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: ZN25N

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2018645.490447
FMO2-HF: Nuclear repulsion 1945109.793761
FMO2-HF: Total energy -73535.696686
FMO2-MP2: Total energy -73748.469141


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.
-21.498-23.11117.693-6.506-9.5730.038
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 : 0.016 / 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   
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].
3A3ILE0-0.0110.0063.738-4.250-2.5680.019-0.796-0.9050.002
4A4ARG10.8870.9256.1072.9212.9210.0000.0000.0000.000
5A5SER0-0.050-0.0598.0750.8350.8350.0000.0000.0000.000
6A6ALA00.1050.0468.321-0.579-0.5790.0000.0000.0000.000
7A7SER00.008-0.0018.3680.0760.0760.0000.0000.0000.000
8A8ASP-1-0.773-0.8474.436-5.059-4.947-0.001-0.005-0.1060.000
9A9ILE0-0.010-0.0093.869-2.864-2.5890.002-0.096-0.1820.000
10A10ARG10.8110.8806.1671.6951.6950.0000.0000.0000.000
11A11ASP-1-0.898-0.9522.471-4.621-3.7630.396-0.444-0.811-0.003
12A12VAL0-0.042-0.0152.4001.8362.5994.305-1.359-3.7090.001
13A13PHE00.024-0.0053.4402.6142.5790.0670.249-0.2810.001
14A14ILE0-0.011-0.0085.8410.6890.6890.0000.0000.0000.000
15A15ASN0-0.105-0.0621.779-10.163-15.78112.911-3.993-3.2990.037
16A16ALA0-0.0110.0085.046-0.366-0.312-0.001-0.001-0.0510.000
17A17GLY0-0.057-0.0277.446-0.625-0.6250.0000.0000.0000.000
18A18ILE0-0.085-0.0229.682-0.340-0.3400.0000.0000.0000.000
19A19LYS10.9130.9369.937-0.389-0.3890.0000.0000.0000.000
20A20GLY00.0500.00510.933-0.139-0.1390.0000.0000.0000.000
21A21GLU-1-0.914-0.94511.669-0.238-0.2380.0000.0000.0000.000
22A22GLU-1-0.828-0.91314.4420.3060.3060.0000.0000.0000.000
23A23TYR00.0160.01110.275-0.107-0.1070.0000.0000.0000.000
24A24ASP-1-0.762-0.85513.086-0.787-0.7870.0000.0000.0000.000
25A25ALA0-0.0090.00515.109-0.011-0.0110.0000.0000.0000.000
26A26ALA00.002-0.00116.0030.0010.0010.0000.0000.0000.000
27A27TRP00.0030.00712.787-0.040-0.0400.0000.0000.0000.000
28A28ASN0-0.058-0.04616.537-0.031-0.0310.0000.0000.0000.000
29A29SER0-0.039-0.01119.8830.0540.0540.0000.0000.0000.000
30A30PHE00.001-0.01621.980-0.026-0.0260.0000.0000.0000.000
31A31VAL00.0500.00922.670-0.013-0.0130.0000.0000.0000.000
32A32VAL00.0430.04117.839-0.001-0.0010.0000.0000.0000.000
33A33LYS10.9720.98620.9400.3020.3020.0000.0000.0000.000
34A34SER0-0.072-0.03323.1800.0000.0000.0000.0000.0000.000
35A35LEU00.0520.01420.8150.0030.0030.0000.0000.0000.000
36A36VAL0-0.033-0.00419.398-0.010-0.0100.0000.0000.0000.000
37A37ALA0-0.0090.00722.026-0.003-0.0030.0000.0000.0000.000
38A38GLN00.0150.00125.6840.0110.0110.0000.0000.0000.000
39A39GLN00.007-0.00418.9740.0000.0000.0000.0000.0000.000
40A40GLU-1-0.895-0.93424.054-0.397-0.3970.0000.0000.0000.000
41A41LYS10.8010.88025.5700.2090.2090.0000.0000.0000.000
42A42ALA00.0220.01326.7600.0160.0160.0000.0000.0000.000
43A43ALA00.0020.00625.4450.0130.0130.0000.0000.0000.000
44A44ALA0-0.004-0.00827.5860.0140.0140.0000.0000.0000.000
45A45ASP-1-0.837-0.90130.598-0.178-0.1780.0000.0000.0000.000
46A46VAL0-0.045-0.01229.3460.0160.0160.0000.0000.0000.000
47A47GLN0-0.097-0.03932.2180.0050.0050.0000.0000.0000.000
48A48LEU0-0.0110.00124.5670.0030.0030.0000.0000.0000.000
49A49ARG10.9510.96928.7130.1910.1910.0000.0000.0000.000
50A50GLY0-0.024-0.01425.040-0.017-0.0170.0000.0000.0000.000
51A51VAL0-0.0520.01520.0550.0150.0150.0000.0000.0000.000
52A52PRO00.049-0.01320.958-0.016-0.0160.0000.0000.0000.000
53A53ALA0-0.040-0.01022.5450.0210.0210.0000.0000.0000.000
54A54MET0-0.0080.01124.531-0.003-0.0030.0000.0000.0000.000
55A55PHE00.0330.01127.0000.0080.0080.0000.0000.0000.000
56A56VAL00.0230.01629.4940.0020.0020.0000.0000.0000.000
57A57ASN00.0330.00232.1370.0020.0020.0000.0000.0000.000
58A58GLY0-0.0080.00532.6160.0020.0020.0000.0000.0000.000
59A59LYS10.8730.96033.9950.0880.0880.0000.0000.0000.000
60A60TYR00.0370.01834.809-0.001-0.0010.0000.0000.0000.000
61A61GLN00.0000.01830.736-0.008-0.0080.0000.0000.0000.000
62A62LEU0-0.005-0.01329.3480.0110.0110.0000.0000.0000.000
63A63ASN0-0.061-0.04230.982-0.025-0.0250.0000.0000.0000.000
64A64PRO00.045-0.00127.9230.0120.0120.0000.0000.0000.000
65A65GLN00.012-0.00330.4820.0130.0130.0000.0000.0000.000
66A66GLY0-0.0310.00133.1290.0060.0060.0000.0000.0000.000
67A67MET0-0.092-0.01930.9410.0090.0090.0000.0000.0000.000
68A68ASP-1-0.853-0.90434.626-0.036-0.0360.0000.0000.0000.000
69A69THR0-0.008-0.01330.7510.0010.0010.0000.0000.0000.000
70A70SER0-0.079-0.05233.0950.0000.0000.0000.0000.0000.000
71A71ASN0-0.036-0.02131.9300.0060.0060.0000.0000.0000.000
72A72MET00.0610.02324.690-0.011-0.0110.0000.0000.0000.000
73A73ASP-1-0.884-0.93928.6290.0240.0240.0000.0000.0000.000
74A74VAL0-0.017-0.02029.9790.0000.0000.0000.0000.0000.000
75A75PHE00.0000.01226.152-0.006-0.0060.0000.0000.0000.000
76A76VAL00.005-0.00225.439-0.009-0.0090.0000.0000.0000.000
77A77GLN0-0.023-0.01128.1260.0000.0000.0000.0000.0000.000
78A78GLN00.0740.03231.046-0.006-0.0060.0000.0000.0000.000
79A79TYR00.0400.00726.658-0.011-0.0110.0000.0000.0000.000
80A80ALA0-0.018-0.02828.012-0.005-0.0050.0000.0000.0000.000
81A81ASP-1-0.848-0.89629.5730.0000.0000.0000.0000.0000.000
82A82THR0-0.043-0.02732.7050.0000.0000.0000.0000.0000.000
83A83VAL0-0.009-0.01028.450-0.004-0.0040.0000.0000.0000.000
84A84LYS10.8150.89831.7520.0030.0030.0000.0000.0000.000
85A85TYR0-0.037-0.02633.7160.0020.0020.0000.0000.0000.000
86A86LEU0-0.011-0.00833.7950.0000.0000.0000.0000.0000.000
87A87SER0-0.080-0.03133.030-0.006-0.0060.0000.0000.0000.000
88A88GLU-1-0.838-0.89035.174-0.001-0.0010.0000.0000.0000.000
89A93TYR0-0.041-0.04537.118-0.001-0.0010.0000.0000.0000.000
90A94GLU-1-0.805-0.87940.398-0.046-0.0460.0000.0000.0000.000
91A95ASP-1-0.817-0.89740.225-0.089-0.0890.0000.0000.0000.000
92A96GLY0-0.025-0.01539.6540.0030.0030.0000.0000.0000.000
93A97LYS10.7980.89239.0560.0470.0470.0000.0000.0000.000
94A98GLN00.0690.04135.038-0.010-0.0100.0000.0000.0000.000
95A99TYR0-0.044-0.02434.124-0.008-0.0080.0000.0000.0000.000
96A100THR0-0.0070.00735.2630.0020.0020.0000.0000.0000.000
97A101THR0-0.011-0.03736.612-0.002-0.0020.0000.0000.0000.000
98A102LEU0-0.029-0.01033.493-0.003-0.0030.0000.0000.0000.000
99A103GLU-1-0.912-0.97437.947-0.098-0.0980.0000.0000.0000.000
100A104LYS10.8870.94239.4360.1210.1210.0000.0000.0000.000
101A105PRO0-0.045-0.02137.787-0.007-0.0070.0000.0000.0000.000
102A106VAL00.0240.02732.8130.0000.0000.0000.0000.0000.000
103A107ALA00.008-0.00435.5580.0050.0050.0000.0000.0000.000
104A108GLY0-0.008-0.01235.056-0.007-0.0070.0000.0000.0000.000
105A109ALA0-0.0210.00731.452-0.008-0.0080.0000.0000.0000.000
106A110PRO0-0.007-0.01427.1680.0140.0140.0000.0000.0000.000
107A111GLN00.0260.00530.026-0.005-0.0050.0000.0000.0000.000
108A112VAL00.0540.02326.8070.0000.0000.0000.0000.0000.000
109A113LEU0-0.060-0.02124.1820.0010.0010.0000.0000.0000.000
110A114GLU-1-0.809-0.88219.756-0.262-0.2620.0000.0000.0000.000
111A115PHE0-0.011-0.01021.819-0.021-0.0210.0000.0000.0000.000
112A116PHE00.035-0.00713.9320.0190.0190.0000.0000.0000.000
113A117SER00.0680.01316.235-0.053-0.0530.0000.0000.0000.000
114A118PHE00.0430.01710.6730.0270.0270.0000.0000.0000.000
115A119PHE00.0370.01912.044-0.136-0.1360.0000.0000.0000.000
116A120CYS0-0.067-0.00414.3490.1550.1550.0000.0000.0000.000
117A121PRO00.0600.02716.0450.0080.0080.0000.0000.0000.000
118A122HIS00.0300.00717.0770.0210.0210.0000.0000.0000.000
119A124TYR00.0550.02911.130-0.014-0.0140.0000.0000.0000.000
120A125GLN00.0190.00415.0760.0980.0980.0000.0000.0000.000
121A126PHE0-0.001-0.01518.0850.0530.0530.0000.0000.0000.000
122A127GLU-1-0.784-0.85614.710-0.123-0.1230.0000.0000.0000.000
123A128GLU-1-0.921-0.97212.5430.1310.1310.0000.0000.0000.000
124A129VAL0-0.052-0.02115.8430.0260.0260.0000.0000.0000.000
125A130LEU0-0.039-0.03418.7400.0320.0320.0000.0000.0000.000
126A131HIS0-0.0150.01816.9900.0130.0130.0000.0000.0000.000
127A132ILE0-0.010-0.00120.8030.0200.0200.0000.0000.0000.000
128A133SER00.001-0.04119.1390.0150.0150.0000.0000.0000.000
129A134ASP-1-0.803-0.90620.3170.1380.1380.0000.0000.0000.000
130A135ASN0-0.032-0.02522.1070.0230.0230.0000.0000.0000.000
131A136VAL00.0060.00324.8570.0050.0050.0000.0000.0000.000
132A137LYS10.8690.94119.008-0.041-0.0410.0000.0000.0000.000
133A138LYS10.8480.92622.034-0.112-0.1120.0000.0000.0000.000
134A139LYS10.8050.91127.617-0.001-0.0010.0000.0000.0000.000
135A140LEU0-0.029-0.00127.579-0.008-0.0080.0000.0000.0000.000
136A141PRO0-0.014-0.00230.6650.0110.0110.0000.0000.0000.000
137A142GLU-1-0.864-0.93832.5710.0520.0520.0000.0000.0000.000
138A143GLY0-0.034-0.01332.764-0.008-0.0080.0000.0000.0000.000
139A144VAL0-0.046-0.01130.401-0.014-0.0140.0000.0000.0000.000
140A145LYS10.9590.98724.7100.0730.0730.0000.0000.0000.000
141A146MET0-0.012-0.00722.775-0.004-0.0040.0000.0000.0000.000
142A147THR0-0.057-0.02922.9580.0100.0100.0000.0000.0000.000
143A148LYS10.8430.89417.4210.2550.2550.0000.0000.0000.000
144A149TYR0-0.014-0.00820.144-0.007-0.0070.0000.0000.0000.000
145A150HIS00.0240.01714.923-0.097-0.0970.0000.0000.0000.000
146A151VAL0-0.033-0.01618.4780.0320.0320.0000.0000.0000.000
147A152ASN0-0.061-0.04018.870-0.060-0.0600.0000.0000.0000.000
148A153PHE00.0000.00020.396-0.024-0.0240.0000.0000.0000.000
149A154MET0-0.017-0.02118.1820.0250.0250.0000.0000.0000.000
150A155GLY00.0560.02316.381-0.070-0.0700.0000.0000.0000.000
151A156GLY0-0.0090.00116.535-0.087-0.0870.0000.0000.0000.000
152A157ASP-1-0.860-0.93517.335-0.784-0.7840.0000.0000.0000.000
153A158LEU00.0350.0359.9170.0260.0260.0000.0000.0000.000
154A159GLY00.0310.01813.489-0.111-0.1110.0000.0000.0000.000
155A160LYS10.8440.91415.8360.7850.7850.0000.0000.0000.000
156A161ASP-1-0.842-0.91912.494-1.309-1.3090.0000.0000.0000.000
157A162LEU0-0.009-0.0049.5440.0050.0050.0000.0000.0000.000
158A163THR0-0.023-0.01313.0100.1410.1410.0000.0000.0000.000
159A164GLN0-0.036-0.02015.8340.1000.1000.0000.0000.0000.000
160A165ALA00.005-0.00311.1000.0940.0940.0000.0000.0000.000
161A166TRP00.003-0.02213.0360.0960.0960.0000.0000.0000.000
162A167ALA00.000-0.00215.0130.1230.1230.0000.0000.0000.000
163A168VAL00.0130.01013.4830.1030.1030.0000.0000.0000.000
164A169ALA0-0.012-0.00213.2900.1120.1120.0000.0000.0000.000
165A170MET0-0.0350.00114.9150.1020.1020.0000.0000.0000.000
166A171ALA0-0.088-0.03418.3240.0520.0520.0000.0000.0000.000
167A172LEU0-0.078-0.04714.2510.0400.0400.0000.0000.0000.000
168A173GLY00.0130.03117.9740.0680.0680.0000.0000.0000.000
169A174VAL0-0.083-0.05413.0790.1010.1010.0000.0000.0000.000
170A175GLU-1-0.806-0.92113.3480.0020.0020.0000.0000.0000.000
171A176ASP-1-0.911-0.95013.5570.1320.1320.0000.0000.0000.000
172A177LYS10.8780.95710.809-0.645-0.6450.0000.0000.0000.000
173A178VAL00.009-0.0038.7190.3380.3380.0000.0000.0000.000
174A179THR00.000-0.0118.825-0.428-0.4280.0000.0000.0000.000
175A180VAL00.0640.0319.201-0.299-0.2990.0000.0000.0000.000
176A181PRO0-0.0020.0034.764-0.534-0.441-0.001-0.003-0.0880.000
177A182LEU0-0.0040.0034.717-1.842-1.778-0.001-0.004-0.0590.000
178A183PHE00.0290.0086.960-0.432-0.4320.0000.0000.0000.000
179A184GLU-1-0.914-0.9525.992-0.215-0.2150.0000.0000.0000.000
180A185GLY00.0060.0034.251-0.158-0.158-0.001-0.0380.0390.000
181A186VAL0-0.004-0.0014.8240.1000.120-0.001-0.008-0.0110.000
182A187GLN0-0.040-0.0428.4500.5060.5060.0000.0000.0000.000
183A188LYS10.8870.9484.7270.7930.912-0.001-0.008-0.1100.000
184A189THR0-0.031-0.0068.5870.4220.4220.0000.0000.0000.000
185A189LEU0-0.117-0.0369.6410.3760.3760.0000.0000.0000.000