FMO DATABASE

FMODB ID: R8L28

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	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	-390166.353102
FMO2-HF: Nuclear repulsion	359858.584731
FMO2-HF: Total energy	-30307.768371
FMO2-MP2: Total energy	-30391.173545

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.
-11.805	-12.646	23.896	-8.019	-15.038	0.04

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 : 0.089 / q_NPA : 0.002

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	0.886	0.914	2.493	-9.479	-3.747	5.680	-3.954	-7.458	0.043
4	A	15	VAL	0	0.031	0.012	1.645	-0.869	-7.323	18.202	-4.573	-7.176	-0.003
5	A	16	VAL	0	0.063	0.041	3.263	-0.577	-0.696	0.014	0.508	-0.404	0.000
6	A	17	GLU	-1	-0.762	-0.850	5.621	1.514	1.514	0.000	0.000	0.000	0.000
7	A	18	GLN	0	0.041	0.026	6.316	-0.470	-0.470	0.000	0.000	0.000	0.000
8	A	19	LYS	1	0.870	0.919	7.028	-0.590	-0.590	0.000	0.000	0.000	0.000
9	A	20	GLN	0	-0.020	-0.015	8.763	-0.225	-0.225	0.000	0.000	0.000	0.000
10	A	21	MET	0	0.007	0.006	10.645	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	22	LYS	1	0.901	0.938	10.808	-0.776	-0.776	0.000	0.000	0.000	0.000
12	A	23	ASP	-1	-0.789	-0.871	12.714	0.206	0.206	0.000	0.000	0.000	0.000
13	A	24	PHE	0	-0.012	0.001	14.568	-0.049	-0.049	0.000	0.000	0.000	0.000
14	A	25	MET	0	-0.037	-0.029	14.286	-0.031	-0.031	0.000	0.000	0.000	0.000
15	A	26	ARG	1	0.840	0.918	15.344	-0.248	-0.248	0.000	0.000	0.000	0.000
16	A	27	LEU	0	0.036	0.031	18.859	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	28	TYR	0	0.036	0.015	21.117	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	29	SER	0	0.049	0.022	21.864	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	30	ASN	0	0.019	-0.007	21.707	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	31	LEU	0	-0.028	-0.003	24.761	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	32	VAL	0	-0.020	-0.010	26.225	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.923	-0.962	27.576	0.116	0.116	0.000	0.000	0.000	0.000
23	A	34	ARG	1	0.867	0.944	28.737	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	35	CYS	0	-0.015	-0.009	30.507	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	36	PHE	0	-0.002	0.005	32.178	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	37	THR	0	-0.031	-0.027	32.455	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	38	ASP	-1	-0.924	-0.967	34.836	0.057	0.057	0.000	0.000	0.000	0.000
28	A	39	CYS	0	-0.169	-0.069	36.634	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	40	VAL	0	-0.047	-0.006	36.750	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	41	ASN	0	0.004	0.001	39.271	0.002	0.002	0.000	0.000	0.000	0.000
31	A	42	ASP	-1	-0.870	-0.905	42.117	0.044	0.044	0.000	0.000	0.000	0.000
32	A	43	PHE	0	-0.017	-0.019	39.244	0.003	0.003	0.000	0.000	0.000	0.000
33	A	44	THR	0	-0.068	-0.031	44.449	0.000	0.000	0.000	0.000	0.000	0.000
34	A	45	THR	0	-0.015	-0.005	45.096	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	46	SER	0	0.003	-0.007	42.106	0.001	0.001	0.000	0.000	0.000	0.000
36	A	47	LYS	1	0.901	0.939	41.071	-0.052	-0.052	0.000	0.000	0.000	0.000
37	A	48	LEU	0	0.045	0.044	36.591	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	49	THR	0	0.052	0.019	41.258	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	50	ASN	0	-0.027	-0.026	42.746	0.001	0.001	0.000	0.000	0.000	0.000
40	A	51	LYS	1	1.015	0.979	43.005	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	52	GLU	-1	-0.708	-0.850	39.937	0.054	0.054	0.000	0.000	0.000	0.000
42	A	53	GLN	0	0.000	0.013	38.296	0.003	0.003	0.000	0.000	0.000	0.000
43	A	54	THR	0	-0.041	-0.022	38.086	0.000	0.000	0.000	0.000	0.000	0.000
44	A	56	ILE	0	0.088	0.031	33.504	0.000	0.000	0.000	0.000	0.000	0.000
45	A	57	MET	0	-0.024	0.033	34.145	0.004	0.004	0.000	0.000	0.000	0.000
46	A	58	LYS	1	0.970	0.967	34.701	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	60	SER	0	0.005	-0.039	30.603	0.004	0.004	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-0.961	-0.967	30.140	0.034	0.034	0.000	0.000	0.000	0.000
49	A	62	LYS	1	0.945	0.961	31.240	-0.033	-0.033	0.000	0.000	0.000	0.000
50	A	63	PHE	0	0.015	0.005	25.200	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	64	LEU	0	0.027	0.017	25.193	0.000	0.000	0.000	0.000	0.000	0.000
52	A	65	LYS	1	0.885	0.930	26.875	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	66	HIS	0	-0.027	-0.007	27.388	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	67	SER	0	-0.005	-0.020	23.260	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	68	GLU	-1	-0.894	-0.920	23.875	0.008	0.008	0.000	0.000	0.000	0.000
56	A	69	ARG	1	0.948	0.973	24.939	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	70	VAL	0	0.015	-0.004	23.290	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	71	GLY	0	0.056	0.037	21.345	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	72	GLN	0	-0.019	-0.028	21.331	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	73	ARG	1	0.819	0.915	23.377	0.029	0.029	0.000	0.000	0.000	0.000
61	A	74	PHE	0	-0.016	0.001	16.316	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	75	GLN	0	0.005	-0.008	16.194	0.013	0.013	0.000	0.000	0.000	0.000
63	A	76	GLU	-1	-0.889	-0.948	19.895	-0.079	-0.079	0.000	0.000	0.000	0.000
64	A	77	GLN	0	-0.047	-0.035	21.592	0.001	0.001	0.000	0.000	0.000	0.000
65	A	78	ASN	0	-0.036	0.003	14.787	0.020	0.020	0.000	0.000	0.000	0.000
66	A	79	ALA	0	-0.047	-0.012	18.136	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	80	ALA	0	-0.021	0.002	19.343	-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)