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: 6G3VZ

Calculation Name: 1UN2-A-Xray372

Preferred Name: Thiol:disulfide interchange protein DsbA

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1UN2

Chain ID: A

ChEMBL ID: CHEMBL3559645

UniProt ID: P0AEG4

Base Structure: X-ray

Registration Date: 2023-09-26

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2018121.910479
FMO2-HF: Nuclear repulsion 1944587.5689
FMO2-HF: Total energy -73534.341579
FMO2-MP2: Total energy -73747.109881


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:1:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-22.785-22.09115.358-6.777-9.2750.052
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.007
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].
3A3ILE00.0020.0113.655-4.006-2.2190.015-0.893-0.9090.003
4A4ARG10.8910.9346.0212.5122.5120.0000.0000.0000.000
5A5SER0-0.008-0.0068.1840.5800.5800.0000.0000.0000.000
6A6ALA00.1070.0448.958-0.286-0.2860.0000.0000.0000.000
7A7SER00.0050.0008.6700.3080.3080.0000.0000.0000.000
8A8ASP-1-0.816-0.9004.789-4.905-4.758-0.001-0.005-0.1410.000
9A9ILE0-0.015-0.0134.806-0.403-0.344-0.001-0.003-0.0550.000
10A10ARG10.8220.9087.0001.5391.5390.0000.0000.0000.000
11A11ASP-1-0.913-0.9612.450-4.811-4.0610.331-0.356-0.726-0.003
12A12VAL0-0.035-0.0092.3240.5712.4263.156-1.646-3.3650.011
13A13PHE00.026-0.0043.6000.9250.8390.0200.319-0.2530.001
14A14ILE0-0.012-0.0086.0520.1740.1740.0000.0000.0000.000
15A15ASN0-0.110-0.0661.834-11.433-15.56611.843-4.130-3.5800.040
16A16ALA0-0.0210.0065.100-0.590-0.515-0.0010.000-0.0730.000
17A17GLY0-0.061-0.0287.205-0.886-0.8860.0000.0000.0000.000
18A18ILE0-0.055-0.0099.475-0.475-0.4750.0000.0000.0000.000
19A19LYS10.9900.98810.229-0.490-0.4900.0000.0000.0000.000
20A20GLY00.0540.00811.371-0.063-0.0630.0000.0000.0000.000
21A21GLU-1-0.922-0.94712.055-0.054-0.0540.0000.0000.0000.000
22A22GLU-1-0.924-0.97615.0420.5600.5600.0000.0000.0000.000
23A23TYR00.0110.00811.239-0.023-0.0230.0000.0000.0000.000
24A24ASP-1-0.768-0.87513.636-0.330-0.3300.0000.0000.0000.000
25A25ALA0-0.0130.00615.702-0.038-0.0380.0000.0000.0000.000
26A26ALA00.003-0.00316.755-0.024-0.0240.0000.0000.0000.000
27A27TRP0-0.011-0.00313.697-0.019-0.0190.0000.0000.0000.000
28A28ASN0-0.068-0.06117.277-0.064-0.0640.0000.0000.0000.000
29A29SER0-0.035-0.00120.5850.0100.0100.0000.0000.0000.000
30A30PHE00.004-0.01522.709-0.019-0.0190.0000.0000.0000.000
31A31VAL00.0500.01122.681-0.014-0.0140.0000.0000.0000.000
32A32VAL00.0330.03518.6880.0000.0000.0000.0000.0000.000
33A33LYS10.9720.98621.6360.0840.0840.0000.0000.0000.000
34A34SER0-0.074-0.04023.994-0.014-0.0140.0000.0000.0000.000
35A35LEU00.0530.01920.986-0.007-0.0070.0000.0000.0000.000
36A36VAL0-0.016-0.00120.794-0.004-0.0040.0000.0000.0000.000
37A37ALA0-0.0040.00522.413-0.014-0.0140.0000.0000.0000.000
38A38GLN00.0250.01125.881-0.010-0.0100.0000.0000.0000.000
39A39GLN0-0.008-0.01519.0020.0200.0200.0000.0000.0000.000
40A40GLU-1-0.944-0.96523.927-0.157-0.1570.0000.0000.0000.000
41A41LYS10.8480.90925.5640.0260.0260.0000.0000.0000.000
42A42ALA0-0.0050.00226.6330.0040.0040.0000.0000.0000.000
43A43ALA00.0090.00725.3390.0050.0050.0000.0000.0000.000
44A44ALA0-0.017-0.01327.4430.0010.0010.0000.0000.0000.000
45A45ASP-1-0.857-0.92530.439-0.027-0.0270.0000.0000.0000.000
46A46VAL0-0.061-0.01829.2120.0060.0060.0000.0000.0000.000
47A47GLN0-0.058-0.02132.102-0.007-0.0070.0000.0000.0000.000
48A48LEU0-0.024-0.00424.348-0.002-0.0020.0000.0000.0000.000
49A49ARG10.9490.96428.5660.0640.0640.0000.0000.0000.000
50A50GLY0-0.025-0.01524.909-0.018-0.0180.0000.0000.0000.000
51A51VAL0-0.0580.01719.8390.0160.0160.0000.0000.0000.000
52A52PRO00.052-0.01520.917-0.021-0.0210.0000.0000.0000.000
53A53ALA0-0.041-0.01322.474-0.001-0.0010.0000.0000.0000.000
54A54MET0-0.0020.01524.0830.0120.0120.0000.0000.0000.000
55A55PHE00.0340.00926.945-0.007-0.0070.0000.0000.0000.000
56A56VAL00.0260.01729.4400.0120.0120.0000.0000.0000.000
57A57ASN00.0400.00732.090-0.004-0.0040.0000.0000.0000.000
58A58GLY0-0.019-0.00132.543-0.005-0.0050.0000.0000.0000.000
59A59LYS10.9150.97633.910-0.023-0.0230.0000.0000.0000.000
60A60TYR00.0410.01334.766-0.008-0.0080.0000.0000.0000.000
61A61GLN00.0120.02630.5470.0040.0040.0000.0000.0000.000
62A62LEU0-0.009-0.01729.2980.0000.0000.0000.0000.0000.000
63A63ASN0-0.068-0.04830.931-0.016-0.0160.0000.0000.0000.000
64A64PRO00.029-0.01827.9390.0040.0040.0000.0000.0000.000
65A65GLN00.025-0.00230.7320.0100.0100.0000.0000.0000.000
66A66GLY0-0.0230.00533.100-0.001-0.0010.0000.0000.0000.000
67A67MET0-0.090-0.01330.8550.0070.0070.0000.0000.0000.000
68A68ASP-1-0.857-0.89634.6310.0340.0340.0000.0000.0000.000
69A69THR0-0.007-0.01530.9540.0040.0040.0000.0000.0000.000
70A70SER0-0.078-0.05833.135-0.003-0.0030.0000.0000.0000.000
71A71ASN0-0.027-0.01431.9150.0050.0050.0000.0000.0000.000
72A72MET00.0510.01724.473-0.005-0.0050.0000.0000.0000.000
73A73ASP-1-0.887-0.94028.6590.1160.1160.0000.0000.0000.000
74A74VAL0-0.018-0.02329.8810.0060.0060.0000.0000.0000.000
75A75PHE0-0.0060.01226.121-0.001-0.0010.0000.0000.0000.000
76A76VAL00.003-0.00325.467-0.002-0.0020.0000.0000.0000.000
77A77GLN0-0.017-0.00628.1830.0110.0110.0000.0000.0000.000
78A78GLN00.0820.04131.057-0.006-0.0060.0000.0000.0000.000
79A79TYR00.0340.01126.623-0.009-0.0090.0000.0000.0000.000
80A80ALA0-0.004-0.02328.0800.0000.0000.0000.0000.0000.000
81A81ASP-1-0.902-0.93329.6130.0970.0970.0000.0000.0000.000
82A82THR0-0.055-0.04132.676-0.004-0.0040.0000.0000.0000.000
83A83VAL0-0.004-0.00628.411-0.004-0.0040.0000.0000.0000.000
84A84LYS10.9130.96831.758-0.102-0.1020.0000.0000.0000.000
85A85TYR0-0.013-0.01133.742-0.002-0.0020.0000.0000.0000.000
86A86LEU0-0.023-0.01033.526-0.002-0.0020.0000.0000.0000.000
87A87SER0-0.095-0.03732.267-0.006-0.0060.0000.0000.0000.000
88A88GLU-1-0.958-0.97035.1690.0910.0910.0000.0000.0000.000
89A93TYR0-0.049-0.04337.139-0.002-0.0020.0000.0000.0000.000
90A94GLU-1-0.847-0.92840.4020.0270.0270.0000.0000.0000.000
91A95ASP-1-0.832-0.90440.2420.0070.0070.0000.0000.0000.000
92A96GLY0-0.023-0.01639.609-0.002-0.0020.0000.0000.0000.000
93A97LYS10.8360.93339.057-0.028-0.0280.0000.0000.0000.000
94A98GLN00.0680.04435.135-0.007-0.0070.0000.0000.0000.000
95A99TYR0-0.030-0.00934.1010.0020.0020.0000.0000.0000.000
96A100THR0-0.0060.01135.190-0.005-0.0050.0000.0000.0000.000
97A101THR0-0.024-0.04736.5500.0050.0050.0000.0000.0000.000
98A102LEU0-0.035-0.01333.461-0.005-0.0050.0000.0000.0000.000
99A103GLU-1-0.930-0.96437.854-0.014-0.0140.0000.0000.0000.000
100A104LYS10.8850.93139.3080.0300.0300.0000.0000.0000.000
101A105PRO0-0.030-0.01437.701-0.002-0.0020.0000.0000.0000.000
102A106VAL00.0220.03132.575-0.002-0.0020.0000.0000.0000.000
103A107ALA00.007-0.00835.4620.0080.0080.0000.0000.0000.000
104A108GLY0-0.016-0.01634.959-0.004-0.0040.0000.0000.0000.000
105A109ALA0-0.0190.00631.3030.0030.0030.0000.0000.0000.000
106A110PRO0-0.013-0.01427.1210.0070.0070.0000.0000.0000.000
107A111GLN00.0340.00629.9590.0030.0030.0000.0000.0000.000
108A112VAL00.0520.02326.494-0.008-0.0080.0000.0000.0000.000
109A113LEU0-0.061-0.02024.1650.0170.0170.0000.0000.0000.000
110A114GLU-1-0.834-0.92119.7760.0700.0700.0000.0000.0000.000
111A115PHE0-0.019-0.01321.7430.0010.0010.0000.0000.0000.000
112A116PHE00.040-0.01013.879-0.008-0.0080.0000.0000.0000.000
113A117SER00.0620.01016.114-0.043-0.0430.0000.0000.0000.000
114A118PHE00.0380.01510.5560.0170.0170.0000.0000.0000.000
115A119PHE00.0260.00811.933-0.118-0.1180.0000.0000.0000.000
116A120CYS0-0.086-0.00714.2140.0740.0740.0000.0000.0000.000
117A121PRO00.0540.02216.0080.0310.0310.0000.0000.0000.000
118A122HIS00.0480.01517.0270.0270.0270.0000.0000.0000.000
119A124TYR00.0500.02411.148-0.008-0.0080.0000.0000.0000.000
120A125GLN00.0270.00415.0690.0750.0750.0000.0000.0000.000
121A126PHE00.014-0.00918.1100.0360.0360.0000.0000.0000.000
122A127GLU-1-0.875-0.93514.7350.2990.2990.0000.0000.0000.000
123A128GLU-1-0.869-0.93712.4960.5060.5060.0000.0000.0000.000
124A129VAL0-0.084-0.03615.853-0.007-0.0070.0000.0000.0000.000
125A130LEU0-0.051-0.03918.7070.0080.0080.0000.0000.0000.000
126A131HIS00.0220.03517.2520.0000.0000.0000.0000.0000.000
127A132ILE0-0.026-0.00620.7970.0040.0040.0000.0000.0000.000
128A133SER00.0490.00819.4190.0010.0010.0000.0000.0000.000
129A134ASP-1-0.899-0.95119.1800.3750.3750.0000.0000.0000.000
130A135ASN0-0.073-0.05322.041-0.011-0.0110.0000.0000.0000.000
131A136VAL00.0390.01424.728-0.010-0.0100.0000.0000.0000.000
132A137LYS10.9160.96419.529-0.319-0.3190.0000.0000.0000.000
133A138LYS10.9300.97222.831-0.268-0.2680.0000.0000.0000.000
134A139LYS10.8430.92927.495-0.133-0.1330.0000.0000.0000.000
135A140LEU0-0.0110.00627.295-0.015-0.0150.0000.0000.0000.000
136A141PRO0-0.0100.00230.7060.0090.0090.0000.0000.0000.000
137A142GLU-1-0.868-0.93632.5450.1830.1830.0000.0000.0000.000
138A143GLY0-0.029-0.01532.472-0.012-0.0120.0000.0000.0000.000
139A144VAL0-0.045-0.01230.219-0.011-0.0110.0000.0000.0000.000
140A145LYS10.9590.99224.994-0.158-0.1580.0000.0000.0000.000
141A146MET0-0.016-0.00422.293-0.016-0.0160.0000.0000.0000.000
142A147THR0-0.072-0.03622.9300.0290.0290.0000.0000.0000.000
143A148LYS10.8790.93416.302-0.189-0.1890.0000.0000.0000.000
144A149TYR0-0.0190.00220.0590.0070.0070.0000.0000.0000.000
145A150HIS00.0260.01514.776-0.045-0.0450.0000.0000.0000.000
146A151VAL0-0.030-0.01418.3430.0040.0040.0000.0000.0000.000
147A152ASN0-0.021-0.00818.698-0.040-0.0400.0000.0000.0000.000
148A153PHE00.000-0.00120.365-0.033-0.0330.0000.0000.0000.000
149A154MET0-0.018-0.02417.7400.0120.0120.0000.0000.0000.000
150A155GLY00.0510.02116.241-0.028-0.0280.0000.0000.0000.000
151A156GLY0-0.025-0.00816.702-0.072-0.0720.0000.0000.0000.000
152A157ASP-1-0.905-0.96117.332-0.527-0.5270.0000.0000.0000.000
153A158LEU00.0120.01910.3140.0320.0320.0000.0000.0000.000
154A159GLY00.0260.01313.938-0.016-0.0160.0000.0000.0000.000
155A160LYS10.9250.95916.0070.4570.4570.0000.0000.0000.000
156A161ASP-1-0.826-0.91013.563-0.694-0.6940.0000.0000.0000.000
157A162LEU0-0.009-0.0029.5380.0870.0870.0000.0000.0000.000
158A163THR0-0.020-0.00213.2700.1490.1490.0000.0000.0000.000
159A164GLN0-0.038-0.00316.5230.0380.0380.0000.0000.0000.000
160A165ALA00.012-0.00511.6440.0790.0790.0000.0000.0000.000
161A166TRP0-0.007-0.02813.0620.1530.1530.0000.0000.0000.000
162A167ALA0-0.001-0.00114.9660.0760.0760.0000.0000.0000.000
163A168VAL00.0150.01013.9680.0400.0400.0000.0000.0000.000
164A169ALA0-0.012-0.00413.1270.0830.0830.0000.0000.0000.000
165A170MET0-0.035-0.00114.7560.0330.0330.0000.0000.0000.000
166A171ALA0-0.089-0.03418.4260.0040.0040.0000.0000.0000.000
167A172LEU0-0.070-0.04514.270-0.006-0.0060.0000.0000.0000.000
168A173GLY00.0130.03317.8280.0390.0390.0000.0000.0000.000
169A174VAL0-0.082-0.05312.6320.0840.0840.0000.0000.0000.000
170A175GLU-1-0.822-0.93112.8310.6010.6010.0000.0000.0000.000
171A176ASP-1-0.906-0.95313.3210.6450.6450.0000.0000.0000.000
172A177LYS10.8840.95410.449-1.088-1.0880.0000.0000.0000.000
173A178VAL00.013-0.0088.2280.5330.5330.0000.0000.0000.000
174A179THR00.016-0.0048.808-0.259-0.2590.0000.0000.0000.000
175A180VAL00.0680.0388.332-0.216-0.2160.0000.0000.0000.000
176A181PRO00.0010.0144.949-0.385-0.3850.0000.0000.0000.000
177A182LEU0-0.016-0.0024.709-1.594-1.516-0.001-0.004-0.0720.000
178A183PHE00.0190.0036.886-0.603-0.6030.0000.0000.0000.000
179A184GLU-1-0.979-0.9805.9170.1020.1020.0000.0000.0000.000
180A185GLY00.0120.0024.116-0.431-0.421-0.001-0.0410.0310.000
181A186VAL00.0030.0044.734-0.054-0.034-0.001-0.009-0.0100.000
182A187GLN0-0.035-0.0348.3140.2590.2590.0000.0000.0000.000
183A188LYS10.9340.9674.4110.5310.663-0.001-0.009-0.1220.000
184A189THR0-0.063-0.0228.4790.2450.2450.0000.0000.0000.000
185A189LEU0-0.070-0.0089.6480.1710.1710.0000.0000.0000.000