FMO DATABASE

FMODB ID: ZVZ8N

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	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	-355794.985387
FMO2-HF: Nuclear repulsion	326510.840408
FMO2-HF: Total energy	-29284.144979
FMO2-MP2: Total energy	-29363.830126

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.
-17.052	-12.782	8.758	-5.195	-7.833	0.01

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 : 0.013

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	0.068	0.022	2.459	-7.063	-3.394	2.649	-2.617	-3.701	0.001
4	B	18	LYS	1	0.949	0.972	2.093	-8.337	-8.270	6.091	-2.448	-3.710	0.009
5	B	19	ILE	0	0.003	0.000	3.762	-1.844	-1.310	0.018	-0.130	-0.422	0.000
6	B	20	GLN	0	0.049	0.039	6.165	0.177	0.177	0.000	0.000	0.000	0.000
7	B	21	ALA	0	-0.038	-0.014	7.791	-0.089	-0.089	0.000	0.000	0.000	0.000
8	B	22	ALA	0	-0.010	0.003	9.584	-0.077	-0.077	0.000	0.000	0.000	0.000
9	B	23	GLU	-1	-0.863	-0.949	10.586	-0.012	-0.012	0.000	0.000	0.000	0.000
10	B	24	ALA	0	-0.006	-0.002	12.268	-0.017	-0.017	0.000	0.000	0.000	0.000
11	B	25	GLU	-1	-0.906	-0.953	13.573	0.185	0.185	0.000	0.000	0.000	0.000
12	B	26	LEU	0	-0.023	-0.018	14.863	-0.033	-0.033	0.000	0.000	0.000	0.000
13	B	27	ASP	-1	-0.950	-0.946	16.842	0.096	0.096	0.000	0.000	0.000	0.000
14	B	28	LEU	0	0.026	0.022	18.026	-0.018	-0.018	0.000	0.000	0.000	0.000
15	B	29	VAL	0	-0.005	-0.014	19.253	-0.016	-0.016	0.000	0.000	0.000	0.000
16	B	30	THR	0	-0.041	-0.030	20.934	-0.019	-0.019	0.000	0.000	0.000	0.000
17	B	31	ASP	-1	-0.765	-0.858	22.569	0.077	0.077	0.000	0.000	0.000	0.000
18	B	32	MET	0	-0.045	-0.011	23.694	-0.003	-0.003	0.000	0.000	0.000	0.000
19	B	33	PHE	0	0.011	0.000	25.231	-0.007	-0.007	0.000	0.000	0.000	0.000
20	B	34	ASN	0	-0.017	-0.016	26.946	-0.006	-0.006	0.000	0.000	0.000	0.000
21	B	35	LYS	1	0.826	0.880	25.742	-0.085	-0.085	0.000	0.000	0.000	0.000
22	B	36	LEU	0	0.000	0.021	29.397	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	37	VAL	0	-0.005	0.004	31.175	-0.003	-0.003	0.000	0.000	0.000	0.000
24	B	38	ASN	0	-0.049	-0.039	32.289	-0.004	-0.004	0.000	0.000	0.000	0.000
25	B	39	ASN	0	-0.107	-0.058	32.749	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	40	CYS	0	-0.007	-0.012	35.190	0.004	0.004	0.000	0.000	0.000	0.000
27	B	41	TYR	0	0.041	0.021	37.044	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	42	LYS	1	0.944	0.963	36.819	-0.031	-0.031	0.000	0.000	0.000	0.000
29	B	43	LYS	1	0.879	0.948	38.616	-0.039	-0.039	0.000	0.000	0.000	0.000
30	B	44	CYS	0	-0.109	-0.037	40.961	0.004	0.004	0.000	0.000	0.000	0.000
31	B	45	ILE	0	-0.001	0.021	41.356	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	46	ASN	0	-0.013	0.001	44.213	0.001	0.001	0.000	0.000	0.000	0.000
33	B	47	THR	0	0.029	0.002	45.848	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	48	SER	0	-0.041	-0.025	48.564	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	49	TYR	0	-0.050	-0.034	52.077	0.000	0.000	0.000	0.000	0.000	0.000
36	B	50	SER	0	-0.005	0.020	49.046	0.000	0.000	0.000	0.000	0.000	0.000
37	B	51	GLU	-1	-0.863	-0.946	50.629	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	52	GLY	0	-0.065	-0.023	47.590	0.001	0.001	0.000	0.000	0.000	0.000
39	B	53	GLU	-1	-0.997	-0.984	46.319	0.001	0.001	0.000	0.000	0.000	0.000
40	B	54	LEU	0	0.007	0.002	40.831	0.002	0.002	0.000	0.000	0.000	0.000
41	B	55	ASN	0	0.089	0.042	45.084	0.001	0.001	0.000	0.000	0.000	0.000
42	B	56	LYS	1	0.939	0.960	42.884	-0.013	-0.013	0.000	0.000	0.000	0.000
43	B	57	ASN	0	0.000	0.007	45.750	0.002	0.002	0.000	0.000	0.000	0.000
44	B	58	GLU	-1	-0.788	-0.887	44.180	0.013	0.013	0.000	0.000	0.000	0.000
45	B	59	SER	0	-0.007	-0.012	41.638	0.001	0.001	0.000	0.000	0.000	0.000
46	B	60	SER	0	-0.069	-0.042	40.995	0.002	0.002	0.000	0.000	0.000	0.000
47	B	62	LEU	0	0.036	0.011	37.554	0.003	0.003	0.000	0.000	0.000	0.000
48	B	63	ASP	-1	-0.869	-0.942	37.123	0.021	0.021	0.000	0.000	0.000	0.000
49	B	64	ARG	1	0.911	0.947	36.783	-0.022	-0.022	0.000	0.000	0.000	0.000
50	B	66	VAL	0	0.049	0.017	31.499	0.005	0.005	0.000	0.000	0.000	0.000
51	B	67	ALA	0	-0.008	0.002	32.520	0.005	0.005	0.000	0.000	0.000	0.000
52	B	68	LYS	1	0.822	0.878	33.268	-0.047	-0.047	0.000	0.000	0.000	0.000
53	B	69	TYR	0	0.013	0.025	28.888	0.005	0.005	0.000	0.000	0.000	0.000
54	B	70	PHE	0	0.038	0.014	25.281	0.007	0.007	0.000	0.000	0.000	0.000
55	B	71	GLU	-1	-0.824	-0.884	29.251	0.066	0.066	0.000	0.000	0.000	0.000
56	B	72	THR	0	-0.030	-0.034	31.350	0.005	0.005	0.000	0.000	0.000	0.000
57	B	73	ASN	0	-0.003	-0.013	25.292	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	74	VAL	0	-0.011	0.008	26.648	0.011	0.011	0.000	0.000	0.000	0.000
59	B	75	GLN	0	0.030	0.033	27.903	0.006	0.006	0.000	0.000	0.000	0.000
60	B	76	VAL	0	0.016	-0.004	27.576	0.003	0.003	0.000	0.000	0.000	0.000
61	B	77	GLY	0	0.034	0.023	25.460	0.007	0.007	0.000	0.000	0.000	0.000
62	B	78	GLU	-1	-0.937	-0.980	26.119	0.117	0.117	0.000	0.000	0.000	0.000
63	B	79	ASN	0	-0.117	-0.073	28.409	-0.004	-0.004	0.000	0.000	0.000	0.000
64	B	80	MET	0	0.016	-0.002	24.153	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	81	GLN	0	-0.026	0.007	24.170	0.017	0.017	0.000	0.000	0.000	0.000
66	B	82	LYS	1	0.913	0.967	26.271	-0.092	-0.092	0.000	0.000	0.000	0.000
67	B	83	MET	0	-0.095	-0.042	27.233	-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)