FMO DATABASE

FMODB ID: 7GY7K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-983233.98445
FMO2-HF: Nuclear repulsion	937526.85691
FMO2-HF: Total energy	-45707.12754
FMO2-MP2: Total energy	-45844.162894

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.
-10.402	-0.926	7.1	-4.964	-11.61	-0.031

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 : 0.011 / q_NPA : 0.010

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

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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	-0.932	-0.977	2.747	-3.837	-1.509	1.165	-1.616	-1.876	-0.009
4	A	93	THR	0	-0.002	-0.016	5.146	-0.071	0.069	-0.001	-0.004	-0.134	0.000
5	A	94	THR	0	-0.030	-0.044	2.163	-0.943	-0.078	1.708	-0.691	-1.882	-0.004
6	A	95	TYR	0	-0.063	-0.040	2.420	-2.435	-0.395	0.808	-0.770	-2.078	-0.003
7	A	96	GLU	-1	-0.779	-0.866	3.799	-0.820	-0.564	0.022	-0.037	-0.241	0.000
8	A	97	ARG	1	0.863	0.911	7.090	0.840	0.840	0.000	0.000	0.000	0.000
9	A	98	LEU	0	0.022	0.023	2.652	-0.719	0.006	0.231	-0.191	-0.765	-0.002
10	A	99	ALA	0	-0.009	-0.003	6.629	0.249	0.249	0.000	0.000	0.000	0.000
11	A	100	GLU	-1	-0.894	-0.919	8.391	-0.511	-0.511	0.000	0.000	0.000	0.000
12	A	101	GLU	-1	-0.877	-0.940	10.139	-0.520	-0.520	0.000	0.000	0.000	0.000
13	A	102	THR	0	-0.066	-0.048	9.196	0.078	0.078	0.000	0.000	0.000	0.000
14	A	103	LEU	0	-0.036	-0.023	11.834	0.086	0.086	0.000	0.000	0.000	0.000
15	A	104	ASP	-1	-0.836	-0.927	14.276	-0.405	-0.405	0.000	0.000	0.000	0.000
16	A	105	SER	0	0.019	0.015	15.389	0.046	0.046	0.000	0.000	0.000	0.000
17	A	106	LEU	0	-0.040	-0.030	14.297	0.041	0.041	0.000	0.000	0.000	0.000
18	A	107	ALA	0	-0.007	0.002	17.651	0.037	0.037	0.000	0.000	0.000	0.000
19	A	108	GLU	-1	-0.890	-0.942	20.065	-0.259	-0.259	0.000	0.000	0.000	0.000
20	A	109	PHE	0	-0.006	-0.010	20.578	0.028	0.028	0.000	0.000	0.000	0.000
21	A	110	PHE	0	-0.011	-0.023	19.222	0.022	0.022	0.000	0.000	0.000	0.000
22	A	111	GLU	-1	-0.905	-0.944	23.561	-0.221	-0.221	0.000	0.000	0.000	0.000
23	A	112	ASP	-1	-0.819	-0.896	25.489	-0.149	-0.149	0.000	0.000	0.000	0.000
24	A	113	LEU	0	-0.034	-0.034	25.333	0.018	0.018	0.000	0.000	0.000	0.000
25	A	114	ALA	0	-0.007	0.009	28.120	0.010	0.010	0.000	0.000	0.000	0.000
26	A	115	ASP	-1	-0.926	-0.943	30.597	-0.123	-0.123	0.000	0.000	0.000	0.000
27	A	116	LYS	1	0.712	0.849	29.664	0.158	0.158	0.000	0.000	0.000	0.000
28	A	117	PRO	0	-0.023	-0.022	33.183	0.000	0.000	0.000	0.000	0.000	0.000
29	A	118	TYR	0	-0.041	-0.026	28.894	0.009	0.009	0.000	0.000	0.000	0.000
30	A	119	THR	0	-0.007	0.003	30.029	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	120	PHE	0	-0.027	-0.006	33.051	0.009	0.009	0.000	0.000	0.000	0.000
32	A	121	GLU	-1	-0.922	-0.962	34.604	-0.091	-0.091	0.000	0.000	0.000	0.000
33	A	122	ASP	-1	-0.821	-0.890	35.117	-0.112	-0.112	0.000	0.000	0.000	0.000
34	A	123	TYR	0	-0.083	-0.049	26.362	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	124	ASP	-1	-0.874	-0.941	28.422	-0.168	-0.168	0.000	0.000	0.000	0.000
36	A	125	VAL	0	-0.045	-0.018	23.455	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	126	SER	0	-0.013	0.001	24.618	0.004	0.004	0.000	0.000	0.000	0.000
38	A	127	PHE	0	-0.025	-0.022	16.579	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	128	GLY	0	0.047	0.020	19.969	0.019	0.019	0.000	0.000	0.000	0.000
40	A	129	SER	0	-0.059	-0.038	18.365	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	130	GLY	0	0.025	0.016	14.717	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	131	VAL	0	-0.041	-0.029	14.710	-0.042	-0.042	0.000	0.000	0.000	0.000
43	A	132	LEU	0	0.017	0.027	17.442	0.018	0.018	0.000	0.000	0.000	0.000
44	A	133	THR	0	-0.027	-0.020	19.100	0.004	0.004	0.000	0.000	0.000	0.000
45	A	134	VAL	0	0.038	0.018	21.874	0.003	0.003	0.000	0.000	0.000	0.000
46	A	135	LYS	1	0.809	0.897	24.414	0.132	0.132	0.000	0.000	0.000	0.000
47	A	136	LEU	0	0.021	-0.002	26.132	0.002	0.002	0.000	0.000	0.000	0.000
48	A	137	GLY	0	0.033	0.016	29.382	0.005	0.005	0.000	0.000	0.000	0.000
49	A	138	GLY	0	-0.019	-0.037	32.938	0.000	0.000	0.000	0.000	0.000	0.000
50	A	139	ASP	-1	-0.992	-0.992	34.645	-0.087	-0.087	0.000	0.000	0.000	0.000
51	A	140	LEU	0	-0.032	-0.010	30.588	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	141	GLY	0	-0.019	0.002	29.464	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	142	THR	0	-0.025	-0.035	25.062	0.000	0.000	0.000	0.000	0.000	0.000
54	A	143	TYR	0	-0.024	-0.030	20.810	0.004	0.004	0.000	0.000	0.000	0.000
55	A	144	VAL	0	-0.016	-0.006	18.987	0.002	0.002	0.000	0.000	0.000	0.000
56	A	145	ILE	0	0.009	-0.001	14.366	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	146	ASN	0	-0.032	-0.015	13.889	0.043	0.043	0.000	0.000	0.000	0.000
58	A	147	LYS	1	0.870	0.949	9.755	0.831	0.831	0.000	0.000	0.000	0.000
59	A	148	GLN	0	0.018	0.011	9.430	0.084	0.084	0.000	0.000	0.000	0.000
60	A	149	THR	0	0.030	-0.013	7.680	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	150	PRO	0	-0.062	-0.032	8.040	-0.138	-0.138	0.000	0.000	0.000	0.000
62	A	151	ASN	0	-0.049	-0.035	9.335	0.167	0.167	0.000	0.000	0.000	0.000
63	A	152	LYS	1	0.846	0.930	3.239	1.270	2.304	0.027	-0.363	-0.698	0.000
64	A	153	GLN	0	0.013	0.005	4.743	-0.258	-0.153	-0.001	-0.006	-0.099	0.000
65	A	154	ILE	0	0.007	0.031	7.402	-0.048	-0.048	0.000	0.000	0.000	0.000
66	A	155	TRP	0	-0.085	-0.063	9.864	0.107	0.107	0.000	0.000	0.000	0.000
67	A	156	LEU	0	0.061	0.028	13.346	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	157	SER	0	-0.002	-0.004	16.547	0.031	0.031	0.000	0.000	0.000	0.000
69	A	158	SER	0	0.007	-0.017	20.291	0.003	0.003	0.000	0.000	0.000	0.000
70	A	159	PRO	0	-0.022	-0.005	22.603	0.012	0.012	0.000	0.000	0.000	0.000
71	A	160	SER	0	-0.062	-0.030	25.475	0.015	0.015	0.000	0.000	0.000	0.000
72	A	161	SER	0	-0.056	-0.072	22.399	0.008	0.008	0.000	0.000	0.000	0.000
73	A	162	GLY	0	0.028	0.020	23.048	0.003	0.003	0.000	0.000	0.000	0.000
74	A	163	PRO	0	-0.024	-0.013	19.421	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	164	LYS	1	0.869	0.943	16.221	0.192	0.192	0.000	0.000	0.000	0.000
76	A	165	ARG	1	0.877	0.948	12.025	0.213	0.213	0.000	0.000	0.000	0.000
77	A	166	TYR	0	0.022	0.015	10.124	0.061	0.061	0.000	0.000	0.000	0.000
78	A	167	ASP	-1	-0.770	-0.859	6.980	-0.473	-0.473	0.000	0.000	0.000	0.000
79	A	168	TRP	0	0.004	0.007	2.671	-3.154	-1.536	3.144	-1.263	-3.500	-0.013
80	A	169	THR	0	0.011	-0.020	4.526	0.134	0.240	-0.001	-0.009	-0.096	0.000
81	A	170	GLY	0	-0.013	-0.007	4.706	0.318	0.373	-0.001	-0.002	-0.050	0.000
82	A	171	LYS	1	0.811	0.900	5.666	0.247	0.247	0.000	0.000	0.000	0.000
83	A	172	ASN	0	0.013	0.013	7.564	0.020	0.020	0.000	0.000	0.000	0.000
84	A	173	TRP	0	0.009	0.007	4.296	-0.432	-0.228	-0.001	-0.012	-0.191	0.000
85	A	174	VAL	0	0.007	-0.004	8.499	0.110	0.110	0.000	0.000	0.000	0.000
86	A	175	TYR	0	0.001	0.019	10.621	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	176	SER	0	-0.036	-0.050	11.331	0.054	0.054	0.000	0.000	0.000	0.000
88	A	177	HIS	0	-0.067	-0.018	13.180	0.050	0.050	0.000	0.000	0.000	0.000
89	A	178	ASP	-1	-0.895	-0.961	16.602	-0.134	-0.134	0.000	0.000	0.000	0.000
90	A	179	GLY	0	-0.019	-0.003	14.822	0.016	0.016	0.000	0.000	0.000	0.000
91	A	180	VAL	0	-0.033	-0.007	15.310	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	181	SER	0	-0.028	-0.068	12.853	-0.040	-0.040	0.000	0.000	0.000	0.000
93	A	182	LEU	0	-0.013	-0.016	11.784	0.037	0.037	0.000	0.000	0.000	0.000
94	A	183	HIS	0	0.032	0.012	11.588	0.058	0.058	0.000	0.000	0.000	0.000
95	A	184	GLU	-1	-0.841	-0.881	16.160	-0.194	-0.194	0.000	0.000	0.000	0.000
96	A	185	LEU	0	-0.012	-0.004	17.630	0.028	0.028	0.000	0.000	0.000	0.000
97	A	186	LEU	0	0.013	0.013	17.290	0.022	0.022	0.000	0.000	0.000	0.000
98	A	187	ALA	0	0.037	0.022	20.245	0.019	0.019	0.000	0.000	0.000	0.000
99	A	188	ALA	0	-0.029	-0.005	22.235	0.020	0.020	0.000	0.000	0.000	0.000
100	A	189	GLU	-1	-0.758	-0.804	22.648	-0.165	-0.165	0.000	0.000	0.000	0.000
101	A	190	LEU	0	0.047	0.025	22.205	0.013	0.013	0.000	0.000	0.000	0.000
102	A	191	THR	0	-0.020	-0.014	25.866	0.014	0.014	0.000	0.000	0.000	0.000
103	A	192	LYS	1	0.871	0.936	27.869	0.107	0.107	0.000	0.000	0.000	0.000
104	A	193	ALA	0	-0.040	-0.019	28.436	0.009	0.009	0.000	0.000	0.000	0.000
105	A	194	LEU	0	0.043	0.014	27.754	0.006	0.006	0.000	0.000	0.000	0.000
106	A	195	LYS	1	0.877	0.949	31.206	0.092	0.092	0.000	0.000	0.000	0.000
107	A	196	THR	0	0.029	0.022	30.311	0.009	0.009	0.000	0.000	0.000	0.000
108	A	197	LYS	1	0.887	0.944	29.192	0.096	0.096	0.000	0.000	0.000	0.000
109	A	198	LEU	0	0.040	0.029	25.041	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	199	ASP	-1	-0.809	-0.882	21.599	-0.202	-0.202	0.000	0.000	0.000	0.000
111	A	200	LEU	0	0.034	0.032	18.046	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	201	SER	0	-0.071	-0.070	17.613	-0.039	-0.039	0.000	0.000	0.000	0.000
113	A	202	SER	0	-0.043	-0.016	17.773	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	203	LEU	0	0.009	0.036	16.423	0.002	0.002	0.000	0.000	0.000	0.000
115	A	204	ALA	0	0.032	0.018	12.891	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	205	TYR	0	-0.030	-0.030	8.735	-0.068	-0.068	0.000	0.000	0.000	0.000
117	A	206	SER	0	0.066	0.031	10.529	-0.049	-0.049	0.000	0.000	0.000	0.000
118	A	207	GLY	0	-0.029	-0.004	12.148	0.014	0.014	0.000	0.000	0.000	0.000
119	A	208	LYS	1	0.876	0.933	12.677	0.341	0.341	0.000	0.000	0.000	0.000

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