Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 37QQL

Calculation Name: 2PET-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PET

Chain ID: A

ChEMBL ID:

UniProt ID: P50895

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2459715.496726
FMO2-HF: Nuclear repulsion 2368361.625982
FMO2-HF: Total energy -91353.870744
FMO2-MP2: Total energy -91615.888337


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:GLU)


Summations of interaction energy for fragment #1(A: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.
-71.386-72.09929.182-15.941-12.5260.098
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.847 / q_NPA : -0.910
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].
3A3ARG10.8200.8851.602-115.888-119.36928.096-14.188-10.4260.113
4A4LEU00.0260.0044.485-4.571-4.511-0.001-0.019-0.0400.000
5A5SER0-0.031-0.0068.1450.5340.5340.0000.0000.0000.000
6A6VAL00.0290.01611.176-0.602-0.6020.0000.0000.0000.000
7A7PRO0-0.008-0.01414.775-0.006-0.0060.0000.0000.0000.000
8A8PRO00.0430.02817.505-0.343-0.3430.0000.0000.0000.000
9A9LEU0-0.038-0.01119.169-0.555-0.5550.0000.0000.0000.000
10A10VAL00.0010.01221.7390.0770.0770.0000.0000.0000.000
11A11GLU-1-0.854-0.92124.45610.27910.2790.0000.0000.0000.000
12A12VAL00.0130.01128.300-0.009-0.0090.0000.0000.0000.000
13A13MET0-0.035-0.01230.672-0.171-0.1710.0000.0000.0000.000
14A14ARG10.9420.94034.138-7.639-7.6390.0000.0000.0000.000
15A15GLY0-0.059-0.02835.522-0.186-0.1860.0000.0000.0000.000
16A16LYS10.9120.96233.116-8.498-8.4980.0000.0000.0000.000
17A17SER00.0440.02330.256-0.002-0.0020.0000.0000.0000.000
18A18VAL0-0.021-0.00224.9020.0350.0350.0000.0000.0000.000
19A19ILE00.0130.01021.934-0.161-0.1610.0000.0000.0000.000
20A20LEU0-0.043-0.01219.9830.2340.2340.0000.0000.0000.000
21A21ASP-1-0.837-0.92316.27517.97117.9710.0000.0000.0000.000
22A22CYS0-0.032-0.01813.5000.0320.0320.0000.0000.0000.000
23A23THR00.0140.00612.846-0.405-0.4050.0000.0000.0000.000
24A24PRO0-0.0200.0018.0941.2351.2350.0000.0000.0000.000
25A25THR0-0.011-0.0106.847-0.178-0.1780.0000.0000.0000.000
26A26GLY00.0330.0053.5822.3662.4720.001-0.056-0.0510.000
27A27THR0-0.0080.0054.3762.1702.3050.000-0.041-0.0940.000
28A28HIS0-0.020-0.0115.444-1.697-1.6970.0000.0000.0000.000
29A29ASP-1-0.890-0.9788.56416.50816.5080.0000.0000.0000.000
30A30HIS0-0.076-0.04011.471-0.213-0.2130.0000.0000.0000.000
31A31TYR0-0.060-0.0349.7191.7091.7090.0000.0000.0000.000
32A32MET00.0110.01111.625-1.272-1.2720.0000.0000.0000.000
33A33LEU0-0.0160.00112.4701.6411.6410.0000.0000.0000.000
34A34GLU-1-0.808-0.90014.86614.23814.2380.0000.0000.0000.000
35A35TRP0-0.001-0.01016.4190.6530.6530.0000.0000.0000.000
36A36PHE0-0.022-0.01916.561-0.766-0.7660.0000.0000.0000.000
37A37LEU0-0.030-0.00120.8480.0510.0510.0000.0000.0000.000
38A38THR0-0.006-0.01220.5340.2670.2670.0000.0000.0000.000
39A39ASP-1-0.847-0.85023.31210.54810.5480.0000.0000.0000.000
40A40ARG10.9780.96024.739-10.053-10.0530.0000.0000.0000.000
41A41SER0-0.086-0.08726.1880.0970.0970.0000.0000.0000.000
42A42GLY00.0150.01122.6610.0960.0960.0000.0000.0000.000
43A43ALA0-0.016-0.00322.3660.3840.3840.0000.0000.0000.000
44A44ARG10.8250.87515.369-16.684-16.6840.0000.0000.0000.000
45A45PRO0-0.061-0.02322.757-0.002-0.0020.0000.0000.0000.000
46A46ARG10.9220.95219.015-13.531-13.5310.0000.0000.0000.000
47A47LEU0-0.053-0.01622.576-0.498-0.4980.0000.0000.0000.000
48A48ALA00.021-0.00822.072-0.489-0.4890.0000.0000.0000.000
49A49SER0-0.0260.00019.4710.4060.4060.0000.0000.0000.000
50A50ALA00.0050.00018.166-0.723-0.7230.0000.0000.0000.000
51A51GLU-1-0.861-0.91316.09915.90715.9070.0000.0000.0000.000
52A52MET0-0.019-0.01114.728-0.822-0.8220.0000.0000.0000.000
53A53GLN00.0910.03814.8730.8150.8150.0000.0000.0000.000
54A54GLY00.0140.01716.099-0.861-0.8610.0000.0000.0000.000
55A55SER0-0.127-0.06118.049-0.153-0.1530.0000.0000.0000.000
56A56GLU-1-0.897-0.94120.16911.51811.5180.0000.0000.0000.000
57A57LEU0-0.033-0.00519.3910.6500.6500.0000.0000.0000.000
58A58GLN0-0.037-0.01220.341-0.728-0.7280.0000.0000.0000.000
59A59VAL00.014-0.00220.9840.5800.5800.0000.0000.0000.000
60A60THR0-0.036-0.00823.203-0.551-0.5510.0000.0000.0000.000
61A61MET0-0.046-0.02024.3240.5090.5090.0000.0000.0000.000
62A62HIS0-0.008-0.02322.652-0.512-0.5120.0000.0000.0000.000
63A63ASP-1-0.863-0.96627.2089.6459.6450.0000.0000.0000.000
64A64THR0-0.042-0.03728.968-0.239-0.2390.0000.0000.0000.000
65A65ARG10.8510.97029.289-10.195-10.1950.0000.0000.0000.000
66A66GLY00.0200.01733.150-0.104-0.1040.0000.0000.0000.000
67A67ARG10.7590.86830.237-9.837-9.8370.0000.0000.0000.000
68A68SER0-0.048-0.00133.724-0.053-0.0530.0000.0000.0000.000
69A69PRO00.0560.01233.534-0.059-0.0590.0000.0000.0000.000
70A70PRO00.0250.00431.7650.1820.1820.0000.0000.0000.000
71A71TYR00.0250.01726.4480.0630.0630.0000.0000.0000.000
72A72GLN0-0.008-0.01327.151-0.325-0.3250.0000.0000.0000.000
73A73LEU00.0140.01620.7840.2900.2900.0000.0000.0000.000
74A74ASP-1-0.794-0.88121.41513.27513.2750.0000.0000.0000.000
75A75SER0-0.016-0.02022.6060.3350.3350.0000.0000.0000.000
76A76GLN0-0.009-0.00117.9870.7430.7430.0000.0000.0000.000
77A77GLY00.0410.02517.6040.8140.8140.0000.0000.0000.000
78A78ARG10.8360.92317.837-14.351-14.3510.0000.0000.0000.000
79A79LEU00.0100.01619.768-0.736-0.7360.0000.0000.0000.000
80A80VAL0-0.001-0.00522.195-0.021-0.0210.0000.0000.0000.000
81A81LEU0-0.050-0.02924.828-0.273-0.2730.0000.0000.0000.000
82A82ALA00.0620.01528.240-0.068-0.0680.0000.0000.0000.000
83A83GLU-1-0.968-0.98331.5408.1758.1750.0000.0000.0000.000
84A84ALA00.0190.01730.813-0.066-0.0660.0000.0000.0000.000
85A85GLN00.0790.03132.505-0.498-0.4980.0000.0000.0000.000
86A86VAL00.0450.02432.9210.2610.2610.0000.0000.0000.000
87A87GLY0-0.010-0.00533.0250.1840.1840.0000.0000.0000.000
88A88ASP-1-0.777-0.86628.94810.02410.0240.0000.0000.0000.000
89A89GLU-1-0.865-0.91028.10410.16410.1640.0000.0000.0000.000
90A90ARG10.8520.92526.005-10.544-10.5440.0000.0000.0000.000
91A91ASP-1-0.856-0.93421.52012.95412.9540.0000.0000.0000.000
92A92TYR0-0.079-0.07020.652-0.417-0.4170.0000.0000.0000.000
93A93VAL0-0.015-0.01015.3390.5490.5490.0000.0000.0000.000
94A95VAL0-0.001-0.01311.7101.2981.2980.0000.0000.0000.000
95A96VAL00.0430.0227.965-1.082-1.0820.0000.0000.0000.000
96A97ARG10.9100.9409.316-16.022-16.0220.0000.0000.0000.000
97A98ALA00.0700.0225.896-1.468-1.4680.0000.0000.0000.000
98A99GLY00.0420.0326.9911.0291.0290.0000.0000.0000.000
99A100ALA0-0.019-0.0197.0841.1401.1400.0000.0000.0000.000
100A101ALA00.0040.0163.0272.2732.7580.121-0.169-0.4380.000
101A102GLY00.0230.0162.7574.0776.0050.966-1.465-1.428-0.015
102A103THR0-0.063-0.0374.992-3.726-3.672-0.001-0.003-0.0490.000
103A104ALA00.0260.0155.3793.1113.1110.0000.0000.0000.000
104A105GLU-1-0.807-0.8817.42817.24517.2450.0000.0000.0000.000
105A106ALA0-0.0130.00110.5711.3261.3260.0000.0000.0000.000
106A107THR0-0.009-0.01112.913-1.214-1.2140.0000.0000.0000.000
107A108ALA00.0040.01416.6490.3010.3010.0000.0000.0000.000
108A109ARG10.9010.97319.405-11.768-11.7680.0000.0000.0000.000
109A110LEU0-0.027-0.00923.0750.0440.0440.0000.0000.0000.000
110A111ASN00.005-0.01825.569-0.276-0.2760.0000.0000.0000.000
111A112VAL0-0.003-0.01128.9740.0180.0180.0000.0000.0000.000
112A113PHE0-0.0120.00230.862-0.267-0.2670.0000.0000.0000.000
113A114ALA0-0.035-0.03235.146-0.059-0.0590.0000.0000.0000.000
114A115LYS10.9270.97738.614-7.068-7.0680.0000.0000.0000.000
115A116PRO00.0120.00941.622-0.044-0.0440.0000.0000.0000.000
116A117GLU-1-0.890-0.93344.4866.4866.4860.0000.0000.0000.000
117A118ALA0-0.023-0.01947.8260.0190.0190.0000.0000.0000.000
118A119THR0-0.037-0.04450.3620.0150.0150.0000.0000.0000.000
119A120GLU-1-0.867-0.91651.7685.6585.6580.0000.0000.0000.000
120A121VAL0-0.018-0.03054.8390.0660.0660.0000.0000.0000.000
121A122SER0-0.045-0.02057.496-0.055-0.0550.0000.0000.0000.000
122A123PRO0-0.022-0.00860.3940.0020.0020.0000.0000.0000.000
123A124ASN00.0530.02363.062-0.101-0.1010.0000.0000.0000.000
124A125LYS10.9370.95065.386-4.880-4.8800.0000.0000.0000.000
125A126GLY0-0.016-0.00868.485-0.084-0.0840.0000.0000.0000.000
126A127THR00.0180.00169.055-0.049-0.0490.0000.0000.0000.000
127A128LEU0-0.0280.02466.044-0.031-0.0310.0000.0000.0000.000
128A129SER00.0650.01570.272-0.076-0.0760.0000.0000.0000.000
129A130VAL0-0.036-0.01071.3580.0410.0410.0000.0000.0000.000
130A131MET0-0.039-0.02573.174-0.022-0.0220.0000.0000.0000.000
131A132GLU-1-0.884-0.90570.8154.4414.4410.0000.0000.0000.000
132A133ASP-1-0.890-0.92471.6544.5234.5230.0000.0000.0000.000
133A134SER0-0.055-0.06167.9900.0470.0470.0000.0000.0000.000
134A135ALA0-0.004-0.00263.1730.0000.0000.0000.0000.0000.000
135A136GLN00.000-0.01064.8260.0090.0090.0000.0000.0000.000
136A137GLU-1-0.894-0.94461.1675.2535.2530.0000.0000.0000.000
137A138ILE0-0.017-0.01161.378-0.078-0.0780.0000.0000.0000.000
138A139ALA00.015-0.00859.820-0.066-0.0660.0000.0000.0000.000
139A140THR00.0230.03755.5390.0800.0800.0000.0000.0000.000
140A141CYS0-0.0500.00152.9510.0000.0000.0000.0000.0000.000
141A142ASN0-0.020-0.02051.4100.1450.1450.0000.0000.0000.000
142A143SER00.0380.03046.8210.0270.0270.0000.0000.0000.000
143A144ARG10.9530.95447.022-5.943-5.9430.0000.0000.0000.000
144A145ASN0-0.026-0.03743.6680.1350.1350.0000.0000.0000.000
145A146GLY00.0250.01941.3520.0320.0320.0000.0000.0000.000
146A147ASN0-0.073-0.02634.009-0.157-0.1570.0000.0000.0000.000
147A148PRO00.0850.02535.0970.0460.0460.0000.0000.0000.000
148A149ALA0-0.010-0.01137.203-0.182-0.1820.0000.0000.0000.000
149A150PRO00.0090.01840.5320.1000.1000.0000.0000.0000.000
150A151LYS10.9450.96740.692-7.650-7.6500.0000.0000.0000.000
151A152ILE00.0160.00445.064-0.012-0.0120.0000.0000.0000.000
152A153THR0-0.0120.02448.5050.0510.0510.0000.0000.0000.000
153A154TRP00.0350.00251.065-0.074-0.0740.0000.0000.0000.000
154A155TYR0-0.015-0.01350.8750.1000.1000.0000.0000.0000.000
155A156ARG10.9340.96357.094-5.133-5.1330.0000.0000.0000.000
156A157ASN00.0040.00560.7340.0140.0140.0000.0000.0000.000
157A158GLY0-0.0040.00158.535-0.004-0.0040.0000.0000.0000.000
158A159GLN0-0.028-0.01057.0830.1260.1260.0000.0000.0000.000
159A160ARG10.9430.96950.447-6.301-6.3010.0000.0000.0000.000
160A161LEU0-0.010-0.01154.919-0.066-0.0660.0000.0000.0000.000
161A162GLU-1-0.989-0.99652.8326.0666.0660.0000.0000.0000.000
162A163VAL0-0.0270.00054.119-0.081-0.0810.0000.0000.0000.000
163A164PRO00.0070.02152.1930.1370.1370.0000.0000.0000.000
164A165VAL00.013-0.01849.274-0.049-0.0490.0000.0000.0000.000
165A166GLU-1-0.934-0.96350.8236.1876.1870.0000.0000.0000.000
166A167MET0-0.012-0.00354.547-0.099-0.0990.0000.0000.0000.000
167A168ASN0-0.034-0.02757.831-0.083-0.0830.0000.0000.0000.000
168A169PRO00.026-0.00460.798-0.006-0.0060.0000.0000.0000.000
169A170GLU-1-0.876-0.93262.0594.8334.8330.0000.0000.0000.000
170A171GLY00.0300.00360.367-0.044-0.0440.0000.0000.0000.000
171A172TYR0-0.0210.00056.0970.0350.0350.0000.0000.0000.000
172A173MET00.0090.01249.989-0.080-0.0800.0000.0000.0000.000
173A174THR00.0300.02453.0490.0920.0920.0000.0000.0000.000
174A175SER0-0.029-0.03348.4230.0710.0710.0000.0000.0000.000
175A176ARG10.9770.98948.488-6.341-6.3410.0000.0000.0000.000
176A177THR00.0050.00942.3340.0290.0290.0000.0000.0000.000
177A178VAL0-0.002-0.00545.525-0.022-0.0220.0000.0000.0000.000
178A179ARG10.8790.94636.538-8.099-8.0990.0000.0000.0000.000
179A180GLU-1-0.824-0.88142.8086.5396.5390.0000.0000.0000.000
180A181ALA00.019-0.00142.5360.1790.1790.0000.0000.0000.000
181A182SER0-0.0020.00441.4780.1580.1580.0000.0000.0000.000
182A183GLY00.0130.00238.3880.2140.2140.0000.0000.0000.000
183A184LEU0-0.053-0.01738.5870.1970.1970.0000.0000.0000.000
184A185LEU0-0.032-0.01338.083-0.107-0.1070.0000.0000.0000.000
185A186SER0-0.024-0.03842.0430.0110.0110.0000.0000.0000.000
186A187LEU0-0.063-0.01445.5000.0090.0090.0000.0000.0000.000
187A188THR00.0100.00747.299-0.124-0.1240.0000.0000.0000.000
188A189SER0-0.006-0.01550.6870.0650.0650.0000.0000.0000.000
189A190THR00.0440.01452.641-0.032-0.0320.0000.0000.0000.000
190A191LEU0-0.0110.01556.1530.0580.0580.0000.0000.0000.000
191A192TYR00.004-0.00558.003-0.062-0.0620.0000.0000.0000.000
192A193LEU0-0.001-0.02260.4230.0680.0680.0000.0000.0000.000
193A194ARG10.8380.93162.941-4.784-4.7840.0000.0000.0000.000
194A195LEU0-0.063-0.01666.0970.0190.0190.0000.0000.0000.000
195A196ARG10.9110.93967.304-4.753-4.7530.0000.0000.0000.000
196A197LYS10.9840.97970.575-4.256-4.2560.0000.0000.0000.000
197A198ASP-1-0.860-0.94270.6074.4354.4350.0000.0000.0000.000
198A199ASP-1-0.778-0.88866.6884.8924.8920.0000.0000.0000.000
199A200ARG10.8620.93368.958-4.218-4.2180.0000.0000.0000.000
200A201ASP-1-0.909-0.95370.7194.4014.4010.0000.0000.0000.000
201A202ALA0-0.082-0.01765.2030.0390.0390.0000.0000.0000.000
202A203SER0-0.016-0.00163.183-0.005-0.0050.0000.0000.0000.000
203A204PHE00.0330.00060.7400.0480.0480.0000.0000.0000.000
204A205HIS00.0020.00154.639-0.129-0.1290.0000.0000.0000.000
205A207ALA00.0120.00150.483-0.021-0.0210.0000.0000.0000.000
206A208ALA00.0310.02846.6280.0420.0420.0000.0000.0000.000
207A209HIS0-0.041-0.04444.0790.1100.1100.0000.0000.0000.000
208A210TYR00.010-0.00440.475-0.011-0.0110.0000.0000.0000.000
209A211SER00.0160.00536.2660.0080.0080.0000.0000.0000.000
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211A213PRO00.0360.01531.3630.0650.0650.0000.0000.0000.000
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