FMO DATABASE

FMODB ID: 94952

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-863431.542781
FMO2-HF: Nuclear repulsion	820397.552782
FMO2-HF: Total energy	-43033.989999
FMO2-MP2: Total energy	-43157.959317

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.
-46.046	-37.202	4.448	-5.772	-7.521	-0.028

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 : 0.018 / q_NPA : -0.011

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	-0.060	-0.031	3.656	-4.545	-2.026	-0.022	-1.268	-1.229	0.000
4	A	1	THR	0	0.011	0.008	4.726	-0.261	-0.189	-0.001	-0.007	-0.063	0.000
5	A	2	THR	0	-0.023	-0.003	7.487	-0.437	-0.437	0.000	0.000	0.000	0.000
6	A	3	PHE	0	-0.011	-0.006	5.285	1.519	1.519	0.000	0.000	0.000	0.000
7	A	4	ASN	0	-0.009	-0.004	7.407	-0.977	-0.977	0.000	0.000	0.000	0.000
8	A	5	ILE	0	-0.005	0.007	7.342	0.318	0.318	0.000	0.000	0.000	0.000
9	A	6	GLN	0	-0.005	-0.016	5.842	0.565	0.565	0.000	0.000	0.000	0.000
10	A	7	ASP	-1	-0.914	-0.959	8.154	-2.232	-2.232	0.000	0.000	0.000	0.000
11	A	8	GLY	0	0.048	0.028	9.355	-0.333	-0.333	0.000	0.000	0.000	0.000
12	A	9	PRO	0	0.006	-0.025	8.292	-0.118	-0.118	0.000	0.000	0.000	0.000
13	A	10	ASP	-1	-0.814	-0.894	3.805	-6.861	-6.499	0.002	-0.137	-0.228	-0.001
14	A	11	PHE	0	-0.004	-0.004	6.123	-0.781	-0.781	0.000	0.000	0.000	0.000
15	A	12	GLN	0	0.019	-0.001	8.960	0.205	0.205	0.000	0.000	0.000	0.000
16	A	13	ASP	-1	-0.979	-0.995	2.611	-25.031	-21.977	0.253	-1.732	-1.576	-0.023
17	A	14	ARG	1	0.942	0.972	2.141	-5.162	-2.325	4.216	-2.628	-4.425	-0.004
18	A	15	VAL	0	-0.034	-0.014	5.851	1.273	1.273	0.000	0.000	0.000	0.000
19	A	16	VAL	0	-0.071	-0.025	9.642	0.201	0.201	0.000	0.000	0.000	0.000
20	A	17	ASN	0	-0.017	-0.007	8.162	0.836	0.836	0.000	0.000	0.000	0.000
21	A	18	SER	0	-0.038	-0.006	8.372	-0.322	-0.322	0.000	0.000	0.000	0.000
22	A	19	GLU	-1	-0.935	-0.967	8.511	-1.859	-1.859	0.000	0.000	0.000	0.000
23	A	20	THR	0	-0.095	-0.046	9.670	0.349	0.349	0.000	0.000	0.000	0.000
24	A	21	PRO	0	-0.026	-0.015	12.249	-0.114	-0.114	0.000	0.000	0.000	0.000
25	A	22	VAL	0	0.031	0.028	11.137	0.086	0.086	0.000	0.000	0.000	0.000
26	A	23	VAL	0	-0.003	-0.003	13.454	0.018	0.018	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.005	0.003	13.285	0.086	0.086	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.931	-0.977	14.837	0.381	0.381	0.000	0.000	0.000	0.000
29	A	26	PHE	0	0.043	0.036	16.168	0.061	0.061	0.000	0.000	0.000	0.000
30	A	27	HIS	0	-0.002	-0.038	14.983	0.003	0.003	0.000	0.000	0.000	0.000
31	A	28	ALA	0	0.088	0.044	19.392	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	29	GLN	0	0.025	0.007	19.564	0.020	0.020	0.000	0.000	0.000	0.000
33	A	30	TRP	0	-0.075	-0.056	22.827	0.025	0.025	0.000	0.000	0.000	0.000
34	A	31	CYS	0	-0.022	0.049	24.257	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	32	GLY	0	-0.031	-0.023	25.053	0.038	0.038	0.000	0.000	0.000	0.000
36	A	33	PRO	0	0.018	-0.016	26.065	0.036	0.036	0.000	0.000	0.000	0.000
37	A	34	CYS	0	0.059	0.016	21.206	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	35	LYS	1	0.938	0.980	21.396	-0.332	-0.332	0.000	0.000	0.000	0.000
39	A	36	ILE	0	-0.064	-0.014	22.909	0.035	0.035	0.000	0.000	0.000	0.000
40	A	37	LEU	0	-0.023	-0.021	20.590	0.033	0.033	0.000	0.000	0.000	0.000
41	A	38	GLY	0	0.102	0.057	18.085	0.010	0.010	0.000	0.000	0.000	0.000
42	A	39	PRO	0	0.012	-0.004	17.350	0.065	0.065	0.000	0.000	0.000	0.000
43	A	40	ARG	1	0.869	0.947	18.386	-0.273	-0.273	0.000	0.000	0.000	0.000
44	A	41	LEU	0	0.028	-0.005	16.268	0.002	0.002	0.000	0.000	0.000	0.000
45	A	42	GLU	-1	-0.769	-0.873	11.681	1.759	1.759	0.000	0.000	0.000	0.000
46	A	43	LYS	1	0.926	0.969	14.374	-0.625	-0.625	0.000	0.000	0.000	0.000
47	A	44	MET	0	-0.057	-0.030	16.690	0.002	0.002	0.000	0.000	0.000	0.000
48	A	45	VAL	0	0.037	0.023	11.784	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	46	ALA	0	0.013	0.008	12.266	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	47	LYS	1	0.862	0.925	13.313	-0.541	-0.541	0.000	0.000	0.000	0.000
51	A	48	GLN	0	0.014	0.017	14.802	-0.126	-0.126	0.000	0.000	0.000	0.000
52	A	49	HIS	0	-0.083	-0.042	12.444	-0.171	-0.171	0.000	0.000	0.000	0.000
53	A	50	GLY	0	0.105	0.039	10.517	-0.052	-0.052	0.000	0.000	0.000	0.000
54	A	51	LYS	1	0.856	0.941	11.280	-0.316	-0.316	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.023	-0.001	13.241	-0.105	-0.105	0.000	0.000	0.000	0.000
56	A	53	VAL	0	0.001	0.012	7.834	0.300	0.300	0.000	0.000	0.000	0.000
57	A	54	MET	0	-0.043	-0.017	9.655	-0.143	-0.143	0.000	0.000	0.000	0.000
58	A	55	ALA	0	0.035	0.018	9.494	0.438	0.438	0.000	0.000	0.000	0.000
59	A	56	LYS	1	0.814	0.900	10.463	-2.081	-2.081	0.000	0.000	0.000	0.000
60	A	57	VAL	0	0.044	0.007	11.709	0.010	0.010	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.845	-0.913	13.976	0.336	0.336	0.000	0.000	0.000	0.000
62	A	59	ILE	0	0.006	-0.038	16.354	-0.095	-0.095	0.000	0.000	0.000	0.000
63	A	60	ASP	-1	-0.905	-0.945	18.929	0.025	0.025	0.000	0.000	0.000	0.000
64	A	61	ASP	-1	-0.977	-0.960	15.148	0.292	0.292	0.000	0.000	0.000	0.000
65	A	62	HIS	0	-0.070	-0.040	11.695	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	63	THR	0	-0.001	-0.010	16.322	-0.046	-0.046	0.000	0.000	0.000	0.000
67	A	64	ASP	-1	-0.886	-0.957	15.940	-0.760	-0.760	0.000	0.000	0.000	0.000
68	A	65	LEU	0	0.038	0.025	12.396	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	66	ALA	0	-0.037	-0.012	17.190	0.017	0.017	0.000	0.000	0.000	0.000
70	A	67	ILE	0	-0.038	-0.022	20.238	0.028	0.028	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.954	-0.970	17.173	-0.981	-0.981	0.000	0.000	0.000	0.000
72	A	69	TYR	0	-0.034	-0.028	15.663	0.026	0.026	0.000	0.000	0.000	0.000
73	A	70	GLU	-1	-1.000	-0.992	20.963	-0.288	-0.288	0.000	0.000	0.000	0.000
74	A	71	VAL	0	-0.061	-0.014	20.440	0.050	0.050	0.000	0.000	0.000	0.000
75	A	72	SER	0	-0.002	-0.005	23.697	0.016	0.016	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.044	-0.029	25.798	0.028	0.028	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.041	0.062	21.780	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	75	PRO	0	-0.007	-0.033	22.222	0.017	0.017	0.000	0.000	0.000	0.000
79	A	76	THR	0	-0.029	-0.035	21.771	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	77	VAL	0	-0.008	-0.003	18.181	0.009	0.009	0.000	0.000	0.000	0.000
81	A	78	LEU	0	0.012	0.013	18.018	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	79	ALA	0	-0.014	-0.008	17.842	0.022	0.022	0.000	0.000	0.000	0.000
83	A	80	MET	0	-0.002	-0.010	14.798	0.014	0.014	0.000	0.000	0.000	0.000
84	A	81	LYS	1	0.964	0.966	15.696	0.723	0.723	0.000	0.000	0.000	0.000
85	A	82	ASN	0	-0.033	-0.015	15.274	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	83	GLY	0	0.080	0.051	14.582	0.021	0.021	0.000	0.000	0.000	0.000
87	A	84	ASP	-1	-0.906	-0.930	15.440	-0.782	-0.782	0.000	0.000	0.000	0.000
88	A	85	VAL	0	-0.027	-0.032	18.635	0.021	0.021	0.000	0.000	0.000	0.000
89	A	86	VAL	0	-0.044	-0.023	20.072	0.045	0.045	0.000	0.000	0.000	0.000
90	A	87	ASP	-1	-0.898	-0.959	21.914	-0.121	-0.121	0.000	0.000	0.000	0.000
91	A	88	LYS	1	0.937	0.970	22.121	0.191	0.191	0.000	0.000	0.000	0.000
92	A	89	PHE	0	-0.080	-0.028	21.527	0.030	0.030	0.000	0.000	0.000	0.000
93	A	90	VAL	0	0.035	0.022	24.105	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	91	GLY	0	-0.012	0.007	25.784	0.007	0.007	0.000	0.000	0.000	0.000
95	A	92	ILE	0	-0.037	-0.030	25.353	0.011	0.011	0.000	0.000	0.000	0.000
96	A	93	LYS	1	0.957	0.988	24.750	-0.055	-0.055	0.000	0.000	0.000	0.000
97	A	94	ASP	-1	-0.875	-0.934	25.460	0.191	0.191	0.000	0.000	0.000	0.000
98	A	95	GLU	-1	-0.894	-0.988	23.870	0.359	0.359	0.000	0.000	0.000	0.000
99	A	96	ASP	-1	-0.845	-0.903	25.215	0.149	0.149	0.000	0.000	0.000	0.000
100	A	97	GLN	0	-0.055	-0.039	27.113	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	98	LEU	0	0.011	0.001	21.036	-0.025	-0.025	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.862	-0.914	22.240	0.135	0.135	0.000	0.000	0.000	0.000
103	A	100	ALA	0	-0.041	-0.034	23.758	-0.030	-0.030	0.000	0.000	0.000	0.000
104	A	101	PHE	0	-0.022	-0.002	19.390	-0.023	-0.023	0.000	0.000	0.000	0.000
105	A	102	LEU	0	0.034	0.009	17.382	-0.046	-0.046	0.000	0.000	0.000	0.000
106	A	103	LYS	1	0.854	0.913	20.668	-0.127	-0.127	0.000	0.000	0.000	0.000
107	A	104	LYS	1	0.906	0.963	23.175	0.046	0.046	0.000	0.000	0.000	0.000
108	A	105	LEU	0	-0.008	0.012	17.289	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	106	ILE	0	-0.081	-0.025	17.314	-0.049	-0.049	0.000	0.000	0.000	0.000
110	A	107	GLY	0	-0.021	-0.008	19.800	-0.022	-0.022	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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