FMO DATABASE

FMODB ID: QVL6Y

Calculation Name: 3DXR-A-Xray372

Preferred Name: Mitochondrial import inner membrane translocase subunit TIM10

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3DXR

Chain ID: A

ChEMBL ID: CHEMBL1741194

UniProt ID: P87108

Base Structure: X-ray

Registration Date: 2023-09-23

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-389724.23606
FMO2-HF: Nuclear repulsion	359415.992387
FMO2-HF: Total energy	-30308.243673
FMO2-MP2: Total energy	-30391.592945

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:12:PHE)

Summations of interaction energy for fragment #1(A:12:PHE)

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.
-13.989	-8.106	14.597	-6.869	-13.611	0.054

Interaction energy analysis for fragmet #1(A:12:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.117 / q_NPA : 0.026

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	14	LYS	1	0.877	0.910	2.607	-11.049	-4.572	6.444	-4.885	-8.036	0.059
4	A	15	VAL	0	0.038	0.015	1.892	-3.593	-4.317	8.140	-2.168	-5.248	-0.005
5	A	16	VAL	0	0.052	0.038	3.415	-0.448	-0.318	0.013	0.184	-0.327	0.000
6	A	17	GLU	-1	-0.756	-0.849	5.919	1.606	1.606	0.000	0.000	0.000	0.000
7	A	18	GLN	0	0.039	0.026	6.544	-0.306	-0.306	0.000	0.000	0.000	0.000
8	A	19	LYS	1	0.859	0.908	7.222	0.250	0.250	0.000	0.000	0.000	0.000
9	A	20	GLN	0	-0.018	-0.012	8.941	-0.087	-0.087	0.000	0.000	0.000	0.000
10	A	21	MET	0	0.004	0.004	10.879	0.031	0.031	0.000	0.000	0.000	0.000
11	A	22	LYS	1	0.893	0.931	10.902	-0.176	-0.176	0.000	0.000	0.000	0.000
12	A	23	ASP	-1	-0.753	-0.843	12.909	-0.242	-0.242	0.000	0.000	0.000	0.000
13	A	24	PHE	0	-0.025	-0.002	14.765	0.000	0.000	0.000	0.000	0.000	0.000
14	A	25	MET	0	-0.029	-0.026	14.641	0.004	0.004	0.000	0.000	0.000	0.000
15	A	26	ARG	1	0.858	0.921	15.276	0.140	0.140	0.000	0.000	0.000	0.000
16	A	27	LEU	0	0.008	0.015	19.019	0.005	0.005	0.000	0.000	0.000	0.000
17	A	28	TYR	0	0.043	0.020	21.331	0.004	0.004	0.000	0.000	0.000	0.000
18	A	29	SER	0	0.062	0.031	22.169	0.005	0.005	0.000	0.000	0.000	0.000
19	A	30	ASN	0	-0.033	-0.032	22.285	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	31	LEU	0	-0.038	-0.011	24.915	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	32	VAL	0	-0.020	-0.012	26.700	0.002	0.002	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.887	-0.942	26.759	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	34	ARG	1	0.794	0.885	28.900	0.035	0.035	0.000	0.000	0.000	0.000
24	A	35	CYS	0	-0.013	-0.020	30.667	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	36	PHE	0	-0.011	0.002	32.339	0.002	0.002	0.000	0.000	0.000	0.000
26	A	37	THR	0	-0.031	-0.031	32.594	0.002	0.002	0.000	0.000	0.000	0.000
27	A	38	ASP	-1	-0.848	-0.895	35.078	-0.030	-0.030	0.000	0.000	0.000	0.000
28	A	39	CYS	0	-0.141	-0.053	36.806	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	40	VAL	0	-0.038	-0.002	37.012	0.001	0.001	0.000	0.000	0.000	0.000
30	A	41	ASN	0	-0.001	-0.003	39.425	0.001	0.001	0.000	0.000	0.000	0.000
31	A	42	ASP	-1	-0.836	-0.872	42.254	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	43	PHE	0	-0.017	-0.019	39.237	0.001	0.001	0.000	0.000	0.000	0.000
33	A	44	THR	0	-0.071	-0.048	44.568	0.001	0.001	0.000	0.000	0.000	0.000
34	A	45	THR	0	-0.052	-0.026	45.704	0.001	0.001	0.000	0.000	0.000	0.000
35	A	46	SER	0	0.017	0.002	42.199	0.000	0.000	0.000	0.000	0.000	0.000
36	A	47	LYS	1	0.912	0.945	41.212	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	48	LEU	0	0.029	0.037	36.722	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	49	THR	0	0.035	-0.017	41.436	0.000	0.000	0.000	0.000	0.000	0.000
39	A	50	ASN	0	0.002	-0.013	42.947	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	51	LYS	1	0.966	0.956	43.225	0.013	0.013	0.000	0.000	0.000	0.000
41	A	52	GLU	-1	-0.665	-0.797	40.118	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	53	GLN	0	-0.024	-0.002	38.505	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	54	THR	0	-0.055	-0.027	38.314	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	56	ILE	0	0.085	0.025	33.619	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	57	MET	0	-0.023	0.014	34.374	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	58	LYS	1	0.965	0.968	34.952	0.023	0.023	0.000	0.000	0.000	0.000
47	A	60	SER	0	0.027	-0.014	30.852	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-0.994	-0.981	30.390	-0.051	-0.051	0.000	0.000	0.000	0.000
49	A	62	LYS	1	0.955	0.969	31.502	0.043	0.043	0.000	0.000	0.000	0.000
50	A	63	PHE	0	0.024	0.008	25.606	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	64	LEU	0	0.028	0.019	25.512	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	65	LYS	1	0.860	0.908	27.143	0.070	0.070	0.000	0.000	0.000	0.000
53	A	66	HIS	0	-0.026	-0.002	27.591	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	67	SER	0	0.016	-0.012	23.310	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	68	GLU	-1	-0.893	-0.916	23.913	-0.111	-0.111	0.000	0.000	0.000	0.000
56	A	69	ARG	1	0.943	0.970	24.915	0.083	0.083	0.000	0.000	0.000	0.000
57	A	70	VAL	0	0.025	-0.002	23.208	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	71	GLY	0	0.049	0.034	21.283	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	72	GLN	0	-0.019	-0.024	21.404	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	73	ARG	1	0.794	0.875	23.574	0.133	0.133	0.000	0.000	0.000	0.000
61	A	74	PHE	0	-0.007	0.000	16.148	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	75	GLN	0	0.010	-0.002	16.118	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	76	GLU	-1	-0.862	-0.904	20.133	-0.167	-0.167	0.000	0.000	0.000	0.000
64	A	77	GLN	0	-0.048	-0.033	21.745	0.006	0.006	0.000	0.000	0.000	0.000
65	A	78	ASN	0	-0.032	-0.002	15.236	0.003	0.003	0.000	0.000	0.000	0.000
66	A	79	ALA	0	-0.056	-0.013	18.503	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	80	ALA	0	-0.015	0.006	19.686	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:PHE)