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: 3J4LL

Calculation Name: 2AUA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AUA

Chain ID: A

ChEMBL ID:

UniProt ID: Q81DM5

Base Structure: X-ray

Registration Date: 2023-09-23

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2371897.486984
FMO2-HF: Nuclear repulsion 2286822.192735
FMO2-HF: Total energy -85075.294249
FMO2-MP2: Total energy -85324.726764


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:-11:LEU)


Summations of interaction energy for fragment #1(A:-11:LEU)
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.
-2.0342.151.305-1.665-3.8240.004
Interaction energy analysis for fragmet #1(A:-11:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.014
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].
3A-9THR0-0.028-0.0092.359-2.5420.8701.288-1.530-3.1700.004
4A-8GLU-1-0.895-0.9464.3730.0660.299-0.001-0.025-0.2070.000
5A-7ASN0-0.058-0.0347.4850.2890.2890.0000.0000.0000.000
6A-6LEU0-0.014-0.0093.490-0.5100.0290.018-0.110-0.4470.000
7A-5TYR00.0260.0177.0710.0900.0900.0000.0000.0000.000
8A-4PHE0-0.070-0.04410.730-0.068-0.0680.0000.0000.0000.000
9A-3GLN00.0100.02412.248-0.026-0.0260.0000.0000.0000.000
10A-2SER00.015-0.00312.4480.1070.1070.0000.0000.0000.000
11A-1ASN0-0.060-0.0369.9410.1510.1510.0000.0000.0000.000
12A0ALA0-0.0070.00013.3470.0260.0260.0000.0000.0000.000
13A1MET00.0040.00516.830-0.012-0.0120.0000.0000.0000.000
14A2ASN0-0.020-0.02519.3030.0200.0200.0000.0000.0000.000
15A3GLU-1-0.906-0.92920.4650.1220.1220.0000.0000.0000.000
16A4THR0-0.048-0.02322.5360.0120.0120.0000.0000.0000.000
17A5GLU-1-0.795-0.88024.3940.1020.1020.0000.0000.0000.000
18A6PHE0-0.060-0.02726.9990.0000.0000.0000.0000.0000.000
19A7TYR0-0.008-0.00730.770-0.003-0.0030.0000.0000.0000.000
20A8ALA0-0.0060.00934.0980.0030.0030.0000.0000.0000.000
21A9TYR00.0030.01036.614-0.004-0.0040.0000.0000.0000.000
22A10HIS0-0.007-0.01039.149-0.001-0.0010.0000.0000.0000.000
23A11ILE00.0320.02741.152-0.002-0.0020.0000.0000.0000.000
24A12VAL00.0020.01642.4180.0000.0000.0000.0000.0000.000
25A13THR00.0270.00044.869-0.001-0.0010.0000.0000.0000.000
26A14ARG10.9060.95544.072-0.016-0.0160.0000.0000.0000.000
27A15LYS10.9840.97244.114-0.005-0.0050.0000.0000.0000.000
28A16LYS10.8320.91543.858-0.011-0.0110.0000.0000.0000.000
29A17MET0-0.0090.02039.295-0.001-0.0010.0000.0000.0000.000
30A18HIS0-0.031-0.01137.918-0.001-0.0010.0000.0000.0000.000
31A19ILE00.012-0.01337.0720.0010.0010.0000.0000.0000.000
32A20GLY00.0220.00934.016-0.003-0.0030.0000.0000.0000.000
33A21GLN0-0.0300.00333.532-0.003-0.0030.0000.0000.0000.000
34A22MET00.0220.01128.0190.0040.0040.0000.0000.0000.000
35A23ILE0-0.076-0.05431.877-0.005-0.0050.0000.0000.0000.000
36A24PRO0-0.0020.01428.9810.0050.0050.0000.0000.0000.000
37A25PHE0-0.002-0.00729.433-0.004-0.0040.0000.0000.0000.000
38A26ASN00.0370.01024.1420.0020.0020.0000.0000.0000.000
39A27LYS10.8880.94022.4880.0040.0040.0000.0000.0000.000
40A28ASN0-0.0150.00226.803-0.001-0.0010.0000.0000.0000.000
41A29GLN00.0610.05028.1770.0010.0010.0000.0000.0000.000
42A30HIS00.0800.06332.3370.0030.0030.0000.0000.0000.000
43A31ASN0-0.007-0.00835.921-0.004-0.0040.0000.0000.0000.000
44A32THR0-0.015-0.02838.147-0.003-0.0030.0000.0000.0000.000
45A33LEU0-0.0100.00741.164-0.002-0.0020.0000.0000.0000.000
46A34TYR00.0370.01339.1060.0010.0010.0000.0000.0000.000
47A35HIS0-0.046-0.04039.0270.0000.0000.0000.0000.0000.000
48A36PHE0-0.075-0.03542.959-0.002-0.0020.0000.0000.0000.000
49A37PHE0-0.018-0.02945.028-0.001-0.0010.0000.0000.0000.000
50A38PHE0-0.017-0.01441.6610.0000.0000.0000.0000.0000.000
51A39GLU-1-0.853-0.90041.0370.0080.0080.0000.0000.0000.000
52A40ARG10.8380.94745.363-0.014-0.0140.0000.0000.0000.000
53A41GLU-1-0.857-0.92448.8380.0070.0070.0000.0000.0000.000
54A42GLN0-0.074-0.03852.0280.0000.0000.0000.0000.0000.000
55A43LEU00.0110.02054.8440.0000.0000.0000.0000.0000.000
56A44ASN0-0.069-0.05358.1360.0000.0000.0000.0000.0000.000
57A45ALA00.013-0.01861.168-0.001-0.0010.0000.0000.0000.000
58A46ASN0-0.110-0.04663.509-0.001-0.0010.0000.0000.0000.000
59A47GLY0-0.0180.00159.1290.0000.0000.0000.0000.0000.000
60A48GLU-1-0.840-0.90258.3750.0050.0050.0000.0000.0000.000
61A49ASP-1-0.736-0.88555.5420.0090.0090.0000.0000.0000.000
62A50GLY00.014-0.01757.0620.0000.0000.0000.0000.0000.000
63A51ILE00.0070.00554.8000.0000.0000.0000.0000.0000.000
64A52GLN0-0.0030.01658.0820.0000.0000.0000.0000.0000.000
65A53ILE00.0130.00660.1000.0000.0000.0000.0000.0000.000
66A54LEU0-0.011-0.00859.5830.0000.0000.0000.0000.0000.000
67A55ASN0-0.045-0.03859.5870.0000.0000.0000.0000.0000.000
68A56ASN0-0.070-0.01963.5200.0000.0000.0000.0000.0000.000
69A57HIS0-0.072-0.05265.954-0.001-0.0010.0000.0000.0000.000
70A58TYR0-0.077-0.03466.1080.0000.0000.0000.0000.0000.000
71A59LYS10.8950.93068.011-0.006-0.0060.0000.0000.0000.000
72A60ASN0-0.046-0.02871.2260.0000.0000.0000.0000.0000.000
73A61ASP-1-0.865-0.90670.4210.0100.0100.0000.0000.0000.000
74A62GLU-1-0.897-0.92971.7230.0090.0090.0000.0000.0000.000
75A63LEU0-0.018-0.02165.3360.0000.0000.0000.0000.0000.000
76A64HIS0-0.040-0.01069.8540.0000.0000.0000.0000.0000.000
77A65ILE0-0.013-0.00565.374-0.001-0.0010.0000.0000.0000.000
78A66ASN00.000-0.01169.2640.0000.0000.0000.0000.0000.000
79A67ASN0-0.003-0.01568.6620.0000.0000.0000.0000.0000.000
80A68GLU-1-0.838-0.91463.8620.0050.0050.0000.0000.0000.000
81A69ASN00.0720.04364.0780.0000.0000.0000.0000.0000.000
82A70ALA00.0330.02163.7600.0010.0010.0000.0000.0000.000
83A71LYS10.9670.98361.066-0.008-0.0080.0000.0000.0000.000
84A72VAL0-0.0030.00658.6780.0010.0010.0000.0000.0000.000
85A73VAL00.0230.01558.9310.0010.0010.0000.0000.0000.000
86A74ILE0-0.019-0.00259.0850.0010.0010.0000.0000.0000.000
87A75SER0-0.030-0.02556.7710.0010.0010.0000.0000.0000.000
88A76TYR00.0360.02252.1620.0010.0010.0000.0000.0000.000
89A77MET00.0030.01854.1460.0010.0010.0000.0000.0000.000
90A78ASP-1-0.834-0.91454.3170.0190.0190.0000.0000.0000.000
91A79GLN0-0.072-0.05048.7030.0010.0010.0000.0000.0000.000
92A80THR00.0410.00749.8160.0010.0010.0000.0000.0000.000
93A81ILE0-0.035-0.00749.5950.0020.0020.0000.0000.0000.000
94A82ARG10.8020.88048.707-0.019-0.0190.0000.0000.0000.000
95A83ALA00.0470.02345.7120.0020.0020.0000.0000.0000.000
96A84ALA0-0.0150.00444.8250.0020.0020.0000.0000.0000.000
97A85ARG10.7940.88844.963-0.029-0.0290.0000.0000.0000.000
98A86GLU-1-0.720-0.84041.6120.0400.0400.0000.0000.0000.000
99A87THR0-0.010-0.00940.6580.0020.0020.0000.0000.0000.000
100A88ILE0-0.056-0.02340.1810.0030.0030.0000.0000.0000.000
101A89VAL00.013-0.00139.1810.0030.0030.0000.0000.0000.000
102A90GLU-1-0.735-0.81033.8580.0610.0610.0000.0000.0000.000
103A91MET0-0.035-0.02235.6580.0030.0030.0000.0000.0000.000
104A92VAL0-0.024-0.02535.9330.0040.0040.0000.0000.0000.000
105A93ARG10.8110.90929.607-0.070-0.0700.0000.0000.0000.000
106A94LEU0-0.025-0.02530.7400.0060.0060.0000.0000.0000.000
107A95GLN0-0.074-0.03131.0950.0050.0050.0000.0000.0000.000
108A96GLU-1-0.860-0.90732.2490.0710.0710.0000.0000.0000.000
109A97PHE0-0.044-0.01931.3870.0020.0020.0000.0000.0000.000
110A98PRO0-0.0030.01127.320-0.002-0.0020.0000.0000.0000.000
111A99GLU-1-0.886-0.95326.7570.1150.1150.0000.0000.0000.000
112A100TYR0-0.0220.00227.7320.0010.0010.0000.0000.0000.000
113A101PRO0-0.0100.00130.771-0.004-0.0040.0000.0000.0000.000
114A102SER00.021-0.01131.765-0.004-0.0040.0000.0000.0000.000
115A103ARG10.8540.88133.957-0.045-0.0450.0000.0000.0000.000
116A104LEU0-0.032-0.00436.277-0.004-0.0040.0000.0000.0000.000
117A105SER0-0.061-0.05732.019-0.003-0.0030.0000.0000.0000.000
118A106CYS0-0.070-0.01032.5800.0040.0040.0000.0000.0000.000
119A107LEU0-0.0050.01234.567-0.006-0.0060.0000.0000.0000.000
120A108TYR0-0.022-0.02136.5550.0040.0040.0000.0000.0000.000
121A109ALA0-0.032-0.01437.610-0.003-0.0030.0000.0000.0000.000
122A110ALA00.0140.00639.7200.0010.0010.0000.0000.0000.000
123A111LYS10.8890.92338.343-0.066-0.0660.0000.0000.0000.000
124A112SER0-0.029-0.04539.2500.0010.0010.0000.0000.0000.000
125A113TYR00.015-0.02441.776-0.001-0.0010.0000.0000.0000.000
126A114GLU-1-0.842-0.91344.2590.0400.0400.0000.0000.0000.000
127A115ASP-1-0.817-0.89943.7720.0470.0470.0000.0000.0000.000
128A116ALA0-0.0020.00143.820-0.002-0.0020.0000.0000.0000.000
129A117LEU00.0090.00145.724-0.002-0.0020.0000.0000.0000.000
130A118LYS10.8080.90347.591-0.044-0.0440.0000.0000.0000.000
131A119TRP0-0.020-0.01944.734-0.003-0.0030.0000.0000.0000.000
132A120LYS10.8160.90748.972-0.024-0.0240.0000.0000.0000.000
133A121ALA00.0160.01050.689-0.002-0.0020.0000.0000.0000.000
134A122LEU0-0.0150.00250.705-0.001-0.0010.0000.0000.0000.000
135A123PHE0-0.013-0.02646.767-0.001-0.0010.0000.0000.0000.000
136A124ASP-1-0.771-0.86052.9840.0200.0200.0000.0000.0000.000
137A125SER0-0.103-0.04156.010-0.001-0.0010.0000.0000.0000.000
138A126TYR0-0.039-0.03355.255-0.001-0.0010.0000.0000.0000.000
139A127ASN0-0.096-0.04457.355-0.001-0.0010.0000.0000.0000.000
140A128ARG10.8960.96448.332-0.025-0.0250.0000.0000.0000.000
141A129GLU-1-0.878-0.93652.9010.0150.0150.0000.0000.0000.000
142A130VAL0-0.045-0.02948.5400.0010.0010.0000.0000.0000.000
143A131LEU0-0.080-0.03747.499-0.001-0.0010.0000.0000.0000.000
144A132GLN0-0.018-0.03144.4010.0000.0000.0000.0000.0000.000
145A133ILE0-0.0110.01544.1400.0010.0010.0000.0000.0000.000
146A134VAL0-0.034-0.01739.787-0.001-0.0010.0000.0000.0000.000
147A135LYS10.8310.91237.377-0.041-0.0410.0000.0000.0000.000
148A136LEU0-0.021-0.02034.489-0.003-0.0030.0000.0000.0000.000
149A137ARG10.8350.89126.109-0.081-0.0810.0000.0000.0000.000
150A138VAL0-0.006-0.00528.856-0.005-0.0050.0000.0000.0000.000
151A139ILE00.0190.01422.8370.0080.0080.0000.0000.0000.000
152A140GLY00.0350.00725.158-0.007-0.0070.0000.0000.0000.000
153A141SER0-0.029-0.00626.1360.0120.0120.0000.0000.0000.000
154A142SER00.026-0.01828.531-0.009-0.0090.0000.0000.0000.000
155A143PHE00.0110.01432.1700.0050.0050.0000.0000.0000.000
156A144GLU-1-0.840-0.88534.8750.0650.0650.0000.0000.0000.000
157A145GLY00.0410.03338.2860.0010.0010.0000.0000.0000.000
158A146ASP-1-0.683-0.83140.7230.0420.0420.0000.0000.0000.000
159A147GLY00.0460.01544.3800.0000.0000.0000.0000.0000.000
160A148ASN0-0.066-0.04746.016-0.004-0.0040.0000.0000.0000.000
161A149LEU0-0.062-0.02544.081-0.002-0.0020.0000.0000.0000.000
162A150LEU0-0.0370.01042.5270.0010.0010.0000.0000.0000.000
163A151PRO0-0.019-0.01444.817-0.002-0.0020.0000.0000.0000.000
164A152LYS10.8550.93047.972-0.036-0.0360.0000.0000.0000.000
165A153GLU-1-0.891-0.94550.8320.0280.0280.0000.0000.0000.000
166A154ASP-1-0.826-0.92053.2800.0270.0270.0000.0000.0000.000
167A155GLY00.0320.00853.8860.0000.0000.0000.0000.0000.000
168A156ILE0-0.060-0.00751.0690.0000.0000.0000.0000.0000.000
169A157PRO00.028-0.00151.8810.0000.0000.0000.0000.0000.000
170A158PHE00.1010.02746.7320.0020.0020.0000.0000.0000.000
171A159SER00.0050.00846.5340.0010.0010.0000.0000.0000.000
172A160GLN00.0580.02146.9270.0010.0010.0000.0000.0000.000
173A161LYS10.7950.91047.057-0.028-0.0280.0000.0000.0000.000
174A162ILE00.0280.01141.7580.0020.0020.0000.0000.0000.000
175A163GLU-1-0.981-0.98642.8970.0460.0460.0000.0000.0000.000
176A164GLN0-0.007-0.01844.2490.0020.0020.0000.0000.0000.000
177A165ALA00.0500.03041.1120.0020.0020.0000.0000.0000.000
178A166ARG10.8390.89839.082-0.056-0.0560.0000.0000.0000.000
179A167LYS10.8970.93740.183-0.045-0.0450.0000.0000.0000.000
180A168TYR00.0150.01638.9850.0020.0020.0000.0000.0000.000
181A169TRP0-0.009-0.02135.5390.0020.0020.0000.0000.0000.000
182A170LYS10.8840.94836.963-0.065-0.0650.0000.0000.0000.000
183A171GLY00.0460.04838.6560.0030.0030.0000.0000.0000.000
184A172ASN0-0.076-0.04240.2980.0000.0000.0000.0000.0000.000
185A173ILE0-0.021-0.01642.6400.0020.0020.0000.0000.0000.000
186A174ARG10.7560.85345.323-0.046-0.0460.0000.0000.0000.000
187A175ASN0-0.034-0.02843.829-0.002-0.0020.0000.0000.0000.000
188A176GLU-1-0.812-0.89045.7240.0420.0420.0000.0000.0000.000
189A177LEU00.0080.00146.0740.0010.0010.0000.0000.0000.000
190A178PRO0-0.0050.01041.330-0.001-0.0010.0000.0000.0000.000
191A179GLU-1-0.863-0.93441.2050.0400.0400.0000.0000.0000.000
192A180LEU0-0.042-0.02435.4020.0030.0030.0000.0000.0000.000
193A181LEU0-0.001-0.00535.251-0.004-0.0040.0000.0000.0000.000
194A182ILE00.0180.00132.5210.0060.0060.0000.0000.0000.000
195A183ASN00.0420.02227.964-0.002-0.0020.0000.0000.0000.000
196A184GLY00.0440.00926.2780.0070.0070.0000.0000.0000.000
197A185GLU-1-0.891-0.96024.8390.0210.0210.0000.0000.0000.000
198A186ILE0-0.027-0.00727.4540.0060.0060.0000.0000.0000.000
199A187GLU-1-0.853-0.93230.5080.0320.0320.0000.0000.0000.000
200A188VAL0-0.023-0.00432.3570.0040.0040.0000.0000.0000.000
201A189VAL00.0110.00333.210-0.003-0.0030.0000.0000.0000.000
202A190GLU-1-0.827-0.91936.0800.0360.0360.0000.0000.0000.000
203A191ILE0-0.0130.00139.8160.0010.0010.0000.0000.0000.000
204A192ILE0-0.042-0.01341.9860.0000.0000.0000.0000.0000.000
205A193ASP-1-0.813-0.90245.0490.0250.0250.0000.0000.0000.000
206A194ASP-1-0.793-0.89347.7310.0140.0140.0000.0000.0000.000
207A195PHE0-0.0060.00649.308-0.002-0.0020.0000.0000.0000.000