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: 6N48Z

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2084849.142333
FMO2-HF: Nuclear repulsion 2010212.08139
FMO2-HF: Total energy -74637.060944
FMO2-MP2: Total energy -74857.867761


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.
-7.985-1.1486.582-5.566-7.853-0.037
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 : -0.064 / 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].
3A2PRO00.0290.0283.857-0.3321.621-0.020-0.967-0.9660.003
4A3ALA0-0.008-0.0116.0180.2510.2510.0000.0000.0000.000
5A4VAL00.0300.0057.0080.1860.1860.0000.0000.0000.000
6A5THR0-0.071-0.0398.7980.1870.1870.0000.0000.0000.000
7A6GLN0-0.0400.0003.4041.5151.9820.018-0.105-0.3810.000
8A7HIS00.0120.0022.776-2.480-0.7360.395-0.674-1.4640.002
9A8ALA00.030-0.0012.348-5.917-3.7193.852-3.185-2.866-0.037
10A9PRO0-0.0080.0002.287-1.338-0.1462.307-1.629-1.870-0.005
11A10TYR0-0.036-0.0163.2211.0290.2970.0310.995-0.2940.000
12A11PHE00.0090.0085.307-0.289-0.274-0.001-0.001-0.0120.000
13A12LYS10.8940.9298.8530.0380.0380.0000.0000.0000.000
14A13GLY0-0.0010.01012.216-0.051-0.0510.0000.0000.0000.000
15A14THR0-0.0100.00715.6890.0200.0200.0000.0000.0000.000
16A15ALA00.0240.01118.740-0.016-0.0160.0000.0000.0000.000
17A16VAL0-0.058-0.02120.6640.0040.0040.0000.0000.0000.000
18A17VAL00.020-0.01121.7140.0020.0020.0000.0000.0000.000
19A18ASN00.0130.00324.7320.0000.0000.0000.0000.0000.000
20A19GLY00.0070.00128.148-0.001-0.0010.0000.0000.0000.000
21A20GLU-1-0.935-0.95127.7340.0250.0250.0000.0000.0000.000
22A21PHE0-0.055-0.03224.5140.0000.0000.0000.0000.0000.000
23A22LYS11.0000.99520.759-0.077-0.0770.0000.0000.0000.000
24A23ASP-1-0.862-0.93217.7170.0190.0190.0000.0000.0000.000
25A24LEU0-0.024-0.01115.5180.0120.0120.0000.0000.0000.000
26A25SER0-0.048-0.05710.948-0.045-0.0450.0000.0000.0000.000
27A26LEU00.0220.0065.7160.0100.0100.0000.0000.0000.000
28A27ASP-1-0.821-0.8889.7900.6150.6150.0000.0000.0000.000
29A28ASP-1-0.862-0.91311.4910.1680.1680.0000.0000.0000.000
30A29PHE0-0.041-0.03812.156-0.044-0.0440.0000.0000.0000.000
31A30LYS10.9070.9749.387-0.919-0.9190.0000.0000.0000.000
32A31GLY0-0.057-0.03113.072-0.050-0.0500.0000.0000.0000.000
33A32LYS10.8840.95415.041-0.228-0.2280.0000.0000.0000.000
34A33TYR0-0.029-0.03014.2540.0330.0330.0000.0000.0000.000
35A34LEU0-0.033-0.01410.809-0.022-0.0220.0000.0000.0000.000
36A35VAL00.0010.00213.536-0.006-0.0060.0000.0000.0000.000
37A36LEU00.0080.00810.414-0.003-0.0030.0000.0000.0000.000
38A37PHE0-0.027-0.03214.015-0.033-0.0330.0000.0000.0000.000
39A38PHE00.0550.02810.8450.0080.0080.0000.0000.0000.000
40A39TYR0-0.050-0.06816.8050.0150.0150.0000.0000.0000.000
41A40PRO0-0.0060.00520.244-0.004-0.0040.0000.0000.0000.000
42A41LEU00.033-0.00221.787-0.007-0.0070.0000.0000.0000.000
43A42ASP-1-0.749-0.84024.433-0.048-0.0480.0000.0000.0000.000
44A43PHE0-0.036-0.02226.554-0.001-0.0010.0000.0000.0000.000
45A44THR0-0.029-0.00927.2600.0010.0010.0000.0000.0000.000
46A45PHE00.011-0.01029.6220.0050.0050.0000.0000.0000.000
47A46VAL00.0370.02226.6240.0040.0040.0000.0000.0000.000
48A47CYS0-0.0250.03825.0460.0020.0020.0000.0000.0000.000
49A48PRO00.0710.05026.2610.0030.0030.0000.0000.0000.000
50A49THR0-0.072-0.04728.6420.0060.0060.0000.0000.0000.000
51A50GLU-1-0.711-0.82623.694-0.047-0.0470.0000.0000.0000.000
52A51ILE00.0060.00923.4770.0070.0070.0000.0000.0000.000
53A52VAL0-0.009-0.01125.6680.0070.0070.0000.0000.0000.000
54A53ALA0-0.0150.01227.4340.0050.0050.0000.0000.0000.000
55A54PHE00.010-0.01421.2270.0070.0070.0000.0000.0000.000
56A55SER00.0100.00625.2410.0080.0080.0000.0000.0000.000
57A56ASP-1-0.831-0.87926.9970.0170.0170.0000.0000.0000.000
58A57LYS10.8110.90426.885-0.037-0.0370.0000.0000.0000.000
59A58ALA00.0000.00624.9420.0060.0060.0000.0000.0000.000
60A59ASN00.0260.00725.2530.0040.0040.0000.0000.0000.000
61A60GLU-1-0.764-0.86527.1600.0590.0590.0000.0000.0000.000
62A61PHE0-0.045-0.03320.8630.0050.0050.0000.0000.0000.000
63A62HIS0-0.034-0.02222.1630.0080.0080.0000.0000.0000.000
64A63ASP-1-0.909-0.95424.1270.0810.0810.0000.0000.0000.000
65A64VAL0-0.114-0.04522.0680.0040.0040.0000.0000.0000.000
66A65ASN0-0.043-0.02518.9440.0080.0080.0000.0000.0000.000
67A66CYS0-0.022-0.00418.2840.0240.0240.0000.0000.0000.000
68A67GLU-1-0.850-0.91116.7820.0920.0920.0000.0000.0000.000
69A68VAL0-0.020-0.01617.306-0.001-0.0010.0000.0000.0000.000
70A69VAL0-0.005-0.00515.4730.0000.0000.0000.0000.0000.000
71A70ALA00.0000.02316.772-0.017-0.0170.0000.0000.0000.000
72A71VAL0-0.005-0.00613.9700.0050.0050.0000.0000.0000.000
73A72SER00.006-0.00817.268-0.008-0.0080.0000.0000.0000.000
74A73VAL00.0210.00917.496-0.003-0.0030.0000.0000.0000.000
75A74ASP-1-0.830-0.88819.564-0.084-0.0840.0000.0000.0000.000
76A75SER0-0.0060.01921.5170.0020.0020.0000.0000.0000.000
77A76HIS00.0570.01022.440-0.001-0.0010.0000.0000.0000.000
78A77PHE00.016-0.00424.1170.0070.0070.0000.0000.0000.000
79A78SER00.0040.00826.0150.0040.0040.0000.0000.0000.000
80A79HIS10.8180.88020.4500.0630.0630.0000.0000.0000.000
81A80LEU00.0210.02726.1600.0040.0040.0000.0000.0000.000
82A81ALA00.0030.00828.9970.0030.0030.0000.0000.0000.000
83A82TRP00.002-0.00525.3600.0010.0010.0000.0000.0000.000
84A83ILE0-0.008-0.01026.7180.0020.0020.0000.0000.0000.000
85A84ASN0-0.043-0.02030.7930.0050.0050.0000.0000.0000.000
86A85THR0-0.0320.00433.526-0.001-0.0010.0000.0000.0000.000
87A86PRO00.0140.00034.5530.0010.0010.0000.0000.0000.000
88A87ARG10.8280.86431.554-0.007-0.0070.0000.0000.0000.000
89A88LYS10.8950.94635.8230.0010.0010.0000.0000.0000.000
90A89ASN0-0.034-0.01738.0370.0000.0000.0000.0000.0000.000
91A90GLY00.0430.03334.622-0.002-0.0020.0000.0000.0000.000
92A91GLY0-0.009-0.00532.439-0.004-0.0040.0000.0000.0000.000
93A92LEU00.0020.00526.8310.0010.0010.0000.0000.0000.000
94A93GLY00.0110.01231.1150.0040.0040.0000.0000.0000.000
95A94HIS0-0.003-0.01230.903-0.004-0.0040.0000.0000.0000.000
96A95MET0-0.041-0.01526.532-0.002-0.0020.0000.0000.0000.000
97A96ASN0-0.037-0.02427.0100.0030.0030.0000.0000.0000.000
98A97ILE00.0070.00421.7970.0070.0070.0000.0000.0000.000
99A98ALA00.0000.01719.267-0.005-0.0050.0000.0000.0000.000
100A99LEU00.004-0.00620.534-0.008-0.0080.0000.0000.0000.000
101A100LEU00.0350.00913.8050.0050.0050.0000.0000.0000.000
102A101SER0-0.099-0.07518.431-0.015-0.0150.0000.0000.0000.000
103A102ASP-1-0.722-0.85914.381-0.260-0.2600.0000.0000.0000.000
104A103LEU00.005-0.00316.597-0.017-0.0170.0000.0000.0000.000
105A104THR0-0.015-0.02214.954-0.004-0.0040.0000.0000.0000.000
106A105LYS10.8750.95715.7120.1490.1490.0000.0000.0000.000
107A106GLN0-0.024-0.0129.6470.0550.0550.0000.0000.0000.000
108A107ILE00.0340.0239.788-0.105-0.1050.0000.0000.0000.000
109A108SER0-0.013-0.0489.812-0.091-0.0910.0000.0000.0000.000
110A109ARG10.7490.85011.1740.3700.3700.0000.0000.0000.000
111A110ASP-1-0.853-0.9186.045-0.939-0.9390.0000.0000.0000.000
112A111TYR0-0.070-0.0716.439-0.389-0.3890.0000.0000.0000.000
113A112GLY0-0.032-0.0088.6020.1060.1060.0000.0000.0000.000
114A113VAL0-0.008-0.00111.1950.0940.0940.0000.0000.0000.000
115A114LEU0-0.046-0.01113.8870.0610.0610.0000.0000.0000.000
116A115LEU00.0100.00915.790-0.015-0.0150.0000.0000.0000.000
117A116GLU-1-0.781-0.89015.918-0.334-0.3340.0000.0000.0000.000
118A117GLY0-0.053-0.01019.5010.0150.0150.0000.0000.0000.000
119A118SER0-0.024-0.01722.6480.0120.0120.0000.0000.0000.000
120A119GLY0-0.0060.01420.3780.0110.0110.0000.0000.0000.000
121A120LEU0-0.021-0.01820.0080.0100.0100.0000.0000.0000.000
122A121ALA00.0300.01016.357-0.016-0.0160.0000.0000.0000.000
123A122LEU00.0250.00617.4700.0300.0300.0000.0000.0000.000
124A123ARG10.7890.86417.9000.0640.0640.0000.0000.0000.000
125A124GLY00.0050.00315.2600.0130.0130.0000.0000.0000.000
126A125LEU0-0.032-0.01815.6150.0060.0060.0000.0000.0000.000
127A126PHE00.0080.0029.969-0.024-0.0240.0000.0000.0000.000
128A127ILE0-0.006-0.00112.7400.0150.0150.0000.0000.0000.000
129A128ILE0-0.020-0.0098.2590.0280.0280.0000.0000.0000.000
130A129ASP-1-0.746-0.85710.9260.5650.5650.0000.0000.0000.000
131A130PRO00.0460.02611.3160.0550.0550.0000.0000.0000.000
132A131ASN0-0.007-0.01910.9130.1110.1110.0000.0000.0000.000
133A132GLY00.0060.0037.2580.2490.2490.0000.0000.0000.000
134A133VAL0-0.030-0.0055.9810.0720.0720.0000.0000.0000.000
135A134ILE0-0.0100.0096.177-0.197-0.1970.0000.0000.0000.000
136A135LYS10.8100.8778.883-0.341-0.3410.0000.0000.0000.000
137A136HIS0-0.015-0.01912.364-0.031-0.0310.0000.0000.0000.000
138A137LEU0-0.0020.01710.300-0.016-0.0160.0000.0000.0000.000
139A138SER0-0.0130.00013.6530.0170.0170.0000.0000.0000.000
140A139VAL00.0210.00415.589-0.023-0.0230.0000.0000.0000.000
141A140ASN0-0.054-0.01018.2980.0150.0150.0000.0000.0000.000
142A141ASP-1-0.821-0.91021.319-0.112-0.1120.0000.0000.0000.000
143A142LEU0-0.008-0.03022.0980.0100.0100.0000.0000.0000.000
144A143PRO0-0.0160.00025.1220.0070.0070.0000.0000.0000.000
145A144VAL0-0.0060.00726.7880.0070.0070.0000.0000.0000.000
146A145GLY00.0180.01325.572-0.006-0.0060.0000.0000.0000.000
147A146ARG10.7690.85318.5800.0750.0750.0000.0000.0000.000
148A147SER00.0130.01124.7350.0050.0050.0000.0000.0000.000
149A148VAL00.0450.01624.0930.0020.0020.0000.0000.0000.000
150A149GLU-1-0.833-0.92224.7950.0470.0470.0000.0000.0000.000
151A150GLU-1-0.826-0.91622.9110.0550.0550.0000.0000.0000.000
152A151THR0-0.013-0.00419.1820.0050.0050.0000.0000.0000.000
153A152LEU00.0010.00120.9910.0150.0150.0000.0000.0000.000
154A153ARG10.7870.88323.306-0.053-0.0530.0000.0000.0000.000
155A154LEU0-0.016-0.01019.0600.0120.0120.0000.0000.0000.000
156A155VAL0-0.0090.00117.9950.0200.0200.0000.0000.0000.000
157A156LYS10.9180.95919.939-0.057-0.0570.0000.0000.0000.000
158A157ALA00.0100.01221.6170.0060.0060.0000.0000.0000.000
159A158PHE0-0.012-0.02916.6360.0130.0130.0000.0000.0000.000
160A159GLN00.0270.00819.1750.0060.0060.0000.0000.0000.000
161A160TYR0-0.037-0.01321.0090.0020.0020.0000.0000.0000.000
162A161VAL0-0.021-0.02619.582-0.001-0.0010.0000.0000.0000.000
163A162GLU-1-0.856-0.89915.9120.3390.3390.0000.0000.0000.000
164A163THR0-0.058-0.02220.696-0.003-0.0030.0000.0000.0000.000
165A164HIS10.8510.92724.153-0.134-0.1340.0000.0000.0000.000
166A165GLY00.0150.02523.902-0.008-0.0080.0000.0000.0000.000
167A166GLU-1-0.883-0.92224.9470.0920.0920.0000.0000.0000.000
168A167VAL0-0.002-0.01622.4950.0100.0100.0000.0000.0000.000
169A168CYS00.0240.00723.596-0.009-0.0090.0000.0000.0000.000
170A169PRO0-0.028-0.00924.9670.0010.0010.0000.0000.0000.000
171A170ALA00.0290.01726.3380.0030.0030.0000.0000.0000.000
172A171ASN0-0.035-0.03427.349-0.002-0.0020.0000.0000.0000.000
173A172TRP0-0.0020.02425.3870.0000.0000.0000.0000.0000.000
174A173THR00.0550.02627.625-0.001-0.0010.0000.0000.0000.000
175A174PRO00.0220.00228.3750.0030.0030.0000.0000.0000.000
176A175ASP-1-0.890-0.94130.3780.0600.0600.0000.0000.0000.000
177A176SER0-0.096-0.02930.780-0.002-0.0020.0000.0000.0000.000
178A177PRO00.004-0.02032.0440.0040.0040.0000.0000.0000.000
179A178THR0-0.034-0.03027.7220.0020.0020.0000.0000.0000.000
180A179ILE0-0.031-0.01228.242-0.006-0.0060.0000.0000.0000.000
181A180LYS10.9300.96128.013-0.073-0.0730.0000.0000.0000.000
182A181PRO00.0010.02124.824-0.009-0.0090.0000.0000.0000.000
183A182SER00.012-0.01027.0980.0030.0030.0000.0000.0000.000
184A183PRO00.0400.01229.805-0.006-0.0060.0000.0000.0000.000
185A184ALA0-0.0010.00032.554-0.004-0.0040.0000.0000.0000.000
186A185ALA00.0450.00932.296-0.003-0.0030.0000.0000.0000.000
187A186SER0-0.0130.00231.175-0.002-0.0020.0000.0000.0000.000
188A187LYS10.9330.95932.995-0.063-0.0630.0000.0000.0000.000
189A188GLU-1-0.783-0.85335.6630.0680.0680.0000.0000.0000.000
190A189TYR00.0100.00532.290-0.002-0.0020.0000.0000.0000.000
191A190PHE00.019-0.00831.361-0.003-0.0030.0000.0000.0000.000
192A191GLN0-0.007-0.01036.570-0.005-0.0050.0000.0000.0000.000
193A192LYS10.8130.91035.002-0.068-0.0680.0000.0000.0000.000
194A193VAL0-0.016-0.00735.357-0.002-0.0020.0000.0000.0000.000
195A194ASN0-0.049-0.00137.412-0.005-0.0050.0000.0000.0000.000