0	-0.018	0.014	20.314	0.076	0.076	0.000	0.000	0.000	0.000
101	A	1931	THR	0	0.013	-0.018	20.962	0.360	0.360	0.000	0.000	0.000	0.000
102	A	1932	ALA	0	0.033	0.017	17.552	0.023	0.023	0.000	0.000	0.000	0.000
103	A	1933	PHE	0	0.010	0.007	19.373	0.030	0.030	0.000	0.000	0.000	0.000
104	A	1934	SER	0	-0.018	-0.014	21.891	0.285	0.285	0.000	0.000	0.000	0.000
105	A	1935	ARG	1	0.893	0.965	16.202	13.989	13.989	0.000	0.000	0.000	0.000
106	A	1936	LEU	0	0.002	0.000	18.413	0.052	0.052	0.000	0.000	0.000	0.000
107	A	1937	ILE	0	-0.013	-0.012	20.841	0.175	0.175	0.000	0.000	0.000	0.000
108	A	1938	LEU	0	-0.053	-0.009	24.353	0.366	0.366	0.000	0.000	0.000	0.000
109	A	1939	ILE	0	0.011	0.005	18.910	0.220	0.220	0.000	0.000	0.000	0.000
110	A	1940	LEU	0	-0.017	-0.014	21.064	0.155	0.155	0.000	0.000	0.000	0.000
111	A	1941	ARG	1	0.956	0.987	24.248	8.893	8.893	0.000	0.000	0.000	0.000
112	A	1942	ALA	0	0.019	0.005	25.687	0.276	0.276	0.000	0.000	0.000	0.000
113	A	1943	LEU	0	-0.035	-0.017	21.271	0.142	0.142	0.000	0.000	0.000	0.000
114	A	1944	HIS	0	-0.042	-0.020	25.987	0.019	0.019	0.000	0.000	0.000	0.000
115	A	1945	VAL	0	-0.047	-0.008	28.916	0.161	0.161	0.000	0.000	0.000	0.000
116	A	1946	ASN	0	0.019	-0.001	29.690	0.068	0.068	0.000	0.000	0.000	0.000
117	A	1947	ASN	0	0.011	-0.007	24.809	-0.293	-0.293	0.000	0.000	0.000	0.000
118	A	1948	ASP	-1	-0.865	-0.930	26.314	-9.945	-9.945	0.000	0.000	0.000	0.000
119	A	1949	ARG	1	0.900	0.950	27.183	9.533	9.533	0.000	0.000	0.000	0.000
120	A	1950	ALA	0	0.030	0.009	24.603	-0.237	-0.237	0.000	0.000	0.000	0.000
121	A	1951	LYS	1	0.958	0.976	22.319	10.693	10.693	0.000	0.000	0.000	0.000
122	A	1952	VAL	0	-0.063	-0.024	22.312	-0.406	-0.406	0.000	0.000	0.000	0.000
123	A	1953	ILE	0	-0.067	-0.025	23.749	-0.200	-0.200	0.000	0.000	0.000	0.000
124	A	1954	LEU	0	0.008	0.003	18.894	-0.286	-0.286	0.000	0.000	0.000	0.000
125	A	1955	LYS	1	0.917	0.960	17.918	13.840	13.840	0.000	0.000	0.000	0.000
126	A	1956	PRO	0	0.026	0.019	19.592	0.526	0.526	0.000	0.000	0.000	0.000
127	A	1957	ASP	-1	-0.783	-0.857	20.199	-13.678	-13.678	0.000	0.000	0.000	0.000
128	A	1958	LYS	1	0.906	0.940	20.552	11.461	11.461	0.000	0.000	0.000	0.000
129	A	1959	THR	0	-0.109	-0.082	17.236	-0.554	-0.554	0.000	0.000	0.000	0.000
130	A	1960	THR	0	-0.003	0.017	16.226	-0.709	-0.709	0.000	0.000	0.000	0.000
131	A	1961	ILE	0	-0.033	-0.018	10.128	0.376	0.376	0.000	0.000	0.000	0.000
132	A	1962	THR	0	0.014	0.014	10.796	0.576	0.576	0.000	0.000	0.000	0.000
133	A	1963	GLU	-1	-0.896	-0.946	5.605	-31.467	-31.467	0.000	0.000	0.000	0.000
134	A	1964	PRO	0	0.017	0.008	5.055	1.489	1.489	0.000	0.000	0.000	0.000
135	A	1965	HIS	0	-0.096	-0.055	3.401	-1.034	0.310	0.163	-0.680	-0.827	-0.006
136	A	1966	HIS	0	-0.032	-0.007	6.192	0.784	0.784	0.000	0.000	0.000	0.000
137	A	1967	ILE	0	-0.045	-0.037	8.856	0.317	0.317	0.000	0.000	0.000	0.000
138	A	1968	TRP	0	-0.085	-0.046	12.362	1.284	1.284	0.000	0.000	0.000	0.000
139	A	1969	PRO	0	-0.047	-0.019	12.241	-1.059	-1.059	0.000	0.000	0.000	0.000
140	A	1970	THR	0	-0.034	-0.027	9.777	0.385	0.385	0.000	0.000	0.000	0.000
141	A	1971	LEU	0	-0.037	-0.015	12.368	0.464	0.464	0.000	0.000	0.000	0.000
142	A	1972	THR	0	-0.005	-0.009	14.899	-0.015	-0.015	0.000	0.000	0.000	0.000
143	A	1973	ASP	-1	-0.895	-0.961	16.756	-14.466	-14.466	0.000	0.000	0.000	0.000
144	A	1974	GLU	-1	-0.924	-0.962	18.923	-11.365	-11.365	0.000	0.000	0.000	0.000
145	A	1975	GLU	-1	-0.906	-0.955	17.768	-14.638	-14.638	0.000	0.000	0.000	0.000
146	A	1976	TRP	0	0.024	0.001	14.772	0.825	0.825	0.000	0.000	0.000	0.000
147	A	1977	ILE	0	0.019	0.029	20.192	0.508	0.508	0.000	0.000	0.000	0.000
148	A	1978	LYS	1	0.930	0.967	23.693	10.931	10.931	0.000	0.000	0.000	0.000
149	A	1979	VAL	0	0.035	0.017	20.852	0.403	0.403	0.000	0.000	0.000	0.000
150	A	1980	GLU	-1	-0.878	-0.951	21.837	-11.438	-11.438	0.000	0.000	0.000	0.000
151	A	1981	VAL	0	-0.029	-0.015	24.987	0.378	0.378	0.000	0.000	0.000	0.000
152	A	1982	GLN	0	0.012	-0.003	25.973	-0.047	-0.047	0.000	0.000	0.000	0.000
153	A	1983	LEU	0	0.001	-0.002	22.870	0.247	0.247	0.000	0.000	0.000	0.000
154	A	1984	LYS	1	0.914	0.956	27.572	9.751	9.751	0.000	0.000	0.000	0.000
155	A	1985	ASP	-1	-0.885	-0.939	30.314	-8.423	-8.423	0.000	0.000	0.000	0.000
156	A	1986	LEU	0	-0.093	-0.033	28.025	0.205	0.205	0.000	0.000	0.000	0.000
157	A	1987	ILE	0	-0.056	-0.040	28.861	0.187	0.187	0.000	0.000	0.000	0.000
158	A	1988	LEU	0	-0.052	-0.023	32.719	0.223	0.223	0.000	0.000	0.000	0.000
159	A	1989	ALA	0	-0.062	-0.023	35.195	0.224	0.224	0.000	0.000	0.000	0.000
160	A	1990	ASP	-1	-0.986	-0.975	35.329	-7.606	-7.606	0.000	0.000	0.000	0.000

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