Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: Z6Z1N

Calculation Name: 5JCG-A-Xray372

Preferred Name: Thioredoxin-dependent peroxide reductase, mitochondrial

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5JCG

Chain ID: A

ChEMBL ID: CHEMBL4295742

UniProt ID: P30048

Base Structure: X-ray

Registration Date: 2023-06-22

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2091852.550943
FMO2-HF: Nuclear repulsion 2017215.327175
FMO2-HF: Total energy -74637.223769
FMO2-MP2: Total energy -74858.183362


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:0:THR)


Summations of interaction energy for fragment #1(A:0:THR)
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.
-8.386-1.46.402-5.711-7.676-0.034
Interaction energy analysis for fragmet #1(A:0:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.036
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   
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].
3A2PRO00.0380.0293.867-0.2501.645-0.021-0.947-0.9270.002
4A3ALA0-0.012-0.0146.1330.2140.2140.0000.0000.0000.000
5A4VAL00.0330.0137.0020.2560.2560.0000.0000.0000.000
6A5THR0-0.076-0.0358.8150.1680.1680.0000.0000.0000.000
7A6GLN0-0.033-0.0073.5220.9971.5420.020-0.160-0.4040.001
8A7HIS0-0.013-0.0112.610-2.436-0.6790.689-0.776-1.6700.003
9A8ALA00.0400.0092.341-5.144-3.3543.515-2.888-2.417-0.031
10A9PRO0-0.0060.0022.226-2.035-0.6172.195-1.668-1.945-0.009
11A10TYR0-0.037-0.0293.2541.0200.5940.0050.730-0.3090.000
12A11PHE00.0130.0055.251-0.239-0.232-0.001-0.002-0.0040.000
13A12LYS10.8950.9209.0180.0590.0590.0000.0000.0000.000
14A13GLY0-0.0090.00912.294-0.048-0.0480.0000.0000.0000.000
15A14THR0-0.007-0.00815.8540.0180.0180.0000.0000.0000.000
16A15ALA00.000-0.00618.725-0.018-0.0180.0000.0000.0000.000
17A16VAL0-0.045-0.01620.6720.0050.0050.0000.0000.0000.000
18A17VAL00.0350.00121.6380.0020.0020.0000.0000.0000.000
19A18ASN00.0140.00624.631-0.001-0.0010.0000.0000.0000.000
20A19GLY00.0040.01227.766-0.001-0.0010.0000.0000.0000.000
21A20GLU-1-0.949-0.96627.6360.0240.0240.0000.0000.0000.000
22A21PHE0-0.042-0.03324.609-0.003-0.0030.0000.0000.0000.000
23A22LYS10.9050.94819.073-0.094-0.0940.0000.0000.0000.000
24A23ASP-1-0.858-0.90717.562-0.002-0.0020.0000.0000.0000.000
25A24LEU0-0.026-0.01115.6150.0200.0200.0000.0000.0000.000
26A25SER0-0.027-0.05410.952-0.047-0.0470.0000.0000.0000.000
27A26LEU00.0130.0085.4370.0210.0210.0000.0000.0000.000
28A27ASP-1-0.811-0.8659.6870.5630.5630.0000.0000.0000.000
29A28ASP-1-0.826-0.89611.6700.1470.1470.0000.0000.0000.000
30A29PHE00.003-0.00311.825-0.031-0.0310.0000.0000.0000.000
31A30LYS10.8790.9549.336-0.974-0.9740.0000.0000.0000.000
32A31GLY0-0.054-0.03712.800-0.058-0.0580.0000.0000.0000.000
33A32LYS10.8570.93214.631-0.258-0.2580.0000.0000.0000.000
34A33TYR0-0.029-0.04714.0710.0420.0420.0000.0000.0000.000
35A34LEU0-0.027-0.00510.745-0.021-0.0210.0000.0000.0000.000
36A35VAL00.0050.00613.681-0.002-0.0020.0000.0000.0000.000
37A36LEU00.0090.01010.275-0.002-0.0020.0000.0000.0000.000
38A37PHE0-0.030-0.03014.038-0.028-0.0280.0000.0000.0000.000
39A38PHE00.0620.03411.0680.0050.0050.0000.0000.0000.000
40A39TYR0-0.029-0.04916.9800.0200.0200.0000.0000.0000.000
41A40PRO00.0050.00620.136-0.009-0.0090.0000.0000.0000.000
42A41LEU00.031-0.00422.012-0.009-0.0090.0000.0000.0000.000
43A42ASP-1-0.741-0.84524.380-0.051-0.0510.0000.0000.0000.000
44A43PHE0-0.050-0.03726.550-0.002-0.0020.0000.0000.0000.000
45A44THR0-0.023-0.00127.0770.0020.0020.0000.0000.0000.000
46A45PHE00.023-0.01029.8400.0040.0040.0000.0000.0000.000
47A46VAL00.0260.01926.9930.0040.0040.0000.0000.0000.000
48A47CYS0-0.0260.04325.1460.0020.0020.0000.0000.0000.000
49A48PRO00.0590.04726.2990.0040.0040.0000.0000.0000.000
50A49THR0-0.066-0.04428.7100.0060.0060.0000.0000.0000.000
51A50GLU-1-0.721-0.82023.798-0.045-0.0450.0000.0000.0000.000
52A51ILE00.0070.00723.3220.0080.0080.0000.0000.0000.000
53A52VAL0-0.006-0.01125.4610.0070.0070.0000.0000.0000.000
54A53ALA0-0.0030.01727.4940.0060.0060.0000.0000.0000.000
55A54PHE00.013-0.01521.1000.0070.0070.0000.0000.0000.000
56A55SER00.0160.01924.9400.0090.0090.0000.0000.0000.000
57A56ASP-1-0.849-0.89526.7490.0190.0190.0000.0000.0000.000
58A57LYS10.7990.88626.848-0.044-0.0440.0000.0000.0000.000
59A58ALA00.0070.01324.6680.0070.0070.0000.0000.0000.000
60A59ASN0-0.011-0.01124.8830.0040.0040.0000.0000.0000.000
61A60GLU-1-0.770-0.86626.5670.0670.0670.0000.0000.0000.000
62A61PHE0-0.043-0.02620.5540.0060.0060.0000.0000.0000.000
63A62HIS0-0.009-0.01121.6390.0100.0100.0000.0000.0000.000
64A63ASP-1-0.885-0.94223.7490.0860.0860.0000.0000.0000.000
65A64VAL0-0.101-0.04421.8470.0030.0030.0000.0000.0000.000
66A65ASN0-0.042-0.02418.9530.0090.0090.0000.0000.0000.000
67A66CYS0-0.053-0.01618.1020.0280.0280.0000.0000.0000.000
68A67GLU-1-0.852-0.91816.5300.0910.0910.0000.0000.0000.000
69A68VAL0-0.024-0.01817.538-0.002-0.0020.0000.0000.0000.000
70A69VAL0-0.019-0.00615.225-0.002-0.0020.0000.0000.0000.000
71A70ALA00.0300.03316.789-0.017-0.0170.0000.0000.0000.000
72A71VAL0-0.028-0.01814.1330.0030.0030.0000.0000.0000.000
73A72SER00.007-0.01617.449-0.006-0.0060.0000.0000.0000.000
74A73VAL00.0060.00517.7480.0000.0000.0000.0000.0000.000
75A74ASP-1-0.793-0.85719.648-0.090-0.0900.0000.0000.0000.000
76A75SER0-0.0020.01321.5000.0000.0000.0000.0000.0000.000
77A76HIS00.0440.01122.251-0.001-0.0010.0000.0000.0000.000
78A77PHE00.0240.00023.8550.0080.0080.0000.0000.0000.000
79A78SER0-0.0180.01225.7550.0030.0030.0000.0000.0000.000
80A79HIS10.8510.88620.4460.0710.0710.0000.0000.0000.000
81A80LEU00.0330.03326.0860.0050.0050.0000.0000.0000.000
82A81ALA00.0070.01128.7840.0040.0040.0000.0000.0000.000
83A82TRP0-0.015-0.01125.3130.0020.0020.0000.0000.0000.000
84A83ILE00.002-0.00326.4190.0020.0020.0000.0000.0000.000
85A84ASN0-0.067-0.03930.6530.0050.0050.0000.0000.0000.000
86A85THR0-0.0290.00733.3470.0000.0000.0000.0000.0000.000
87A86PRO00.0090.00034.3380.0010.0010.0000.0000.0000.000
88A87ARG10.8270.86231.155-0.008-0.0080.0000.0000.0000.000
89A88LYS10.8770.94035.6560.0020.0020.0000.0000.0000.000
90A89ASN0-0.035-0.01937.7950.0010.0010.0000.0000.0000.000
91A90GLY00.0320.02634.509-0.002-0.0020.0000.0000.0000.000
92A91GLY00.0090.00432.472-0.004-0.0040.0000.0000.0000.000
93A92LEU00.0100.00526.6920.0020.0020.0000.0000.0000.000
94A93GLY00.0040.00731.0480.0050.0050.0000.0000.0000.000
95A94HIS0-0.002-0.01030.258-0.005-0.0050.0000.0000.0000.000
96A95MET0-0.038-0.01426.206-0.003-0.0030.0000.0000.0000.000
97A96ASN0-0.050-0.02526.8410.0030.0030.0000.0000.0000.000
98A97ILE00.0230.00821.7370.0080.0080.0000.0000.0000.000
99A98ALA00.0040.01618.952-0.006-0.0060.0000.0000.0000.000
100A99LEU00.0130.00220.379-0.008-0.0080.0000.0000.0000.000
101A100LEU00.0250.01013.6810.0050.0050.0000.0000.0000.000
102A101SER0-0.078-0.04818.310-0.013-0.0130.0000.0000.0000.000
103A102ASP-1-0.705-0.83214.615-0.285-0.2850.0000.0000.0000.000
104A103LEU00.0300.01316.750-0.015-0.0150.0000.0000.0000.000
105A104THR0-0.001-0.00415.0380.0000.0000.0000.0000.0000.000
106A105LYS10.7760.88816.0590.1510.1510.0000.0000.0000.000
107A106GLN00.0170.0079.6740.0570.0570.0000.0000.0000.000
108A107ILE00.0170.00810.006-0.107-0.1070.0000.0000.0000.000
109A108SER0-0.006-0.05310.147-0.080-0.0800.0000.0000.0000.000
110A109ARG10.7230.83711.4090.3910.3910.0000.0000.0000.000
111A110ASP-1-0.839-0.9076.133-1.000-1.0000.0000.0000.0000.000
112A111TYR0-0.066-0.0686.422-0.349-0.3490.0000.0000.0000.000
113A112GLY0-0.026-0.0078.6990.1020.1020.0000.0000.0000.000
114A113VAL0-0.027-0.01611.2240.1030.1030.0000.0000.0000.000
115A114LEU0-0.057-0.01414.0690.0630.0630.0000.0000.0000.000
116A115LEU00.0160.01216.018-0.013-0.0130.0000.0000.0000.000
117A116GLU-1-0.733-0.85816.099-0.336-0.3360.0000.0000.0000.000
118A117GLY0-0.035-0.01419.6470.0170.0170.0000.0000.0000.000
119A118SER0-0.094-0.05422.4080.0200.0200.0000.0000.0000.000
120A119GLY0-0.0070.01520.7510.0110.0110.0000.0000.0000.000
121A120LEU0-0.014-0.00620.3330.0050.0050.0000.0000.0000.000
122A121ALA00.0250.01216.765-0.020-0.0200.0000.0000.0000.000
123A122LEU00.0440.01017.5430.0310.0310.0000.0000.0000.000
124A123ARG10.7920.86218.1740.0630.0630.0000.0000.0000.000
125A124GLY00.0130.00315.4200.0170.0170.0000.0000.0000.000
126A125LEU0-0.046-0.03015.4700.0050.0050.0000.0000.0000.000
127A126PHE0-0.0020.0029.710-0.018-0.0180.0000.0000.0000.000
128A127ILE00.0080.00812.8440.0100.0100.0000.0000.0000.000
129A128ILE0-0.010-0.0068.3420.0370.0370.0000.0000.0000.000
130A129ASP-1-0.727-0.84510.5450.6360.6360.0000.0000.0000.000
131A130PRO00.0440.03111.1460.0580.0580.0000.0000.0000.000
132A131ASN0-0.001-0.01610.7580.0760.0760.0000.0000.0000.000
133A132GLY00.0250.0227.0570.2970.2970.0000.0000.0000.000
134A133VAL0-0.038-0.0156.0130.0210.0210.0000.0000.0000.000
135A134ILE0-0.0070.0066.076-0.237-0.2370.0000.0000.0000.000
136A135LYS10.8030.8758.706-0.370-0.3700.0000.0000.0000.000
137A136HIS0-0.007-0.01812.229-0.033-0.0330.0000.0000.0000.000
138A137LEU0-0.0080.01010.268-0.012-0.0120.0000.0000.0000.000
139A138SER0-0.019-0.00213.5520.0150.0150.0000.0000.0000.000
140A139VAL00.023-0.00615.647-0.027-0.0270.0000.0000.0000.000
141A140ASN0-0.063-0.01918.3790.0130.0130.0000.0000.0000.000
142A141ASP-1-0.824-0.91321.225-0.111-0.1110.0000.0000.0000.000
143A142LEU00.003-0.01622.1420.0110.0110.0000.0000.0000.000
144A143PRO0-0.022-0.00225.1180.0070.0070.0000.0000.0000.000
145A144VAL0-0.0030.00326.7390.0080.0080.0000.0000.0000.000
146A145GLY00.0200.02425.568-0.006-0.0060.0000.0000.0000.000
147A146ARG10.7670.84318.6930.0740.0740.0000.0000.0000.000
148A147SER00.0080.00924.5050.0040.0040.0000.0000.0000.000
149A148VAL00.0520.02423.7940.0040.0040.0000.0000.0000.000
150A149GLU-1-0.793-0.89924.2990.0540.0540.0000.0000.0000.000
151A150GLU-1-0.841-0.91222.3930.0670.0670.0000.0000.0000.000
152A151THR0-0.022-0.01818.9230.0080.0080.0000.0000.0000.000
153A152LEU0-0.010-0.00120.7170.0170.0170.0000.0000.0000.000
154A153ARG10.7660.86823.123-0.061-0.0610.0000.0000.0000.000
155A154LEU0-0.017-0.01018.7360.0130.0130.0000.0000.0000.000
156A155VAL0-0.015-0.00817.7640.0220.0220.0000.0000.0000.000
157A156LYS10.9040.94719.683-0.063-0.0630.0000.0000.0000.000
158A157ALA00.0050.00621.2850.0050.0050.0000.0000.0000.000
159A158PHE0-0.021-0.02616.4580.0140.0140.0000.0000.0000.000
160A159GLN00.0420.01218.9390.0010.0010.0000.0000.0000.000
161A160TYR0-0.021-0.00720.816-0.002-0.0020.0000.0000.0000.000
162A161VAL0-0.018-0.02019.505-0.001-0.0010.0000.0000.0000.000
163A162GLU-1-0.848-0.88015.8560.3530.3530.0000.0000.0000.000
164A163THR0-0.051-0.02620.540-0.006-0.0060.0000.0000.0000.000
165A164HIS10.8500.92124.009-0.148-0.1480.0000.0000.0000.000
166A165GLY00.0090.02923.764-0.010-0.0100.0000.0000.0000.000
167A166GLU-1-0.860-0.91024.7930.0980.0980.0000.0000.0000.000
168A167VAL0-0.007-0.01422.4060.0120.0120.0000.0000.0000.000
169A168CYS00.0300.01523.527-0.010-0.0100.0000.0000.0000.000
170A169PRO0-0.035-0.00724.7430.0030.0030.0000.0000.0000.000
171A170ALA00.0370.01526.2080.0020.0020.0000.0000.0000.000
172A171ASN0-0.031-0.03227.180-0.002-0.0020.0000.0000.0000.000
173A172TRP0-0.0100.02324.9940.0010.0010.0000.0000.0000.000
174A173THR00.0420.01627.2900.0000.0000.0000.0000.0000.000
175A174PRO00.0560.01827.6220.0030.0030.0000.0000.0000.000
176A175ASP-1-0.896-0.94229.8380.0660.0660.0000.0000.0000.000
177A176SER0-0.080-0.01830.486-0.004-0.0040.0000.0000.0000.000
178A177PRO00.004-0.02331.3480.0060.0060.0000.0000.0000.000
179A178THR0-0.042-0.02527.3150.0020.0020.0000.0000.0000.000
180A179ILE0-0.012-0.00628.163-0.007-0.0070.0000.0000.0000.000
181A180LYS10.8710.91527.917-0.078-0.0780.0000.0000.0000.000
182A181PRO00.0290.02724.664-0.010-0.0100.0000.0000.0000.000
183A182SER00.019-0.00426.9100.0010.0010.0000.0000.0000.000
184A183PRO00.0420.02529.335-0.005-0.0050.0000.0000.0000.000
185A184ALA00.0090.01832.149-0.005-0.0050.0000.0000.0000.000
186A185ALA00.0510.01332.185-0.003-0.0030.0000.0000.0000.000
187A186SER0-0.003-0.00630.844-0.003-0.0030.0000.0000.0000.000
188A187LYS10.8790.92232.640-0.068-0.0680.0000.0000.0000.000
189A188GLU-1-0.789-0.85335.2050.0740.0740.0000.0000.0000.000
190A189TYR00.002-0.00232.200-0.003-0.0030.0000.0000.0000.000
191A190PHE00.012-0.00931.475-0.003-0.0030.0000.0000.0000.000
192A191GLN00.0220.00736.534-0.004-0.0040.0000.0000.0000.000
193A192LYS10.8210.91234.251-0.075-0.0750.0000.0000.0000.000
194A193VAL0-0.032-0.00935.148-0.001-0.0010.0000.0000.0000.000
195A194ASN0-0.063-0.01137.143-0.005-0.0050.0000.0000.0000.000