FMO DATABASE

FMODB ID: MVYKZ

Calculation Name: 1UVZ-A-Xray372

Preferred Name: Thioredoxin, mitochondrial

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1UVZ

Chain ID: A

ChEMBL ID: CHEMBL2189153

UniProt ID: Q99757

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	110
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864635.844365
FMO2-HF: Nuclear repulsion	821600.943877
FMO2-HF: Total energy	-43034.900488
FMO2-MP2: Total energy	-43158.848675

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:-2:HIS)

Summations of interaction energy for fragment #1(A:-2:HIS)

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.
-46.736	-36.829	4.971	-5.683	-9.195	-0.033

Interaction energy analysis for fragmet #1(A:-2:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.014

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	A	0	SER	0	-0.054	-0.026	3.617	-4.395	-1.923	-0.021	-1.238	-1.213	0.000
4	A	1	THR	0	0.041	0.014	4.710	-0.264	-0.188	-0.001	-0.007	-0.067	0.000
5	A	2	THR	0	-0.094	-0.054	7.475	-0.452	-0.452	0.000	0.000	0.000	0.000
6	A	3	PHE	0	0.007	0.002	5.256	1.588	1.588	0.000	0.000	0.000	0.000
7	A	4	ASN	0	0.001	0.003	7.385	-0.845	-0.845	0.000	0.000	0.000	0.000
8	A	5	ILE	0	0.007	0.008	6.918	0.370	0.370	0.000	0.000	0.000	0.000
9	A	6	GLN	0	-0.051	-0.039	5.366	0.989	0.989	0.000	0.000	0.000	0.000
10	A	7	ASP	-1	-0.887	-0.941	8.208	-1.983	-1.983	0.000	0.000	0.000	0.000
11	A	8	GLY	0	0.053	0.025	9.111	-0.357	-0.357	0.000	0.000	0.000	0.000
12	A	9	PRO	0	0.005	-0.021	8.253	-0.153	-0.153	0.000	0.000	0.000	0.000
13	A	10	ASP	-1	-0.806	-0.892	3.440	-6.951	-6.239	0.016	-0.337	-0.391	-0.002
14	A	11	PHE	0	0.009	-0.001	5.774	-1.100	-1.100	0.000	0.000	0.000	0.000
15	A	12	GLN	0	-0.019	-0.020	8.568	0.224	0.224	0.000	0.000	0.000	0.000
16	A	13	ASP	-1	-0.958	-0.983	2.415	-26.833	-23.377	0.608	-2.070	-1.994	-0.032
17	A	14	ARG	1	0.917	0.958	2.322	-5.550	-2.398	4.370	-2.030	-5.493	0.001
18	A	15	VAL	0	-0.028	-0.013	5.336	1.416	1.455	-0.001	-0.001	-0.037	0.000
19	A	16	VAL	0	-0.059	-0.019	9.133	0.206	0.206	0.000	0.000	0.000	0.000
20	A	17	ASN	0	-0.005	0.005	7.739	0.933	0.933	0.000	0.000	0.000	0.000
21	A	18	SER	0	-0.034	-0.006	8.049	-0.331	-0.331	0.000	0.000	0.000	0.000
22	A	19	GLU	-1	-0.937	-0.966	8.692	-1.916	-1.916	0.000	0.000	0.000	0.000
23	A	20	THR	0	-0.108	-0.047	9.594	0.532	0.532	0.000	0.000	0.000	0.000
24	A	21	PRO	0	-0.001	-0.009	11.889	-0.133	-0.133	0.000	0.000	0.000	0.000
25	A	22	VAL	0	0.021	0.018	10.430	0.082	0.082	0.000	0.000	0.000	0.000
26	A	23	VAL	0	0.000	0.001	13.340	0.031	0.031	0.000	0.000	0.000	0.000
27	A	24	VAL	0	-0.004	-0.004	12.919	0.082	0.082	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.919	-0.971	14.643	0.344	0.344	0.000	0.000	0.000	0.000
29	A	26	PHE	0	0.048	0.032	15.776	0.066	0.066	0.000	0.000	0.000	0.000
30	A	27	HIS	0	-0.023	-0.039	14.985	0.005	0.005	0.000	0.000	0.000	0.000
31	A	28	ALA	0	0.084	0.039	19.086	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	29	GLN	0	-0.002	-0.008	19.058	0.025	0.025	0.000	0.000	0.000	0.000
33	A	30	TRP	0	-0.063	-0.050	22.610	0.024	0.024	0.000	0.000	0.000	0.000
34	A	31	CYS	0	0.011	0.049	24.024	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	32	GLY	0	-0.024	-0.020	25.030	0.037	0.037	0.000	0.000	0.000	0.000
36	A	33	PRO	0	0.008	-0.019	26.040	0.034	0.034	0.000	0.000	0.000	0.000
37	A	34	CYS	0	0.040	0.013	21.207	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	35	LYS	1	0.898	0.951	21.371	-0.324	-0.324	0.000	0.000	0.000	0.000
39	A	36	ILE	0	-0.046	-0.006	22.878	0.035	0.035	0.000	0.000	0.000	0.000
40	A	37	LEU	0	-0.024	-0.021	20.650	0.031	0.031	0.000	0.000	0.000	0.000
41	A	38	GLY	0	0.098	0.059	18.065	0.009	0.009	0.000	0.000	0.000	0.000
42	A	39	PRO	0	0.000	-0.010	17.325	0.064	0.064	0.000	0.000	0.000	0.000
43	A	40	ARG	1	0.804	0.911	18.356	-0.251	-0.251	0.000	0.000	0.000	0.000
44	A	41	LEU	0	0.031	-0.003	16.356	0.000	0.000	0.000	0.000	0.000	0.000
45	A	42	GLU	-1	-0.736	-0.838	11.632	1.725	1.725	0.000	0.000	0.000	0.000
46	A	43	LYS	1	0.926	0.968	14.349	-0.583	-0.583	0.000	0.000	0.000	0.000
47	A	44	MET	0	-0.068	-0.029	16.665	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	45	VAL	0	0.042	0.022	11.809	-0.054	-0.054	0.000	0.000	0.000	0.000
49	A	46	ALA	0	0.022	0.015	12.252	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	47	LYS	1	0.874	0.936	13.290	-0.465	-0.465	0.000	0.000	0.000	0.000
51	A	48	GLN	0	-0.014	0.004	14.772	-0.114	-0.114	0.000	0.000	0.000	0.000
52	A	49	HIS	0	-0.095	-0.058	12.439	-0.144	-0.144	0.000	0.000	0.000	0.000
53	A	50	GLY	0	0.108	0.043	10.523	-0.057	-0.057	0.000	0.000	0.000	0.000
54	A	51	LYS	1	0.864	0.950	11.279	-0.275	-0.275	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.022	-0.003	13.268	-0.099	-0.099	0.000	0.000	0.000	0.000
56	A	53	VAL	0	-0.011	0.005	7.734	0.298	0.298	0.000	0.000	0.000	0.000
57	A	54	MET	0	-0.040	-0.015	9.640	-0.138	-0.138	0.000	0.000	0.000	0.000
58	A	55	ALA	0	0.034	0.024	9.487	0.455	0.455	0.000	0.000	0.000	0.000
59	A	56	LYS	1	0.812	0.901	10.759	-1.849	-1.849	0.000	0.000	0.000	0.000
60	A	57	VAL	0	0.042	0.007	11.362	0.019	0.019	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.813	-0.898	13.626	0.356	0.356	0.000	0.000	0.000	0.000
62	A	59	ILE	0	0.007	-0.028	16.078	-0.090	-0.090	0.000	0.000	0.000	0.000
63	A	60	ASP	-1	-0.886	-0.940	18.633	0.050	0.050	0.000	0.000	0.000	0.000
64	A	61	ASP	-1	-0.965	-0.955	14.867	0.311	0.311	0.000	0.000	0.000	0.000
65	A	62	HIS	0	-0.096	-0.055	11.767	-0.065	-0.065	0.000	0.000	0.000	0.000
66	A	63	THR	0	-0.001	-0.012	16.074	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	64	ASP	-1	-0.872	-0.945	15.743	-0.713	-0.713	0.000	0.000	0.000	0.000
68	A	65	LEU	0	0.032	0.022	12.443	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	66	ALA	0	-0.036	-0.014	16.841	0.013	0.013	0.000	0.000	0.000	0.000
70	A	67	ILE	0	-0.038	-0.020	19.875	0.027	0.027	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.900	-0.926	16.617	-1.032	-1.032	0.000	0.000	0.000	0.000
72	A	69	TYR	0	-0.083	-0.069	15.637	0.008	0.008	0.000	0.000	0.000	0.000
73	A	70	GLU	-1	-0.995	-0.990	20.545	-0.292	-0.292	0.000	0.000	0.000	0.000
74	A	71	VAL	0	-0.069	-0.020	19.960	0.049	0.049	0.000	0.000	0.000	0.000
75	A	72	SER	0	0.007	-0.004	23.290	0.016	0.016	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.052	-0.026	25.395	0.029	0.029	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.034	0.051	21.532	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	75	PRO	0	-0.015	-0.029	22.238	0.017	0.017	0.000	0.000	0.000	0.000
79	A	76	THR	0	-0.011	-0.023	21.216	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	77	VAL	0	-0.013	-0.005	18.223	0.006	0.006	0.000	0.000	0.000	0.000
81	A	78	LEU	0	0.012	0.009	17.501	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	79	ALA	0	-0.026	-0.008	17.420	0.016	0.016	0.000	0.000	0.000	0.000
83	A	80	MET	0	0.000	-0.012	14.426	0.006	0.006	0.000	0.000	0.000	0.000
84	A	81	LYS	1	0.940	0.950	15.295	0.837	0.837	0.000	0.000	0.000	0.000
85	A	82	ASN	0	-0.019	-0.006	14.796	0.067	0.067	0.000	0.000	0.000	0.000
86	A	83	GLY	0	0.089	0.055	14.098	0.028	0.028	0.000	0.000	0.000	0.000
87	A	84	ASP	-1	-0.900	-0.927	14.958	-0.789	-0.789	0.000	0.000	0.000	0.000
88	A	85	VAL	0	-0.038	-0.036	18.117	0.018	0.018	0.000	0.000	0.000	0.000
89	A	86	VAL	0	-0.042	-0.023	19.376	0.048	0.048	0.000	0.000	0.000	0.000
90	A	87	ASP	-1	-0.889	-0.945	21.386	-0.148	-0.148	0.000	0.000	0.000	0.000
91	A	88	LYS	1	0.906	0.956	21.608	0.239	0.239	0.000	0.000	0.000	0.000
92	A	89	PHE	0	-0.051	-0.015	21.541	0.032	0.032	0.000	0.000	0.000	0.000
93	A	90	VAL	0	0.033	0.024	24.024	0.000	0.000	0.000	0.000	0.000	0.000
94	A	91	GLY	0	-0.020	-0.004	25.766	0.008	0.008	0.000	0.000	0.000	0.000
95	A	92	ILE	0	-0.026	-0.021	25.341	0.009	0.009	0.000	0.000	0.000	0.000
96	A	93	LYS	1	0.932	0.986	24.686	-0.052	-0.052	0.000	0.000	0.000	0.000
97	A	94	ASP	-1	-0.843	-0.913	25.443	0.163	0.163	0.000	0.000	0.000	0.000
98	A	95	GLU	-1	-0.797	-0.933	23.701	0.330	0.330	0.000	0.000	0.000	0.000
99	A	96	ASP	-1	-0.872	-0.920	25.200	0.131	0.131	0.000	0.000	0.000	0.000
100	A	97	GLN	0	-0.089	-0.073	27.147	-0.041	-0.041	0.000	0.000	0.000	0.000
101	A	98	LEU	0	0.012	0.004	21.020	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.874	-0.920	22.235	0.128	0.128	0.000	0.000	0.000	0.000
103	A	100	ALA	0	-0.031	-0.026	23.755	-0.031	-0.031	0.000	0.000	0.000	0.000
104	A	101	PHE	0	-0.003	0.003	19.133	-0.025	-0.025	0.000	0.000	0.000	0.000
105	A	102	LEU	0	0.031	0.009	17.415	-0.048	-0.048	0.000	0.000	0.000	0.000
106	A	103	LYS	1	0.851	0.907	20.670	-0.105	-0.105	0.000	0.000	0.000	0.000
107	A	104	LYS	1	0.913	0.968	23.179	0.081	0.081	0.000	0.000	0.000	0.000
108	A	105	LEU	0	-0.006	0.010	17.037	-0.028	-0.028	0.000	0.000	0.000	0.000
109	A	106	ILE	0	-0.080	-0.027	17.367	-0.049	-0.049	0.000	0.000	0.000	0.000
110	A	107	GLY	0	-0.017	-0.004	19.828	-0.023	-0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:HIS)