FMO DATABASE

FMODB ID: 7278K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-868488.136501
FMO2-HF: Nuclear repulsion	825452.791047
FMO2-HF: Total energy	-43035.345454
FMO2-MP2: Total energy	-43159.431465

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.
-55.612	-50.12	12.431	-7.642	-10.28	-0.066

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 : -0.006 / 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	A	0	SER	0	-0.035	-0.024	3.336	-3.485	-1.016	-0.006	-1.224	-1.239	0.001
4	A	1	THR	0	0.040	0.018	4.504	-0.196	-0.083	-0.001	-0.011	-0.101	0.000
5	A	2	THR	0	-0.105	-0.065	7.219	-0.534	-0.534	0.000	0.000	0.000	0.000
6	A	3	PHE	0	0.007	0.009	4.931	1.817	1.817	0.000	0.000	0.000	0.000
7	A	4	ASN	0	0.009	0.005	7.290	-0.934	-0.934	0.000	0.000	0.000	0.000
8	A	5	ILE	0	0.037	0.031	7.223	0.699	0.699	0.000	0.000	0.000	0.000
9	A	6	GLN	0	-0.102	-0.059	5.593	1.113	1.113	0.000	0.000	0.000	0.000
10	A	7	ASP	-1	-0.846	-0.923	8.167	-2.047	-2.047	0.000	0.000	0.000	0.000
11	A	8	GLY	0	0.090	0.046	8.992	-0.340	-0.340	0.000	0.000	0.000	0.000
12	A	9	PRO	0	-0.018	-0.021	8.119	-0.283	-0.283	0.000	0.000	0.000	0.000
13	A	10	ASP	-1	-0.765	-0.864	3.539	-5.019	-4.446	0.011	-0.235	-0.348	-0.002
14	A	11	PHE	0	0.026	0.004	5.619	-0.925	-0.925	0.000	0.000	0.000	0.000
15	A	12	GLN	0	-0.027	-0.034	8.240	0.208	0.208	0.000	0.000	0.000	0.000
16	A	13	ASP	-1	-0.920	-0.962	1.792	-39.184	-40.110	8.847	-4.359	-3.562	-0.068
17	A	14	ARG	1	0.832	0.912	2.292	-6.084	-2.864	3.581	-1.812	-4.988	0.003
18	A	15	VAL	0	-0.026	-0.014	5.303	1.673	1.716	-0.001	-0.001	-0.042	0.000
19	A	16	VAL	0	-0.045	-0.009	9.116	0.222	0.222	0.000	0.000	0.000	0.000
20	A	17	ASN	0	-0.005	-0.003	7.173	1.193	1.193	0.000	0.000	0.000	0.000
21	A	18	SER	0	-0.046	-0.011	7.987	-0.252	-0.252	0.000	0.000	0.000	0.000
22	A	19	GLU	-1	-0.944	-0.972	8.591	-1.960	-1.960	0.000	0.000	0.000	0.000
23	A	20	THR	0	-0.059	-0.024	9.584	0.350	0.350	0.000	0.000	0.000	0.000
24	A	21	PRO	0	-0.012	-0.009	11.519	-0.136	-0.136	0.000	0.000	0.000	0.000
25	A	22	VAL	0	0.012	0.009	10.491	0.077	0.077	0.000	0.000	0.000	0.000
26	A	23	VAL	0	-0.017	-0.015	12.511	0.036	0.036	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.037	0.025	12.757	0.168	0.168	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.914	-0.973	14.229	0.468	0.468	0.000	0.000	0.000	0.000
29	A	26	PHE	0	0.054	0.030	15.912	0.110	0.110	0.000	0.000	0.000	0.000
30	A	27	HIS	0	-0.024	-0.038	15.534	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	28	ALA	0	0.101	0.047	19.501	-0.050	-0.050	0.000	0.000	0.000	0.000
32	A	29	GLN	0	-0.030	-0.014	19.124	0.025	0.025	0.000	0.000	0.000	0.000
33	A	30	TRP	0	-0.056	-0.046	22.582	0.021	0.021	0.000	0.000	0.000	0.000
34	A	31	CYS	0	-0.043	0.003	24.270	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	32	GLY	0	-0.001	-0.006	24.669	0.038	0.038	0.000	0.000	0.000	0.000
36	A	33	PRO	0	0.011	-0.018	25.520	0.038	0.038	0.000	0.000	0.000	0.000
37	A	34	CYS	0	0.044	0.038	20.779	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	35	LYS	1	0.864	0.934	21.034	-0.394	-0.394	0.000	0.000	0.000	0.000
39	A	36	ILE	0	-0.044	-0.012	22.479	0.035	0.035	0.000	0.000	0.000	0.000
40	A	37	LEU	0	-0.020	-0.010	20.239	0.019	0.019	0.000	0.000	0.000	0.000
41	A	38	GLY	0	0.102	0.062	17.620	0.012	0.012	0.000	0.000	0.000	0.000
42	A	39	PRO	0	0.002	-0.010	16.879	0.082	0.082	0.000	0.000	0.000	0.000
43	A	40	ARG	1	0.792	0.899	17.929	-0.305	-0.305	0.000	0.000	0.000	0.000
44	A	41	LEU	0	0.041	0.004	15.687	0.007	0.007	0.000	0.000	0.000	0.000
45	A	42	GLU	-1	-0.737	-0.845	11.232	2.037	2.037	0.000	0.000	0.000	0.000
46	A	43	LYS	1	0.932	0.967	13.973	-0.620	-0.620	0.000	0.000	0.000	0.000
47	A	44	MET	0	-0.091	-0.041	16.492	-0.032	-0.032	0.000	0.000	0.000	0.000
48	A	45	VAL	0	0.045	0.019	11.244	-0.082	-0.082	0.000	0.000	0.000	0.000
49	A	46	ALA	0	0.032	0.032	12.178	-0.027	-0.027	0.000	0.000	0.000	0.000
50	A	47	LYS	1	0.887	0.941	13.211	-0.498	-0.498	0.000	0.000	0.000	0.000
51	A	48	GLN	0	-0.024	-0.004	13.947	-0.155	-0.155	0.000	0.000	0.000	0.000
52	A	49	HIS	0	-0.094	-0.058	12.092	-0.186	-0.186	0.000	0.000	0.000	0.000
53	A	50	GLY	0	0.099	0.046	9.967	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	51	LYS	1	0.847	0.931	10.934	-0.355	-0.355	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.005	0.003	12.486	-0.104	-0.104	0.000	0.000	0.000	0.000
56	A	53	VAL	0	-0.007	0.013	7.126	0.314	0.314	0.000	0.000	0.000	0.000
57	A	54	MET	0	-0.078	-0.030	8.871	-0.186	-0.186	0.000	0.000	0.000	0.000
58	A	55	ALA	0	0.063	0.038	8.774	0.549	0.549	0.000	0.000	0.000	0.000
59	A	56	LYS	1	0.792	0.891	10.225	-2.291	-2.291	0.000	0.000	0.000	0.000
60	A	57	VAL	0	0.031	0.006	11.799	0.086	0.086	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.793	-0.889	14.011	0.423	0.423	0.000	0.000	0.000	0.000
62	A	59	ILE	0	0.029	-0.006	16.651	-0.094	-0.094	0.000	0.000	0.000	0.000
63	A	60	ASP	-1	-0.873	-0.924	19.147	0.134	0.134	0.000	0.000	0.000	0.000
64	A	61	ASP	-1	-0.960	-0.965	15.002	0.444	0.444	0.000	0.000	0.000	0.000
65	A	62	HIS	0	-0.069	-0.048	11.909	-0.082	-0.082	0.000	0.000	0.000	0.000
66	A	63	THR	0	-0.023	-0.033	16.092	-0.050	-0.050	0.000	0.000	0.000	0.000
67	A	64	ASP	-1	-0.891	-0.942	15.599	-0.658	-0.658	0.000	0.000	0.000	0.000
68	A	65	LEU	0	0.038	0.013	12.621	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	66	ALA	0	-0.038	-0.022	16.563	0.014	0.014	0.000	0.000	0.000	0.000
70	A	67	ILE	0	-0.049	-0.024	19.602	0.024	0.024	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.901	-0.924	16.226	-1.116	-1.116	0.000	0.000	0.000	0.000
72	A	69	TYR	0	-0.045	-0.042	15.451	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	70	GLU	-1	-0.973	-0.990	20.449	-0.267	-0.267	0.000	0.000	0.000	0.000
74	A	71	VAL	0	-0.021	-0.007	19.759	0.049	0.049	0.000	0.000	0.000	0.000
75	A	72	SER	0	-0.017	-0.006	23.172	0.026	0.026	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.025	-0.014	25.314	0.028	0.028	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.036	0.054	21.746	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	75	PRO	0	-0.001	-0.023	21.651	0.014	0.014	0.000	0.000	0.000	0.000
79	A	76	THR	0	-0.050	-0.046	21.192	-0.029	-0.029	0.000	0.000	0.000	0.000
80	A	77	VAL	0	-0.030	-0.002	17.689	0.009	0.009	0.000	0.000	0.000	0.000
81	A	78	LEU	0	0.023	0.005	17.164	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	79	ALA	0	-0.033	-0.002	16.991	0.008	0.008	0.000	0.000	0.000	0.000
83	A	80	MET	0	0.030	0.003	14.358	0.010	0.010	0.000	0.000	0.000	0.000
84	A	81	LYS	1	0.942	0.950	14.432	0.969	0.969	0.000	0.000	0.000	0.000
85	A	82	ASN	0	-0.024	-0.012	14.010	0.156	0.156	0.000	0.000	0.000	0.000
86	A	83	GLY	0	0.092	0.068	13.881	-0.074	-0.074	0.000	0.000	0.000	0.000
87	A	84	ASP	-1	-0.933	-0.944	14.807	-0.838	-0.838	0.000	0.000	0.000	0.000
88	A	85	VAL	0	-0.019	-0.025	17.259	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	86	VAL	0	-0.047	-0.032	19.258	0.039	0.039	0.000	0.000	0.000	0.000
90	A	87	ASP	-1	-0.849	-0.921	21.313	-0.109	-0.109	0.000	0.000	0.000	0.000
91	A	88	LYS	1	0.868	0.949	21.515	0.248	0.248	0.000	0.000	0.000	0.000
92	A	89	PHE	0	-0.041	-0.012	20.948	0.029	0.029	0.000	0.000	0.000	0.000
93	A	90	VAL	0	0.065	0.035	23.577	0.002	0.002	0.000	0.000	0.000	0.000
94	A	91	GLY	0	0.010	0.003	25.290	0.007	0.007	0.000	0.000	0.000	0.000
95	A	92	ILE	0	-0.019	-0.013	24.905	0.002	0.002	0.000	0.000	0.000	0.000
96	A	93	LYS	1	0.846	0.944	23.837	-0.126	-0.126	0.000	0.000	0.000	0.000
97	A	94	ASP	-1	-0.806	-0.886	25.098	0.204	0.204	0.000	0.000	0.000	0.000
98	A	95	GLU	-1	-0.796	-0.925	23.005	0.397	0.397	0.000	0.000	0.000	0.000
99	A	96	ASP	-1	-0.886	-0.926	24.615	0.161	0.161	0.000	0.000	0.000	0.000
100	A	97	GLN	0	-0.067	-0.067	26.491	-0.043	-0.043	0.000	0.000	0.000	0.000
101	A	98	LEU	0	0.016	0.003	20.474	-0.027	-0.027	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.894	-0.931	21.572	0.184	0.184	0.000	0.000	0.000	0.000
103	A	100	ALA	0	-0.032	-0.016	23.062	-0.035	-0.035	0.000	0.000	0.000	0.000
104	A	101	PHE	0	-0.009	-0.009	18.122	-0.032	-0.032	0.000	0.000	0.000	0.000
105	A	102	LEU	0	0.028	0.001	16.664	-0.045	-0.045	0.000	0.000	0.000	0.000
106	A	103	LYS	1	0.850	0.912	19.943	-0.141	-0.141	0.000	0.000	0.000	0.000
107	A	104	LYS	1	0.816	0.905	22.721	0.089	0.089	0.000	0.000	0.000	0.000
108	A	105	LEU	0	-0.034	0.004	16.107	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	106	ILE	0	-0.053	-0.022	16.752	-0.066	-0.066	0.000	0.000	0.000	0.000
110	A	107	GLY	0	-0.035	-0.006	19.161	-0.022	-0.022	0.000	0.000	0.000	0.000

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