FMO DATABASE

FMODB ID: 2NMQR

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	OptH
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	-355880.744943
FMO2-HF: Nuclear repulsion	326597.557841
FMO2-HF: Total energy	-29283.187103
FMO2-MP2: Total energy	-29363.000371

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.
-6.656	-5.352	10.068	-4.602	-6.769	0.016

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 : -0.019 / q_NPA : -0.024

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	0.084	0.025	3.193	-0.702	1.635	0.166	-0.976	-1.526	0.003
4	B	18	LYS	1	0.945	0.983	2.043	-3.891	-5.566	9.844	-3.500	-4.669	0.011
5	B	19	ILE	0	0.024	0.016	3.705	-2.087	-1.445	0.058	-0.126	-0.574	0.002
6	B	20	GLN	0	0.013	0.022	6.059	0.120	0.120	0.000	0.000	0.000	0.000
7	B	21	ALA	0	-0.032	-0.017	7.493	-0.163	-0.163	0.000	0.000	0.000	0.000
8	B	22	ALA	0	-0.012	0.003	9.256	-0.056	-0.056	0.000	0.000	0.000	0.000
9	B	23	GLU	-1	-0.872	-0.952	10.367	0.340	0.340	0.000	0.000	0.000	0.000
10	B	24	ALA	0	-0.009	-0.018	11.804	-0.026	-0.026	0.000	0.000	0.000	0.000
11	B	25	GLU	-1	-0.948	-0.968	12.996	-0.145	-0.145	0.000	0.000	0.000	0.000
12	B	26	LEU	0	-0.033	-0.035	14.442	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	27	ASP	-1	-0.947	-0.941	16.179	0.041	0.041	0.000	0.000	0.000	0.000
14	B	28	LEU	0	0.048	0.019	17.534	-0.006	-0.006	0.000	0.000	0.000	0.000
15	B	29	VAL	0	-0.045	-0.027	17.733	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	30	THR	0	-0.060	-0.035	20.267	0.001	0.001	0.000	0.000	0.000	0.000
17	B	31	ASP	-1	-0.821	-0.905	22.054	-0.004	-0.004	0.000	0.000	0.000	0.000
18	B	32	MET	0	-0.017	-0.011	23.209	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	33	PHE	0	0.021	0.010	24.721	0.000	0.000	0.000	0.000	0.000	0.000
20	B	34	ASN	0	0.032	0.002	26.035	0.003	0.003	0.000	0.000	0.000	0.000
21	B	35	LYS	1	0.875	0.947	26.136	0.010	0.010	0.000	0.000	0.000	0.000
22	B	36	LEU	0	-0.016	0.018	28.690	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	37	VAL	0	-0.001	0.003	30.542	0.000	0.000	0.000	0.000	0.000	0.000
24	B	38	ASN	0	-0.025	-0.023	31.692	0.001	0.001	0.000	0.000	0.000	0.000
25	B	39	ASN	0	-0.109	-0.069	32.017	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	40	CYS	0	-0.048	-0.029	34.730	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	41	TYR	0	0.038	0.038	36.620	0.000	0.000	0.000	0.000	0.000	0.000
28	B	42	LYS	1	0.954	0.970	37.143	0.006	0.006	0.000	0.000	0.000	0.000
29	B	43	LYS	1	0.875	0.941	37.849	0.020	0.020	0.000	0.000	0.000	0.000
30	B	44	CYS	0	-0.099	-0.041	40.567	-0.004	-0.004	0.000	0.000	0.000	0.000
31	B	45	ILE	0	0.000	0.022	40.863	0.001	0.001	0.000	0.000	0.000	0.000
32	B	46	ASN	0	0.017	0.020	43.608	0.001	0.001	0.000	0.000	0.000	0.000
33	B	47	THR	0	0.019	-0.001	45.328	0.000	0.000	0.000	0.000	0.000	0.000
34	B	48	SER	0	-0.018	-0.012	48.037	0.001	0.001	0.000	0.000	0.000	0.000
35	B	49	TYR	0	-0.073	-0.042	51.639	0.000	0.000	0.000	0.000	0.000	0.000
36	B	50	SER	0	0.000	0.018	48.089	0.000	0.000	0.000	0.000	0.000	0.000
37	B	51	GLU	-1	-0.895	-0.956	50.258	0.006	0.006	0.000	0.000	0.000	0.000
38	B	52	GLY	0	-0.024	-0.013	46.680	0.000	0.000	0.000	0.000	0.000	0.000
39	B	53	GLU	-1	-1.021	-0.985	45.434	0.003	0.003	0.000	0.000	0.000	0.000
40	B	54	LEU	0	0.000	0.012	40.289	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	55	ASN	0	0.100	0.051	44.674	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	56	LYS	1	0.959	0.978	43.664	0.007	0.007	0.000	0.000	0.000	0.000
43	B	57	ASN	0	0.024	-0.009	45.294	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	58	GLU	-1	-0.831	-0.914	43.496	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	59	SER	0	-0.028	-0.043	41.341	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	60	SER	0	-0.070	-0.031	40.461	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	62	LEU	0	0.054	0.019	37.313	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	63	ASP	-1	-0.867	-0.915	36.299	-0.016	-0.016	0.000	0.000	0.000	0.000
49	B	64	ARG	1	0.927	0.939	36.028	0.015	0.015	0.000	0.000	0.000	0.000
50	B	66	VAL	0	0.043	0.000	31.110	-0.003	-0.003	0.000	0.000	0.000	0.000
51	B	67	ALA	0	-0.010	0.000	31.832	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	68	LYS	1	0.991	0.979	32.653	0.026	0.026	0.000	0.000	0.000	0.000
53	B	69	TYR	0	-0.012	0.015	27.982	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	70	PHE	0	0.026	0.015	25.025	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	71	GLU	-1	-0.958	-0.976	28.756	-0.053	-0.053	0.000	0.000	0.000	0.000
56	B	72	THR	0	-0.051	-0.046	30.963	-0.003	-0.003	0.000	0.000	0.000	0.000
57	B	73	ASN	0	-0.004	-0.004	24.779	0.002	0.002	0.000	0.000	0.000	0.000
58	B	74	VAL	0	0.043	0.026	25.845	-0.006	-0.006	0.000	0.000	0.000	0.000
59	B	75	GLN	0	0.024	0.032	27.261	-0.008	-0.008	0.000	0.000	0.000	0.000
60	B	76	VAL	0	-0.012	-0.022	27.332	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	77	GLY	0	-0.018	-0.010	25.188	-0.004	-0.004	0.000	0.000	0.000	0.000
62	B	78	GLU	-1	-0.955	-0.988	25.624	-0.101	-0.101	0.000	0.000	0.000	0.000
63	B	79	ASN	0	-0.090	-0.055	27.818	0.002	0.002	0.000	0.000	0.000	0.000
64	B	80	MET	0	-0.017	-0.021	24.098	0.001	0.001	0.000	0.000	0.000	0.000
65	B	81	GLN	0	-0.014	0.008	23.963	-0.017	-0.017	0.000	0.000	0.000	0.000
66	B	82	LYS	1	0.903	0.970	25.961	0.073	0.073	0.000	0.000	0.000	0.000
67	B	83	MET	0	-0.037	-0.001	26.363	-0.001	-0.001	0.000	0.000	0.000	0.000

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