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: 2JM8R

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2081854.409295
FMO2-HF: Nuclear repulsion 2007218.028024
FMO2-HF: Total energy -74636.38127
FMO2-MP2: Total energy -74857.10298


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.
-14.137-4.9656.483-7.021-8.632-0.042
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 : -0.035 / q_NPA : -0.008
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].
3A2PRO00.0340.0343.857-0.9381.633-0.021-1.375-1.1740.006
4A3ALA0-0.011-0.0156.0230.5240.5240.0000.0000.0000.000
5A4VAL00.0290.0057.0210.0630.0630.0000.0000.0000.000
6A5THR0-0.095-0.0498.403-0.179-0.1790.0000.0000.0000.000
7A6GLN0-0.0300.0013.015-4.250-2.7540.104-0.847-0.753-0.008
8A7HIS00.0380.0142.636-1.6750.3480.618-0.958-1.6830.005
9A8ALA00.035-0.0022.332-7.471-4.9273.765-3.361-2.948-0.039
10A9PRO0-0.0170.0002.478-0.2600.8721.991-1.335-1.787-0.006
11A10TYR00.0120.0163.3650.8100.1990.0270.856-0.2720.000
12A11PHE00.0030.0005.336-0.462-0.445-0.001-0.001-0.0150.000
13A12LYS10.9430.9638.860-0.232-0.2320.0000.0000.0000.000
14A13GLY0-0.0030.00812.229-0.082-0.0820.0000.0000.0000.000
15A14THR00.0020.01415.6920.0290.0290.0000.0000.0000.000
16A15ALA00.0170.00718.783-0.036-0.0360.0000.0000.0000.000
17A16VAL0-0.064-0.02220.6860.0090.0090.0000.0000.0000.000
18A17VAL00.024-0.01021.761-0.003-0.0030.0000.0000.0000.000
19A18ASN00.0150.00424.717-0.004-0.0040.0000.0000.0000.000
20A19GLY0-0.005-0.00428.107-0.001-0.0010.0000.0000.0000.000
21A20GLU-1-0.933-0.95127.7330.1050.1050.0000.0000.0000.000
22A21PHE0-0.065-0.03824.5060.0010.0010.0000.0000.0000.000
23A22LYS11.0020.99821.033-0.216-0.2160.0000.0000.0000.000
24A23ASP-1-0.907-0.95917.6650.2140.2140.0000.0000.0000.000
25A24LEU0-0.0100.00015.4690.0060.0060.0000.0000.0000.000
26A25SER0-0.026-0.01211.0180.0150.0150.0000.0000.0000.000
27A26LEU00.020-0.0015.693-0.039-0.0390.0000.0000.0000.000
28A27ASP-1-0.887-0.9499.7891.5671.5670.0000.0000.0000.000
29A28ASP-1-0.906-0.95211.5930.4540.4540.0000.0000.0000.000
30A29PHE0-0.057-0.04012.327-0.105-0.1050.0000.0000.0000.000
31A30LYS10.9611.0019.658-1.782-1.7820.0000.0000.0000.000
32A31GLY0-0.061-0.03113.344-0.086-0.0860.0000.0000.0000.000
33A32LYS10.9130.96915.272-0.428-0.4280.0000.0000.0000.000
34A33TYR00.0230.00114.4580.0510.0510.0000.0000.0000.000
35A34LEU0-0.021-0.00710.981-0.005-0.0050.0000.0000.0000.000
36A35VAL0-0.008-0.00513.571-0.063-0.0630.0000.0000.0000.000
37A36LEU00.0100.01110.1980.0270.0270.0000.0000.0000.000
38A37PHE0-0.035-0.03813.924-0.097-0.0970.0000.0000.0000.000
39A38PHE00.0550.02611.0990.0360.0360.0000.0000.0000.000
40A39TYR0-0.077-0.09016.952-0.002-0.0020.0000.0000.0000.000
41A40PRO0-0.0080.00420.3280.0080.0080.0000.0000.0000.000
42A41LEU00.025-0.00521.8220.0000.0000.0000.0000.0000.000
43A42ASP-1-0.737-0.83724.484-0.078-0.0780.0000.0000.0000.000
44A43PHE0-0.035-0.02026.638-0.001-0.0010.0000.0000.0000.000
45A44THR0-0.026-0.00827.351-0.005-0.0050.0000.0000.0000.000
46A45PHE00.008-0.01129.7520.0080.0080.0000.0000.0000.000
47A46VAL00.0430.02226.8200.0070.0070.0000.0000.0000.000
48A47CYS0-0.0390.03625.152-0.004-0.0040.0000.0000.0000.000
49A48PRO00.0770.05326.3230.0040.0040.0000.0000.0000.000
50A49THR0-0.079-0.04928.7120.0080.0080.0000.0000.0000.000
51A50GLU-1-0.702-0.82823.672-0.189-0.1890.0000.0000.0000.000
52A51ILE00.0060.00923.4560.0090.0090.0000.0000.0000.000
53A52VAL0-0.026-0.02025.5340.0150.0150.0000.0000.0000.000
54A53ALA0-0.0020.01927.2680.0090.0090.0000.0000.0000.000
55A54PHE00.006-0.01721.0350.0080.0080.0000.0000.0000.000
56A55SER00.0070.00225.1760.0190.0190.0000.0000.0000.000
57A56ASP-1-0.855-0.92126.951-0.003-0.0030.0000.0000.0000.000
58A57LYS10.9010.96427.1170.0280.0280.0000.0000.0000.000
59A58ALA00.0060.00624.9650.0040.0040.0000.0000.0000.000
60A59ASN00.0450.01725.3100.0070.0070.0000.0000.0000.000
61A60GLU-1-0.893-0.93927.4450.0130.0130.0000.0000.0000.000
62A61PHE0-0.042-0.03420.637-0.003-0.0030.0000.0000.0000.000
63A62HIS0-0.005-0.00822.3490.0140.0140.0000.0000.0000.000
64A63ASP-1-0.922-0.95324.2430.1020.1020.0000.0000.0000.000
65A64VAL0-0.122-0.04722.1270.0040.0040.0000.0000.0000.000
66A65ASN0-0.022-0.01119.1160.0070.0070.0000.0000.0000.000
67A66CYS0-0.034-0.00618.2020.0260.0260.0000.0000.0000.000
68A67GLU-1-0.875-0.93116.8710.1760.1760.0000.0000.0000.000
69A68VAL0-0.010-0.00917.348-0.021-0.0210.0000.0000.0000.000
70A69VAL00.0000.00015.2870.0190.0190.0000.0000.0000.000
71A70ALA0-0.0010.01816.668-0.043-0.0430.0000.0000.0000.000
72A71VAL0-0.018-0.00914.1240.0320.0320.0000.0000.0000.000
73A72SER00.0230.01517.419-0.030-0.0300.0000.0000.0000.000
74A73VAL00.0210.00417.4200.0140.0140.0000.0000.0000.000
75A74ASP-1-0.847-0.89619.569-0.110-0.1100.0000.0000.0000.000
76A75SER00.0100.02221.5550.0140.0140.0000.0000.0000.000
77A76HIS00.0690.01922.404-0.007-0.0070.0000.0000.0000.000
78A77PHE00.006-0.00824.2010.0040.0040.0000.0000.0000.000
79A78SER0-0.0010.00426.1290.0040.0040.0000.0000.0000.000
80A79HIS10.8260.89120.6450.0570.0570.0000.0000.0000.000
81A80LEU00.0260.02726.2820.0000.0000.0000.0000.0000.000
82A81ALA00.0000.00629.0910.0010.0010.0000.0000.0000.000
83A82TRP00.005-0.00425.440-0.003-0.0030.0000.0000.0000.000
84A83ILE0-0.012-0.01126.684-0.001-0.0010.0000.0000.0000.000
85A84ASN0-0.045-0.02130.7810.0040.0040.0000.0000.0000.000
86A85THR0-0.0190.00133.602-0.003-0.0030.0000.0000.0000.000
87A86PRO00.014-0.00334.5640.0000.0000.0000.0000.0000.000
88A87ARG10.8710.92732.0740.0140.0140.0000.0000.0000.000
89A88LYS10.8840.94135.7870.0190.0190.0000.0000.0000.000
90A89ASN0-0.035-0.01838.085-0.005-0.0050.0000.0000.0000.000
91A90GLY00.0500.03934.756-0.002-0.0020.0000.0000.0000.000
92A91GLY0-0.012-0.00632.564-0.006-0.0060.0000.0000.0000.000
93A92LEU0-0.0100.00226.893-0.003-0.0030.0000.0000.0000.000
94A93GLY00.0010.00131.0620.0030.0030.0000.0000.0000.000
95A94HIS00.015-0.00231.244-0.003-0.0030.0000.0000.0000.000
96A95MET0-0.037-0.01526.481-0.011-0.0110.0000.0000.0000.000
97A96ASN0-0.034-0.01727.0060.0150.0150.0000.0000.0000.000
98A97ILE00.0030.00021.6530.0090.0090.0000.0000.0000.000
99A98ALA00.0010.01619.231-0.003-0.0030.0000.0000.0000.000
100A99LEU00.003-0.00720.457-0.022-0.0220.0000.0000.0000.000
101A100LEU00.0410.00913.9440.0200.0200.0000.0000.0000.000
102A101SER0-0.104-0.07718.473-0.035-0.0350.0000.0000.0000.000
103A102ASP-1-0.730-0.87414.350-0.247-0.2470.0000.0000.0000.000
104A103LEU0-0.003-0.00516.618-0.034-0.0340.0000.0000.0000.000
105A104THR0-0.021-0.02014.812-0.026-0.0260.0000.0000.0000.000
106A105LYS10.9010.97915.6640.1990.1990.0000.0000.0000.000
107A106GLN0-0.030-0.0129.9410.0110.0110.0000.0000.0000.000
108A107ILE00.0300.0239.779-0.143-0.1430.0000.0000.0000.000
109A108SER0-0.013-0.0409.806-0.165-0.1650.0000.0000.0000.000
110A109ARG10.7870.88011.1300.3920.3920.0000.0000.0000.000
111A110ASP-1-0.867-0.9305.945-0.963-0.9630.0000.0000.0000.000
112A111TYR0-0.071-0.0636.457-0.661-0.6610.0000.0000.0000.000
113A112GLY0-0.031-0.0098.6220.0220.0220.0000.0000.0000.000
114A113VAL0-0.0010.00311.1210.0910.0910.0000.0000.0000.000
115A114LEU0-0.049-0.01513.8120.1160.1160.0000.0000.0000.000
116A115LEU00.0100.00915.709-0.044-0.0440.0000.0000.0000.000
117A116GLU-1-0.809-0.91215.919-0.452-0.4520.0000.0000.0000.000
118A117GLY0-0.049-0.00719.3270.0370.0370.0000.0000.0000.000
119A118SER0-0.006-0.01022.5230.0190.0190.0000.0000.0000.000
120A119GLY0-0.0200.00120.2540.0260.0260.0000.0000.0000.000
121A120LEU0-0.004-0.01619.9810.0280.0280.0000.0000.0000.000
122A121ALA00.0410.01416.416-0.036-0.0360.0000.0000.0000.000
123A122LEU00.0170.00417.4770.0510.0510.0000.0000.0000.000
124A123ARG10.8130.89417.9840.2130.2130.0000.0000.0000.000
125A124GLY00.0000.00515.392-0.008-0.0080.0000.0000.0000.000
126A125LEU0-0.022-0.01515.5270.0600.0600.0000.0000.0000.000
127A126PHE0-0.0010.0019.877-0.098-0.0980.0000.0000.0000.000
128A127ILE0-0.002-0.00212.6280.1000.1000.0000.0000.0000.000
129A128ILE0-0.021-0.0098.146-0.078-0.0780.0000.0000.0000.000
130A129ASP-1-0.775-0.88911.0850.6540.6540.0000.0000.0000.000
131A130PRO00.0280.01011.5410.1300.1300.0000.0000.0000.000
132A131ASN0-0.061-0.04810.5190.4360.4360.0000.0000.0000.000
133A132GLY00.0090.0177.5450.4580.4580.0000.0000.0000.000
134A133VAL0-0.0200.0026.2100.1620.1620.0000.0000.0000.000
135A134ILE0-0.0090.0076.185-0.060-0.0600.0000.0000.0000.000
136A135LYS10.9100.9508.884-0.234-0.2340.0000.0000.0000.000
137A136HIS0-0.005-0.01412.371-0.028-0.0280.0000.0000.0000.000
138A137LEU00.0060.01710.574-0.007-0.0070.0000.0000.0000.000
139A138SER0-0.029-0.00613.6510.0330.0330.0000.0000.0000.000
140A139VAL00.0350.00915.708-0.009-0.0090.0000.0000.0000.000
141A140ASN0-0.0360.00718.4240.0030.0030.0000.0000.0000.000
142A141ASP-1-0.825-0.91021.400-0.321-0.3210.0000.0000.0000.000
143A142LEU0-0.002-0.03322.3120.0220.0220.0000.0000.0000.000
144A143PRO0-0.029-0.01025.1840.0200.0200.0000.0000.0000.000
145A144VAL0-0.0060.00826.8930.0190.0190.0000.0000.0000.000
146A145GLY00.0120.00425.714-0.017-0.0170.0000.0000.0000.000
147A146ARG10.7640.84418.6600.2530.2530.0000.0000.0000.000
148A147SER00.0150.00924.5840.0240.0240.0000.0000.0000.000
149A148VAL00.0460.02023.996-0.011-0.0110.0000.0000.0000.000
150A149GLU-1-0.910-0.95324.755-0.038-0.0380.0000.0000.0000.000
151A150GLU-1-0.840-0.94122.851-0.150-0.1500.0000.0000.0000.000
152A151THR0-0.017-0.01119.110-0.014-0.0140.0000.0000.0000.000
153A152LEU00.0290.01720.9950.0110.0110.0000.0000.0000.000
154A153ARG10.8040.90123.3260.1380.1380.0000.0000.0000.000
155A154LEU0-0.009-0.01018.8030.0120.0120.0000.0000.0000.000
156A155VAL00.0030.00918.1110.0120.0120.0000.0000.0000.000
157A156LYS10.9750.98620.0180.0100.0100.0000.0000.0000.000
158A157ALA00.0150.00921.6760.0160.0160.0000.0000.0000.000
159A158PHE0-0.015-0.02716.5180.0090.0090.0000.0000.0000.000
160A159GLN0-0.017-0.01619.1820.0190.0190.0000.0000.0000.000
161A160TYR0-0.030-0.00621.0130.0210.0210.0000.0000.0000.000
162A161VAL0-0.022-0.02819.5660.0080.0080.0000.0000.0000.000
163A162GLU-1-0.952-0.97316.3120.3190.3190.0000.0000.0000.000
164A163THR0-0.057-0.01820.7080.0170.0170.0000.0000.0000.000
165A164HIS10.8500.92724.163-0.083-0.0830.0000.0000.0000.000
166A165GLY00.0190.02623.921-0.007-0.0070.0000.0000.0000.000
167A166GLU-1-0.945-0.96624.9650.0050.0050.0000.0000.0000.000
168A167VAL0-0.002-0.01322.4540.0020.0020.0000.0000.0000.000
169A168CYS00.0180.00423.6600.0070.0070.0000.0000.0000.000
170A169PRO0-0.023-0.00524.983-0.019-0.0190.0000.0000.0000.000
171A170ALA00.0340.01926.351-0.006-0.0060.0000.0000.0000.000
172A171ASN0-0.034-0.03427.3560.0030.0030.0000.0000.0000.000
173A172TRP0-0.0130.02325.3140.0060.0060.0000.0000.0000.000
174A173THR00.0720.03427.630-0.008-0.0080.0000.0000.0000.000
175A174PRO0-0.002-0.02328.3250.0040.0040.0000.0000.0000.000
176A175ASP-1-0.882-0.93230.3810.0110.0110.0000.0000.0000.000
177A176SER0-0.102-0.02130.735-0.005-0.0050.0000.0000.0000.000
178A177PRO00.003-0.02132.0550.0060.0060.0000.0000.0000.000
179A178THR0-0.019-0.01227.821-0.007-0.0070.0000.0000.0000.000
180A179ILE0-0.042-0.01827.7390.0020.0020.0000.0000.0000.000
181A180LYS10.9620.99327.988-0.014-0.0140.0000.0000.0000.000
182A181PRO00.0240.03024.732-0.011-0.0110.0000.0000.0000.000
183A182SER00.010-0.01226.627-0.001-0.0010.0000.0000.0000.000
184A183PRO00.0450.01729.329-0.002-0.0020.0000.0000.0000.000
185A184ALA0-0.008-0.00431.941-0.002-0.0020.0000.0000.0000.000
186A185ALA00.0440.00831.901-0.001-0.0010.0000.0000.0000.000
187A186SER0-0.012-0.00130.719-0.001-0.0010.0000.0000.0000.000
188A187LYS10.9380.96232.6520.0440.0440.0000.0000.0000.000
189A188GLU-1-0.864-0.92335.6790.0040.0040.0000.0000.0000.000
190A189TYR0-0.029-0.01232.481-0.001-0.0010.0000.0000.0000.000
191A190PHE00.022-0.00830.978-0.002-0.0020.0000.0000.0000.000
192A191GLN0-0.0030.00336.401-0.004-0.0040.0000.0000.0000.000
193A192LYS10.9020.96835.0450.0130.0130.0000.0000.0000.000
194A193VAL0-0.019-0.00935.3560.0020.0020.0000.0000.0000.000
195A194ASN0-0.046-0.00837.315-0.008-0.0080.0000.0000.0000.000