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: MVZZZ

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2129270.226866
FMO2-HF: Nuclear repulsion 2045372.434714
FMO2-HF: Total energy -83897.792152
FMO2-MP2: Total energy -84141.656117


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.
-7.754-3.9720.639-1.411-3.0090.005
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 : -0.933 / q_NPA : -0.982
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].
3E3GLN0-0.0020.0122.544-9.691-7.0670.341-0.968-1.9960.005
4E4LEU00.004-0.0075.964-4.048-4.0480.0000.0000.0000.000
5E5VAL00.004-0.0089.6981.0851.0850.0000.0000.0000.000
6E6GLU-1-0.761-0.87412.06320.47220.4720.0000.0000.0000.000
7E7SER0-0.058-0.02815.753-0.241-0.2410.0000.0000.0000.000
8E8GLY00.0410.00118.683-0.279-0.2790.0000.0000.0000.000
9E9GLY0-0.0030.01221.653-0.601-0.6010.0000.0000.0000.000
10E10GLY00.0050.00123.476-0.175-0.1750.0000.0000.0000.000
11E11LEU0-0.044-0.01626.589-0.082-0.0820.0000.0000.0000.000
12E12VAL00.0170.01729.499-0.192-0.1920.0000.0000.0000.000
13E13LYS10.8870.96032.235-8.494-8.4940.0000.0000.0000.000
14E14ALA00.0560.02935.5450.0910.0910.0000.0000.0000.000
15E15GLY0-0.063-0.03936.643-0.267-0.2670.0000.0000.0000.000
16E16GLY0-0.050-0.01735.245-0.088-0.0880.0000.0000.0000.000
17E17SER0-0.009-0.04732.160-0.020-0.0200.0000.0000.0000.000
18E18LEU0-0.017-0.00825.846-0.079-0.0790.0000.0000.0000.000
19E19ILE0-0.019-0.00924.788-0.014-0.0140.0000.0000.0000.000
20E20LEU0-0.0220.01120.8850.1790.1790.0000.0000.0000.000
21E21SER00.0000.00119.579-0.063-0.0630.0000.0000.0000.000
22E22CYS0-0.055-0.03014.369-0.078-0.0780.0000.0000.0000.000
23E23GLY00.0670.06113.869-0.735-0.7350.0000.0000.0000.000
24E24VAL0-0.030-0.0289.3401.2731.2730.0000.0000.0000.000
25E25SER00.0480.0185.701-2.369-2.3690.0000.0000.0000.000
26E26ASN0-0.066-0.0482.994-5.102-3.9440.298-0.443-1.0130.000
27E27PHE00.003-0.0075.4310.0230.0230.0000.0000.0000.000
28E28ARG10.8340.9138.236-18.876-18.8760.0000.0000.0000.000
29E29ILE00.0360.00112.0220.0720.0720.0000.0000.0000.000
30E30SER0-0.039-0.01214.057-0.356-0.3560.0000.0000.0000.000
31E31ALA0-0.033-0.00214.050-0.916-0.9160.0000.0000.0000.000
32E32HIS0-0.040-0.02611.3860.6200.6200.0000.0000.0000.000
33E33THR0-0.010-0.00615.945-0.846-0.8460.0000.0000.0000.000
34E34MET0-0.0220.00012.7991.0871.0870.0000.0000.0000.000
35E35ASN0-0.026-0.03516.065-1.975-1.9750.0000.0000.0000.000
36E36TRP0-0.0070.00917.1970.9980.9980.0000.0000.0000.000
37E37VAL0-0.009-0.01517.991-0.848-0.8480.0000.0000.0000.000
38E38ARG10.7950.88719.828-11.126-11.1260.0000.0000.0000.000
39E39ARG10.8860.94919.864-15.214-15.2140.0000.0000.0000.000
40E40VAL00.0300.02522.376-0.095-0.0950.0000.0000.0000.000
41E41PRO00.014-0.02025.4710.2300.2300.0000.0000.0000.000
42E42GLY0-0.0180.00627.563-0.052-0.0520.0000.0000.0000.000
43E43GLY00.0310.02424.867-0.100-0.1000.0000.0000.0000.000
44E44GLY0-0.0080.00623.5670.6680.6680.0000.0000.0000.000
45E45LEU0-0.005-0.01018.7300.0850.0850.0000.0000.0000.000
46E46GLU-1-0.824-0.90122.88910.81910.8190.0000.0000.0000.000
47E47TRP0-0.0050.00120.9270.3380.3380.0000.0000.0000.000
48E48VAL0-0.026-0.01022.530-0.627-0.6270.0000.0000.0000.000
49E49ALA00.009-0.01222.688-0.650-0.6500.0000.0000.0000.000
50E50SER0-0.0070.01121.2360.6970.6970.0000.0000.0000.000
51E51ILE0-0.0070.00319.720-0.736-0.7360.0000.0000.0000.000
52E52SER00.0660.02620.7760.5350.5350.0000.0000.0000.000
53E52THR00.0580.02519.1190.0590.0590.0000.0000.0000.000
54E53SER00.027-0.00321.594-0.518-0.5180.0000.0000.0000.000
55E54SER0-0.041-0.02423.545-0.396-0.3960.0000.0000.0000.000
56E55THR0-0.052-0.00325.439-0.470-0.4700.0000.0000.0000.000
57E56TYR0-0.036-0.03826.437-0.536-0.5360.0000.0000.0000.000
58E57ARG10.8660.92125.721-10.637-10.6370.0000.0000.0000.000
59E58ASP-1-0.797-0.86625.69810.20310.2030.0000.0000.0000.000
60E59TYR0-0.016-0.01925.8820.5810.5810.0000.0000.0000.000
61E60ALA00.0710.04127.180-0.309-0.3090.0000.0000.0000.000
62E61ASP-1-0.839-0.92828.9179.1509.1500.0000.0000.0000.000
63E62ALA0-0.042-0.01530.979-0.201-0.2010.0000.0000.0000.000
64E63VAL0-0.006-0.00827.641-0.137-0.1370.0000.0000.0000.000
65E64LYS10.8730.94431.088-9.666-9.6660.0000.0000.0000.000
66E65GLY0-0.0040.00232.633-0.279-0.2790.0000.0000.0000.000
67E66ARG10.6780.82131.878-9.824-9.8240.0000.0000.0000.000
68E67PHE00.0450.00426.6710.0830.0830.0000.0000.0000.000
69E68THR0-0.056-0.02928.173-0.306-0.3060.0000.0000.0000.000
70E69VAL00.0140.03622.2140.2710.2710.0000.0000.0000.000
71E70SER0-0.026-0.01923.595-0.634-0.6340.0000.0000.0000.000
72E71ARG10.7560.86717.645-14.573-14.5730.0000.0000.0000.000
73E72ASP-1-0.869-0.92819.69013.05413.0540.0000.0000.0000.000
74E73ASP-1-0.799-0.91418.11615.42015.4200.0000.0000.0000.000
75E74LEU0-0.044-0.01717.6460.5140.5140.0000.0000.0000.000
76E75GLU-1-0.905-0.95617.50315.33615.3360.0000.0000.0000.000
77E76ASP-1-0.825-0.86813.42320.08420.0840.0000.0000.0000.000
78E77PHE00.0160.01314.7781.0401.0400.0000.0000.0000.000
79E78VAL0-0.041-0.01916.429-0.829-0.8290.0000.0000.0000.000
80E79TYR00.007-0.01718.7590.0980.0980.0000.0000.0000.000
81E80LEU00.006-0.00521.949-0.196-0.1960.0000.0000.0000.000
82E81GLN0-0.0010.00224.079-0.347-0.3470.0000.0000.0000.000
83E82MET00.0000.01725.566-0.080-0.0800.0000.0000.0000.000
84E82HIS00.0700.03529.465-0.323-0.3230.0000.0000.0000.000
85E82LYS10.9300.95833.256-7.935-7.9350.0000.0000.0000.000
86E82MET0-0.0190.01328.562-0.020-0.0200.0000.0000.0000.000
87E83ARG10.9400.97133.475-9.176-9.1760.0000.0000.0000.000
88E84VAL00.0620.02033.0210.2470.2470.0000.0000.0000.000
89E85GLU-1-0.837-0.92332.2089.3809.3800.0000.0000.0000.000
90E86ASP-1-0.764-0.84029.32910.46010.4600.0000.0000.0000.000
91E87THR0-0.0230.00027.7630.4990.4990.0000.0000.0000.000
92E88ALA0-0.021-0.01024.225-0.116-0.1160.0000.0000.0000.000
93E89ILE0-0.033-0.00418.674-0.029-0.0290.0000.0000.0000.000
94E90TYR0-0.011-0.02920.285-0.158-0.1580.0000.0000.0000.000
95E91TYR00.013-0.00314.822-0.154-0.1540.0000.0000.0000.000
96E93ALA00.0360.00712.5881.6271.6270.0000.0000.0000.000
97E94ARG10.8340.8927.942-29.348-29.3480.0000.0000.0000.000
98E95LYS10.8220.89512.781-14.490-14.4900.0000.0000.0000.000
99E96GLY00.014-0.00112.178-0.191-0.1910.0000.0000.0000.000
100E97SER0-0.040-0.04211.2880.0290.0290.0000.0000.0000.000
101E98ASP-1-0.888-0.9349.46326.59026.5900.0000.0000.0000.000
102E99ARG10.8660.92710.815-16.561-16.5610.0000.0000.0000.000
103E100LEU00.0030.01512.452-0.563-0.5630.0000.0000.0000.000
104E100SER0-0.055-0.03415.062-1.046-1.0460.0000.0000.0000.000
105E100ASP-1-0.904-0.94318.75512.43812.4380.0000.0000.0000.000
106E100ASN0-0.047-0.02820.8830.2150.2150.0000.0000.0000.000
107E100ASP-1-0.744-0.83515.42217.55517.5550.0000.0000.0000.000
108E100PRO0-0.0070.00714.247-0.695-0.6950.0000.0000.0000.000
109E100PHE0-0.022-0.02613.7020.0770.0770.0000.0000.0000.000
110E101ASP-1-0.773-0.8459.23727.08527.0850.0000.0000.0000.000
111E102ALA00.0140.0157.0872.9832.9830.0000.0000.0000.000
112E103TRP0-0.035-0.0438.664-3.970-3.9700.0000.0000.0000.000
113E104GLY00.0440.0429.4963.0593.0590.0000.0000.0000.000
114E105PRO0-0.025-0.02110.396-1.011-1.0110.0000.0000.0000.000
115E106GLY00.0020.00012.460-1.355-1.3550.0000.0000.0000.000
116E107THR0-0.044-0.02516.073-0.509-0.5090.0000.0000.0000.000
117E108VAL00.010-0.00319.221-0.460-0.4600.0000.0000.0000.000
118E109VAL00.0070.01122.477-0.323-0.3230.0000.0000.0000.000
119E110THR0-0.008-0.00825.603-0.133-0.1330.0000.0000.0000.000
120E111VAL00.002-0.00428.978-0.169-0.1690.0000.0000.0000.000
121E112SER0-0.023-0.01632.267-0.190-0.1900.0000.0000.0000.000
122E113PRO00.040-0.00535.415-0.099-0.0990.0000.0000.0000.000
123E114ALA0-0.028-0.00538.404-0.175-0.1750.0000.0000.0000.000
124E115SER00.0220.02239.7900.0930.0930.0000.0000.0000.000
125E116THR0-0.056-0.03540.997-0.058-0.0580.0000.0000.0000.000
126E117LYS10.9040.95143.615-6.992-6.9920.0000.0000.0000.000
127E118GLY00.0620.03945.590-0.034-0.0340.0000.0000.0000.000
128E119PRO0-0.039-0.01548.6210.1010.1010.0000.0000.0000.000
129E120SER0-0.036-0.01350.386-0.088-0.0880.0000.0000.0000.000
130E121VAL00.006-0.00452.3970.0400.0400.0000.0000.0000.000
131E122PHE00.0190.00551.544-0.098-0.0980.0000.0000.0000.000
132E123PRO0-0.0020.00456.8080.0100.0100.0000.0000.0000.000
133E124LEU0-0.032-0.01756.5090.0460.0460.0000.0000.0000.000
134E125ALA0-0.002-0.01060.488-0.074-0.0740.0000.0000.0000.000
135E126PRO00.0580.04463.9460.0320.0320.0000.0000.0000.000
136E127SER0-0.027-0.02466.043-0.017-0.0170.0000.0000.0000.000
137E128SER0-0.005-0.00768.269-0.023-0.0230.0000.0000.0000.000
138E129LYS10.9710.98271.226-4.410-4.4100.0000.0000.0000.000
139E130SER00.016-0.00569.2720.0570.0570.0000.0000.0000.000
140E133THR00.0170.02070.540-0.036-0.0360.0000.0000.0000.000
141E134SER00.0090.00472.830-0.041-0.0410.0000.0000.0000.000
142E135GLY00.0110.00875.3110.0520.0520.0000.0000.0000.000
143E136GLY00.0040.00675.270-0.048-0.0480.0000.0000.0000.000
144E137THR0-0.019-0.01369.644-0.033-0.0330.0000.0000.0000.000
145E138ALA0-0.0070.01269.3590.0370.0370.0000.0000.0000.000
146E139ALA00.013-0.00164.3050.0010.0010.0000.0000.0000.000
147E140LEU0-0.0150.00663.9600.0100.0100.0000.0000.0000.000
148E141GLY00.0460.00560.9050.0090.0090.0000.0000.0000.000
149E142CYS0-0.112-0.01858.157-0.032-0.0320.0000.0000.0000.000
150E143LEU00.0370.02551.7850.0490.0490.0000.0000.0000.000
151E144VAL0-0.019-0.00851.325-0.012-0.0120.0000.0000.0000.000
152E145LYS10.8630.90646.012-6.810-6.8100.0000.0000.0000.000
153E146ASP-1-0.806-0.88145.1447.0467.0460.0000.0000.0000.000
154E147TYR0-0.040-0.03546.261-0.045-0.0450.0000.0000.0000.000
155E148PHE00.0220.01138.7880.1550.1550.0000.0000.0000.000
156E149PRO00.0270.02342.390-0.063-0.0630.0000.0000.0000.000
157E150GLU-1-0.751-0.87244.0756.6416.6410.0000.0000.0000.000
158E151PRO0-0.011-0.00446.4800.0310.0310.0000.0000.0000.000
159E152VAL0-0.007-0.02349.479-0.028-0.0280.0000.0000.0000.000
160E153THR0-0.049-0.01352.447-0.056-0.0560.0000.0000.0000.000
161E154VAL00.001-0.01355.7980.0000.0000.0000.0000.0000.000
162E156SER0-0.0080.00758.445-0.026-0.0260.0000.0000.0000.000
163E157TRP00.0270.02161.3710.0040.0040.0000.0000.0000.000
164E162ASN00.0250.00065.0850.0080.0080.0000.0000.0000.000
165E163SER0-0.008-0.01366.411-0.066-0.0660.0000.0000.0000.000
166E164GLY0-0.013-0.00166.186-0.010-0.0100.0000.0000.0000.000
167E165ALA0-0.032-0.00267.020-0.027-0.0270.0000.0000.0000.000
168E166LEU0-0.038-0.00868.022-0.058-0.0580.0000.0000.0000.000
169E167THR00.017-0.00466.6100.0640.0640.0000.0000.0000.000
170E168SER0-0.003-0.00966.7230.0740.0740.0000.0000.0000.000
171E169GLY00.0540.02366.880-0.005-0.0050.0000.0000.0000.000
172E171VAL0-0.028-0.00961.9270.0420.0420.0000.0000.0000.000
173E172HIS0-0.0050.00659.3990.0830.0830.0000.0000.0000.000
174E173THR00.001-0.01355.3250.0190.0190.0000.0000.0000.000
175E174PHE0-0.0130.00353.0820.0130.0130.0000.0000.0000.000
176E175PRO00.0150.00149.8140.0400.0400.0000.0000.0000.000
177E176ALA0-0.0140.01047.1280.0040.0040.0000.0000.0000.000
178E177VAL00.0160.00944.6810.0810.0810.0000.0000.0000.000
179E178LEU0-0.044-0.02238.063-0.018-0.0180.0000.0000.0000.000
180E179GLN0-0.024-0.02341.276-0.028-0.0280.0000.0000.0000.000
181E180SER00.0530.02236.9930.0850.0850.0000.0000.0000.000
182E182SER00.0050.00536.5540.2390.2390.0000.0000.0000.000
183E183GLY00.0310.01737.4190.1330.1330.0000.0000.0000.000
184E184LEU0-0.105-0.05638.172-0.069-0.0690.0000.0000.0000.000
185E185TYR00.0400.02441.5100.0720.0720.0000.0000.0000.000
186E186SER0-0.057-0.04444.831-0.084-0.0840.0000.0000.0000.000
187E187LEU00.0480.04548.0010.0330.0330.0000.0000.0000.000
188E188SER00.0390.01551.118-0.019-0.0190.0000.0000.0000.000
189E189SER0-0.028-0.01754.604-0.039-0.0390.0000.0000.0000.000
190E190VAL00.019-0.00557.940-0.032-0.0320.0000.0000.0000.000
191E191VAL00.0320.01960.997-0.014-0.0140.0000.0000.0000.000
192E192THR0-0.024-0.00464.7020.0040.0040.0000.0000.0000.000
193E193VAL00.0090.00367.533-0.035-0.0350.0000.0000.0000.000
194E194PRO00.0550.02770.9730.0090.0090.0000.0000.0000.000
195E195SER00.0250.00273.6110.0280.0280.0000.0000.0000.000
196E196SER00.002-0.00274.5850.0190.0190.0000.0000.0000.000
197E197SER0-0.032-0.01674.258-0.012-0.0120.0000.0000.0000.000
198E198LEU00.010-0.00170.5360.0310.0310.0000.0000.0000.000
199E199GLY0-0.029-0.00674.0330.0250.0250.0000.0000.0000.000
200E200THR0-0.025-0.01976.364-0.050-0.0500.0000.0000.0000.000
201E203GLN0-0.052-0.01372.879-0.044-0.0440.0000.0000.0000.000
202E205THR00.0030.01571.1800.0650.0650.0000.0000.0000.000
203E206TYR00.0270.00367.4460.0010.0010.0000.0000.0000.000
204E207ILE00.007-0.00264.8680.0560.0560.0000.0000.0000.000
205E209ASN00.038-0.01161.5170.0000.0000.0000.0000.0000.000
206E210VAL00.0230.01354.8970.0520.0520.0000.0000.0000.000
207E211ASN00.000-0.00956.3540.0240.0240.0000.0000.0000.000
208E212HIS00.0280.03147.357-0.055-0.0550.0000.0000.0000.000
209E213LYS10.9840.97252.074-5.826-5.8260.0000.0000.0000.000
210E214PRO00.0110.01846.989-0.024-0.0240.0000.0000.0000.000
211E215SER0-0.027-0.03248.3310.0020.0020.0000.0000.0000.000
212E216ASN0-0.025-0.00649.599-0.144-0.1440.0000.0000.0000.000
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