FMO DATABASE

FMODB ID: V21K1

Calculation Name: 1EKG-A-Xray309

Preferred Name: Frataxin, mitochondrial

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1EKG

Chain ID: A

ChEMBL ID: CHEMBL2321640

UniProt ID: Q16595

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-987404.187629
FMO2-HF: Nuclear repulsion	941527.013049
FMO2-HF: Total energy	-45877.17458
FMO2-MP2: Total energy	-46014.753443

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:89:ACE )

Summations of interaction energy for fragment #1(A:89:ACE )

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.
1.906	3.155	0.014	-0.446	-0.816	0.001

Interaction energy analysis for fragmet #1(A:89:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.003

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	91	ASP	-1	-0.800	-0.851	3.882	0.023	0.751	-0.003	-0.327	-0.398	0.001
4	A	92	GLU	-1	-0.881	-0.976	6.897	-0.185	-0.185	0.000	0.000	0.000	0.000
5	A	93	THR	0	0.006	0.016	8.924	0.078	0.078	0.000	0.000	0.000	0.000
6	A	94	THR	0	-0.023	-0.047	7.528	0.126	0.126	0.000	0.000	0.000	0.000
7	A	95	TYR	0	-0.060	-0.041	6.438	0.079	0.079	0.000	0.000	0.000	0.000
8	A	96	GLU	-1	-0.857	-0.924	8.080	0.014	0.014	0.000	0.000	0.000	0.000
9	A	97	ARG	1	0.954	0.988	11.770	0.300	0.300	0.000	0.000	0.000	0.000
10	A	98	LEU	0	0.029	0.018	7.163	0.029	0.029	0.000	0.000	0.000	0.000
11	A	99	ALA	0	-0.023	-0.007	10.625	0.075	0.075	0.000	0.000	0.000	0.000
12	A	100	GLU	-1	-0.985	-0.982	11.973	-0.090	-0.090	0.000	0.000	0.000	0.000
13	A	101	GLU	-1	-0.855	-0.931	14.477	-0.134	-0.134	0.000	0.000	0.000	0.000
14	A	102	THR	0	-0.098	-0.060	12.647	0.028	0.028	0.000	0.000	0.000	0.000
15	A	103	LEU	0	-0.055	-0.046	15.133	0.024	0.024	0.000	0.000	0.000	0.000
16	A	104	ASP	-1	-0.820	-0.903	17.450	-0.059	-0.059	0.000	0.000	0.000	0.000
17	A	105	SER	0	-0.006	0.004	18.641	0.008	0.008	0.000	0.000	0.000	0.000
18	A	106	LEU	0	-0.046	-0.038	17.171	0.011	0.011	0.000	0.000	0.000	0.000
19	A	107	ALA	0	-0.006	-0.001	20.787	0.006	0.006	0.000	0.000	0.000	0.000
20	A	108	GLU	-1	-0.876	-0.926	23.282	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	109	PHE	0	-0.004	-0.009	23.638	0.005	0.005	0.000	0.000	0.000	0.000
22	A	110	PHE	0	-0.044	-0.049	21.993	0.006	0.006	0.000	0.000	0.000	0.000
23	A	111	GLU	-1	-0.922	-0.945	26.741	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	112	ASP	-1	-0.884	-0.930	28.833	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	113	LEU	0	-0.124	-0.089	28.110	0.002	0.002	0.000	0.000	0.000	0.000
26	A	114	ALA	0	-0.007	0.003	31.357	0.002	0.002	0.000	0.000	0.000	0.000
27	A	115	ASP	-1	-0.877	-0.917	33.799	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	116	LYS	1	0.803	0.915	32.740	0.000	0.000	0.000	0.000	0.000	0.000
29	A	117	PRO	0	-0.009	-0.022	36.277	0.001	0.001	0.000	0.000	0.000	0.000
30	A	118	TYR	0	-0.023	-0.018	31.741	0.000	0.000	0.000	0.000	0.000	0.000
31	A	119	THR	0	-0.015	0.013	32.828	0.003	0.003	0.000	0.000	0.000	0.000
32	A	120	PHE	0	-0.011	-0.007	35.545	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	121	GLU	-1	-0.929	-0.964	37.137	0.011	0.011	0.000	0.000	0.000	0.000
34	A	122	ASP	-1	-0.909	-0.958	37.731	0.023	0.023	0.000	0.000	0.000	0.000
35	A	123	TYR	0	-0.107	-0.056	29.043	0.005	0.005	0.000	0.000	0.000	0.000
36	A	124	ASP	-1	-0.930	-0.977	32.124	0.013	0.013	0.000	0.000	0.000	0.000
37	A	125	VAL	0	-0.002	0.004	26.512	0.006	0.006	0.000	0.000	0.000	0.000
38	A	126	SER	0	-0.010	0.005	27.460	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	127	PHE	0	0.002	-0.010	19.651	0.011	0.011	0.000	0.000	0.000	0.000
40	A	128	GLY	0	0.052	0.025	23.486	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	129	SER	0	-0.043	-0.028	21.829	0.005	0.005	0.000	0.000	0.000	0.000
42	A	130	GLY	0	0.011	0.007	18.283	0.007	0.007	0.000	0.000	0.000	0.000
43	A	131	VAL	0	-0.034	-0.021	18.278	0.021	0.021	0.000	0.000	0.000	0.000
44	A	132	LEU	0	0.024	0.025	20.453	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	133	THR	0	-0.034	-0.032	22.238	0.015	0.015	0.000	0.000	0.000	0.000
46	A	134	VAL	0	0.042	0.023	24.517	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	135	LYS	1	0.932	0.980	27.040	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	136	LEU	0	0.005	-0.009	28.293	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	137	GLY	0	0.053	0.028	31.671	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	138	GLY	0	0.011	-0.010	35.192	0.003	0.003	0.000	0.000	0.000	0.000
51	A	139	ASP	-1	-1.017	-1.012	36.397	0.037	0.037	0.000	0.000	0.000	0.000
52	A	140	LEU	0	-0.010	0.002	32.394	0.004	0.004	0.000	0.000	0.000	0.000
53	A	141	GLY	0	-0.042	-0.016	30.846	0.005	0.005	0.000	0.000	0.000	0.000
54	A	142	THR	0	-0.024	-0.034	26.971	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	143	TYR	0	-0.047	-0.054	22.645	0.005	0.005	0.000	0.000	0.000	0.000
56	A	144	VAL	0	-0.020	0.001	21.206	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	145	ILE	0	0.012	0.002	16.937	0.020	0.020	0.000	0.000	0.000	0.000
58	A	146	ASN	0	-0.013	-0.004	16.658	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	147	LYS	1	0.888	0.946	13.408	0.104	0.104	0.000	0.000	0.000	0.000
60	A	148	GLN	0	0.020	-0.006	12.071	0.016	0.016	0.000	0.000	0.000	0.000
61	A	149	THR	0	0.083	0.020	10.527	0.083	0.083	0.000	0.000	0.000	0.000
62	A	150	PRO	0	-0.069	-0.014	9.622	0.021	0.021	0.000	0.000	0.000	0.000
63	A	151	ASN	0	-0.052	-0.027	9.125	0.074	0.074	0.000	0.000	0.000	0.000
64	A	152	LYS	1	0.831	0.914	4.455	0.497	0.597	0.000	-0.011	-0.088	0.000
65	A	153	GLN	0	0.002	-0.010	6.581	0.052	0.052	0.000	0.000	0.000	0.000
66	A	154	ILE	0	0.007	0.039	9.265	-0.130	-0.130	0.000	0.000	0.000	0.000
67	A	155	TRP	0	-0.079	-0.047	12.223	0.015	0.015	0.000	0.000	0.000	0.000
68	A	156	LEU	0	0.057	0.034	15.283	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	157	SER	0	-0.038	-0.015	18.212	0.015	0.015	0.000	0.000	0.000	0.000
70	A	158	SER	0	0.029	-0.020	21.784	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	159	PRO	0	-0.021	-0.001	23.858	0.003	0.003	0.000	0.000	0.000	0.000
72	A	160	SER	0	-0.052	-0.023	26.604	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	161	SER	0	-0.084	-0.088	23.118	0.006	0.006	0.000	0.000	0.000	0.000
74	A	162	GLY	0	0.004	0.013	23.588	0.012	0.012	0.000	0.000	0.000	0.000
75	A	163	PRO	0	-0.030	-0.022	19.940	0.002	0.002	0.000	0.000	0.000	0.000
76	A	164	LYS	1	0.927	0.979	16.406	-0.164	-0.164	0.000	0.000	0.000	0.000
77	A	165	ARG	1	0.891	0.959	12.508	-0.334	-0.334	0.000	0.000	0.000	0.000
78	A	166	TYR	0	0.003	0.002	10.980	0.031	0.031	0.000	0.000	0.000	0.000
79	A	167	ASP	-1	-0.798	-0.898	5.847	1.205	1.205	0.000	0.000	0.000	0.000
80	A	168	TRP	0	-0.003	0.009	3.314	-0.332	-0.130	0.017	-0.080	-0.139	0.000
81	A	169	THR	0	0.006	-0.029	4.332	0.224	0.443	0.000	-0.028	-0.191	0.000
82	A	170	GLY	0	-0.011	-0.010	6.242	-0.088	-0.088	0.000	0.000	0.000	0.000
83	A	171	LYS	1	0.876	0.938	6.859	-0.096	-0.096	0.000	0.000	0.000	0.000
84	A	172	ASN	0	0.001	0.019	9.158	0.027	0.027	0.000	0.000	0.000	0.000
85	A	173	TRP	0	0.036	0.010	7.333	0.088	0.088	0.000	0.000	0.000	0.000
86	A	174	VAL	0	-0.019	-0.003	9.514	-0.060	-0.060	0.000	0.000	0.000	0.000
87	A	175	TYR	0	-0.033	0.006	10.571	0.109	0.109	0.000	0.000	0.000	0.000
88	A	176	SER	0	0.008	-0.015	10.636	-0.073	-0.073	0.000	0.000	0.000	0.000
89	A	177	HIS	0	-0.041	-0.019	12.188	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	178	ASP	-1	-0.857	-0.936	15.855	0.200	0.200	0.000	0.000	0.000	0.000
91	A	179	GLY	0	-0.029	-0.011	14.011	-0.026	-0.026	0.000	0.000	0.000	0.000
92	A	180	VAL	0	-0.012	0.008	15.086	-0.027	-0.027	0.000	0.000	0.000	0.000
93	A	181	SER	0	-0.014	-0.025	13.985	0.027	0.027	0.000	0.000	0.000	0.000
94	A	182	LEU	0	0.036	0.000	13.973	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	183	HIS	0	0.054	0.009	14.773	0.003	0.003	0.000	0.000	0.000	0.000
96	A	184	GLU	-1	-0.906	-0.939	17.831	0.103	0.103	0.000	0.000	0.000	0.000
97	A	185	LEU	0	-0.009	0.001	18.867	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	186	LEU	0	0.023	0.006	19.501	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	187	ALA	0	0.046	0.034	22.068	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	188	ALA	0	-0.027	0.003	23.667	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	189	GLU	-1	-0.764	-0.803	24.003	0.095	0.095	0.000	0.000	0.000	0.000
102	A	190	LEU	0	0.045	0.021	24.837	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	191	THR	0	-0.021	-0.014	27.772	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	192	LYS	1	0.884	0.937	29.577	-0.062	-0.062	0.000	0.000	0.000	0.000
105	A	193	ALA	0	-0.038	-0.020	30.380	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	194	LEU	0	0.035	0.016	30.302	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	195	LYS	1	0.878	0.951	33.472	-0.033	-0.033	0.000	0.000	0.000	0.000
108	A	196	THR	0	0.012	0.007	32.448	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	197	LYS	1	0.890	0.946	31.084	-0.031	-0.031	0.000	0.000	0.000	0.000
110	A	198	LEU	0	0.028	0.030	27.360	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	199	ASP	-1	-0.847	-0.921	24.280	0.022	0.022	0.000	0.000	0.000	0.000
112	A	200	LEU	0	0.029	0.013	20.996	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	201	SER	0	-0.039	-0.027	20.299	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	202	SER	0	-0.057	-0.039	20.433	-0.011	-0.011	0.000	0.000	0.000	0.000
115	A	203	LEU	0	-0.003	0.033	19.300	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	204	ALA	0	0.019	0.007	16.454	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	205	TYR	0	-0.033	-0.029	11.951	0.001	0.001	0.000	0.000	0.000	0.000
118	A	206	SER	0	0.040	0.020	13.349	0.029	0.029	0.000	0.000	0.000	0.000
119	A	207	GLY	0	-0.057	-0.030	14.216	0.027	0.027	0.000	0.000	0.000	0.000
120	A	208	LYS	1	0.816	0.904	14.822	0.042	0.042	0.000	0.000	0.000	0.000
121	A	209	NME	0	0.075	0.051	18.581	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:89:ACE )