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: 7244K

Calculation Name: 2OQJ-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OQJ

Chain ID: E

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2135796.996776
FMO2-HF: Nuclear repulsion 2051898.983619
FMO2-HF: Total energy -83898.013158
FMO2-MP2: Total energy -84141.986344


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(E:1:GLU)


Summations of interaction energy for fragment #1(E:1:GLU)
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.
-26.799-26.8711.805-5.16-6.5740.042
Interaction energy analysis for fragmet #1(E:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.889 / q_NPA : -0.952
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].
3E3GLN0-0.029-0.0051.823-24.125-25.23310.679-4.474-5.0970.038
4E4LEU00.000-0.0175.565-4.632-4.6320.0000.0000.0000.000
5E5VAL0-0.006-0.0079.3461.3471.3470.0000.0000.0000.000
6E6GLU-1-0.748-0.86812.01320.96220.9620.0000.0000.0000.000
7E7SER0-0.052-0.02615.781-0.204-0.2040.0000.0000.0000.000
8E8GLY00.0440.01318.776-0.320-0.3200.0000.0000.0000.000
9E9GLY00.0190.01521.499-0.579-0.5790.0000.0000.0000.000
10E10GLY0-0.005-0.01023.064-0.120-0.1200.0000.0000.0000.000
11E11LEU0-0.036-0.01326.232-0.106-0.1060.0000.0000.0000.000
12E12VAL00.0110.01129.322-0.127-0.1270.0000.0000.0000.000
13E13LYS10.8360.93132.019-8.582-8.5820.0000.0000.0000.000
14E14ALA00.0350.01535.5970.0640.0640.0000.0000.0000.000
15E15GLY0-0.042-0.02936.621-0.261-0.2610.0000.0000.0000.000
16E16GLY0-0.029-0.00935.509-0.092-0.0920.0000.0000.0000.000
17E17SER0-0.024-0.04532.100-0.035-0.0350.0000.0000.0000.000
18E18LEU0-0.0170.00025.753-0.108-0.1080.0000.0000.0000.000
19E19ILE0-0.020-0.01824.929-0.140-0.1400.0000.0000.0000.000
20E20LEU0-0.0170.01420.8800.2070.2070.0000.0000.0000.000
21E21SER0-0.013-0.01419.626-0.151-0.1510.0000.0000.0000.000
22E22CYS0-0.044-0.02313.879-0.108-0.1080.0000.0000.0000.000
23E23GLY00.0620.05913.713-1.165-1.1650.0000.0000.0000.000
24E24VAL0-0.021-0.0219.3041.2831.2830.0000.0000.0000.000
25E25SER00.0230.0115.792-1.868-1.8680.0000.0000.0000.000
26E26ASN0-0.031-0.0332.717-7.199-6.1621.126-0.686-1.4770.004
27E27PHE0-0.015-0.0125.546-1.065-1.0650.0000.0000.0000.000
28E28ARG10.8280.8938.196-19.227-19.2270.0000.0000.0000.000
29E29ILE00.021-0.00812.054-0.067-0.0670.0000.0000.0000.000
30E30SER0-0.007-0.00314.028-0.386-0.3860.0000.0000.0000.000
31E31ALA0-0.053-0.00613.697-0.956-0.9560.0000.0000.0000.000
32E32HIS0-0.029-0.02011.5540.8740.8740.0000.0000.0000.000
33E33THR00.0050.00715.951-0.820-0.8200.0000.0000.0000.000
34E34MET0-0.0230.00712.5181.0681.0680.0000.0000.0000.000
35E35ASN0-0.030-0.03415.923-2.005-2.0050.0000.0000.0000.000
36E36TRP0-0.0090.00216.9260.9830.9830.0000.0000.0000.000
37E37VAL0-0.007-0.00517.713-0.841-0.8410.0000.0000.0000.000
38E38ARG10.7820.87919.550-11.176-11.1760.0000.0000.0000.000
39E39ARG10.8870.94519.736-15.165-15.1650.0000.0000.0000.000
40E40VAL00.0410.03122.346-0.018-0.0180.0000.0000.0000.000
41E41PRO00.007-0.01825.8340.1910.1910.0000.0000.0000.000
42E42GLY0-0.0070.01227.779-0.090-0.0900.0000.0000.0000.000
43E43GLY0-0.0010.01024.769-0.095-0.0950.0000.0000.0000.000
44E44GLY00.0120.01223.5830.6380.6380.0000.0000.0000.000
45E45LEU0-0.015-0.01718.4880.2270.2270.0000.0000.0000.000
46E46GLU-1-0.816-0.89522.52710.89810.8980.0000.0000.0000.000
47E47TRP0-0.002-0.00420.7590.3030.3030.0000.0000.0000.000
48E48VAL0-0.032-0.01322.261-0.593-0.5930.0000.0000.0000.000
49E49ALA00.022-0.00622.390-0.637-0.6370.0000.0000.0000.000
50E50SER0-0.0260.00521.0430.6520.6520.0000.0000.0000.000
51E51ILE00.0110.00019.311-0.707-0.7070.0000.0000.0000.000
52E52SER00.0480.01520.5200.5440.5440.0000.0000.0000.000
53E52THR00.0670.03218.8710.1440.1440.0000.0000.0000.000
54E53SER00.0240.00821.283-0.529-0.5290.0000.0000.0000.000
55E54SER0-0.037-0.02123.241-0.417-0.4170.0000.0000.0000.000
56E55THR0-0.044-0.01225.045-0.422-0.4220.0000.0000.0000.000
57E56TYR0-0.023-0.02826.188-0.526-0.5260.0000.0000.0000.000
58E57ARG10.8740.92825.434-10.722-10.7220.0000.0000.0000.000
59E58ASP-1-0.803-0.86225.61310.01810.0180.0000.0000.0000.000
60E59TYR0-0.009-0.01725.7260.5930.5930.0000.0000.0000.000
61E60ALA00.0680.05326.847-0.383-0.3830.0000.0000.0000.000
62E61ASP-1-0.812-0.91428.5209.3079.3070.0000.0000.0000.000
63E62ALA0-0.030-0.00430.522-0.238-0.2380.0000.0000.0000.000
64E63VAL0-0.022-0.01627.269-0.131-0.1310.0000.0000.0000.000
65E64LYS10.8520.92430.762-9.703-9.7030.0000.0000.0000.000
66E65GLY00.0110.01331.968-0.289-0.2890.0000.0000.0000.000
67E66ARG10.6590.81231.541-9.883-9.8830.0000.0000.0000.000
68E67PHE00.0340.00726.3580.0800.0800.0000.0000.0000.000
69E68THR0-0.050-0.03528.023-0.357-0.3570.0000.0000.0000.000
70E69VAL00.0030.02722.2950.2440.2440.0000.0000.0000.000
71E70SER0-0.043-0.03623.146-0.687-0.6870.0000.0000.0000.000
72E71ARG10.7310.84717.492-14.641-14.6410.0000.0000.0000.000
73E72ASP-1-0.837-0.91119.44413.28613.2860.0000.0000.0000.000
74E73ASP-1-0.822-0.91718.31215.43315.4330.0000.0000.0000.000
75E74LEU0-0.055-0.01718.5370.1530.1530.0000.0000.0000.000
76E75GLU-1-0.911-0.95617.61015.94015.9400.0000.0000.0000.000
77E76ASP-1-0.800-0.85513.29820.67920.6790.0000.0000.0000.000
78E77PHE00.0150.01214.5981.0781.0780.0000.0000.0000.000
79E78VAL0-0.028-0.02516.202-0.721-0.7210.0000.0000.0000.000
80E79TYR00.012-0.00818.5430.2520.2520.0000.0000.0000.000
81E80LEU0-0.011-0.01121.561-0.283-0.2830.0000.0000.0000.000
82E81GLN00.0410.03323.709-0.309-0.3090.0000.0000.0000.000
83E82MET0-0.0160.00025.2630.0100.0100.0000.0000.0000.000
84E82HIS00.0710.02328.989-0.296-0.2960.0000.0000.0000.000
85E82LYS10.9150.96032.824-8.028-8.0280.0000.0000.0000.000
86E82MET0-0.0090.01728.020-0.027-0.0270.0000.0000.0000.000
87E83ARG10.9000.93632.854-9.241-9.2410.0000.0000.0000.000
88E84VAL00.0470.02032.7550.2580.2580.0000.0000.0000.000
89E85GLU-1-0.821-0.90731.8709.4359.4350.0000.0000.0000.000
90E86ASP-1-0.763-0.84528.97410.47110.4710.0000.0000.0000.000
91E87THR0-0.025-0.00527.6710.4750.4750.0000.0000.0000.000
92E88ALA0-0.010-0.00724.006-0.121-0.1210.0000.0000.0000.000
93E89ILE0-0.0170.01018.469-0.052-0.0520.0000.0000.0000.000
94E90TYR0-0.007-0.03420.106-0.244-0.2440.0000.0000.0000.000
95E91TYR00.0070.00014.602-0.111-0.1110.0000.0000.0000.000
96E93ALA00.0460.01412.1921.6521.6520.0000.0000.0000.000
97E94ARG10.8400.8957.979-28.300-28.3000.0000.0000.0000.000
98E95LYS10.8080.88912.903-14.506-14.5060.0000.0000.0000.000
99E96GLY00.007-0.00811.954-0.068-0.0680.0000.0000.0000.000
100E97SER0-0.036-0.04211.159-0.055-0.0550.0000.0000.0000.000
101E98ASP-1-0.882-0.9409.03225.57825.5780.0000.0000.0000.000
102E99ARG10.8380.91010.435-16.484-16.4840.0000.0000.0000.000
103E100LEU0-0.0020.01111.762-0.736-0.7360.0000.0000.0000.000
104E100SER0-0.029-0.03214.915-1.023-1.0230.0000.0000.0000.000
105E100ASP-1-0.903-0.95318.49712.49212.4920.0000.0000.0000.000
106E100ASN0-0.055-0.03820.4530.0560.0560.0000.0000.0000.000
107E100ASP-1-0.741-0.79715.10017.23217.2320.0000.0000.0000.000
108E100PRO00.0000.01214.095-0.675-0.6750.0000.0000.0000.000
109E100PHE0-0.017-0.01813.608-0.125-0.1250.0000.0000.0000.000
110E101ASP-1-0.774-0.8499.08526.03326.0330.0000.0000.0000.000
111E102ALA0-0.0030.0096.8302.4162.4160.0000.0000.0000.000
112E103TRP0-0.023-0.0438.348-3.888-3.8880.0000.0000.0000.000
113E104GLY00.0450.0428.8183.2513.2510.0000.0000.0000.000
114E105PRO0-0.043-0.0269.971-0.928-0.9280.0000.0000.0000.000
115E106GLY00.006-0.00212.149-1.514-1.5140.0000.0000.0000.000
116E107THR0-0.055-0.03115.718-0.368-0.3680.0000.0000.0000.000
117E108VAL00.0070.00218.828-0.486-0.4860.0000.0000.0000.000
118E109VAL00.0070.00922.195-0.268-0.2680.0000.0000.0000.000
119E110THR0-0.019-0.01325.453-0.087-0.0870.0000.0000.0000.000
120E111VAL00.0060.00728.895-0.180-0.1800.0000.0000.0000.000
121E112SER00.0210.00132.119-0.248-0.2480.0000.0000.0000.000
122E113PRO00.043-0.00535.226-0.101-0.1010.0000.0000.0000.000
123E114ALA0-0.0280.00538.301-0.207-0.2070.0000.0000.0000.000
124E115SER00.0090.00839.5410.0730.0730.0000.0000.0000.000
125E116THR0-0.063-0.06040.500-0.043-0.0430.0000.0000.0000.000
126E117LYS10.8580.91043.598-6.967-6.9670.0000.0000.0000.000
127E118GLY00.0540.03845.408-0.026-0.0260.0000.0000.0000.000
128E119PRO0-0.033-0.01748.5290.0920.0920.0000.0000.0000.000
129E120SER0-0.040-0.00550.256-0.028-0.0280.0000.0000.0000.000
130E121VAL00.0120.00051.9400.0460.0460.0000.0000.0000.000
131E122PHE0-0.001-0.00651.369-0.080-0.0800.0000.0000.0000.000
132E123PRO0-0.0030.00856.6790.0070.0070.0000.0000.0000.000
133E124LEU0-0.029-0.01356.5220.0240.0240.0000.0000.0000.000
134E125ALA00.013-0.00460.502-0.074-0.0740.0000.0000.0000.000
135E126PRO00.0290.03363.9810.0280.0280.0000.0000.0000.000
136E127SER0-0.006-0.01965.606-0.024-0.0240.0000.0000.0000.000
137E128SER0-0.005-0.00467.945-0.026-0.0260.0000.0000.0000.000
138E129LYS10.9630.99271.087-4.445-4.4450.0000.0000.0000.000
139E130SER00.027-0.00869.2340.0570.0570.0000.0000.0000.000
140E133THR00.0080.02570.548-0.045-0.0450.0000.0000.0000.000
141E134SER0-0.001-0.00472.480-0.054-0.0540.0000.0000.0000.000
142E135GLY00.004-0.00175.0780.0510.0510.0000.0000.0000.000
143E136GLY00.0030.01475.687-0.046-0.0460.0000.0000.0000.000
144E137THR0-0.037-0.02069.909-0.034-0.0340.0000.0000.0000.000
145E138ALA00.0120.01669.2650.0290.0290.0000.0000.0000.000
146E139ALA00.013-0.00464.3860.0040.0040.0000.0000.0000.000
147E140LEU0-0.0220.00764.084-0.003-0.0030.0000.0000.0000.000
148E141GLY00.0490.00360.6860.0180.0180.0000.0000.0000.000
149E142CYS0-0.0660.00557.897-0.041-0.0410.0000.0000.0000.000
150E143LEU00.0420.03651.5450.0500.0500.0000.0000.0000.000
151E144VAL00.000-0.00351.148-0.038-0.0380.0000.0000.0000.000
152E145LYS10.8480.91445.995-6.853-6.8530.0000.0000.0000.000
153E146ASP-1-0.789-0.87244.9377.0467.0460.0000.0000.0000.000
154E147TYR0-0.014-0.01445.777-0.008-0.0080.0000.0000.0000.000
155E148PHE00.0320.00638.6900.1760.1760.0000.0000.0000.000
156E149PRO00.0290.02942.278-0.053-0.0530.0000.0000.0000.000
157E150GLU-1-0.759-0.87143.8226.6296.6290.0000.0000.0000.000
158E151PRO0-0.016-0.00346.4720.0450.0450.0000.0000.0000.000
159E152VAL0-0.016-0.02649.434-0.039-0.0390.0000.0000.0000.000
160E153THR0-0.044-0.01352.149-0.061-0.0610.0000.0000.0000.000
161E154VAL0-0.003-0.02155.7690.0190.0190.0000.0000.0000.000
162E156SER0-0.0150.00358.392-0.019-0.0190.0000.0000.0000.000
163E157TRP00.0280.00961.2900.0130.0130.0000.0000.0000.000
164E162ASN00.0240.00365.1050.0090.0090.0000.0000.0000.000
165E163SER0-0.011-0.01466.224-0.069-0.0690.0000.0000.0000.000
166E164GLY0-0.0040.00366.3020.0030.0030.0000.0000.0000.000
167E165ALA0-0.035-0.00767.159-0.024-0.0240.0000.0000.0000.000
168E166LEU0-0.037-0.00967.724-0.058-0.0580.0000.0000.0000.000
169E167THR00.024-0.00166.3240.0650.0650.0000.0000.0000.000
170E168SER00.0270.00566.5760.0730.0730.0000.0000.0000.000
171E169GLY00.0490.02167.038-0.008-0.0080.0000.0000.0000.000
172E171VAL0-0.048-0.01462.0050.0520.0520.0000.0000.0000.000
173E172HIS00.0010.00959.5290.0810.0810.0000.0000.0000.000
174E173THR0-0.008-0.01355.263-0.004-0.0040.0000.0000.0000.000
175E174PHE0-0.0090.00752.7780.0100.0100.0000.0000.0000.000
176E175PRO00.0250.00049.4920.0270.0270.0000.0000.0000.000
177E176ALA0-0.0180.01146.8310.0030.0030.0000.0000.0000.000
178E177VAL00.006-0.00144.4850.0940.0940.0000.0000.0000.000
179E178LEU0-0.040-0.01837.925-0.032-0.0320.0000.0000.0000.000
180E179GLN0-0.017-0.02141.190-0.035-0.0350.0000.0000.0000.000
181E180SER00.0420.01036.9170.0780.0780.0000.0000.0000.000
182E182SER00.0030.00636.4390.2410.2410.0000.0000.0000.000
183E183GLY00.0490.03337.0190.1270.1270.0000.0000.0000.000
184E184LEU0-0.084-0.04537.849-0.057-0.0570.0000.0000.0000.000
185E185TYR00.0290.01941.6010.0590.0590.0000.0000.0000.000
186E186SER0-0.074-0.05344.624-0.087-0.0870.0000.0000.0000.000
187E187LEU00.0560.03647.8540.0470.0470.0000.0000.0000.000
188E188SER00.0380.01351.063-0.020-0.0200.0000.0000.0000.000
189E189SER0-0.017-0.00654.691-0.040-0.0400.0000.0000.0000.000
190E190VAL00.015-0.01158.071-0.011-0.0110.0000.0000.0000.000
191E191VAL00.0180.01261.162-0.014-0.0140.0000.0000.0000.000
192E192THR0-0.016-0.00264.834-0.004-0.0040.0000.0000.0000.000
193E193VAL00.0110.00367.456-0.037-0.0370.0000.0000.0000.000
194E194PRO00.0680.03770.8820.0120.0120.0000.0000.0000.000
195E195SER00.005-0.00773.4210.0170.0170.0000.0000.0000.000
196E196SER00.0160.00574.4190.0220.0220.0000.0000.0000.000
197E197SER0-0.019-0.01373.941-0.004-0.0040.0000.0000.0000.000
198E198LEU0-0.001-0.00770.3030.0170.0170.0000.0000.0000.000
199E199GLY0-0.030-0.00173.7630.0250.0250.0000.0000.0000.000
200E200THR0-0.040-0.02576.278-0.051-0.0510.0000.0000.0000.000
201E203GLN0-0.063-0.02672.729-0.051-0.0510.0000.0000.0000.000
202E205THR00.0000.01170.9790.0640.0640.0000.0000.0000.000
203E206TYR00.0220.00267.394-0.007-0.0070.0000.0000.0000.000
204E207ILE00.008-0.01064.7290.0440.0440.0000.0000.0000.000
205E209ASN00.0450.00361.475-0.017-0.0170.0000.0000.0000.000
206E210VAL00.0020.00954.7540.0450.0450.0000.0000.0000.000
207E211ASN00.006-0.01456.194-0.015-0.0150.0000.0000.0000.000
208E212HIS00.0210.03147.128-0.068-0.0680.0000.0000.0000.000
209E213LYS10.9970.98751.780-5.879-5.8790.0000.0000.0000.000
210E214PRO00.0200.01746.642-0.029-0.0290.0000.0000.0000.000
211E215SER00.0180.01447.5890.0790.0790.0000.0000.0000.000
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