FMO DATABASE

FMODB ID: M3RYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-980797.454006
FMO2-HF: Nuclear repulsion	935090.477205
FMO2-HF: Total energy	-45706.976801
FMO2-MP2: Total energy	-45844.010999

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.
-9.376	-2.372	9.009	-4.68	-11.334	-0.024

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 : 0.012 / q_NPA : 0.004

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	-0.904	-0.976	2.827	-4.531	-2.020	0.382	-1.371	-1.523	-0.006
4	A	93	THR	0	0.004	0.000	5.460	0.058	0.058	0.000	0.000	0.000	0.000
5	A	94	THR	0	-0.027	-0.039	2.278	-0.891	-0.388	2.459	-0.819	-2.143	-0.002
6	A	95	TYR	0	-0.070	-0.036	2.845	-1.813	-0.208	0.188	-0.479	-1.314	-0.003
7	A	96	GLU	-1	-0.775	-0.863	3.976	-0.708	-0.462	0.010	-0.051	-0.204	0.000
8	A	97	ARG	1	0.880	0.938	7.034	0.899	0.899	0.000	0.000	0.000	0.000
9	A	98	LEU	0	0.033	0.020	2.769	-0.760	-0.010	0.222	-0.194	-0.778	-0.002
10	A	99	ALA	0	-0.013	-0.001	6.821	0.279	0.279	0.000	0.000	0.000	0.000
11	A	100	GLU	-1	-0.919	-0.941	8.305	-0.520	-0.520	0.000	0.000	0.000	0.000
12	A	101	GLU	-1	-0.873	-0.939	10.185	-0.540	-0.540	0.000	0.000	0.000	0.000
13	A	102	THR	0	-0.076	-0.054	8.833	0.082	0.082	0.000	0.000	0.000	0.000
14	A	103	LEU	0	-0.046	-0.037	11.404	0.096	0.096	0.000	0.000	0.000	0.000
15	A	104	ASP	-1	-0.848	-0.920	13.914	-0.420	-0.420	0.000	0.000	0.000	0.000
16	A	105	SER	0	0.004	0.009	14.995	0.055	0.055	0.000	0.000	0.000	0.000
17	A	106	LEU	0	-0.036	-0.031	14.009	0.047	0.047	0.000	0.000	0.000	0.000
18	A	107	ALA	0	-0.002	0.002	17.403	0.040	0.040	0.000	0.000	0.000	0.000
19	A	108	GLU	-1	-0.900	-0.938	19.652	-0.258	-0.258	0.000	0.000	0.000	0.000
20	A	109	PHE	0	-0.005	-0.017	20.350	0.030	0.030	0.000	0.000	0.000	0.000
21	A	110	PHE	0	-0.027	-0.035	19.074	0.023	0.023	0.000	0.000	0.000	0.000
22	A	111	GLU	-1	-0.912	-0.941	23.520	-0.223	-0.223	0.000	0.000	0.000	0.000
23	A	112	ASP	-1	-0.829	-0.891	25.285	-0.156	-0.156	0.000	0.000	0.000	0.000
24	A	113	LEU	0	-0.047	-0.035	25.295	0.018	0.018	0.000	0.000	0.000	0.000
25	A	114	ALA	0	-0.012	0.005	28.166	0.011	0.011	0.000	0.000	0.000	0.000
26	A	115	ASP	-1	-0.893	-0.926	30.565	-0.126	-0.126	0.000	0.000	0.000	0.000
27	A	116	LYS	1	0.680	0.824	29.162	0.164	0.164	0.000	0.000	0.000	0.000
28	A	117	PRO	0	-0.008	-0.021	33.160	0.002	0.002	0.000	0.000	0.000	0.000
29	A	118	TYR	0	-0.019	-0.018	28.717	0.007	0.007	0.000	0.000	0.000	0.000
30	A	119	THR	0	-0.020	0.010	29.828	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	120	PHE	0	-0.008	-0.006	32.811	0.008	0.008	0.000	0.000	0.000	0.000
32	A	121	GLU	-1	-0.919	-0.959	34.325	-0.092	-0.092	0.000	0.000	0.000	0.000
33	A	122	ASP	-1	-0.836	-0.903	35.009	-0.113	-0.113	0.000	0.000	0.000	0.000
34	A	123	TYR	0	-0.078	-0.039	26.109	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	124	ASP	-1	-0.915	-0.973	29.226	-0.164	-0.164	0.000	0.000	0.000	0.000
36	A	125	VAL	0	-0.020	0.000	23.379	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	126	SER	0	0.013	0.016	24.480	0.008	0.008	0.000	0.000	0.000	0.000
38	A	127	PHE	0	-0.007	-0.013	16.142	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	128	GLY	0	0.051	0.026	20.098	0.015	0.015	0.000	0.000	0.000	0.000
40	A	129	SER	0	-0.045	-0.029	18.231	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	130	GLY	0	0.014	0.004	14.871	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	131	VAL	0	-0.042	-0.022	15.171	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	132	LEU	0	0.015	0.022	17.415	0.020	0.020	0.000	0.000	0.000	0.000
44	A	133	THR	0	-0.033	-0.031	19.360	0.007	0.007	0.000	0.000	0.000	0.000
45	A	134	VAL	0	0.038	0.019	21.884	0.005	0.005	0.000	0.000	0.000	0.000
46	A	135	LYS	1	0.817	0.901	24.427	0.133	0.133	0.000	0.000	0.000	0.000
47	A	136	LEU	0	0.017	-0.004	26.215	0.001	0.001	0.000	0.000	0.000	0.000
48	A	137	GLY	0	0.046	0.023	29.301	0.004	0.004	0.000	0.000	0.000	0.000
49	A	138	GLY	0	0.007	-0.009	32.852	0.000	0.000	0.000	0.000	0.000	0.000
50	A	139	ASP	-1	-1.025	-1.018	34.537	-0.084	-0.084	0.000	0.000	0.000	0.000
51	A	140	LEU	0	-0.017	-0.004	30.517	0.000	0.000	0.000	0.000	0.000	0.000
52	A	141	GLY	0	-0.041	-0.012	29.224	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	142	THR	0	-0.025	-0.037	25.074	0.000	0.000	0.000	0.000	0.000	0.000
54	A	143	TYR	0	-0.041	-0.041	20.839	0.005	0.005	0.000	0.000	0.000	0.000
55	A	144	VAL	0	-0.017	-0.003	19.286	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	145	ILE	0	0.007	0.000	14.413	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	146	ASN	0	-0.017	-0.007	14.509	0.035	0.035	0.000	0.000	0.000	0.000
58	A	147	LYS	1	0.891	0.954	10.202	0.805	0.805	0.000	0.000	0.000	0.000
59	A	148	GLN	0	0.015	0.011	9.919	0.087	0.087	0.000	0.000	0.000	0.000
60	A	149	THR	0	0.040	-0.018	8.307	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	150	PRO	0	-0.053	-0.018	8.459	-0.126	-0.126	0.000	0.000	0.000	0.000
62	A	151	ASN	0	-0.066	-0.043	9.289	0.178	0.178	0.000	0.000	0.000	0.000
63	A	152	LYS	1	0.839	0.922	3.346	0.756	1.645	0.007	-0.356	-0.541	0.000
64	A	153	GLN	0	-0.005	-0.010	5.498	-0.089	-0.089	0.000	0.000	0.000	0.000
65	A	154	ILE	0	-0.001	0.027	7.983	-0.043	-0.043	0.000	0.000	0.000	0.000
66	A	155	TRP	0	-0.082	-0.061	10.444	0.113	0.113	0.000	0.000	0.000	0.000
67	A	156	LEU	0	0.062	0.034	13.949	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	157	SER	0	-0.002	0.001	16.904	0.036	0.036	0.000	0.000	0.000	0.000
69	A	158	SER	0	0.005	-0.027	20.639	0.000	0.000	0.000	0.000	0.000	0.000
70	A	159	PRO	0	-0.020	-0.002	22.663	0.013	0.013	0.000	0.000	0.000	0.000
71	A	160	SER	0	-0.057	-0.027	25.541	0.015	0.015	0.000	0.000	0.000	0.000
72	A	161	SER	0	-0.050	-0.063	22.369	0.009	0.009	0.000	0.000	0.000	0.000
73	A	162	GLY	0	0.017	0.019	23.421	0.007	0.007	0.000	0.000	0.000	0.000
74	A	163	PRO	0	-0.025	-0.019	19.601	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	164	LYS	1	0.888	0.958	16.287	0.177	0.177	0.000	0.000	0.000	0.000
76	A	165	ARG	1	0.891	0.958	12.502	0.147	0.147	0.000	0.000	0.000	0.000
77	A	166	TYR	0	0.003	0.002	10.015	0.052	0.052	0.000	0.000	0.000	0.000
78	A	167	ASP	-1	-0.773	-0.865	6.894	-0.360	-0.360	0.000	0.000	0.000	0.000
79	A	168	TRP	0	0.011	0.015	2.438	-2.146	-2.067	5.744	-1.373	-4.451	-0.011
80	A	169	THR	0	0.018	-0.009	4.591	0.161	0.265	-0.001	-0.008	-0.095	0.000
81	A	170	GLY	0	-0.009	-0.014	3.929	0.239	0.358	0.000	-0.023	-0.096	0.000
82	A	171	LYS	1	0.803	0.895	4.965	0.257	0.300	-0.001	0.000	-0.041	0.000
83	A	172	ASN	0	-0.011	-0.003	7.663	0.032	0.032	0.000	0.000	0.000	0.000
84	A	173	TRP	0	0.023	0.009	4.646	-0.369	-0.214	-0.001	-0.006	-0.148	0.000
85	A	174	VAL	0	-0.009	-0.003	8.702	0.103	0.103	0.000	0.000	0.000	0.000
86	A	175	TYR	0	-0.003	0.018	10.864	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	176	SER	0	-0.006	-0.039	11.653	0.037	0.037	0.000	0.000	0.000	0.000
88	A	177	HIS	0	-0.075	-0.029	13.359	0.039	0.039	0.000	0.000	0.000	0.000
89	A	178	ASP	-1	-0.864	-0.944	16.904	-0.108	-0.108	0.000	0.000	0.000	0.000
90	A	179	GLY	0	-0.024	-0.005	14.897	0.006	0.006	0.000	0.000	0.000	0.000
91	A	180	VAL	0	-0.026	0.001	15.685	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	181	SER	0	-0.037	-0.069	12.956	-0.039	-0.039	0.000	0.000	0.000	0.000
93	A	182	LEU	0	-0.001	-0.013	11.522	0.034	0.034	0.000	0.000	0.000	0.000
94	A	183	HIS	0	0.049	0.012	11.689	0.054	0.054	0.000	0.000	0.000	0.000
95	A	184	GLU	-1	-0.857	-0.880	16.172	-0.179	-0.179	0.000	0.000	0.000	0.000
96	A	185	LEU	0	-0.015	-0.006	17.611	0.028	0.028	0.000	0.000	0.000	0.000
97	A	186	LEU	0	0.018	0.008	17.150	0.021	0.021	0.000	0.000	0.000	0.000
98	A	187	ALA	0	0.037	0.030	20.213	0.019	0.019	0.000	0.000	0.000	0.000
99	A	188	ALA	0	-0.028	-0.004	22.142	0.020	0.020	0.000	0.000	0.000	0.000
100	A	189	GLU	-1	-0.759	-0.812	22.787	-0.156	-0.156	0.000	0.000	0.000	0.000
101	A	190	LEU	0	0.046	0.020	22.253	0.013	0.013	0.000	0.000	0.000	0.000
102	A	191	THR	0	-0.014	-0.004	25.855	0.014	0.014	0.000	0.000	0.000	0.000
103	A	192	LYS	1	0.882	0.937	27.968	0.102	0.102	0.000	0.000	0.000	0.000
104	A	193	ALA	0	-0.041	-0.022	28.442	0.009	0.009	0.000	0.000	0.000	0.000
105	A	194	LEU	0	0.037	0.015	27.786	0.005	0.005	0.000	0.000	0.000	0.000
106	A	195	LYS	1	0.878	0.952	31.322	0.089	0.089	0.000	0.000	0.000	0.000
107	A	196	THR	0	0.018	0.010	30.032	0.007	0.007	0.000	0.000	0.000	0.000
108	A	197	LYS	1	0.892	0.949	29.055	0.095	0.095	0.000	0.000	0.000	0.000
109	A	198	LEU	0	0.027	0.031	24.908	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	199	ASP	-1	-0.814	-0.895	21.872	-0.200	-0.200	0.000	0.000	0.000	0.000
111	A	200	LEU	0	0.014	0.018	18.296	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	201	SER	0	-0.040	-0.048	17.876	-0.042	-0.042	0.000	0.000	0.000	0.000
113	A	202	SER	0	-0.041	-0.019	17.717	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	203	LEU	0	0.002	0.030	16.163	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	204	ALA	0	0.013	0.007	12.656	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	205	TYR	0	-0.029	-0.030	8.700	-0.088	-0.088	0.000	0.000	0.000	0.000
117	A	206	SER	0	0.061	0.030	10.584	-0.042	-0.042	0.000	0.000	0.000	0.000
118	A	207	GLY	0	-0.035	-0.007	12.141	0.023	0.023	0.000	0.000	0.000	0.000
119	A	208	LYS	1	0.891	0.942	12.836	0.370	0.370	0.000	0.000	0.000	0.000

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