FMO DATABASE

FMODB ID: KGV53

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

Total energy (hartree)

FMO2-HF: Electronic energy	-389671.321589
FMO2-HF: Nuclear repulsion	359362.664411
FMO2-HF: Total energy	-30308.657178
FMO2-MP2: Total energy	-30391.923345

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.
-10.53	-3.267	6.776	-4.424	-9.615	0.034

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 : 0.104 / q_NPA : 0.043

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	14	LYS	1	0.843	0.909	2.653	-7.994	-3.474	4.544	-3.111	-5.953	0.031
4	A	15	VAL	0	0.010	-0.002	2.281	-4.349	-1.975	2.232	-1.234	-3.372	0.003
5	A	16	VAL	0	0.027	0.024	4.257	-0.202	0.167	0.000	-0.079	-0.290	0.000
6	A	17	GLU	-1	-0.763	-0.851	6.427	0.963	0.963	0.000	0.000	0.000	0.000
7	A	18	GLN	0	0.041	0.026	7.149	-0.058	-0.058	0.000	0.000	0.000	0.000
8	A	19	LYS	1	0.869	0.923	8.154	0.596	0.596	0.000	0.000	0.000	0.000
9	A	20	GLN	0	-0.001	-0.003	9.893	0.077	0.077	0.000	0.000	0.000	0.000
10	A	21	MET	0	-0.005	-0.005	12.008	0.068	0.068	0.000	0.000	0.000	0.000
11	A	22	LYS	1	0.903	0.946	11.476	0.359	0.359	0.000	0.000	0.000	0.000
12	A	23	ASP	-1	-0.745	-0.841	13.850	-0.368	-0.368	0.000	0.000	0.000	0.000
13	A	24	PHE	0	-0.005	0.013	15.661	0.033	0.033	0.000	0.000	0.000	0.000
14	A	25	MET	0	-0.005	-0.012	15.162	0.025	0.025	0.000	0.000	0.000	0.000
15	A	26	ARG	1	0.855	0.915	15.319	0.286	0.286	0.000	0.000	0.000	0.000
16	A	27	LEU	0	-0.003	0.006	19.797	0.018	0.018	0.000	0.000	0.000	0.000
17	A	28	TYR	0	0.018	0.004	21.812	0.016	0.016	0.000	0.000	0.000	0.000
18	A	29	SER	0	0.029	0.007	22.902	0.012	0.012	0.000	0.000	0.000	0.000
19	A	30	ASN	0	-0.047	-0.052	22.694	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	31	LEU	0	-0.021	-0.001	25.516	0.009	0.009	0.000	0.000	0.000	0.000
21	A	32	VAL	0	-0.019	-0.008	27.590	0.008	0.008	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.863	-0.914	27.376	-0.095	-0.095	0.000	0.000	0.000	0.000
23	A	34	ARG	1	0.796	0.885	29.154	0.084	0.084	0.000	0.000	0.000	0.000
24	A	35	CYS	0	0.009	-0.006	31.031	0.001	0.001	0.000	0.000	0.000	0.000
25	A	36	PHE	0	0.011	0.010	33.003	0.005	0.005	0.000	0.000	0.000	0.000
26	A	37	THR	0	-0.036	-0.037	33.062	0.005	0.005	0.000	0.000	0.000	0.000
27	A	38	ASP	-1	-0.839	-0.885	35.544	-0.063	-0.063	0.000	0.000	0.000	0.000
28	A	39	CYS	0	-0.131	-0.059	37.432	0.001	0.001	0.000	0.000	0.000	0.000
29	A	40	VAL	0	-0.033	-0.003	37.763	0.002	0.002	0.000	0.000	0.000	0.000
30	A	41	ASN	0	-0.006	-0.008	40.222	0.000	0.000	0.000	0.000	0.000	0.000
31	A	42	ASP	-1	-0.831	-0.873	43.140	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	43	PHE	0	-0.003	-0.015	40.075	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	44	THR	0	-0.076	-0.054	45.267	0.001	0.001	0.000	0.000	0.000	0.000
34	A	45	THR	0	-0.024	-0.007	46.047	0.001	0.001	0.000	0.000	0.000	0.000
35	A	46	SER	0	-0.017	-0.012	42.703	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	47	LYS	1	0.908	0.937	41.651	0.039	0.039	0.000	0.000	0.000	0.000
37	A	48	LEU	0	0.043	0.049	37.463	0.001	0.001	0.000	0.000	0.000	0.000
38	A	49	THR	0	0.032	-0.019	42.157	0.001	0.001	0.000	0.000	0.000	0.000
39	A	50	ASN	0	0.024	-0.003	43.787	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	51	LYS	1	0.928	0.962	44.282	0.037	0.037	0.000	0.000	0.000	0.000
41	A	52	GLU	-1	-0.662	-0.791	41.027	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	53	GLN	0	-0.038	-0.014	39.622	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	54	THR	0	-0.089	-0.053	39.291	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	56	ILE	0	0.093	0.035	34.463	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	57	MET	0	-0.022	0.010	34.991	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	58	LYS	1	0.955	0.968	35.429	0.046	0.046	0.000	0.000	0.000	0.000
47	A	60	SER	0	0.018	-0.013	31.225	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-0.901	-0.945	30.828	-0.076	-0.076	0.000	0.000	0.000	0.000
49	A	62	LYS	1	0.858	0.928	31.798	0.063	0.063	0.000	0.000	0.000	0.000
50	A	63	PHE	0	0.034	0.012	26.082	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	64	LEU	0	0.009	0.011	25.865	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	65	LYS	1	0.853	0.896	27.051	0.088	0.088	0.000	0.000	0.000	0.000
53	A	66	HIS	0	-0.006	0.009	27.428	0.001	0.001	0.000	0.000	0.000	0.000
54	A	67	SER	0	0.032	0.005	22.792	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	68	GLU	-1	-0.886	-0.911	23.673	-0.120	-0.120	0.000	0.000	0.000	0.000
56	A	69	ARG	1	0.898	0.952	24.821	0.082	0.082	0.000	0.000	0.000	0.000
57	A	70	VAL	0	0.026	-0.003	23.100	0.001	0.001	0.000	0.000	0.000	0.000
58	A	71	GLY	0	0.036	0.022	21.196	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	72	GLN	0	-0.011	-0.014	21.498	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	73	ARG	1	0.775	0.857	23.483	0.104	0.104	0.000	0.000	0.000	0.000
61	A	74	PHE	0	0.014	0.015	16.092	0.005	0.005	0.000	0.000	0.000	0.000
62	A	75	GLN	0	0.008	-0.016	15.592	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	76	GLU	-1	-0.824	-0.871	19.644	-0.104	-0.104	0.000	0.000	0.000	0.000
64	A	77	GLN	0	-0.051	-0.032	21.386	0.007	0.007	0.000	0.000	0.000	0.000
65	A	78	ASN	0	-0.033	-0.006	14.492	0.003	0.003	0.000	0.000	0.000	0.000
66	A	79	ALA	0	-0.055	-0.015	17.568	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	80	ALA	0	-0.020	0.003	19.297	0.013	0.013	0.000	0.000	0.000	0.000

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