FMO DATABASE

FMODB ID: G56G1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1042138.615828
FMO2-HF: Nuclear repulsion	993904.736011
FMO2-HF: Total energy	-48233.879816
FMO2-MP2: Total energy	-48371.882747

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.
-20.031	-15.224	12.76	-5.247	-12.321	-0.043

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 : -0.049 / q_NPA : -0.033

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	0.005	0.018	3.564	-0.517	1.470	-0.013	-0.919	-1.055	0.000
4	A	6	VAL	0	0.020	0.016	2.139	0.162	0.816	2.593	-1.043	-2.204	0.000
5	A	7	GLY	0	-0.034	-0.010	4.801	-0.916	-0.851	-0.001	-0.018	-0.046	0.000
6	A	8	LYS	1	0.819	0.927	8.121	-0.415	-0.415	0.000	0.000	0.000	0.000
7	A	9	GLN	0	-0.030	-0.012	9.595	0.160	0.160	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.015	-0.012	10.392	-0.103	-0.103	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.002	0.009	13.045	0.002	0.002	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.021	-0.015	12.026	-0.047	-0.047	0.000	0.000	0.000	0.000
11	A	13	VAL	0	-0.012	-0.009	16.550	0.026	0.026	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.763	-0.879	19.277	-0.214	-0.214	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.836	-0.916	21.219	-0.126	-0.126	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.835	-0.905	22.082	-0.249	-0.249	0.000	0.000	0.000	0.000
15	A	17	GLN	0	0.026	-0.003	18.938	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	18	VAL	0	0.004	0.024	18.902	-0.034	-0.034	0.000	0.000	0.000	0.000
17	A	19	PHE	0	0.023	-0.002	17.521	-0.076	-0.076	0.000	0.000	0.000	0.000
18	A	20	ARG	1	0.859	0.913	16.453	0.103	0.103	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.026	-0.032	14.580	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.051	-0.018	12.964	-0.130	-0.130	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.005	-0.001	12.011	-0.188	-0.188	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.807	-0.891	10.076	-0.664	-0.664	0.000	0.000	0.000	0.000
23	A	25	SER	0	-0.015	0.001	8.548	-0.417	-0.417	0.000	0.000	0.000	0.000
24	A	26	TRP	0	-0.018	-0.018	7.265	-0.811	-0.811	0.000	0.000	0.000	0.000
25	A	27	PHE	0	0.038	0.009	7.098	-0.584	-0.584	0.000	0.000	0.000	0.000
26	A	28	SER	0	0.041	0.023	4.988	-0.224	-0.224	0.000	0.000	0.000	0.000
27	A	29	SER	0	-0.119	-0.066	2.760	-6.231	-4.265	0.213	-1.043	-1.136	-0.012
28	A	30	LEU	0	-0.047	-0.031	2.148	-10.841	-9.739	4.205	-2.219	-3.089	-0.029
29	A	31	GLY	0	0.013	0.002	2.531	-2.003	-0.361	5.403	-2.855	-4.190	-0.007
30	A	32	ALA	0	-0.038	-0.002	3.022	3.245	0.636	0.360	2.850	-0.601	0.005
31	A	33	THR	0	-0.031	-0.023	6.417	-0.191	-0.191	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.017	-0.031	8.530	-0.126	-0.126	0.000	0.000	0.000	0.000
33	A	35	VAL	0	0.002	0.008	10.903	0.094	0.094	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.017	-0.011	12.530	-0.057	-0.057	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.003	0.011	16.619	0.026	0.026	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.028	-0.024	20.395	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.746	-0.857	22.584	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.072	0.008	24.389	0.007	0.007	0.000	0.000	0.000	0.000
39	A	41	VAL	0	-0.045	-0.032	25.947	0.009	0.009	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.865	-0.931	24.593	0.011	0.011	0.000	0.000	0.000	0.000
41	A	43	ALA	0	-0.024	-0.019	22.412	0.016	0.016	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.021	-0.007	23.517	0.013	0.013	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.960	-0.975	26.544	0.068	0.068	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.014	-0.006	20.485	0.015	0.015	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.011	-0.007	20.945	0.021	0.021	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.009	0.010	24.038	0.004	0.004	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.055	-0.031	25.158	0.002	0.002	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.036	-0.023	16.632	0.021	0.021	0.000	0.000	0.000	0.000
49	A	51	THR	0	-0.024	-0.025	20.078	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	52	PRO	0	-0.043	0.010	15.884	0.044	0.044	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.787	-0.898	13.463	0.271	0.271	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.024	-0.022	13.837	-0.045	-0.045	0.000	0.000	0.000	0.000
53	A	55	MET	0	-0.009	0.008	16.163	0.019	0.019	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.003	0.005	14.693	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	57	CYS	0	0.011	-0.001	18.051	0.013	0.013	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.658	-0.787	21.361	-0.142	-0.142	0.000	0.000	0.000	0.000
57	A	59	ILE	0	-0.033	-0.026	24.232	0.015	0.015	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.033	-0.025	27.460	0.011	0.011	0.000	0.000	0.000	0.000
59	A	61	MET	0	-0.037	0.007	24.769	0.000	0.000	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.037	0.028	27.937	0.012	0.012	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.796	0.861	29.875	0.032	0.032	0.000	0.000	0.000	0.000
62	A	64	MET	0	-0.042	0.007	27.459	0.010	0.010	0.000	0.000	0.000	0.000
63	A	65	ASN	0	0.014	-0.005	30.823	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.057	0.037	27.240	0.007	0.007	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.009	-0.011	27.821	0.006	0.006	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.746	0.858	30.239	0.024	0.024	0.000	0.000	0.000	0.000
67	A	69	LEU	0	0.007	0.016	23.502	0.007	0.007	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.011	0.004	25.659	0.008	0.008	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.786	-0.888	27.897	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	72	HIS	0	-0.005	-0.005	30.746	0.008	0.008	0.000	0.000	0.000	0.000
71	A	73	ILE	0	0.010	0.012	24.655	0.006	0.006	0.000	0.000	0.000	0.000
72	A	74	ARG	1	0.755	0.865	23.869	0.006	0.006	0.000	0.000	0.000	0.000
73	A	75	ASN	0	-0.050	-0.029	30.226	0.003	0.003	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.751	0.872	26.177	-0.077	-0.077	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.015	0.012	31.232	0.007	0.007	0.000	0.000	0.000	0.000
76	A	78	ASP	-1	-0.820	-0.883	25.630	0.070	0.070	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.072	-0.053	25.437	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	80	THR	0	0.010	0.012	20.471	0.003	0.003	0.000	0.000	0.000	0.000
79	A	81	PRO	0	0.059	0.048	18.278	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	82	VAL	0	-0.028	-0.023	19.926	0.001	0.001	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.011	0.015	16.061	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	84	VAL	0	-0.022	-0.013	19.859	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.008	-0.008	17.031	-0.018	-0.018	0.000	0.000	0.000	0.000
84	A	86	SER	0	-0.050	-0.058	21.732	0.008	0.008	0.000	0.000	0.000	0.000
85	A	87	ALA	0	0.018	0.007	25.167	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.040	-0.010	27.657	0.008	0.008	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.878	-0.942	30.199	-0.112	-0.112	0.000	0.000	0.000	0.000
88	A	90	ASN	0	-0.060	-0.041	32.771	0.008	0.008	0.000	0.000	0.000	0.000
89	A	91	MET	0	0.044	0.011	32.097	0.001	0.001	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.018	-0.007	34.322	0.003	0.003	0.000	0.000	0.000	0.000
91	A	93	ASP	-1	-0.815	-0.893	32.239	-0.053	-0.053	0.000	0.000	0.000	0.000
92	A	94	ILE	0	0.057	0.027	28.738	0.003	0.003	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.016	0.003	30.487	0.003	0.003	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.799	0.902	33.126	0.050	0.050	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.059	0.021	27.461	0.006	0.006	0.000	0.000	0.000	0.000
96	A	98	LEU	0	0.010	0.002	27.324	0.005	0.005	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.845	0.920	29.586	0.037	0.037	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.017	0.005	29.811	0.006	0.006	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.027	0.033	27.639	0.007	0.007	0.000	0.000	0.000	0.000
100	A	102	VAL	0	-0.022	-0.016	23.755	0.003	0.003	0.000	0.000	0.000	0.000
101	A	103	GLU	-1	-0.801	-0.911	18.599	-0.046	-0.046	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.799	-0.893	20.762	-0.131	-0.131	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.073	-0.054	22.581	0.002	0.002	0.000	0.000	0.000	0.000
104	A	106	LEU	0	-0.038	0.001	18.120	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.010	0.017	22.184	0.006	0.006	0.000	0.000	0.000	0.000
106	A	108	LYS	1	0.797	0.860	21.682	0.170	0.170	0.000	0.000	0.000	0.000
107	A	109	PRO	0	0.002	-0.035	22.784	0.020	0.020	0.000	0.000	0.000	0.000
108	A	110	VAL	0	-0.016	0.006	17.628	0.005	0.005	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.899	0.993	20.584	0.146	0.146	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.820	-0.937	19.705	-0.234	-0.234	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.032	0.023	13.910	0.010	0.010	0.000	0.000	0.000	0.000
112	A	114	ASN	0	-0.019	-0.031	13.893	-0.114	-0.114	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.834	0.889	15.208	0.144	0.144	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.042	0.019	13.590	0.026	0.026	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.900	0.957	7.984	0.893	0.893	0.000	0.000	0.000	0.000
116	A	118	GLU	-1	-0.867	-0.918	12.474	-0.126	-0.126	0.000	0.000	0.000	0.000
117	A	119	MET	0	-0.025	0.014	15.142	0.005	0.005	0.000	0.000	0.000	0.000
118	A	120	VAL	0	0.026	0.019	10.431	0.023	0.023	0.000	0.000	0.000	0.000
119	A	121	PHE	0	-0.019	-0.017	6.589	0.047	0.047	0.000	0.000	0.000	0.000
120	A	122	ALA	0	-0.023	0.002	12.193	0.030	0.030	0.000	0.000	0.000	0.000
121	A	123	CYS	0	-0.072	-0.006	15.437	0.025	0.025	0.000	0.000	0.000	0.000
122	A	124	LEU	0	0.000	-0.008	10.390	0.026	0.026	0.000	0.000	0.000	0.000
123	A	125	TYR	0	-0.112	-0.085	7.230	0.147	0.147	0.000	0.000	0.000	0.000

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Graph

Overview

Highlights

Manual

Support

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