FMO DATABASE

FMODB ID: 1N7KZ

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	OptHSide
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	-1041005.362773
FMO2-HF: Nuclear repulsion	992771.821559
FMO2-HF: Total energy	-48233.541214
FMO2-MP2: Total energy	-48371.584152

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.
-15.17	-8.97	9.438	-5.014	-10.622	-0.026

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 : -0.033 / 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	0.013	0.010	3.239	-0.857	1.038	0.001	-0.799	-1.096	0.001
4	A	6	VAL	0	0.028	0.023	2.261	-0.161	0.897	2.332	-1.011	-2.379	0.001
5	A	7	GLY	0	-0.039	-0.017	4.894	-0.942	-0.902	-0.001	-0.011	-0.027	0.000
6	A	8	LYS	1	0.832	0.928	8.148	-0.694	-0.694	0.000	0.000	0.000	0.000
7	A	9	GLN	0	0.004	-0.004	9.539	0.134	0.134	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.003	-0.011	10.467	-0.122	-0.122	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.006	0.009	13.122	0.008	0.008	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.011	-0.013	12.362	-0.039	-0.039	0.000	0.000	0.000	0.000
11	A	13	VAL	0	-0.005	-0.007	16.838	0.008	0.008	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.807	-0.918	19.436	-0.096	-0.096	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.824	-0.905	21.322	-0.040	-0.040	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.863	-0.928	22.505	-0.136	-0.136	0.000	0.000	0.000	0.000
15	A	17	GLN	0	0.002	-0.014	19.672	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	18	VAL	0	0.030	0.022	19.399	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	19	PHE	0	0.032	0.012	18.143	-0.050	-0.050	0.000	0.000	0.000	0.000
18	A	20	ARG	1	0.845	0.911	16.917	0.016	0.016	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.022	-0.023	15.034	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.046	-0.009	13.421	-0.094	-0.094	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.012	-0.002	12.488	-0.121	-0.121	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.809	-0.891	10.709	-0.242	-0.242	0.000	0.000	0.000	0.000
23	A	25	SER	0	-0.024	-0.009	9.095	-0.255	-0.255	0.000	0.000	0.000	0.000
24	A	26	TRP	0	0.010	-0.003	7.718	-0.525	-0.525	0.000	0.000	0.000	0.000
25	A	27	PHE	0	0.046	0.011	7.156	-0.385	-0.385	0.000	0.000	0.000	0.000
26	A	28	SER	0	0.028	0.019	5.674	0.045	0.045	0.000	0.000	0.000	0.000
27	A	29	SER	0	-0.125	-0.056	3.439	-2.750	-1.927	0.009	-0.411	-0.422	-0.003
28	A	30	LEU	0	-0.060	-0.041	2.551	-8.711	-6.368	1.176	-1.442	-2.076	-0.015
29	A	31	GLY	0	0.004	-0.006	2.410	-2.820	-0.953	5.681	-3.456	-4.092	-0.013
30	A	32	ALA	0	-0.028	0.013	3.107	2.791	0.965	0.240	2.116	-0.530	0.003
31	A	33	THR	0	-0.034	-0.016	6.497	-0.131	-0.131	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.016	-0.032	8.997	-0.108	-0.108	0.000	0.000	0.000	0.000
33	A	35	VAL	0	0.003	0.009	11.348	0.040	0.040	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.020	-0.007	12.995	-0.046	-0.046	0.000	0.000	0.000	0.000
35	A	37	ALA	0	-0.006	0.002	16.965	0.016	0.016	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.023	-0.018	20.721	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.740	-0.848	22.891	0.022	0.022	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.080	0.007	25.107	0.012	0.012	0.000	0.000	0.000	0.000
39	A	41	VAL	0	-0.064	-0.045	26.373	0.008	0.008	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.862	-0.929	25.209	0.076	0.076	0.000	0.000	0.000	0.000
41	A	43	ALA	0	-0.032	-0.023	22.776	0.016	0.016	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.031	-0.020	24.086	0.014	0.014	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.960	-0.972	26.995	0.116	0.116	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.010	-0.005	20.830	0.013	0.013	0.000	0.000	0.000	0.000
45	A	47	LEU	0	0.009	0.003	21.336	0.022	0.022	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.061	-0.010	24.331	0.003	0.003	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.045	-0.026	25.090	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.064	-0.034	16.790	0.022	0.022	0.000	0.000	0.000	0.000
49	A	51	THR	0	-0.006	-0.015	20.076	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	52	PRO	0	-0.019	0.019	16.238	0.037	0.037	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.782	-0.893	13.264	0.456	0.456	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.023	-0.022	13.256	-0.051	-0.051	0.000	0.000	0.000	0.000
53	A	55	MET	0	-0.021	0.006	15.949	0.023	0.023	0.000	0.000	0.000	0.000
54	A	56	ILE	0	0.006	0.004	15.048	-0.024	-0.024	0.000	0.000	0.000	0.000
55	A	57	CYS	0	-0.001	0.002	18.535	0.009	0.009	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.672	-0.812	21.809	-0.058	-0.058	0.000	0.000	0.000	0.000
57	A	59	ILE	0	-0.034	-0.024	24.574	0.010	0.010	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.009	-0.002	27.747	0.003	0.003	0.000	0.000	0.000	0.000
59	A	61	MET	0	-0.032	0.003	25.423	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.046	0.029	28.428	0.006	0.006	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.810	0.865	30.309	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	64	MET	0	-0.049	0.010	28.227	0.009	0.009	0.000	0.000	0.000	0.000
63	A	65	ASN	0	0.014	-0.006	31.026	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.062	0.031	27.505	0.007	0.007	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.005	-0.010	28.016	0.008	0.008	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.754	0.874	30.383	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	69	LEU	0	0.028	0.024	24.010	0.004	0.004	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.014	0.008	25.466	0.008	0.008	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.793	-0.900	28.044	0.036	0.036	0.000	0.000	0.000	0.000
70	A	72	HIS	0	-0.019	-0.014	30.907	0.005	0.005	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.012	-0.006	24.606	0.004	0.004	0.000	0.000	0.000	0.000
72	A	74	ARG	1	0.764	0.868	23.489	-0.072	-0.072	0.000	0.000	0.000	0.000
73	A	75	ASN	0	-0.046	-0.022	29.823	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.779	0.904	26.614	-0.138	-0.138	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.005	0.007	30.821	0.004	0.004	0.000	0.000	0.000	0.000
76	A	78	ASP	-1	-0.826	-0.892	25.413	0.135	0.135	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.056	-0.047	24.599	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.005	0.005	19.976	0.001	0.001	0.000	0.000	0.000	0.000
79	A	81	PRO	0	0.083	0.063	17.910	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.006	-0.001	19.289	0.008	0.008	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.019	0.017	16.140	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	84	VAL	0	-0.012	-0.010	19.811	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.016	-0.004	17.285	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	86	SER	0	-0.029	-0.049	22.008	0.002	0.002	0.000	0.000	0.000	0.000
85	A	87	ALA	0	-0.010	0.003	25.521	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.025	-0.007	27.920	0.002	0.002	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.887	-0.944	30.329	-0.058	-0.058	0.000	0.000	0.000	0.000
88	A	90	ASN	0	-0.057	-0.036	33.088	0.003	0.003	0.000	0.000	0.000	0.000
89	A	91	MET	0	0.050	0.014	32.484	0.003	0.003	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.002	0.002	34.381	0.003	0.003	0.000	0.000	0.000	0.000
91	A	93	ASP	-1	-0.823	-0.904	32.530	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	94	ILE	0	0.055	0.025	28.832	0.005	0.005	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.008	-0.007	30.522	0.004	0.004	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.803	0.891	32.789	0.002	0.002	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.060	0.026	27.556	0.005	0.005	0.000	0.000	0.000	0.000
96	A	98	LEU	0	0.005	-0.001	27.135	0.005	0.005	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.872	0.935	29.399	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.025	0.001	29.555	0.004	0.004	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.024	0.035	27.419	0.008	0.008	0.000	0.000	0.000	0.000
100	A	102	VAL	0	-0.045	-0.028	23.650	0.007	0.007	0.000	0.000	0.000	0.000
101	A	103	GLU	-1	-0.855	-0.936	18.809	0.052	0.052	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.799	-0.911	20.950	-0.044	-0.044	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.068	-0.044	22.637	0.004	0.004	0.000	0.000	0.000	0.000
104	A	106	LEU	0	-0.048	-0.008	18.381	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.015	0.011	22.472	0.000	0.000	0.000	0.000	0.000	0.000
106	A	108	LYS	1	0.782	0.867	21.815	0.068	0.068	0.000	0.000	0.000	0.000
107	A	109	PRO	0	-0.002	-0.038	23.011	0.012	0.012	0.000	0.000	0.000	0.000
108	A	110	VAL	0	0.051	0.027	18.114	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.884	0.986	21.004	0.082	0.082	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.780	-0.930	19.980	-0.142	-0.142	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.028	0.054	14.024	0.017	0.017	0.000	0.000	0.000	0.000
112	A	114	ASN	0	-0.064	-0.063	14.258	-0.056	-0.056	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.853	0.901	15.620	0.073	0.073	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.012	0.011	13.602	0.021	0.021	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.900	0.962	8.090	0.343	0.343	0.000	0.000	0.000	0.000
116	A	118	GLU	-1	-0.871	-0.925	12.651	-0.039	-0.039	0.000	0.000	0.000	0.000
117	A	119	MET	0	-0.011	0.016	15.169	0.007	0.007	0.000	0.000	0.000	0.000
118	A	120	VAL	0	0.030	0.017	10.408	0.016	0.016	0.000	0.000	0.000	0.000
119	A	121	PHE	0	-0.017	-0.016	6.494	0.062	0.062	0.000	0.000	0.000	0.000
120	A	122	ALA	0	-0.081	-0.026	12.077	0.001	0.001	0.000	0.000	0.000	0.000
121	A	123	CYS	0	-0.074	-0.019	14.640	0.010	0.010	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.018	-0.018	10.078	0.020	0.020	0.000	0.000	0.000	0.000
123	A	125	TYR	0	-0.088	-0.041	6.931	0.082	0.082	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

Support

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