FMO DATABASE

FMODB ID: 76YLK

Calculation Name: 2EA9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EA9

Chain ID: A

ChEMBL ID:

UniProt ID: P52141

Base Structure: X-ray

Registration Date: 2023-09-22

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-779725.023479
FMO2-HF: Nuclear repulsion	738681.139712
FMO2-HF: Total energy	-41043.883767
FMO2-MP2: Total energy	-41160.768138

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:8:MET)

Summations of interaction energy for fragment #1(A:8:MET)

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.
-7.454	-0.432	2.916	-3.732	-6.206	-0.017

Interaction energy analysis for fragmet #1(A:8:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.011

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	10	ASN	0	0.036	0.036	2.910	-0.584	2.354	0.053	-1.341	-1.650	0.003
4	A	11	THR	0	0.008	-0.018	2.662	-3.353	-1.171	1.183	-1.505	-1.860	-0.016
5	A	12	THR	0	0.026	-0.001	3.537	-0.926	-0.413	0.028	-0.018	-0.522	-0.001
6	A	13	TRP	0	0.071	0.040	4.323	-0.023	0.047	0.000	-0.010	-0.061	0.000
7	A	14	GLY	0	0.048	0.034	6.654	0.113	0.113	0.000	0.000	0.000	0.000
8	A	15	LEU	0	-0.052	-0.036	2.805	-0.475	-0.011	0.256	-0.107	-0.613	0.000
9	A	16	GLN	0	-0.044	-0.030	7.060	0.191	0.191	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.855	0.933	9.566	0.596	0.596	0.000	0.000	0.000	0.000
11	A	18	ASP	-1	-0.868	-0.934	12.294	-0.344	-0.344	0.000	0.000	0.000	0.000
12	A	19	ILE	0	-0.018	-0.003	15.203	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	20	THR	0	-0.041	-0.007	15.141	-0.117	-0.117	0.000	0.000	0.000	0.000
14	A	21	PRO	0	-0.027	-0.015	16.713	0.054	0.054	0.000	0.000	0.000	0.000
15	A	22	ARG	1	0.827	0.905	9.555	0.876	0.876	0.000	0.000	0.000	0.000
16	A	23	LEU	0	-0.006	-0.002	12.317	-0.090	-0.090	0.000	0.000	0.000	0.000
17	A	24	GLY	0	-0.009	0.014	9.842	0.127	0.127	0.000	0.000	0.000	0.000
18	A	25	ALA	0	-0.007	-0.020	9.179	-0.307	-0.307	0.000	0.000	0.000	0.000
19	A	26	ARG	1	0.897	0.966	7.828	0.836	0.836	0.000	0.000	0.000	0.000
20	A	27	LEU	0	0.014	0.026	10.247	-0.092	-0.092	0.000	0.000	0.000	0.000
21	A	28	VAL	0	0.010	-0.003	12.450	0.055	0.055	0.000	0.000	0.000	0.000
22	A	29	GLN	0	-0.031	-0.033	14.552	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	30	GLU	-1	-0.883	-0.935	18.013	-0.219	-0.219	0.000	0.000	0.000	0.000
24	A	31	GLY	0	-0.022	-0.011	21.028	0.001	0.001	0.000	0.000	0.000	0.000
25	A	32	ASN	0	-0.025	-0.026	23.124	0.010	0.010	0.000	0.000	0.000	0.000
26	A	33	GLN	0	-0.057	-0.020	22.526	0.001	0.001	0.000	0.000	0.000	0.000
27	A	34	LEU	0	-0.028	-0.021	17.380	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	35	HIS	0	-0.031	-0.003	16.648	-0.061	-0.061	0.000	0.000	0.000	0.000
29	A	36	TYR	0	0.013	-0.014	13.394	-0.093	-0.093	0.000	0.000	0.000	0.000
30	A	37	LEU	0	0.006	0.003	9.997	0.067	0.067	0.000	0.000	0.000	0.000
31	A	38	ALA	0	0.021	0.006	10.562	-0.215	-0.215	0.000	0.000	0.000	0.000
32	A	39	ASP	-1	-0.876	-0.936	6.141	-2.724	-2.724	0.000	0.000	0.000	0.000
33	A	40	ARG	1	0.780	0.895	2.330	0.122	0.977	1.396	-0.751	-1.500	-0.003
34	A	41	ALA	0	0.051	0.036	7.308	0.585	0.585	0.000	0.000	0.000	0.000
35	A	42	SER	0	-0.061	-0.029	6.883	-0.311	-0.311	0.000	0.000	0.000	0.000
36	A	43	ILE	0	0.036	0.014	8.981	0.254	0.254	0.000	0.000	0.000	0.000
37	A	44	THR	0	-0.047	-0.019	10.251	-0.134	-0.134	0.000	0.000	0.000	0.000
38	A	45	GLY	0	0.049	0.024	12.462	0.089	0.089	0.000	0.000	0.000	0.000
39	A	46	LYS	1	0.805	0.879	15.212	0.319	0.319	0.000	0.000	0.000	0.000
40	A	47	PHE	0	0.021	0.029	15.714	0.045	0.045	0.000	0.000	0.000	0.000
41	A	48	SER	0	-0.014	-0.055	20.093	0.010	0.010	0.000	0.000	0.000	0.000
42	A	49	ASP	-1	-0.794	-0.899	23.276	-0.352	-0.352	0.000	0.000	0.000	0.000
43	A	50	ALA	0	0.000	0.010	24.645	0.004	0.004	0.000	0.000	0.000	0.000
44	A	51	GLU	-1	-0.770	-0.856	22.652	-0.361	-0.361	0.000	0.000	0.000	0.000
45	A	52	CYS	0	-0.022	0.002	20.814	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	53	PRO	0	0.054	0.029	22.211	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	54	LYS	1	0.805	0.892	24.584	0.297	0.297	0.000	0.000	0.000	0.000
48	A	55	LEU	0	0.025	0.010	17.306	0.005	0.005	0.000	0.000	0.000	0.000
49	A	56	ASP	-1	-0.880	-0.953	20.292	-0.525	-0.525	0.000	0.000	0.000	0.000
50	A	57	VAL	0	-0.075	-0.029	21.946	0.010	0.010	0.000	0.000	0.000	0.000
51	A	58	VAL	0	-0.031	-0.013	21.625	0.012	0.012	0.000	0.000	0.000	0.000
52	A	59	PHE	0	0.011	0.015	15.027	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	60	PRO	0	0.022	0.007	20.418	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	61	HIS	0	0.001	0.016	22.284	0.032	0.032	0.000	0.000	0.000	0.000
55	A	62	PHE	0	0.055	0.021	20.197	0.018	0.018	0.000	0.000	0.000	0.000
56	A	63	ILE	0	-0.013	0.001	17.114	0.008	0.008	0.000	0.000	0.000	0.000
57	A	64	SER	0	-0.013	-0.011	20.893	0.033	0.033	0.000	0.000	0.000	0.000
58	A	65	GLN	0	-0.024	-0.030	23.706	0.017	0.017	0.000	0.000	0.000	0.000
59	A	66	ILE	0	0.022	0.006	17.997	0.020	0.020	0.000	0.000	0.000	0.000
60	A	67	GLU	-1	-0.801	-0.901	22.089	-0.276	-0.276	0.000	0.000	0.000	0.000
61	A	68	SER	0	-0.013	0.007	23.849	0.030	0.030	0.000	0.000	0.000	0.000
62	A	69	MET	0	-0.023	-0.005	23.371	0.008	0.008	0.000	0.000	0.000	0.000
63	A	70	LEU	0	-0.040	-0.020	19.985	0.019	0.019	0.000	0.000	0.000	0.000
64	A	71	THR	0	-0.071	-0.039	24.214	0.021	0.021	0.000	0.000	0.000	0.000
65	A	72	THR	0	-0.087	-0.076	27.915	0.013	0.013	0.000	0.000	0.000	0.000
66	A	73	GLY	0	-0.015	0.005	26.685	0.014	0.014	0.000	0.000	0.000	0.000
67	A	74	GLU	-1	-0.894	-0.917	26.031	-0.143	-0.143	0.000	0.000	0.000	0.000
68	A	75	LEU	0	-0.010	0.015	18.506	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	76	ASN	0	0.049	0.017	22.022	0.016	0.016	0.000	0.000	0.000	0.000
70	A	77	PRO	0	0.054	0.011	19.561	0.015	0.015	0.000	0.000	0.000	0.000
71	A	78	ARG	1	0.935	0.962	19.198	0.017	0.017	0.000	0.000	0.000	0.000
72	A	79	HIS	0	-0.071	-0.035	20.164	0.042	0.042	0.000	0.000	0.000	0.000
73	A	80	ALA	0	-0.020	-0.002	16.411	-0.021	-0.021	0.000	0.000	0.000	0.000
74	A	81	GLN	0	-0.057	-0.050	17.837	0.033	0.033	0.000	0.000	0.000	0.000
75	A	82	CYS	0	-0.052	-0.009	16.547	-0.029	-0.029	0.000	0.000	0.000	0.000
76	A	83	VAL	0	0.017	0.019	18.407	0.025	0.025	0.000	0.000	0.000	0.000
77	A	84	THR	0	-0.012	-0.023	19.353	-0.031	-0.031	0.000	0.000	0.000	0.000
78	A	85	LEU	0	-0.015	0.008	21.214	0.025	0.025	0.000	0.000	0.000	0.000
79	A	86	TYR	0	0.015	-0.011	22.765	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	87	HIS	0	0.032	0.006	25.159	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	88	ASN	0	-0.021	-0.014	25.994	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	89	GLY	0	0.018	0.016	27.469	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	90	PHE	0	-0.022	0.002	21.252	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	91	THR	0	0.035	0.013	20.698	0.043	0.043	0.000	0.000	0.000	0.000
85	A	92	CYS	0	-0.023	-0.012	17.470	-0.066	-0.066	0.000	0.000	0.000	0.000
86	A	93	GLU	-1	-0.780	-0.840	15.428	-0.383	-0.383	0.000	0.000	0.000	0.000
87	A	94	ALA	0	0.028	-0.001	15.383	-0.079	-0.079	0.000	0.000	0.000	0.000
88	A	95	ASP	-1	-0.708	-0.868	14.102	-0.119	-0.119	0.000	0.000	0.000	0.000
89	A	96	THR	0	0.025	0.031	14.061	-0.060	-0.060	0.000	0.000	0.000	0.000
90	A	97	LEU	0	-0.103	-0.048	10.540	0.049	0.049	0.000	0.000	0.000	0.000
91	A	98	GLY	0	0.019	0.020	14.570	0.062	0.062	0.000	0.000	0.000	0.000
92	A	99	SER	0	-0.076	-0.056	13.118	0.019	0.019	0.000	0.000	0.000	0.000
93	A	100	CYS	0	-0.076	-0.045	15.169	0.014	0.014	0.000	0.000	0.000	0.000
94	A	101	GLY	0	0.045	0.031	16.110	0.003	0.003	0.000	0.000	0.000	0.000
95	A	102	TYR	0	-0.042	-0.019	11.043	-0.064	-0.064	0.000	0.000	0.000	0.000
96	A	103	VAL	0	0.025	0.019	13.826	0.062	0.062	0.000	0.000	0.000	0.000
97	A	104	TYR	0	-0.066	-0.024	7.436	-0.093	-0.093	0.000	0.000	0.000	0.000
98	A	105	ILE	0	0.041	0.006	11.530	0.107	0.107	0.000	0.000	0.000	0.000
99	A	106	ALA	0	-0.029	-0.026	11.741	-0.188	-0.188	0.000	0.000	0.000	0.000
100	A	107	VAL	0	0.025	0.027	13.684	0.098	0.098	0.000	0.000	0.000	0.000
101	A	108	TYR	0	-0.013	-0.048	16.046	-0.055	-0.055	0.000	0.000	0.000	0.000
102	A	109	PRO	0	0.012	0.017	18.719	0.031	0.031	0.000	0.000	0.000	0.000
103	A	110	THR	0	-0.051	-0.034	22.264	0.010	0.010	0.000	0.000	0.000	0.000

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Overview

Highlights

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:MET)