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: 94QQ2

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2127732.51603
FMO2-HF: Nuclear repulsion 2043835.21898
FMO2-HF: Total energy -83897.29705
FMO2-MP2: Total energy -84141.105897


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.
-2.984-0.390999999999990.962-0.793-2.762-0.001
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 : -0.928 / q_NPA : -0.984
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].
3E3GLN00.0080.0163.287-4.368-2.5850.012-0.444-1.3510.001
4E4LEU00.006-0.0065.821-4.020-4.0200.0000.0000.0000.000
5E5VAL00.000-0.0089.5541.0741.0740.0000.0000.0000.000
6E6GLU-1-0.760-0.88611.91120.33720.3370.0000.0000.0000.000
7E7SER0-0.039-0.01915.606-0.256-0.2560.0000.0000.0000.000
8E8GLY00.024-0.00418.531-0.261-0.2610.0000.0000.0000.000
9E9GLY0-0.0040.01421.509-0.589-0.5890.0000.0000.0000.000
10E10GLY00.002-0.00223.339-0.194-0.1940.0000.0000.0000.000
11E11LEU0-0.038-0.01826.456-0.061-0.0610.0000.0000.0000.000
12E12VAL00.0130.01929.377-0.191-0.1910.0000.0000.0000.000
13E13LYS10.9120.96732.101-8.530-8.5300.0000.0000.0000.000
14E14ALA00.0560.02735.4110.0910.0910.0000.0000.0000.000
15E15GLY0-0.061-0.03736.508-0.270-0.2700.0000.0000.0000.000
16E16GLY0-0.045-0.01535.104-0.089-0.0890.0000.0000.0000.000
17E17SER0-0.009-0.03731.997-0.018-0.0180.0000.0000.0000.000
18E18LEU0-0.018-0.01025.825-0.082-0.0820.0000.0000.0000.000
19E19ILE0-0.016-0.00624.675-0.007-0.0070.0000.0000.0000.000
20E20LEU0-0.0240.00420.7410.1630.1630.0000.0000.0000.000
21E21SER00.0000.00519.276-0.099-0.0990.0000.0000.0000.000
22E22CYS0-0.052-0.02514.318-0.047-0.0470.0000.0000.0000.000
23E23GLY00.0670.05913.869-0.720-0.7200.0000.0000.0000.000
24E24VAL0-0.027-0.0219.2801.2711.2710.0000.0000.0000.000
25E25SER00.0370.0155.871-2.454-2.4540.0000.0000.0000.000
26E26ASN0-0.054-0.0452.682-4.868-4.0580.950-0.349-1.411-0.002
27E27PHE0-0.006-0.0145.4370.2550.2550.0000.0000.0000.000
28E28ARG10.8530.9168.227-19.045-19.0450.0000.0000.0000.000
29E29ILE00.0520.01512.0130.1240.1240.0000.0000.0000.000
30E30SER0-0.058-0.01814.047-0.303-0.3030.0000.0000.0000.000
31E31ALA0-0.0100.00814.026-0.884-0.8840.0000.0000.0000.000
32E32HIS0-0.043-0.02211.4400.4570.4570.0000.0000.0000.000
33E33THR0-0.015-0.00615.816-0.914-0.9140.0000.0000.0000.000
34E34MET0-0.0270.00012.7531.1531.1530.0000.0000.0000.000
35E35ASN0-0.009-0.02516.216-2.023-2.0230.0000.0000.0000.000
36E36TRP0-0.0120.00917.0941.0431.0430.0000.0000.0000.000
37E37VAL0-0.004-0.00817.908-0.825-0.8250.0000.0000.0000.000
38E38ARG10.8170.90519.632-11.263-11.2630.0000.0000.0000.000
39E39ARG10.8910.94519.375-15.500-15.5000.0000.0000.0000.000
40E40VAL00.0300.02422.027-0.125-0.1250.0000.0000.0000.000
41E41PRO00.012-0.01825.1460.2550.2550.0000.0000.0000.000
42E42GLY0-0.0140.00527.278-0.051-0.0510.0000.0000.0000.000
43E43GLY00.0280.02224.510-0.097-0.0970.0000.0000.0000.000
44E44GLY0-0.0060.00923.1600.6890.6890.0000.0000.0000.000
45E45LEU0-0.003-0.01418.3600.0690.0690.0000.0000.0000.000
46E46GLU-1-0.848-0.91922.45910.90310.9030.0000.0000.0000.000
47E47TRP0-0.0080.00220.7520.3610.3610.0000.0000.0000.000
48E48VAL0-0.023-0.00822.434-0.650-0.6500.0000.0000.0000.000
49E49ALA00.010-0.01422.585-0.669-0.6690.0000.0000.0000.000
50E50SER00.0030.01721.1160.6940.6940.0000.0000.0000.000
51E51ILE0-0.0080.00319.875-0.755-0.7550.0000.0000.0000.000
52E52SER00.0670.03420.6510.5670.5670.0000.0000.0000.000
53E52THR00.0390.01419.116-0.083-0.0830.0000.0000.0000.000
54E53SER00.0610.01421.465-0.491-0.4910.0000.0000.0000.000
55E54SER0-0.058-0.03423.450-0.411-0.4110.0000.0000.0000.000
56E55THR0-0.041-0.00125.327-0.458-0.4580.0000.0000.0000.000
57E56TYR00.006-0.00326.309-0.544-0.5440.0000.0000.0000.000
58E57ARG10.8660.92625.595-10.672-10.6720.0000.0000.0000.000
59E58ASP-1-0.858-0.91625.57610.46910.4690.0000.0000.0000.000
60E59TYR0-0.033-0.02425.7690.5600.5600.0000.0000.0000.000
61E60ALA00.0760.04427.130-0.284-0.2840.0000.0000.0000.000
62E61ASP-1-0.853-0.94528.8169.1369.1360.0000.0000.0000.000
63E62ALA0-0.040-0.01530.965-0.204-0.2040.0000.0000.0000.000
64E63VAL0-0.014-0.00527.574-0.171-0.1710.0000.0000.0000.000
65E64LYS10.9200.97330.993-9.569-9.5690.0000.0000.0000.000
66E65GLY0-0.015-0.00132.529-0.285-0.2850.0000.0000.0000.000
67E66ARG10.6870.83931.910-9.863-9.8630.0000.0000.0000.000
68E67PHE00.0420.00626.4590.0620.0620.0000.0000.0000.000
69E68THR0-0.056-0.03128.208-0.303-0.3030.0000.0000.0000.000
70E69VAL00.0130.03322.0880.2620.2620.0000.0000.0000.000
71E70SER0-0.033-0.02623.547-0.643-0.6430.0000.0000.0000.000
72E71ARG10.7900.89617.457-14.726-14.7260.0000.0000.0000.000
73E72ASP-1-0.875-0.92119.69213.11313.1130.0000.0000.0000.000
74E73ASP-1-0.821-0.94118.12315.28015.2800.0000.0000.0000.000
75E74LEU0-0.064-0.03917.6460.5060.5060.0000.0000.0000.000
76E75GLU-1-0.910-0.95517.50314.97214.9720.0000.0000.0000.000
77E76ASP-1-0.843-0.87713.38919.89419.8940.0000.0000.0000.000
78E77PHE00.0200.01814.7781.0301.0300.0000.0000.0000.000
79E78VAL0-0.037-0.02116.403-0.778-0.7780.0000.0000.0000.000
80E79TYR00.005-0.01618.7590.0760.0760.0000.0000.0000.000
81E80LEU0-0.004-0.01221.949-0.176-0.1760.0000.0000.0000.000
82E81GLN0-0.005-0.00523.984-0.377-0.3770.0000.0000.0000.000
83E82MET00.0050.02025.504-0.080-0.0800.0000.0000.0000.000
84E82HIS00.0740.03729.343-0.355-0.3550.0000.0000.0000.000
85E82LYS10.9290.95833.117-7.984-7.9840.0000.0000.0000.000
86E82MET0-0.0130.01228.505-0.027-0.0270.0000.0000.0000.000
87E83ARG10.9690.99533.222-9.187-9.1870.0000.0000.0000.000
88E84VAL00.0720.02332.7900.2500.2500.0000.0000.0000.000
89E85GLU-1-0.876-0.94331.9099.3839.3830.0000.0000.0000.000
90E86ASP-1-0.767-0.86729.14310.60310.6030.0000.0000.0000.000
91E87THR0-0.047-0.01427.5200.4840.4840.0000.0000.0000.000
92E88ALA0-0.015-0.01023.910-0.107-0.1070.0000.0000.0000.000
93E89ILE0-0.0310.00018.393-0.047-0.0470.0000.0000.0000.000
94E90TYR0-0.019-0.02320.047-0.142-0.1420.0000.0000.0000.000
95E91TYR00.0280.00514.581-0.167-0.1670.0000.0000.0000.000
96E93ALA00.0320.00512.4891.6701.6700.0000.0000.0000.000
97E94ARG10.8280.8887.295-30.925-30.9250.0000.0000.0000.000
98E95LYS10.8230.90712.666-14.605-14.6050.0000.0000.0000.000
99E96GLY00.015-0.00412.060-0.233-0.2330.0000.0000.0000.000
100E97SER0-0.037-0.02411.1710.0300.0300.0000.0000.0000.000
101E98ASP-1-0.868-0.9259.76627.33527.3350.0000.0000.0000.000
102E99ARG10.8640.92910.811-17.187-17.1870.0000.0000.0000.000
103E100LEU0-0.0050.00512.711-0.575-0.5750.0000.0000.0000.000
104E100SER0-0.069-0.04215.035-1.089-1.0890.0000.0000.0000.000
105E100ASP-1-0.893-0.93918.72712.57112.5710.0000.0000.0000.000
106E100ASN0-0.053-0.02720.7760.2340.2340.0000.0000.0000.000
107E100ASP-1-0.754-0.85315.28817.71317.7130.0000.0000.0000.000
108E100PRO00.000-0.00214.276-0.688-0.6880.0000.0000.0000.000
109E100PHE0-0.020-0.02613.6190.0290.0290.0000.0000.0000.000
110E101ASP-1-0.777-0.8578.95128.64128.6410.0000.0000.0000.000
111E102ALA00.0170.0196.9853.3583.3580.0000.0000.0000.000
112E103TRP0-0.025-0.0368.568-4.263-4.2630.0000.0000.0000.000
113E104GLY00.0240.0339.1823.1313.1310.0000.0000.0000.000
114E105PRO0-0.022-0.02010.283-0.890-0.8900.0000.0000.0000.000
115E106GLY00.002-0.00312.344-1.322-1.3220.0000.0000.0000.000
116E107THR0-0.046-0.02015.930-0.569-0.5690.0000.0000.0000.000
117E108VAL00.010-0.00619.099-0.444-0.4440.0000.0000.0000.000
118E109VAL00.0180.01722.393-0.343-0.3430.0000.0000.0000.000
119E110THR0-0.021-0.02425.488-0.200-0.2000.0000.0000.0000.000
120E111VAL0-0.0030.00328.860-0.173-0.1730.0000.0000.0000.000
121E112SER0-0.029-0.02032.126-0.198-0.1980.0000.0000.0000.000
122E113PRO00.0480.00335.302-0.093-0.0930.0000.0000.0000.000
123E114ALA0-0.030-0.00938.247-0.178-0.1780.0000.0000.0000.000
124E115SER00.0110.01439.6640.0840.0840.0000.0000.0000.000
125E116THR0-0.058-0.02440.869-0.102-0.1020.0000.0000.0000.000
126E117LYS10.9430.96543.496-7.122-7.1220.0000.0000.0000.000
127E118GLY00.0560.03145.461-0.033-0.0330.0000.0000.0000.000
128E119PRO0-0.034-0.01548.4920.0890.0890.0000.0000.0000.000
129E120SER0-0.0180.00250.253-0.114-0.1140.0000.0000.0000.000
130E121VAL0-0.001-0.00652.2680.0350.0350.0000.0000.0000.000
131E122PHE00.0120.00151.376-0.097-0.0970.0000.0000.0000.000
132E123PRO0-0.0100.00156.6770.0090.0090.0000.0000.0000.000
133E124LEU0-0.030-0.01456.4050.0440.0440.0000.0000.0000.000
134E125ALA0-0.002-0.01160.351-0.073-0.0730.0000.0000.0000.000
135E126PRO00.0500.04063.8120.0310.0310.0000.0000.0000.000
136E127SER0-0.024-0.02165.876-0.019-0.0190.0000.0000.0000.000
137E128SER0-0.018-0.01168.135-0.027-0.0270.0000.0000.0000.000
138E129LYS10.9840.98971.089-4.397-4.3970.0000.0000.0000.000
139E130SER00.0220.00269.1820.0580.0580.0000.0000.0000.000
140E133THR00.0090.01270.341-0.039-0.0390.0000.0000.0000.000
141E134SER00.0030.00272.688-0.041-0.0410.0000.0000.0000.000
142E135GLY00.0220.01675.1690.0480.0480.0000.0000.0000.000
143E136GLY00.0240.01375.124-0.047-0.0470.0000.0000.0000.000
144E137THR0-0.044-0.02069.437-0.015-0.0150.0000.0000.0000.000
145E138ALA0-0.0040.00969.2130.0340.0340.0000.0000.0000.000
146E139ALA00.016-0.00164.2180.0010.0010.0000.0000.0000.000
147E140LEU0-0.0140.00663.8030.0100.0100.0000.0000.0000.000
148E141GLY00.0370.00260.7630.0090.0090.0000.0000.0000.000
149E142CYS0-0.101-0.02057.961-0.035-0.0350.0000.0000.0000.000
150E143LEU00.0290.02251.4240.0490.0490.0000.0000.0000.000
151E144VAL0-0.019-0.00751.017-0.013-0.0130.0000.0000.0000.000
152E145LYS10.9490.95746.085-6.767-6.7670.0000.0000.0000.000
153E146ASP-1-0.882-0.94145.1187.0397.0390.0000.0000.0000.000
154E147TYR0-0.0010.01046.126-0.036-0.0360.0000.0000.0000.000
155E148PHE00.0130.00938.4720.1380.1380.0000.0000.0000.000
156E149PRO00.0320.01642.240-0.062-0.0620.0000.0000.0000.000
157E150GLU-1-0.818-0.91543.9316.7226.7220.0000.0000.0000.000
158E151PRO00.0060.00046.3310.0290.0290.0000.0000.0000.000
159E152VAL0-0.004-0.02049.329-0.022-0.0220.0000.0000.0000.000
160E153THR0-0.049-0.01252.299-0.057-0.0570.0000.0000.0000.000
161E154VAL00.001-0.01255.6900.0010.0010.0000.0000.0000.000
162E156SER0-0.0020.01158.297-0.024-0.0240.0000.0000.0000.000
163E157TRP00.0340.02561.3500.0000.0000.0000.0000.0000.000
164E162ASN00.0260.00564.939-0.001-0.0010.0000.0000.0000.000
165E163SER0-0.010-0.01066.269-0.063-0.0630.0000.0000.0000.000
166E164GLY0-0.021-0.00966.038-0.008-0.0080.0000.0000.0000.000
167E165ALA0-0.028-0.00166.872-0.027-0.0270.0000.0000.0000.000
168E166LEU0-0.039-0.00967.637-0.059-0.0590.0000.0000.0000.000
169E167THR00.012-0.00566.4570.0620.0620.0000.0000.0000.000
170E168SER0-0.008-0.01266.5680.0720.0720.0000.0000.0000.000
171E169GLY00.0530.02366.724-0.005-0.0050.0000.0000.0000.000
172E171VAL0-0.022-0.00561.8440.0390.0390.0000.0000.0000.000
173E172HIS0-0.0010.00559.1880.0720.0720.0000.0000.0000.000
174E173THR00.003-0.01355.0970.0150.0150.0000.0000.0000.000
175E174PHE0-0.023-0.00752.9970.0130.0130.0000.0000.0000.000
176E175PRO00.012-0.00149.7520.0400.0400.0000.0000.0000.000
177E176ALA0-0.0130.01146.984-0.002-0.0020.0000.0000.0000.000
178E177VAL00.0260.01444.5040.0800.0800.0000.0000.0000.000
179E178LEU0-0.037-0.01937.825-0.016-0.0160.0000.0000.0000.000
180E179GLN0-0.044-0.03941.128-0.029-0.0290.0000.0000.0000.000
181E180SER00.0360.01436.7450.0980.0980.0000.0000.0000.000
182E182SER00.0140.00836.4180.2320.2320.0000.0000.0000.000
183E183GLY00.0170.01037.2790.1370.1370.0000.0000.0000.000
184E184LEU0-0.098-0.05038.032-0.055-0.0550.0000.0000.0000.000
185E185TYR00.0420.03541.1500.0640.0640.0000.0000.0000.000
186E186SER0-0.052-0.03244.687-0.084-0.0840.0000.0000.0000.000
187E187LEU00.0590.04847.8570.0280.0280.0000.0000.0000.000
188E188SER00.0160.00250.971-0.028-0.0280.0000.0000.0000.000
189E189SER0-0.010-0.00854.458-0.039-0.0390.0000.0000.0000.000
190E190VAL00.013-0.00357.792-0.031-0.0310.0000.0000.0000.000
191E191VAL00.0500.02460.849-0.012-0.0120.0000.0000.0000.000
192E192THR0-0.045-0.01564.5530.0050.0050.0000.0000.0000.000
193E193VAL00.0110.00467.383-0.034-0.0340.0000.0000.0000.000
194E194PRO00.0490.02670.8240.0090.0090.0000.0000.0000.000
195E195SER00.015-0.00173.4690.0270.0270.0000.0000.0000.000
196E196SER00.000-0.00574.4410.0190.0190.0000.0000.0000.000
197E197SER0-0.021-0.02174.389-0.011-0.0110.0000.0000.0000.000
198E198LEU00.004-0.00470.2290.0310.0310.0000.0000.0000.000
199E199GLY0-0.0190.00073.8940.0250.0250.0000.0000.0000.000
200E200THR0-0.016-0.01476.202-0.051-0.0510.0000.0000.0000.000
201E203GLN0-0.0460.00072.755-0.055-0.0550.0000.0000.0000.000
202E205THR0-0.0180.00171.0020.0690.0690.0000.0000.0000.000
203E206TYR00.0300.00167.2500.0020.0020.0000.0000.0000.000
204E207ILE00.0120.00064.7640.0560.0560.0000.0000.0000.000
205E209ASN00.024-0.00761.376-0.008-0.0080.0000.0000.0000.000
206E210VAL00.0230.01554.7140.0470.0470.0000.0000.0000.000
207E211ASN00.005-0.00856.2130.0290.0290.0000.0000.0000.000
208E212HIS00.0220.01647.129-0.042-0.0420.0000.0000.0000.000
209E213LYS10.9710.96751.937-5.800-5.8000.0000.0000.0000.000
210E214PRO0-0.0160.00546.880-0.020-0.0200.0000.0000.0000.000
211E215SER00.0150.00848.138-0.009-0.0090.0000.0000.0000.000
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