FMO DATABASE

FMODB ID: 6Y42Z

Calculation Name: 3DXR-B-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: B

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	-355629.249265
FMO2-HF: Nuclear repulsion	326345.495887
FMO2-HF: Total energy	-29283.753378
FMO2-MP2: Total energy	-29363.500235

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(B:15:SER)

Summations of interaction energy for fragment #1(B:15:SER)

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.
-10.403	-6.316	6.957	-4.525	-6.52	0.018

Interaction energy analysis for fragmet #1(B:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.005

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	B	17	GLN	0	0.086	0.027	3.058	-1.323	1.815	0.258	-1.448	-1.948	0.007
4	B	18	LYS	1	0.945	0.980	2.173	-7.159	-6.853	6.661	-2.893	-4.074	0.010
5	B	19	ILE	0	0.020	0.017	3.822	-1.939	-1.296	0.038	-0.184	-0.498	0.001
6	B	20	GLN	0	0.035	0.031	6.067	0.214	0.214	0.000	0.000	0.000	0.000
7	B	21	ALA	0	-0.036	-0.019	7.569	-0.114	-0.114	0.000	0.000	0.000	0.000
8	B	22	ALA	0	-0.014	0.000	9.271	-0.026	-0.026	0.000	0.000	0.000	0.000
9	B	23	GLU	-1	-0.871	-0.951	10.429	-0.070	-0.070	0.000	0.000	0.000	0.000
10	B	24	ALA	0	-0.013	-0.017	11.885	0.001	0.001	0.000	0.000	0.000	0.000
11	B	25	GLU	-1	-0.945	-0.971	13.077	-0.010	-0.010	0.000	0.000	0.000	0.000
12	B	26	LEU	0	-0.026	-0.027	14.603	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	27	ASP	-1	-0.942	-0.938	16.268	0.012	0.012	0.000	0.000	0.000	0.000
14	B	28	LEU	0	0.036	0.015	17.613	-0.002	-0.002	0.000	0.000	0.000	0.000
15	B	29	VAL	0	-0.037	-0.027	18.331	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	30	THR	0	-0.050	-0.034	20.247	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	31	ASP	-1	-0.780	-0.882	22.142	0.001	0.001	0.000	0.000	0.000	0.000
18	B	32	MET	0	-0.029	-0.007	23.298	0.001	0.001	0.000	0.000	0.000	0.000
19	B	33	PHE	0	0.012	0.005	24.823	0.001	0.001	0.000	0.000	0.000	0.000
20	B	34	ASN	0	0.021	0.004	26.496	0.001	0.001	0.000	0.000	0.000	0.000
21	B	35	LYS	1	0.844	0.926	25.658	0.002	0.002	0.000	0.000	0.000	0.000
22	B	36	LEU	0	-0.014	0.017	28.708	0.001	0.001	0.000	0.000	0.000	0.000
23	B	37	VAL	0	0.003	0.003	30.808	0.001	0.001	0.000	0.000	0.000	0.000
24	B	38	ASN	0	-0.046	-0.037	31.963	0.001	0.001	0.000	0.000	0.000	0.000
25	B	39	ASN	0	-0.113	-0.070	32.271	0.002	0.002	0.000	0.000	0.000	0.000
26	B	40	CYS	0	-0.040	-0.024	34.828	0.002	0.002	0.000	0.000	0.000	0.000
27	B	41	TYR	0	0.040	0.038	36.723	0.000	0.000	0.000	0.000	0.000	0.000
28	B	42	LYS	1	0.956	0.973	36.879	0.006	0.006	0.000	0.000	0.000	0.000
29	B	43	LYS	1	0.880	0.945	38.216	0.004	0.004	0.000	0.000	0.000	0.000
30	B	44	CYS	0	-0.137	-0.054	40.607	0.001	0.001	0.000	0.000	0.000	0.000
31	B	45	ILE	0	-0.005	0.021	40.940	0.000	0.000	0.000	0.000	0.000	0.000
32	B	46	ASN	0	0.015	0.026	43.652	0.001	0.001	0.000	0.000	0.000	0.000
33	B	47	THR	0	0.026	0.001	45.345	0.000	0.000	0.000	0.000	0.000	0.000
34	B	48	SER	0	-0.041	-0.028	48.038	0.000	0.000	0.000	0.000	0.000	0.000
35	B	49	TYR	0	-0.074	-0.042	51.695	0.000	0.000	0.000	0.000	0.000	0.000
36	B	50	SER	0	0.006	0.018	48.259	0.000	0.000	0.000	0.000	0.000	0.000
37	B	51	GLU	-1	-0.887	-0.949	50.330	-0.011	-0.011	0.000	0.000	0.000	0.000
38	B	52	GLY	0	-0.028	-0.014	46.700	0.000	0.000	0.000	0.000	0.000	0.000
39	B	53	GLU	-1	-1.030	-0.989	45.455	-0.013	-0.013	0.000	0.000	0.000	0.000
40	B	54	LEU	0	0.004	0.010	40.467	0.001	0.001	0.000	0.000	0.000	0.000
41	B	55	ASN	0	0.081	0.026	44.683	0.000	0.000	0.000	0.000	0.000	0.000
42	B	56	LYS	1	0.968	0.979	43.766	0.010	0.010	0.000	0.000	0.000	0.000
43	B	57	ASN	0	-0.001	-0.012	45.284	0.000	0.000	0.000	0.000	0.000	0.000
44	B	58	GLU	-1	-0.805	-0.903	43.517	-0.010	-0.010	0.000	0.000	0.000	0.000
45	B	59	SER	0	-0.024	-0.033	41.333	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	60	SER	0	-0.030	-0.015	40.450	0.000	0.000	0.000	0.000	0.000	0.000
47	B	62	LEU	0	0.069	0.027	37.110	0.000	0.000	0.000	0.000	0.000	0.000
48	B	63	ASP	-1	-0.865	-0.916	36.287	-0.013	-0.013	0.000	0.000	0.000	0.000
49	B	64	ARG	1	0.926	0.940	35.998	0.007	0.007	0.000	0.000	0.000	0.000
50	B	66	VAL	0	0.045	-0.001	31.006	0.001	0.001	0.000	0.000	0.000	0.000
51	B	67	ALA	0	-0.014	-0.002	31.952	0.000	0.000	0.000	0.000	0.000	0.000
52	B	68	LYS	1	0.854	0.893	32.772	0.002	0.002	0.000	0.000	0.000	0.000
53	B	69	TYR	0	0.008	0.023	28.314	0.002	0.002	0.000	0.000	0.000	0.000
54	B	70	PHE	0	0.035	0.016	24.963	0.001	0.001	0.000	0.000	0.000	0.000
55	B	71	GLU	-1	-0.867	-0.904	28.861	0.003	0.003	0.000	0.000	0.000	0.000
56	B	72	THR	0	-0.034	-0.045	31.056	0.002	0.002	0.000	0.000	0.000	0.000
57	B	73	ASN	0	-0.004	-0.001	25.070	0.000	0.000	0.000	0.000	0.000	0.000
58	B	74	VAL	0	0.041	0.026	25.915	0.002	0.002	0.000	0.000	0.000	0.000
59	B	75	GLN	0	0.027	0.033	27.349	0.003	0.003	0.000	0.000	0.000	0.000
60	B	76	VAL	0	0.014	-0.013	27.467	0.001	0.001	0.000	0.000	0.000	0.000
61	B	77	GLY	0	-0.014	-0.004	25.239	0.001	0.001	0.000	0.000	0.000	0.000
62	B	78	GLU	-1	-0.949	-0.988	25.671	0.017	0.017	0.000	0.000	0.000	0.000
63	B	79	ASN	0	-0.115	-0.066	27.872	0.000	0.000	0.000	0.000	0.000	0.000
64	B	80	MET	0	0.026	0.002	23.942	0.000	0.000	0.000	0.000	0.000	0.000
65	B	81	GLN	0	-0.016	0.039	23.744	0.003	0.003	0.000	0.000	0.000	0.000
66	B	82	LYS	1	0.903	0.969	25.983	-0.012	-0.012	0.000	0.000	0.000	0.000
67	B	83	MET	0	-0.081	-0.056	26.998	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:15:SER)