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: RY1G8

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2021679.976837
FMO2-HF: Nuclear repulsion 1948143.97279
FMO2-HF: Total energy -73536.004046
FMO2-MP2: Total energy -73748.819759


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.
-19.157-20.52914.582-5.149-8.0610.028
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 : 0.027 / 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].
3A3ILE0-0.0250.0053.865-2.866-1.512-0.001-0.580-0.7730.002
4A4ARG10.8400.9235.9512.9232.9230.0000.0000.0000.000
5A5SER0-0.043-0.0417.9750.8350.8350.0000.0000.0000.000
6A6ALA00.0950.0317.952-0.733-0.7330.0000.0000.0000.000
7A7SER0-0.022-0.0138.0820.0670.0670.0000.0000.0000.000
8A8ASP-1-0.702-0.8214.158-4.609-4.467-0.001-0.010-0.1310.000
9A9ILE0-0.021-0.0073.440-4.485-3.8400.029-0.306-0.368-0.002
10A10ARG10.8420.8975.8471.5201.5200.0000.0000.0000.000
11A11ASP-1-0.894-0.9572.989-2.820-2.1930.069-0.212-0.485-0.002
12A12VAL0-0.044-0.0172.2902.6612.5544.499-1.134-3.259-0.003
13A13PHE00.012-0.0093.6492.0732.2280.0360.019-0.2100.001
14A14ILE0-0.026-0.0045.9990.6040.6040.0000.0000.0000.000
15A15ASN0-0.052-0.0371.821-9.580-14.1229.956-2.853-2.5610.032
16A16ALA00.0020.0265.444-0.499-0.478-0.0010.000-0.0200.000
17A17GLY0-0.020-0.0158.010-0.535-0.5350.0000.0000.0000.000
18A18ILE0-0.089-0.0419.977-0.285-0.2850.0000.0000.0000.000
19A19LYS10.8490.90010.160-0.382-0.3820.0000.0000.0000.000
20A20GLY00.0500.01510.888-0.153-0.1530.0000.0000.0000.000
21A21GLU-1-0.900-0.94311.696-0.237-0.2370.0000.0000.0000.000
22A22GLU-1-0.803-0.88514.2360.2180.2180.0000.0000.0000.000
23A23TYR00.0300.01310.064-0.154-0.1540.0000.0000.0000.000
24A24ASP-1-0.772-0.86612.892-0.819-0.8190.0000.0000.0000.000
25A25ALA00.0010.00514.899-0.008-0.0080.0000.0000.0000.000
26A26ALA00.0070.00715.6270.0030.0030.0000.0000.0000.000
27A27TRP00.0150.01112.516-0.039-0.0390.0000.0000.0000.000
28A28ASN0-0.056-0.03816.446-0.025-0.0250.0000.0000.0000.000
29A29SER0-0.035-0.01319.8350.0610.0610.0000.0000.0000.000
30A30PHE0-0.002-0.01921.919-0.029-0.0290.0000.0000.0000.000
31A31VAL00.0340.01622.281-0.010-0.0100.0000.0000.0000.000
32A32VAL00.0520.03417.544-0.009-0.0090.0000.0000.0000.000
33A33LYS10.9560.97720.5890.3510.3510.0000.0000.0000.000
34A34SER0-0.016-0.01422.9910.0060.0060.0000.0000.0000.000
35A35LEU00.0090.00620.6080.0070.0070.0000.0000.0000.000
36A36VAL0-0.031-0.00118.926-0.018-0.0180.0000.0000.0000.000
37A37ALA0-0.0010.00921.5610.0030.0030.0000.0000.0000.000
38A38GLN00.008-0.00425.1920.0180.0180.0000.0000.0000.000
39A39GLN00.009-0.00918.567-0.017-0.0170.0000.0000.0000.000
40A40GLU-1-0.876-0.92323.522-0.450-0.4500.0000.0000.0000.000
41A41LYS10.8000.88225.2130.2670.2670.0000.0000.0000.000
42A42ALA00.0230.01226.4880.0200.0200.0000.0000.0000.000
43A43ALA00.0110.00325.1160.0160.0160.0000.0000.0000.000
44A44ALA0-0.011-0.00827.2700.0170.0170.0000.0000.0000.000
45A45ASP-1-0.835-0.89030.335-0.224-0.2240.0000.0000.0000.000
46A46VAL0-0.050-0.02028.7200.0180.0180.0000.0000.0000.000
47A47GLN0-0.099-0.05131.8720.0090.0090.0000.0000.0000.000
48A48LEU0-0.020-0.00524.2900.0030.0030.0000.0000.0000.000
49A49ARG10.9540.97028.0620.2200.2200.0000.0000.0000.000
50A50GLY0-0.024-0.00425.056-0.006-0.0060.0000.0000.0000.000
51A51VAL0-0.0340.00119.9130.0050.0050.0000.0000.0000.000
52A52PRO00.022-0.01020.586-0.016-0.0160.0000.0000.0000.000
53A53ALA0-0.033-0.00922.1720.0350.0350.0000.0000.0000.000
54A54MET0-0.0100.00224.237-0.010-0.0100.0000.0000.0000.000
55A55PHE00.0270.01126.7720.0150.0150.0000.0000.0000.000
56A56VAL00.0290.01329.239-0.003-0.0030.0000.0000.0000.000
57A57ASN00.027-0.00231.9670.0030.0030.0000.0000.0000.000
58A58GLY00.0060.01932.7720.0050.0050.0000.0000.0000.000
59A59LYS10.8480.93834.1160.1260.1260.0000.0000.0000.000
60A60TYR00.0310.01834.6120.0040.0040.0000.0000.0000.000
61A61GLN0-0.0010.00630.511-0.014-0.0140.0000.0000.0000.000
62A62LEU00.000-0.00829.1560.0150.0150.0000.0000.0000.000
63A63ASN0-0.066-0.04130.763-0.027-0.0270.0000.0000.0000.000
64A64PRO00.0490.00627.7960.0140.0140.0000.0000.0000.000
65A65GLN0-0.015-0.01829.9830.0140.0140.0000.0000.0000.000
66A66GLY0-0.0120.00833.1180.0090.0090.0000.0000.0000.000
67A67MET0-0.073-0.00730.6140.0070.0070.0000.0000.0000.000
68A68ASP-1-0.855-0.91534.620-0.068-0.0680.0000.0000.0000.000
69A69THR00.002-0.01030.798-0.004-0.0040.0000.0000.0000.000
70A70SER0-0.073-0.05032.8420.0010.0010.0000.0000.0000.000
71A71ASN0-0.044-0.02232.0120.0080.0080.0000.0000.0000.000
72A72MET00.0580.02824.923-0.015-0.0150.0000.0000.0000.000
73A73ASP-1-0.870-0.93028.564-0.031-0.0310.0000.0000.0000.000
74A74VAL0-0.029-0.02129.789-0.003-0.0030.0000.0000.0000.000
75A75PHE00.0150.02025.961-0.007-0.0070.0000.0000.0000.000
76A76VAL0-0.012-0.01025.123-0.009-0.0090.0000.0000.0000.000
77A77GLN0-0.007-0.00727.743-0.002-0.0020.0000.0000.0000.000
78A78GLN00.0600.03330.612-0.006-0.0060.0000.0000.0000.000
79A79TYR00.0630.02026.157-0.008-0.0080.0000.0000.0000.000
80A80ALA0-0.005-0.00827.671-0.005-0.0050.0000.0000.0000.000
81A81ASP-1-0.842-0.88929.316-0.049-0.0490.0000.0000.0000.000
82A82THR0-0.047-0.03332.3590.0030.0030.0000.0000.0000.000
83A83VAL0-0.020-0.02328.015-0.004-0.0040.0000.0000.0000.000
84A84LYS10.7900.89231.2750.0510.0510.0000.0000.0000.000
85A85TYR00.003-0.00533.3450.0030.0030.0000.0000.0000.000
86A86LEU0-0.034-0.01933.2910.0010.0010.0000.0000.0000.000
87A87SER0-0.060-0.04033.076-0.008-0.0080.0000.0000.0000.000
88A88GLU-1-0.839-0.88435.234-0.048-0.0480.0000.0000.0000.000
89A93TYR0-0.053-0.05336.9110.0000.0000.0000.0000.0000.000
90A94GLU-1-0.807-0.88040.107-0.076-0.0760.0000.0000.0000.000
91A95ASP-1-0.774-0.86739.681-0.128-0.1280.0000.0000.0000.000
92A96GLY0-0.015-0.00939.2310.0050.0050.0000.0000.0000.000
93A97LYS10.7770.88438.4590.0800.0800.0000.0000.0000.000
94A98GLN00.0860.05234.750-0.011-0.0110.0000.0000.0000.000
95A99TYR0-0.043-0.03933.714-0.013-0.0130.0000.0000.0000.000
96A100THR0-0.032-0.00834.9350.0040.0040.0000.0000.0000.000
97A101THR0-0.018-0.04436.302-0.006-0.0060.0000.0000.0000.000
98A102LEU0-0.045-0.01133.474-0.003-0.0030.0000.0000.0000.000
99A103GLU-1-0.883-0.95937.894-0.124-0.1240.0000.0000.0000.000
100A104LYS10.8680.93339.2200.1470.1470.0000.0000.0000.000
101A105PRO0-0.021-0.01037.621-0.009-0.0090.0000.0000.0000.000
102A106VAL00.0340.02832.3020.0020.0020.0000.0000.0000.000
103A107ALA0-0.015-0.01835.0520.0020.0020.0000.0000.0000.000
104A108GLY00.000-0.00134.852-0.005-0.0050.0000.0000.0000.000
105A109ALA0-0.0250.00030.951-0.010-0.0100.0000.0000.0000.000
106A110PRO0-0.026-0.02126.8970.0150.0150.0000.0000.0000.000
107A111GLN00.0180.01629.820-0.007-0.0070.0000.0000.0000.000
108A112VAL00.0580.02726.5590.0040.0040.0000.0000.0000.000
109A113LEU0-0.060-0.02524.070-0.005-0.0050.0000.0000.0000.000
110A114GLU-1-0.809-0.88919.572-0.400-0.4000.0000.0000.0000.000
111A115PHE00.002-0.00721.679-0.026-0.0260.0000.0000.0000.000
112A116PHE00.035-0.00213.8120.0320.0320.0000.0000.0000.000
113A117SER00.0640.01415.949-0.056-0.0560.0000.0000.0000.000
114A118PHE00.0550.01510.3580.0210.0210.0000.0000.0000.000
115A119PHE00.0300.02111.927-0.114-0.1140.0000.0000.0000.000
116A120CYS0-0.0360.01313.9940.1880.1880.0000.0000.0000.000
117A121PRO00.0450.02415.6230.0080.0080.0000.0000.0000.000
118A122HIS00.0210.00116.6620.0190.0190.0000.0000.0000.000
119A124TYR00.0410.02911.164-0.011-0.0110.0000.0000.0000.000
120A125GLN00.012-0.00414.8380.1080.1080.0000.0000.0000.000
121A126PHE0-0.014-0.01217.9020.0580.0580.0000.0000.0000.000
122A127GLU-1-0.788-0.85114.430-0.325-0.3250.0000.0000.0000.000
123A128GLU-1-0.905-0.96312.571-0.079-0.0790.0000.0000.0000.000
124A129VAL0-0.052-0.02615.8780.0500.0500.0000.0000.0000.000
125A130LEU0-0.022-0.03218.7340.0390.0390.0000.0000.0000.000
126A131HIS0-0.0240.01516.7770.0220.0220.0000.0000.0000.000
127A132ILE00.0000.02420.6880.0270.0270.0000.0000.0000.000
128A133SER0-0.003-0.04818.9830.0260.0260.0000.0000.0000.000
129A134ASP-1-0.797-0.90619.7960.0030.0030.0000.0000.0000.000
130A135ASN0-0.037-0.02721.8190.0440.0440.0000.0000.0000.000
131A136VAL00.0240.00124.4740.0110.0110.0000.0000.0000.000
132A137LYS10.8440.93518.5100.1080.1080.0000.0000.0000.000
133A138LYS10.8350.91421.9610.0010.0010.0000.0000.0000.000
134A139LYS10.7860.89327.5790.0610.0610.0000.0000.0000.000
135A140LEU0-0.051-0.01627.612-0.001-0.0010.0000.0000.0000.000
136A141PRO0-0.016-0.00330.7150.0110.0110.0000.0000.0000.000
137A142GLU-1-0.853-0.92332.482-0.014-0.0140.0000.0000.0000.000
138A143GLY0-0.045-0.02333.198-0.005-0.0050.0000.0000.0000.000
139A144VAL0-0.056-0.02330.402-0.013-0.0130.0000.0000.0000.000
140A145LYS10.9490.98323.5740.1890.1890.0000.0000.0000.000
141A146MET0-0.0010.00721.741-0.003-0.0030.0000.0000.0000.000
142A147THR0-0.046-0.02522.8210.0050.0050.0000.0000.0000.000
143A148LYS10.8240.88217.3730.4280.4280.0000.0000.0000.000
144A149TYR0-0.010-0.00220.121-0.005-0.0050.0000.0000.0000.000
145A150HIS00.0180.02314.569-0.119-0.1190.0000.0000.0000.000
146A151VAL0-0.040-0.02518.1800.0440.0440.0000.0000.0000.000
147A152ASN0-0.051-0.03618.547-0.069-0.0690.0000.0000.0000.000
148A153PHE0-0.0070.00019.702-0.032-0.0320.0000.0000.0000.000
149A154MET0-0.010-0.00917.7180.0230.0230.0000.0000.0000.000
150A155GLY00.0630.02215.766-0.095-0.0950.0000.0000.0000.000
151A156GLY0-0.0110.00016.022-0.092-0.0920.0000.0000.0000.000
152A157ASP-1-0.839-0.90717.182-0.768-0.7680.0000.0000.0000.000
153A158LEU00.0450.0429.5920.0150.0150.0000.0000.0000.000
154A159GLY00.0300.01413.036-0.147-0.1470.0000.0000.0000.000
155A160LYS10.8100.89015.4470.8290.8290.0000.0000.0000.000
156A161ASP-1-0.856-0.93011.886-1.479-1.4790.0000.0000.0000.000
157A162LEU0-0.004-0.0119.078-0.020-0.0200.0000.0000.0000.000
158A163THR0-0.027-0.01212.4650.1380.1380.0000.0000.0000.000
159A164GLN0-0.030-0.01915.3450.1170.1170.0000.0000.0000.000
160A165ALA00.0100.00510.6630.0950.0950.0000.0000.0000.000
161A166TRP00.001-0.02412.7560.0930.0930.0000.0000.0000.000
162A167ALA0-0.022-0.00914.7760.1310.1310.0000.0000.0000.000
163A168VAL00.007-0.00413.0520.1110.1110.0000.0000.0000.000
164A169ALA0-0.021-0.01313.4830.1120.1120.0000.0000.0000.000
165A170MET0-0.026-0.00414.9800.1230.1230.0000.0000.0000.000
166A171ALA0-0.070-0.03018.3150.0610.0610.0000.0000.0000.000
167A172LEU0-0.067-0.03014.3340.0490.0490.0000.0000.0000.000
168A173GLY0-0.0020.02917.9970.0700.0700.0000.0000.0000.000
169A174VAL0-0.048-0.03013.2220.0840.0840.0000.0000.0000.000
170A175GLU-1-0.825-0.92913.827-0.250-0.2500.0000.0000.0000.000
171A176ASP-1-0.890-0.94313.568-0.161-0.1610.0000.0000.0000.000
172A177LYS10.8180.92711.196-0.570-0.5700.0000.0000.0000.000
173A178VAL00.003-0.0038.9010.1550.1550.0000.0000.0000.000
174A179THR0-0.024-0.0308.765-0.459-0.4590.0000.0000.0000.000
175A180VAL00.0630.0369.271-0.288-0.2880.0000.0000.0000.000
176A181PRO00.0130.0054.772-0.444-0.362-0.001-0.003-0.0780.000
177A182LEU00.0030.0084.803-1.785-1.722-0.001-0.003-0.0580.000
178A183PHE00.0200.0096.916-0.371-0.3710.0000.0000.0000.000
179A184GLU-1-0.877-0.9235.706-0.310-0.3100.0000.0000.0000.000
180A185GLY0-0.0040.0014.137-0.032-0.0190.000-0.0470.0340.000
181A186VAL00.002-0.0054.6720.5420.578-0.001-0.010-0.0250.000
182A187GLN0-0.035-0.0388.3290.6130.6130.0000.0000.0000.000
183A188LYS10.8470.9154.5850.8641.003-0.001-0.010-0.1270.000
184A189THR0-0.043-0.0348.3080.4720.4720.0000.0000.0000.000
185A189LEU0-0.099-0.0369.6070.4140.4140.0000.0000.0000.000