FMO DATABASE

FMODB ID: 39Z1L

Calculation Name: 3LBX-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LBX

Chain ID: B

ChEMBL ID:

UniProt ID: P02549

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	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	184
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1687885.869451
FMO2-HF: Nuclear repulsion	1611506.852991
FMO2-HF: Total energy	-76379.01646
FMO2-MP2: Total energy	-76599.607138

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:1900:GLY)

Summations of interaction energy for fragment #1(B:1900:GLY)

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.
0.918	2.771	0.045	-0.685	-1.212	0

Interaction energy analysis for fragmet #1(B:1900:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.028

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].
3	B	1902	THR	0	0.026	0.015	3.883	-0.720	0.300	-0.001	-0.434	-0.585
4	B	1903	ALA	0	0.031	0.019	3.251	-0.032	0.390	0.047	-0.138	-0.330
5	B	1904	ASP	-1	-0.774	-0.868	4.224	-2.035	-1.624	-0.001	-0.113	-0.297
6	B	1905	LYS	1	0.858	0.927	5.986	0.609	0.609	0.000	0.000	0.000
7	B	1906	PHE	0	-0.011	-0.008	7.969	0.165	0.165	0.000	0.000	0.000
8	B	1907	ARG	1	0.887	0.923	5.475	1.512	1.512	0.000	0.000	0.000
9	B	1908	PHE	0	-0.005	0.013	10.029	0.106	0.106	0.000	0.000	0.000
10	B	1909	PHE	0	0.031	-0.005	12.002	0.082	0.082	0.000	0.000	0.000
11	B	1910	SER	0	-0.052	-0.010	13.181	0.062	0.062	0.000	0.000	0.000
12	B	1911	MET	0	-0.017	-0.002	12.021	0.045	0.045	0.000	0.000	0.000
13	B	1912	ALA	0	0.041	0.019	16.010	0.036	0.036	0.000	0.000	0.000
14	B	1913	ARG	1	0.806	0.882	16.052	0.181	0.181	0.000	0.000	0.000
15	B	1914	ASP	-1	-0.804	-0.880	17.797	-0.152	-0.152	0.000	0.000	0.000
16	B	1915	LEU	0	0.019	0.007	19.313	0.016	0.016	0.000	0.000	0.000
17	B	1916	LEU	0	-0.001	-0.015	21.384	0.016	0.016	0.000	0.000	0.000
18	B	1917	SER	0	-0.067	-0.032	23.596	0.014	0.014	0.000	0.000	0.000
19	B	1918	TRP	0	-0.009	-0.004	24.936	0.004	0.004	0.000	0.000	0.000
20	B	1919	MET	0	-0.016	-0.007	24.252	0.006	0.006	0.000	0.000	0.000
21	B	1920	GLU	-1	-0.860	-0.896	27.969	-0.051	-0.051	0.000	0.000	0.000
22	B	1921	SER	0	-0.010	-0.005	29.609	0.007	0.007	0.000	0.000	0.000
23	B	1922	ILE	0	0.037	0.015	29.817	0.005	0.005	0.000	0.000	0.000
24	B	1923	ILE	0	-0.067	-0.029	30.707	0.004	0.004	0.000	0.000	0.000
25	B	1924	ARG	1	0.902	0.933	31.814	0.056	0.056	0.000	0.000	0.000
26	B	1925	GLN	0	-0.008	0.019	34.399	0.001	0.001	0.000	0.000	0.000
27	B	1926	ILE	0	-0.027	-0.013	34.834	0.003	0.003	0.000	0.000	0.000
28	B	1927	GLU	-1	-0.862	-0.933	37.413	-0.046	-0.046	0.000	0.000	0.000
29	B	1928	THR	0	-0.067	-0.056	39.141	0.003	0.003	0.000	0.000	0.000
30	B	1929	GLN	0	-0.038	-0.005	41.484	0.002	0.002	0.000	0.000	0.000
31	B	1930	GLU	-1	-0.831	-0.907	43.697	-0.031	-0.031	0.000	0.000	0.000
32	B	1931	ARG	0	0.008	0.022	45.955	-0.001	-0.001	0.000	0.000	0.000
33	B	1932	PRO	0	0.006	0.002	47.563	0.000	0.000	0.000	0.000	0.000
34	B	1933	ARG	1	0.785	0.880	50.886	0.025	0.025	0.000	0.000	0.000
35	B	1934	ASP	-1	-0.758	-0.882	49.331	-0.027	-0.027	0.000	0.000	0.000
36	B	1935	VAL	0	0.017	0.030	49.704	0.001	0.001	0.000	0.000	0.000
37	B	1936	SER	0	-0.026	-0.014	52.065	0.001	0.001	0.000	0.000	0.000
38	B	1937	SER	0	0.021	0.006	55.037	0.001	0.001	0.000	0.000	0.000
39	B	1938	VAL	0	0.040	0.019	52.647	0.000	0.000	0.000	0.000	0.000
40	B	1939	GLU	-1	-0.842	-0.940	48.140	-0.036	-0.036	0.000	0.000	0.000
41	B	1940	LEU	0	0.003	-0.004	47.039	-0.002	-0.002	0.000	0.000	0.000
42	B	1941	LEU	0	0.042	0.014	44.793	-0.002	-0.002	0.000	0.000	0.000
43	B	1942	MET	0	0.028	0.029	43.675	-0.002	-0.002	0.000	0.000	0.000
44	B	1943	LYS	1	0.934	0.968	41.582	0.046	0.046	0.000	0.000	0.000
45	B	1944	TYR	0	-0.029	-0.023	39.514	-0.003	-0.003	0.000	0.000	0.000
46	B	1945	HIS	0	0.051	0.019	38.909	-0.003	-0.003	0.000	0.000	0.000
47	B	1946	GLN	0	0.000	-0.003	38.121	-0.002	-0.002	0.000	0.000	0.000
48	B	1947	GLY	0	-0.023	-0.008	37.071	-0.004	-0.004	0.000	0.000	0.000
49	B	1948	ILE	0	0.007	0.010	33.938	-0.005	-0.005	0.000	0.000	0.000
50	B	1949	ASN	0	-0.032	-0.007	33.095	-0.010	-0.010	0.000	0.000	0.000
51	B	1950	ALA	0	0.013	0.004	32.499	-0.006	-0.006	0.000	0.000	0.000
52	B	1951	GLU	-1	-0.798	-0.888	29.713	-0.092	-0.092	0.000	0.000	0.000
53	B	1952	ILE	0	-0.005	-0.003	28.639	-0.010	-0.010	0.000	0.000	0.000
54	B	1953	GLU	-1	-0.859	-0.920	27.514	-0.130	-0.130	0.000	0.000	0.000
55	B	1954	THR	0	-0.088	-0.049	26.947	-0.011	-0.011	0.000	0.000	0.000
56	B	1955	ARG	1	0.814	0.900	23.485	0.100	0.100	0.000	0.000	0.000
57	B	1956	SER	0	-0.034	-0.012	22.730	-0.021	-0.021	0.000	0.000	0.000
58	B	1957	LYS	1	0.973	0.985	20.724	0.133	0.133	0.000	0.000	0.000
59	B	1958	ASN	0	0.026	0.007	18.383	-0.009	-0.009	0.000	0.000	0.000
60	B	1959	PHE	0	0.042	0.007	18.187	-0.025	-0.025	0.000	0.000	0.000
61	B	1960	SER	0	-0.030	-0.013	19.060	-0.012	-0.012	0.000	0.000	0.000
62	B	1961	ALA	0	0.048	0.023	14.556	-0.019	-0.019	0.000	0.000	0.000
63	B	1962	CYS	0	-0.064	-0.021	14.125	-0.053	-0.053	0.000	0.000	0.000
64	B	1963	LEU	0	0.028	-0.011	15.089	-0.027	-0.027	0.000	0.000	0.000
65	B	1964	GLU	-1	-0.936	-0.947	13.571	-0.405	-0.405	0.000	0.000	0.000
66	B	1965	LEU	0	-0.052	-0.027	7.793	-0.052	-0.052	0.000	0.000	0.000
67	B	1966	GLY	0	0.038	0.010	11.442	-0.064	-0.064	0.000	0.000	0.000
68	B	1967	GLU	-1	-0.719	-0.859	13.823	-0.200	-0.200	0.000	0.000	0.000
69	B	1968	SER	0	-0.023	0.005	10.538	-0.059	-0.059	0.000	0.000	0.000
70	B	1969	LEU	0	-0.054	-0.037	7.648	-0.069	-0.069	0.000	0.000	0.000
71	B	1970	LEU	0	-0.020	0.006	10.855	0.083	0.083	0.000	0.000	0.000
72	B	1971	GLN	0	-0.014	0.004	13.062	0.018	0.018	0.000	0.000	0.000
73	B	1972	ARG	1	0.730	0.851	5.496	1.489	1.489	0.000	0.000	0.000
74	B	1973	GLN	0	0.008	0.001	10.285	0.069	0.069	0.000	0.000	0.000
75	B	1974	HIS	0	0.039	0.032	7.377	0.194	0.194	0.000	0.000	0.000
76	B	1975	GLN	0	-0.037	-0.015	10.942	-0.014	-0.014	0.000	0.000	0.000
77	B	1976	ALA	0	-0.006	-0.015	12.639	0.028	0.028	0.000	0.000	0.000
78	B	1977	SER	0	0.022	-0.011	14.322	-0.063	-0.063	0.000	0.000	0.000
79	B	1978	GLU	-1	-0.892	-0.932	15.877	-0.047	-0.047	0.000	0.000	0.000
80	B	1979	GLU	-1	-0.759	-0.864	15.485	-0.079	-0.079	0.000	0.000	0.000
81	B	1980	ILE	0	-0.033	-0.032	11.551	-0.026	-0.026	0.000	0.000	0.000
82	B	1981	ARG	1	0.837	0.899	15.798	0.137	0.137	0.000	0.000	0.000
83	B	1982	GLU	-1	-0.921	-0.967	18.850	-0.056	-0.056	0.000	0.000	0.000
84	B	1983	LYS	1	0.851	0.935	17.430	0.126	0.126	0.000	0.000	0.000
85	B	1984	LEU	0	0.005	0.003	16.652	-0.003	-0.003	0.000	0.000	0.000
86	B	1985	GLN	0	0.028	0.003	19.581	0.003	0.003	0.000	0.000	0.000
87	B	1986	GLN	0	0.015	0.016	22.455	0.001	0.001	0.000	0.000	0.000
88	B	1987	VAL	0	0.004	-0.001	19.761	0.009	0.009	0.000	0.000	0.000
89	B	1988	MET	0	-0.009	-0.007	22.310	0.004	0.004	0.000	0.000	0.000
90	B	1989	SER	0	-0.055	-0.019	24.637	0.009	0.009	0.000	0.000	0.000
91	B	1990	ARG	1	1.018	0.996	26.309	0.081	0.081	0.000	0.000	0.000
92	B	1991	ARG	1	0.926	0.976	24.481	0.141	0.141	0.000	0.000	0.000
93	B	1992	LYS	1	0.841	0.916	27.506	0.082	0.082	0.000	0.000	0.000
94	B	1993	GLU	-1	-0.826	-0.909	30.527	-0.062	-0.062	0.000	0.000	0.000
95	B	1994	MET	0	-0.013	0.005	27.812	0.004	0.004	0.000	0.000	0.000
96	B	1995	ASN	0	0.019	-0.001	30.545	0.002	0.002	0.000	0.000	0.000
97	B	1996	GLU	-1	-0.856	-0.914	33.175	-0.066	-0.066	0.000	0.000	0.000
98	B	1997	LYS	1	0.809	0.891	34.734	0.059	0.059	0.000	0.000	0.000
99	B	1998	TRP	0	-0.037	-0.011	35.190	0.003	0.003	0.000	0.000	0.000
100	B	1999	GLU	-1	-0.844	-0.953	36.842	-0.058	-0.058	0.000	0.000	0.000
101	B	2000	ALA	0	-0.032	-0.006	39.199	0.003	0.003	0.000	0.000	0.000
102	B	2001	ARG	1	0.821	0.897	40.633	0.044	0.044	0.000	0.000	0.000
103	B	2002	TRP	0	-0.040	-0.015	40.821	0.003	0.003	0.000	0.000	0.000
104	B	2003	GLU	-1	-0.808	-0.898	42.774	-0.037	-0.037	0.000	0.000	0.000
105	B	2004	ARG	1	0.833	0.892	45.118	0.035	0.035	0.000	0.000	0.000
106	B	2005	LEU	0	-0.024	-0.003	43.576	0.002	0.002	0.000	0.000	0.000
107	B	2006	ARG	1	0.941	0.975	44.645	0.046	0.046	0.000	0.000	0.000
108	B	2007	MET	0	0.007	0.046	49.051	0.001	0.001	0.000	0.000	0.000
109	B	2008	LEU	0	-0.035	-0.005	50.530	0.002	0.002	0.000	0.000	0.000
110	B	2009	LEU	0	0.018	-0.006	50.351	0.001	0.001	0.000	0.000	0.000
111	B	2010	GLU	-1	-0.755	-0.865	52.903	-0.028	-0.028	0.000	0.000	0.000
112	B	2011	VAL	0	0.001	0.012	55.549	0.001	0.001	0.000	0.000	0.000
113	B	2012	CYS	0	-0.065	-0.028	54.028	0.001	0.001	0.000	0.000	0.000
114	B	2013	GLN	0	-0.050	-0.020	54.612	0.001	0.001	0.000	0.000	0.000
115	B	2014	PHE	0	0.098	0.053	58.814	0.001	0.001	0.000	0.000	0.000
116	B	2015	SER	0	0.028	0.011	60.841	0.001	0.001	0.000	0.000	0.000
117	B	2016	ARG	1	0.754	0.862	59.733	0.025	0.025	0.000	0.000	0.000
118	B	2017	ASP	-1	-0.786	-0.874	62.141	-0.023	-0.023	0.000	0.000	0.000
119	B	2018	ALA	0	0.039	0.023	64.848	0.001	0.001	0.000	0.000	0.000
120	B	2019	SER	0	-0.037	-0.027	65.834	0.001	0.001	0.000	0.000	0.000
121	B	2020	VAL	0	-0.060	-0.033	66.310	0.001	0.001	0.000	0.000	0.000
122	B	2021	ALA	0	-0.001	0.006	68.960	0.001	0.001	0.000	0.000	0.000
123	B	2022	GLU	-1	-0.902	-0.958	70.991	-0.016	-0.016	0.000	0.000	0.000
124	B	2023	ALA	0	-0.033	-0.016	71.835	0.001	0.001	0.000	0.000	0.000
125	B	2024	TRP	0	-0.011	-0.013	73.162	0.000	0.000	0.000	0.000	0.000
126	B	2025	LEU	0	0.001	-0.004	74.959	0.000	0.000	0.000	0.000	0.000
127	B	2026	ILE	0	-0.025	-0.010	76.819	0.001	0.001	0.000	0.000	0.000
128	B	2027	ALA	0	-0.044	-0.019	77.389	0.000	0.000	0.000	0.000	0.000
129	B	2028	GLN	0	-0.007	-0.001	78.914	0.000	0.000	0.000	0.000	0.000
130	B	2029	GLU	-1	-0.872	-0.931	81.470	-0.012	-0.012	0.000	0.000	0.000
131	B	2030	PRO	0	-0.060	-0.039	83.344	0.000	0.000	0.000	0.000	0.000
132	B	2031	TYR	0	-0.076	-0.031	85.610	0.000	0.000	0.000	0.000	0.000
133	B	2032	LEU	0	-0.010	0.003	83.563	0.000	0.000	0.000	0.000	0.000
134	B	2033	ALA	0	0.017	0.016	87.090	0.000	0.000	0.000	0.000	0.000
135	B	2034	SER	0	-0.113	-0.053	89.334	0.000	0.000	0.000	0.000	0.000
136	B	2035	GLY	0	0.021	0.002	92.210	0.000	0.000	0.000	0.000	0.000
137	B	2036	ASP	-1	-0.931	-0.967	95.231	-0.009	-0.009	0.000	0.000	0.000
138	B	2037	PHE	0	0.011	-0.002	93.659	0.000	0.000	0.000	0.000	0.000
139	B	2038	GLY	0	-0.001	0.002	97.613	0.000	0.000	0.000	0.000	0.000
140	B	2039	HIS	0	-0.025	-0.017	100.335	0.000	0.000	0.000	0.000	0.000
141	B	2040	THR	0	-0.020	-0.017	103.368	0.000	0.000	0.000	0.000	0.000
142	B	2041	VAL	0	0.011	0.024	102.148	0.000	0.000	0.000	0.000	0.000
143	B	2042	ASP	-1	-0.732	-0.845	100.946	-0.010	-0.010	0.000	0.000	0.000
144	B	2043	SER	0	-0.033	-0.030	99.334	0.000	0.000	0.000	0.000	0.000
145	B	2044	VAL	0	0.046	0.020	97.803	0.000	0.000	0.000	0.000	0.000
146	B	2045	GLU	-1	-0.916	-0.964	96.495	-0.010	-0.010	0.000	0.000	0.000
147	B	2046	LYS	1	0.759	0.864	94.934	0.009	0.009	0.000	0.000	0.000
148	B	2047	LEU	0	-0.009	0.006	93.299	0.000	0.000	0.000	0.000	0.000
149	B	2048	ILE	0	0.022	0.019	91.953	0.000	0.000	0.000	0.000	0.000
150	B	2049	LYS	1	0.964	0.986	90.475	0.012	0.012	0.000	0.000	0.000
151	B	2050	ARG	1	0.900	0.950	87.937	0.011	0.011	0.000	0.000	0.000
152	B	2051	HIS	0	0.005	0.001	86.481	0.000	0.000	0.000	0.000	0.000
153	B	2052	GLU	-1	-0.889	-0.949	86.205	-0.013	-0.013	0.000	0.000	0.000
154	B	2053	ALA	0	-0.071	-0.039	84.212	0.000	0.000	0.000	0.000	0.000
155	B	2054	PHE	0	0.040	0.028	82.668	0.000	0.000	0.000	0.000	0.000
156	B	2055	GLU	-1	-0.833	-0.904	81.730	-0.014	-0.014	0.000	0.000	0.000
157	B	2056	LYS	1	0.945	0.973	79.567	0.015	0.015	0.000	0.000	0.000
158	B	2057	SER	0	-0.112	-0.071	78.235	-0.001	-0.001	0.000	0.000	0.000
159	B	2058	THR	0	0.026	-0.004	76.939	0.000	0.000	0.000	0.000	0.000
160	B	2059	ALA	0	-0.003	-0.002	76.343	0.000	0.000	0.000	0.000	0.000
161	B	2060	SER	0	-0.054	-0.020	72.982	-0.001	-0.001	0.000	0.000	0.000
162	B	2061	TRP	0	0.022	-0.007	70.107	-0.001	-0.001	0.000	0.000	0.000
163	B	2062	ALA	0	-0.006	0.010	71.551	0.000	0.000	0.000	0.000	0.000
164	B	2063	GLU	-1	-0.930	-0.970	67.629	-0.021	-0.021	0.000	0.000	0.000
165	B	2064	ARG	1	0.886	0.958	67.041	0.019	0.019	0.000	0.000	0.000
166	B	2065	PHE	0	0.031	0.008	67.389	0.000	0.000	0.000	0.000	0.000
167	B	2066	ALA	0	0.049	0.024	68.338	0.000	0.000	0.000	0.000	0.000
168	B	2067	ALA	0	-0.059	-0.034	63.413	-0.001	-0.001	0.000	0.000	0.000
169	B	2068	LEU	0	-0.065	-0.032	63.456	-0.001	-0.001	0.000	0.000	0.000
170	B	2069	GLU	-1	-0.953	-0.958	65.451	-0.019	-0.019	0.000	0.000	0.000
171	B	2070	LYS	1	0.801	0.910	58.492	0.026	0.026	0.000	0.000	0.000
172	B	2071	PRO	0	0.011	0.001	60.436	0.000	0.000	0.000	0.000	0.000
173	B	2072	THR	0	-0.035	-0.027	56.121	-0.001	-0.001	0.000	0.000	0.000
174	B	2073	THR	0	-0.026	-0.062	52.174	0.000	0.000	0.000	0.000	0.000
175	B	2074	LEU	0	-0.044	-0.033	53.667	-0.001	-0.001	0.000	0.000	0.000
176	B	2075	GLU	-1	-0.790	-0.879	55.256	-0.023	-0.023	0.000	0.000	0.000
177	B	2076	LEU	0	-0.045	-0.021	55.447	0.000	0.000	0.000	0.000	0.000
178	B	2077	LYS	1	0.797	0.848	48.695	0.035	0.035	0.000	0.000	0.000
179	B	2078	GLU	-1	-0.858	-0.926	53.998	-0.023	-0.023	0.000	0.000	0.000
180	B	2079	ARG	1	0.909	0.959	56.154	0.025	0.025	0.000	0.000	0.000
181	B	2080	GLN	0	-0.047	-0.021	50.804	-0.001	-0.001	0.000	0.000	0.000
182	B	2081	ILE	0	-0.064	-0.018	53.304	0.000	0.000	0.000	0.000	0.000
183	B	2082	ALA	0	-0.001	0.002	55.402	0.001	0.001	0.000	0.000	0.000
184	B	2083	GLU	-1	-1.033	-1.003	54.926	-0.024	-0.024	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1900:GLY)