FMO DATABASE

FMODB ID: VQ5L1

Calculation Name: 3EOD-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3EOD

Chain ID: A

ChEMBL ID:
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UniProt ID: P0AEV1

Base Structure: X-ray

Registration Date: 2023-09-21

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1040672.031145
FMO2-HF: Nuclear repulsion	992439.321755
FMO2-HF: Total energy	-48232.709391
FMO2-MP2: Total energy	-48370.811184

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:3:GLN)

Summations of interaction energy for fragment #1(A:3:GLN)

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.
-14.649	-6.89	6.093	-5.12	-8.734	-0.011

Interaction energy analysis for fragmet #1(A:3:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.029

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	5	LEU	0	-0.001	0.000	3.259	-1.001	0.893	0.000	-0.804	-1.091	0.001
4	A	6	VAL	0	0.035	0.027	2.309	-0.445	1.022	1.825	-0.963	-2.330	0.006
5	A	7	GLY	0	-0.054	-0.027	4.778	-1.186	-1.146	-0.001	-0.011	-0.028	0.000
6	A	8	LYS	1	0.911	0.976	8.031	-1.048	-1.048	0.000	0.000	0.000	0.000
7	A	9	GLN	0	0.016	-0.008	9.634	0.190	0.190	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.016	-0.013	10.572	-0.149	-0.149	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.005	0.006	13.345	0.001	0.001	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.013	-0.014	13.032	-0.046	-0.046	0.000	0.000	0.000	0.000
11	A	13	VAL	0	-0.009	-0.011	17.396	0.002	0.002	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.834	-0.941	19.911	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.806	-0.899	21.862	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.964	-0.974	23.217	-0.127	-0.127	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.038	-0.033	19.645	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	18	VAL	0	0.058	0.022	19.838	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	19	PHE	0	0.025	0.010	18.574	-0.052	-0.052	0.000	0.000	0.000	0.000
18	A	20	ARG	1	0.886	0.940	17.411	0.000	0.000	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.015	-0.013	15.459	0.001	0.001	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.045	-0.010	13.849	-0.098	-0.098	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.011	-0.004	12.946	-0.118	-0.118	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.812	-0.893	11.214	-0.139	-0.139	0.000	0.000	0.000	0.000
23	A	25	SER	0	-0.021	-0.003	9.585	-0.237	-0.237	0.000	0.000	0.000	0.000
24	A	26	TRP	0	0.019	0.004	8.132	-0.527	-0.527	0.000	0.000	0.000	0.000
25	A	27	PHE	0	0.055	0.012	7.646	-0.326	-0.326	0.000	0.000	0.000	0.000
26	A	28	SER	0	0.020	0.013	6.205	0.234	0.234	0.000	0.000	0.000	0.000
27	A	29	SER	0	-0.136	-0.061	3.919	-1.774	-1.456	0.000	-0.100	-0.218	-0.001
28	A	30	LEU	0	-0.060	-0.041	3.078	-6.915	-4.981	0.222	-0.910	-1.246	-0.006
29	A	31	GLY	0	0.009	-0.003	2.425	-3.116	-0.708	3.964	-2.982	-3.390	-0.014
30	A	32	ALA	0	-0.022	0.015	3.460	1.257	0.955	0.083	0.650	-0.431	0.003
31	A	33	THR	0	-0.038	-0.018	6.972	-0.181	-0.181	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.019	-0.033	9.350	-0.130	-0.130	0.000	0.000	0.000	0.000
33	A	35	VAL	0	0.015	0.015	11.844	0.026	0.026	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.021	-0.007	13.572	-0.049	-0.049	0.000	0.000	0.000	0.000
35	A	37	ALA	0	-0.005	0.002	17.469	0.011	0.011	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.030	-0.022	21.229	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.728	-0.843	23.396	0.049	0.049	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.073	-0.001	25.634	0.016	0.016	0.000	0.000	0.000	0.000
39	A	41	VAL	0	-0.079	-0.044	26.918	0.010	0.010	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.846	-0.925	25.642	0.112	0.112	0.000	0.000	0.000	0.000
41	A	43	ALA	0	-0.036	-0.027	23.288	0.021	0.021	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.031	-0.021	24.608	0.018	0.018	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.956	-0.970	27.519	0.157	0.157	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.023	-0.008	21.326	0.017	0.017	0.000	0.000	0.000	0.000
45	A	47	LEU	0	0.008	0.002	21.655	0.028	0.028	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.075	-0.017	24.629	0.003	0.003	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.040	-0.023	25.203	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.070	-0.043	17.310	0.029	0.029	0.000	0.000	0.000	0.000
49	A	51	THR	0	0.006	-0.009	20.118	-0.051	-0.051	0.000	0.000	0.000	0.000
50	A	52	PRO	0	-0.023	0.018	16.496	0.049	0.049	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.841	-0.917	13.256	0.707	0.707	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.029	-0.025	13.340	-0.064	-0.064	0.000	0.000	0.000	0.000
53	A	55	MET	0	-0.019	0.005	15.954	0.029	0.029	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.003	0.000	14.787	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	57	CYS	0	-0.020	-0.006	18.554	0.003	0.003	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.677	-0.832	22.054	-0.036	-0.036	0.000	0.000	0.000	0.000
57	A	59	ILE	0	-0.029	-0.025	24.857	0.011	0.011	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.018	-0.005	28.074	0.001	0.001	0.000	0.000	0.000	0.000
59	A	61	MET	0	-0.020	0.006	25.981	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.042	0.027	29.195	0.006	0.006	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.810	0.865	30.807	-0.045	-0.045	0.000	0.000	0.000	0.000
62	A	64	MET	0	-0.052	0.011	28.707	0.012	0.012	0.000	0.000	0.000	0.000
63	A	65	ASN	0	0.011	-0.009	31.602	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.056	0.030	27.789	0.009	0.009	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.011	-0.009	28.119	0.011	0.011	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.904	0.965	30.401	-0.042	-0.042	0.000	0.000	0.000	0.000
67	A	69	LEU	0	0.022	0.024	24.418	0.005	0.005	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.006	0.004	25.405	0.010	0.010	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.899	-0.966	28.056	0.066	0.066	0.000	0.000	0.000	0.000
70	A	72	HIS	0	-0.033	-0.020	31.040	0.006	0.006	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.019	-0.020	24.676	0.006	0.006	0.000	0.000	0.000	0.000
72	A	74	ARG	1	0.776	0.877	23.418	-0.128	-0.128	0.000	0.000	0.000	0.000
73	A	75	ASN	0	-0.030	-0.015	29.830	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.796	0.937	27.147	-0.195	-0.195	0.000	0.000	0.000	0.000
75	A	77	GLY	0	-0.006	0.001	30.822	0.005	0.005	0.000	0.000	0.000	0.000
76	A	78	ASP	-1	-0.858	-0.932	25.503	0.204	0.204	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.052	-0.039	24.509	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.010	0.006	19.742	0.004	0.004	0.000	0.000	0.000	0.000
79	A	81	PRO	0	0.090	0.058	17.924	-0.032	-0.032	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.012	0.003	19.301	0.014	0.014	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.022	0.015	16.399	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	84	VAL	0	-0.002	-0.006	19.838	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.019	-0.005	17.394	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	86	SER	0	-0.024	-0.038	22.041	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	87	ALA	0	0.001	-0.005	25.555	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.041	-0.002	27.971	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.886	-0.944	30.367	-0.052	-0.052	0.000	0.000	0.000	0.000
88	A	90	ASN	0	-0.017	-0.007	33.127	0.004	0.004	0.000	0.000	0.000	0.000
89	A	91	MET	0	0.041	0.005	32.391	0.005	0.005	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.006	0.002	34.416	0.005	0.005	0.000	0.000	0.000	0.000
91	A	93	ASP	-1	-0.900	-0.957	32.448	0.013	0.013	0.000	0.000	0.000	0.000
92	A	94	ILE	0	0.026	0.009	28.966	0.007	0.007	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.016	-0.009	30.553	0.007	0.007	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.883	0.935	32.818	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.061	0.029	27.586	0.007	0.007	0.000	0.000	0.000	0.000
96	A	98	LEU	0	0.006	-0.003	27.126	0.008	0.008	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.871	0.935	29.428	-0.025	-0.025	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.023	0.003	29.476	0.004	0.004	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.022	0.034	27.440	0.010	0.010	0.000	0.000	0.000	0.000
100	A	102	VAL	0	-0.045	-0.025	23.720	0.011	0.011	0.000	0.000	0.000	0.000
101	A	103	GLU	-1	-0.894	-0.960	18.913	0.118	0.118	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.844	-0.944	21.047	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.072	-0.042	22.672	0.007	0.007	0.000	0.000	0.000	0.000
104	A	106	LEU	0	-0.050	-0.011	18.437	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.012	0.019	22.512	0.000	0.000	0.000	0.000	0.000	0.000
106	A	108	LYS	1	0.874	0.932	22.744	0.050	0.050	0.000	0.000	0.000	0.000
107	A	109	PRO	0	-0.007	-0.045	23.379	0.012	0.012	0.000	0.000	0.000	0.000
108	A	110	VAL	0	0.023	0.009	17.997	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.906	0.998	21.106	0.083	0.083	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.754	-0.933	20.019	-0.141	-0.141	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.084	0.034	13.672	0.028	0.028	0.000	0.000	0.000	0.000
112	A	114	ASN	0	-0.097	-0.034	14.181	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.926	0.953	15.620	0.058	0.058	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.014	0.017	13.651	0.022	0.022	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.916	0.965	7.303	0.220	0.220	0.000	0.000	0.000	0.000
116	A	118	GLU	-1	-0.883	-0.931	12.700	-0.013	-0.013	0.000	0.000	0.000	0.000
117	A	119	MET	0	-0.033	0.005	15.169	0.016	0.016	0.000	0.000	0.000	0.000
118	A	120	VAL	0	0.035	0.021	10.458	0.022	0.022	0.000	0.000	0.000	0.000
119	A	121	PHE	0	-0.031	-0.026	6.693	0.069	0.069	0.000	0.000	0.000	0.000
120	A	122	ALA	0	-0.078	-0.023	12.114	0.004	0.004	0.000	0.000	0.000	0.000
121	A	123	CYS	0	-0.041	0.007	14.678	0.009	0.009	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.014	-0.018	10.115	0.031	0.031	0.000	0.000	0.000	0.000
123	A	125	TYR	0	-0.062	-0.018	8.347	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLN)