FMO DATABASE

FMODB ID: 9GL92

Calculation Name: 1EKG-A-Xray372

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: 2023-03-13

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-980662.913395
FMO2-HF: Nuclear repulsion	934956.657551
FMO2-HF: Total energy	-45706.255844
FMO2-MP2: Total energy	-45843.303069

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:90:LEU)

Summations of interaction energy for fragment #1(A:90:LEU)

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.
-7.538	-0.79	9.397	-4.805	-11.339	-0.025

Interaction energy analysis for fragmet #1(A:90:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.002

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	92	GLU	-1	-0.877	-0.974	2.816	-4.663	-2.249	0.397	-1.326	-1.486	-0.007
4	A	93	THR	0	0.004	0.015	5.441	0.200	0.200	0.000	0.000	0.000	0.000
5	A	94	THR	0	-0.025	-0.048	2.279	-0.749	-0.118	2.019	-0.766	-1.884	-0.002
6	A	95	TYR	0	-0.061	-0.042	3.069	-1.534	-0.090	0.122	-0.419	-1.147	-0.002
7	A	96	GLU	-1	-0.859	-0.923	3.973	-0.709	-0.484	0.006	-0.050	-0.181	0.000
8	A	97	ARG	1	0.959	0.990	7.032	0.997	0.997	0.000	0.000	0.000	0.000
9	A	98	LEU	0	0.030	0.019	2.749	-0.647	0.023	0.178	-0.168	-0.680	-0.002
10	A	99	ALA	0	-0.025	-0.007	6.803	0.293	0.293	0.000	0.000	0.000	0.000
11	A	100	GLU	-1	-0.987	-0.984	8.340	-0.539	-0.539	0.000	0.000	0.000	0.000
12	A	101	GLU	-1	-0.855	-0.932	10.285	-0.536	-0.536	0.000	0.000	0.000	0.000
13	A	102	THR	0	-0.095	-0.059	9.023	0.097	0.097	0.000	0.000	0.000	0.000
14	A	103	LEU	0	-0.054	-0.045	11.574	0.099	0.099	0.000	0.000	0.000	0.000
15	A	104	ASP	-1	-0.824	-0.904	13.987	-0.459	-0.459	0.000	0.000	0.000	0.000
16	A	105	SER	0	-0.007	0.003	15.174	0.058	0.058	0.000	0.000	0.000	0.000
17	A	106	LEU	0	-0.043	-0.037	14.215	0.047	0.047	0.000	0.000	0.000	0.000
18	A	107	ALA	0	-0.009	-0.002	17.531	0.040	0.040	0.000	0.000	0.000	0.000
19	A	108	GLU	-1	-0.874	-0.925	19.811	-0.252	-0.252	0.000	0.000	0.000	0.000
20	A	109	PHE	0	-0.005	-0.009	20.490	0.031	0.031	0.000	0.000	0.000	0.000
21	A	110	PHE	0	-0.042	-0.048	19.223	0.023	0.023	0.000	0.000	0.000	0.000
22	A	111	GLU	-1	-0.927	-0.946	23.518	-0.233	-0.233	0.000	0.000	0.000	0.000
23	A	112	ASP	-1	-0.879	-0.929	25.457	-0.182	-0.182	0.000	0.000	0.000	0.000
24	A	113	LEU	0	-0.120	-0.087	25.301	0.019	0.019	0.000	0.000	0.000	0.000
25	A	114	ALA	0	-0.014	0.000	28.296	0.012	0.012	0.000	0.000	0.000	0.000
26	A	115	ASP	-1	-0.876	-0.917	30.663	-0.126	-0.126	0.000	0.000	0.000	0.000
27	A	116	LYS	1	0.805	0.916	29.730	0.148	0.148	0.000	0.000	0.000	0.000
28	A	117	PRO	0	-0.010	-0.022	33.303	0.001	0.001	0.000	0.000	0.000	0.000
29	A	118	TYR	0	-0.021	-0.018	29.008	0.007	0.007	0.000	0.000	0.000	0.000
30	A	119	THR	0	-0.015	0.014	29.990	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	120	PHE	0	-0.013	-0.007	32.877	0.008	0.008	0.000	0.000	0.000	0.000
32	A	121	GLU	-1	-0.928	-0.964	34.357	-0.097	-0.097	0.000	0.000	0.000	0.000
33	A	122	ASP	-1	-0.909	-0.958	34.994	-0.117	-0.117	0.000	0.000	0.000	0.000
34	A	123	TYR	0	-0.106	-0.057	26.062	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	124	ASP	-1	-0.929	-0.976	29.341	-0.172	-0.172	0.000	0.000	0.000	0.000
36	A	125	VAL	0	-0.003	0.004	23.410	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	126	SER	0	-0.010	0.006	24.442	0.008	0.008	0.000	0.000	0.000	0.000
38	A	127	PHE	0	0.002	-0.011	16.079	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	128	GLY	0	0.051	0.025	20.295	0.016	0.016	0.000	0.000	0.000	0.000
40	A	129	SER	0	-0.043	-0.028	18.542	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	130	GLY	0	0.014	0.007	15.128	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	131	VAL	0	-0.036	-0.022	15.434	-0.037	-0.037	0.000	0.000	0.000	0.000
43	A	132	LEU	0	0.022	0.026	17.503	0.022	0.022	0.000	0.000	0.000	0.000
44	A	133	THR	0	-0.035	-0.033	19.308	0.006	0.006	0.000	0.000	0.000	0.000
45	A	134	VAL	0	0.045	0.024	21.763	0.007	0.007	0.000	0.000	0.000	0.000
46	A	135	LYS	1	0.926	0.978	24.383	0.141	0.141	0.000	0.000	0.000	0.000
47	A	136	LEU	0	0.006	-0.009	25.973	0.002	0.002	0.000	0.000	0.000	0.000
48	A	137	GLY	0	0.055	0.029	29.273	0.005	0.005	0.000	0.000	0.000	0.000
49	A	138	GLY	0	0.009	-0.010	32.809	0.001	0.001	0.000	0.000	0.000	0.000
50	A	139	ASP	-1	-1.015	-1.013	34.517	-0.090	-0.090	0.000	0.000	0.000	0.000
51	A	140	LEU	0	-0.010	0.003	30.455	0.000	0.000	0.000	0.000	0.000	0.000
52	A	141	GLY	0	-0.041	-0.016	29.108	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	142	THR	0	-0.029	-0.035	24.828	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	143	TYR	0	-0.041	-0.051	20.774	0.005	0.005	0.000	0.000	0.000	0.000
55	A	144	VAL	0	-0.020	0.000	19.164	0.000	0.000	0.000	0.000	0.000	0.000
56	A	145	ILE	0	0.012	0.002	14.371	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	146	ASN	0	-0.014	-0.004	14.578	0.052	0.052	0.000	0.000	0.000	0.000
58	A	147	LYS	1	0.889	0.946	10.378	0.948	0.948	0.000	0.000	0.000	0.000
59	A	148	GLN	0	0.018	-0.007	10.017	0.094	0.094	0.000	0.000	0.000	0.000
60	A	149	THR	0	0.083	0.021	8.271	-0.108	-0.108	0.000	0.000	0.000	0.000
61	A	150	PRO	0	-0.069	-0.015	8.288	-0.193	-0.193	0.000	0.000	0.000	0.000
62	A	151	ASN	0	-0.049	-0.026	9.231	0.156	0.156	0.000	0.000	0.000	0.000
63	A	152	LYS	1	0.834	0.916	3.064	1.820	3.035	0.028	-0.508	-0.735	0.000
64	A	153	GLN	0	0.001	-0.010	5.384	-0.056	-0.056	0.000	0.000	0.000	0.000
65	A	154	ILE	0	0.003	0.038	7.963	-0.053	-0.053	0.000	0.000	0.000	0.000
66	A	155	TRP	0	-0.075	-0.047	10.335	0.125	0.125	0.000	0.000	0.000	0.000
67	A	156	LEU	0	0.057	0.034	13.891	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	157	SER	0	-0.040	-0.015	16.721	0.036	0.036	0.000	0.000	0.000	0.000
69	A	158	SER	0	0.031	-0.019	20.443	0.000	0.000	0.000	0.000	0.000	0.000
70	A	159	PRO	0	-0.021	-0.002	22.518	0.013	0.013	0.000	0.000	0.000	0.000
71	A	160	SER	0	-0.054	-0.025	25.401	0.016	0.016	0.000	0.000	0.000	0.000
72	A	161	SER	0	-0.085	-0.087	22.325	0.008	0.008	0.000	0.000	0.000	0.000
73	A	162	GLY	0	0.004	0.013	23.228	0.007	0.007	0.000	0.000	0.000	0.000
74	A	163	PRO	0	-0.027	-0.021	19.559	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	164	LYS	1	0.924	0.978	16.035	0.182	0.182	0.000	0.000	0.000	0.000
76	A	165	ARG	1	0.893	0.959	12.407	0.212	0.212	0.000	0.000	0.000	0.000
77	A	166	TYR	0	0.005	0.003	9.884	0.070	0.070	0.000	0.000	0.000	0.000
78	A	167	ASP	-1	-0.800	-0.898	6.617	-0.483	-0.483	0.000	0.000	0.000	0.000
79	A	168	TRP	0	0.002	0.010	2.304	-1.879	-2.160	6.650	-1.525	-4.844	-0.012
80	A	169	THR	0	0.013	-0.026	4.542	0.233	0.351	-0.001	-0.010	-0.107	0.000
81	A	170	GLY	0	-0.014	-0.013	3.969	0.280	0.402	0.000	-0.026	-0.095	0.000
82	A	171	LYS	1	0.874	0.936	4.987	0.078	0.120	-0.001	0.000	-0.040	0.000
83	A	172	ASN	0	-0.001	0.019	7.854	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	173	TRP	0	0.038	0.012	4.548	-0.349	-0.201	-0.001	-0.007	-0.140	0.000
85	A	174	VAL	0	-0.017	-0.002	8.743	0.096	0.096	0.000	0.000	0.000	0.000
86	A	175	TYR	0	-0.036	0.005	10.727	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	176	SER	0	0.009	-0.015	11.775	0.033	0.033	0.000	0.000	0.000	0.000
88	A	177	HIS	0	-0.040	-0.020	13.246	0.045	0.045	0.000	0.000	0.000	0.000
89	A	178	ASP	-1	-0.857	-0.937	16.812	-0.089	-0.089	0.000	0.000	0.000	0.000
90	A	179	GLY	0	-0.029	-0.011	14.817	0.010	0.010	0.000	0.000	0.000	0.000
91	A	180	VAL	0	-0.013	0.008	15.707	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	181	SER	0	-0.015	-0.024	13.053	-0.044	-0.044	0.000	0.000	0.000	0.000
93	A	182	LEU	0	0.030	-0.002	11.720	0.027	0.027	0.000	0.000	0.000	0.000
94	A	183	HIS	0	0.060	0.011	12.080	0.049	0.049	0.000	0.000	0.000	0.000
95	A	184	GLU	-1	-0.907	-0.940	16.281	-0.127	-0.127	0.000	0.000	0.000	0.000
96	A	185	LEU	0	-0.008	0.001	17.648	0.023	0.023	0.000	0.000	0.000	0.000
97	A	186	LEU	0	0.024	0.006	17.184	0.019	0.019	0.000	0.000	0.000	0.000
98	A	187	ALA	0	0.047	0.035	20.253	0.017	0.017	0.000	0.000	0.000	0.000
99	A	188	ALA	0	-0.031	0.001	22.207	0.019	0.019	0.000	0.000	0.000	0.000
100	A	189	GLU	-1	-0.762	-0.803	22.784	-0.156	-0.156	0.000	0.000	0.000	0.000
101	A	190	LEU	0	0.045	0.022	22.469	0.012	0.012	0.000	0.000	0.000	0.000
102	A	191	THR	0	-0.018	-0.014	25.896	0.014	0.014	0.000	0.000	0.000	0.000
103	A	192	LYS	1	0.882	0.936	28.008	0.099	0.099	0.000	0.000	0.000	0.000
104	A	193	ALA	0	-0.041	-0.022	28.483	0.008	0.008	0.000	0.000	0.000	0.000
105	A	194	LEU	0	0.038	0.018	27.939	0.005	0.005	0.000	0.000	0.000	0.000
106	A	195	LYS	1	0.877	0.950	31.374	0.087	0.087	0.000	0.000	0.000	0.000
107	A	196	THR	0	0.012	0.008	30.136	0.008	0.008	0.000	0.000	0.000	0.000
108	A	197	LYS	1	0.889	0.945	29.183	0.083	0.083	0.000	0.000	0.000	0.000
109	A	198	LEU	0	0.028	0.030	25.012	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	199	ASP	-1	-0.849	-0.922	22.207	-0.166	-0.166	0.000	0.000	0.000	0.000
111	A	200	LEU	0	0.028	0.013	18.477	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	201	SER	0	-0.028	-0.022	18.114	-0.036	-0.036	0.000	0.000	0.000	0.000
113	A	202	SER	0	-0.062	-0.041	18.020	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	203	LEU	0	-0.002	0.034	16.374	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	204	ALA	0	0.013	0.005	12.858	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	205	TYR	0	-0.035	-0.030	8.771	-0.091	-0.091	0.000	0.000	0.000	0.000
117	A	206	SER	0	0.045	0.023	10.835	-0.032	-0.032	0.000	0.000	0.000	0.000
118	A	207	GLY	0	-0.049	-0.020	12.208	0.025	0.025	0.000	0.000	0.000	0.000
119	A	208	LYS	1	0.887	0.947	13.002	0.321	0.321	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:90:LEU)