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: K2G73

Calculation Name: 1ET9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ET9

Chain ID: A

ChEMBL ID:

UniProt ID: P0C0I6

Base Structure: X-ray

Registration Date: 2023-09-27

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2369736.304732
FMO2-HF: Nuclear repulsion 2290149.808021
FMO2-HF: Total energy -79586.496711
FMO2-MP2: Total energy -79822.223916


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:ASN)


Summations of interaction energy for fragment #1(A:1:ASN)
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.
-18.903-16.07110.071-4.984-7.920.055
Interaction energy analysis for fragmet #1(A:1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.088 / q_NPA : 0.043
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].
3A3TYR00.0210.0201.937-11.641-10.0439.935-5.234-6.2990.050
4A4ASN0-0.0070.0173.037-4.456-3.4640.1380.290-1.4200.005
5A5THR00.0500.0214.714-1.247-1.147-0.001-0.017-0.0830.000
6A6THR00.0620.0298.095-0.305-0.3050.0000.0000.0000.000
7A7ASN00.0050.0036.175-0.107-0.1070.0000.0000.0000.000
8A8ARG10.7700.8725.992-2.545-2.5450.0000.0000.0000.000
9A9HIS00.0120.0169.649-0.183-0.1830.0000.0000.0000.000
10A10ASN0-0.013-0.00511.538-0.112-0.1120.0000.0000.0000.000
11A11LEU00.0230.00610.711-0.079-0.0790.0000.0000.0000.000
12A12GLU-1-0.810-0.91913.2350.4680.4680.0000.0000.0000.000
13A13SER0-0.068-0.04015.394-0.091-0.0910.0000.0000.0000.000
14A14LEU0-0.028-0.00515.825-0.048-0.0480.0000.0000.0000.000
15A15TYR00.028-0.00916.157-0.037-0.0370.0000.0000.0000.000
16A16LYS10.7740.89417.573-0.467-0.4670.0000.0000.0000.000
17A17HIS00.0010.00120.363-0.047-0.0470.0000.0000.0000.000
18A18ASP-1-0.831-0.91523.4240.1730.1730.0000.0000.0000.000
19A19SER0-0.029-0.01524.589-0.009-0.0090.0000.0000.0000.000
20A20ASN0-0.046-0.01921.094-0.016-0.0160.0000.0000.0000.000
21A21LEU0-0.0270.00224.610-0.004-0.0040.0000.0000.0000.000
22A22ILE0-0.043-0.02326.525-0.007-0.0070.0000.0000.0000.000
23A23GLU-1-0.871-0.93729.3910.0940.0940.0000.0000.0000.000
24A24ALA0-0.082-0.05631.6040.0010.0010.0000.0000.0000.000
25A25ASP-1-0.814-0.90835.0160.0640.0640.0000.0000.0000.000
26A26SER0-0.041-0.02537.951-0.001-0.0010.0000.0000.0000.000
27A27ILE0-0.0140.00836.5970.0000.0000.0000.0000.0000.000
28A28LYS10.8850.93239.291-0.049-0.0490.0000.0000.0000.000
29A29ASN0-0.047-0.03437.8940.0020.0020.0000.0000.0000.000
30A30SER00.0320.01038.481-0.002-0.0020.0000.0000.0000.000
31A31PRO0-0.0130.01040.3800.0000.0000.0000.0000.0000.000
32A32ASP-1-0.847-0.92638.8800.0650.0650.0000.0000.0000.000
33A33ILE00.0040.00439.398-0.002-0.0020.0000.0000.0000.000
34A34VAL0-0.012-0.00935.6940.0050.0050.0000.0000.0000.000
35A35THR00.0280.00632.199-0.004-0.0040.0000.0000.0000.000
36A36SER00.006-0.02633.742-0.001-0.0010.0000.0000.0000.000
37A37HIS00.0330.04129.272-0.001-0.0010.0000.0000.0000.000
38A38MET0-0.036-0.00830.2870.0040.0040.0000.0000.0000.000
39A39LEU0-0.022-0.01032.190-0.006-0.0060.0000.0000.0000.000
40A40LYS10.8510.92832.754-0.067-0.0670.0000.0000.0000.000
41A41TYR00.0470.02133.452-0.004-0.0040.0000.0000.0000.000
42A42SER00.0170.00934.8290.0050.0050.0000.0000.0000.000
43A43VAL00.0140.00133.504-0.004-0.0040.0000.0000.0000.000
44A44LYS10.9050.95432.928-0.097-0.0970.0000.0000.0000.000
45A45ASP-1-0.855-0.93933.3150.1150.1150.0000.0000.0000.000
46A46LYS10.8260.93628.762-0.140-0.1400.0000.0000.0000.000
47A47ASN00.0210.00132.409-0.008-0.0080.0000.0000.0000.000
48A48LEU0-0.010-0.00727.9290.0080.0080.0000.0000.0000.000
49A49SER0-0.011-0.03528.521-0.011-0.0110.0000.0000.0000.000
50A50VAL0-0.021-0.01228.3380.0070.0070.0000.0000.0000.000
51A51PHE00.0260.00525.557-0.009-0.0090.0000.0000.0000.000
52A52PHE00.011-0.01627.4070.0020.0020.0000.0000.0000.000
53A53GLU-1-0.833-0.90924.2200.0370.0370.0000.0000.0000.000
54A54LYS10.7910.86826.848-0.035-0.0350.0000.0000.0000.000
55A55ASP-1-0.840-0.91930.5240.0390.0390.0000.0000.0000.000
56A56TRP00.0370.00732.0420.0030.0030.0000.0000.0000.000
57A57ILE0-0.032-0.00329.6190.0000.0000.0000.0000.0000.000
58A58SER00.0150.01733.7440.0010.0010.0000.0000.0000.000
59A59GLN0-0.006-0.01535.2860.0000.0000.0000.0000.0000.000
60A60GLU-1-0.815-0.86335.4380.0390.0390.0000.0000.0000.000
61A61PHE00.014-0.00232.6490.0000.0000.0000.0000.0000.000
62A62LYS10.8580.93136.907-0.050-0.0500.0000.0000.0000.000
63A63ASP-1-0.840-0.90840.1600.0450.0450.0000.0000.0000.000
64A64LYS10.8110.91541.097-0.041-0.0410.0000.0000.0000.000
65A65GLU-1-0.897-0.92940.6350.0510.0510.0000.0000.0000.000
66A66VAL0-0.058-0.03335.853-0.002-0.0020.0000.0000.0000.000
67A67ASP-1-0.746-0.84835.5900.0590.0590.0000.0000.0000.000
68A68ILE0-0.050-0.03430.645-0.001-0.0010.0000.0000.0000.000
69A69TYR0-0.013-0.01625.9100.0050.0050.0000.0000.0000.000
70A70ALA00.0150.01825.870-0.002-0.0020.0000.0000.0000.000
71A71LEU0-0.0080.00720.1070.0040.0040.0000.0000.0000.000
72A72SER0-0.061-0.03623.259-0.011-0.0110.0000.0000.0000.000
73A73ALA0-0.001-0.00120.4020.0210.0210.0000.0000.0000.000
74A74GLN0-0.0030.00522.286-0.012-0.0120.0000.0000.0000.000
75A75GLU-1-0.830-0.88823.5310.1220.1220.0000.0000.0000.000
76A83ARG10.8690.93330.344-0.108-0.1080.0000.0000.0000.000
77A84TYR0-0.026-0.01925.6560.0080.0080.0000.0000.0000.000
78A85GLU-1-0.840-0.89922.4760.1410.1410.0000.0000.0000.000
79A86ALA00.0380.00624.3030.0120.0120.0000.0000.0000.000
80A87PHE0-0.009-0.00321.429-0.010-0.0100.0000.0000.0000.000
81A88GLY00.0400.01624.7540.0000.0000.0000.0000.0000.000
82A89GLY00.0080.00327.2890.0060.0060.0000.0000.0000.000
83A90ILE0-0.037-0.01728.0120.0020.0020.0000.0000.0000.000
84A91THR00.0150.00631.791-0.004-0.0040.0000.0000.0000.000
85A92LEU0-0.011-0.00534.5510.0020.0020.0000.0000.0000.000
86A93THR0-0.022-0.01738.356-0.001-0.0010.0000.0000.0000.000
87A94ASN0-0.020-0.00940.024-0.004-0.0040.0000.0000.0000.000
88A95SER00.0570.02041.8280.0020.0020.0000.0000.0000.000
89A96GLU-1-0.869-0.91142.6390.0300.0300.0000.0000.0000.000
90A97LYS10.7640.88338.337-0.057-0.0570.0000.0000.0000.000
91A98LYS10.8230.88640.927-0.027-0.0270.0000.0000.0000.000
92A99GLU-1-0.845-0.90536.7420.0540.0540.0000.0000.0000.000
93A100ILE00.0040.00834.684-0.004-0.0040.0000.0000.0000.000
94A101LYS10.8120.87933.606-0.044-0.0440.0000.0000.0000.000
95A102VAL00.0560.04028.637-0.005-0.0050.0000.0000.0000.000
96A103PRO00.023-0.00130.0910.0070.0070.0000.0000.0000.000
97A104VAL0-0.015-0.01524.1390.0010.0010.0000.0000.0000.000
98A105ASN0-0.026-0.00825.3230.0070.0070.0000.0000.0000.000
99A106VAL0-0.026-0.02120.5720.0050.0050.0000.0000.0000.000
100A107TRP0-0.0010.00119.940-0.013-0.0130.0000.0000.0000.000
101A108ASP-1-0.760-0.86718.2240.0870.0870.0000.0000.0000.000
102A109LYS10.8060.89213.266-0.073-0.0730.0000.0000.0000.000
103A110SER0-0.006-0.00717.900-0.018-0.0180.0000.0000.0000.000
104A111LYS10.7980.89620.129-0.013-0.0130.0000.0000.0000.000
105A112GLN00.0270.02322.5550.0070.0070.0000.0000.0000.000
106A113GLN0-0.013-0.00722.607-0.012-0.0120.0000.0000.0000.000
107A114PRO0-0.001-0.01625.696-0.004-0.0040.0000.0000.0000.000
108A115PRO00.0320.01627.8960.0070.0070.0000.0000.0000.000
109A116MET0-0.048-0.01224.3970.0150.0150.0000.0000.0000.000
110A117PHE00.0190.01028.953-0.007-0.0070.0000.0000.0000.000
111A118ILE0-0.0280.00126.0130.0120.0120.0000.0000.0000.000
112A119THR0-0.0100.00229.399-0.005-0.0050.0000.0000.0000.000
113A120VAL00.0110.01130.4750.0080.0080.0000.0000.0000.000
114A121ASN00.018-0.00333.126-0.002-0.0020.0000.0000.0000.000
115A122LYS10.9450.97232.124-0.076-0.0760.0000.0000.0000.000
116A123PRO00.0400.04235.8270.0000.0000.0000.0000.0000.000
117A124LYS10.9310.96434.572-0.030-0.0300.0000.0000.0000.000
118A125VAL00.0250.02929.2730.0040.0040.0000.0000.0000.000
119A126THR00.0370.01627.271-0.003-0.0030.0000.0000.0000.000
120A127ALA00.0460.01123.7330.0040.0040.0000.0000.0000.000
121A128GLN00.0130.00622.7290.0160.0160.0000.0000.0000.000
122A129GLU-1-0.761-0.86423.5750.0910.0910.0000.0000.0000.000
123A130VAL00.0150.01023.9760.0080.0080.0000.0000.0000.000
124A131ASP-1-0.735-0.82218.3030.1490.1490.0000.0000.0000.000
125A132ILE0-0.018-0.00720.6750.0220.0220.0000.0000.0000.000
126A133LYS10.7990.89322.163-0.074-0.0740.0000.0000.0000.000
127A134VAL00.0210.01220.1190.0080.0080.0000.0000.0000.000
128A135ARG10.8260.89413.420-0.187-0.1870.0000.0000.0000.000
129A136LYS10.7930.88919.521-0.178-0.1780.0000.0000.0000.000
130A137LEU0-0.032-0.01222.3010.0080.0080.0000.0000.0000.000
131A138LEU00.003-0.00917.1640.0040.0040.0000.0000.0000.000
132A139ILE0-0.002-0.01016.8330.0180.0180.0000.0000.0000.000
133A140LYS10.9120.95518.979-0.176-0.1760.0000.0000.0000.000
134A141LYS10.8690.94621.297-0.134-0.1340.0000.0000.0000.000
135A142TYR00.0000.00817.815-0.029-0.0290.0000.0000.0000.000
136A143ASP-1-0.866-0.91916.8940.5010.5010.0000.0000.0000.000
137A144ILE00.0070.00113.7960.0900.0900.0000.0000.0000.000
138A145TYR0-0.008-0.01610.9510.1010.1010.0000.0000.0000.000
139A146ASN0-0.028-0.01011.3700.2700.2700.0000.0000.0000.000
140A147ASN00.061-0.0019.2260.6150.6150.0000.0000.0000.000
141A148ARG10.9180.97711.439-0.383-0.3830.0000.0000.0000.000
142A149GLU-1-0.833-0.91713.2250.3060.3060.0000.0000.0000.000
143A150GLN0-0.075-0.0376.306-0.134-0.1340.0000.0000.0000.000
144A151LYS10.8990.9499.642-0.293-0.2930.0000.0000.0000.000
145A152TYR0-0.045-0.03010.961-0.183-0.1830.0000.0000.0000.000
146A153SER00.0240.0145.7470.2240.2240.0000.0000.0000.000
147A154LYS10.9951.0136.5520.9040.9040.0000.0000.0000.000
148A155GLY00.0620.0279.0530.0350.0350.0000.0000.0000.000
149A156THR0-0.0170.00412.4580.0070.0070.0000.0000.0000.000
150A157VAL00.0240.01215.2260.0110.0110.0000.0000.0000.000
151A158THR00.0260.01218.675-0.011-0.0110.0000.0000.0000.000
152A159LEU0-0.045-0.02321.2260.0040.0040.0000.0000.0000.000
153A160ASP-1-0.831-0.90524.543-0.020-0.0200.0000.0000.0000.000
154A161LEU0-0.001-0.01327.0750.0080.0080.0000.0000.0000.000
155A162ASN00.032-0.00829.788-0.003-0.0030.0000.0000.0000.000
156A163SER0-0.051-0.02131.954-0.001-0.0010.0000.0000.0000.000
157A164GLY0-0.025-0.00231.384-0.001-0.0010.0000.0000.0000.000
158A165LYS10.7880.87825.604-0.010-0.0100.0000.0000.0000.000
159A166ASP-1-0.845-0.90422.891-0.032-0.0320.0000.0000.0000.000
160A167ILE0-0.068-0.04021.5780.0010.0010.0000.0000.0000.000
161A168VAL0-0.016-0.00116.6260.0040.0040.0000.0000.0000.000
162A169PHE00.001-0.00216.1540.0020.0020.0000.0000.0000.000
163A170ASP-1-0.834-0.9209.508-0.042-0.0420.0000.0000.0000.000
164A171LEU0-0.015-0.00612.3150.0420.0420.0000.0000.0000.000
165A172TYR0-0.052-0.0557.0090.1410.1410.0000.0000.0000.000
166A173TYR0-0.0170.0097.239-0.146-0.1460.0000.0000.0000.000
167A174PHE00.016-0.0134.6920.0200.162-0.001-0.023-0.1180.000
168A175GLY00.0320.0299.4920.0400.0400.0000.0000.0000.000
169A176ASN0-0.082-0.0499.292-0.053-0.0530.0000.0000.0000.000
170A177GLY0-0.0010.0029.8700.0380.0380.0000.0000.0000.000
171A178ASP-1-0.850-0.89710.5650.3370.3370.0000.0000.0000.000
172A179PHE00.030-0.01314.398-0.017-0.0170.0000.0000.0000.000
173A180ASN0-0.002-0.01016.619-0.003-0.0030.0000.0000.0000.000
174A181SER00.010-0.01313.802-0.028-0.0280.0000.0000.0000.000
175A182MET0-0.085-0.02110.741-0.015-0.0150.0000.0000.0000.000
176A183LEU00.0430.02214.745-0.019-0.0190.0000.0000.0000.000
177A184LYS10.9690.99417.917-0.118-0.1180.0000.0000.0000.000
178A185ILE0-0.0190.00115.333-0.017-0.0170.0000.0000.0000.000
179A186TYR0-0.002-0.00718.607-0.006-0.0060.0000.0000.0000.000
180A187SER0-0.018-0.01221.849-0.008-0.0080.0000.0000.0000.000
181A188ASN00.0080.00323.8860.0040.0040.0000.0000.0000.000
182A189ASN00.001-0.00525.8650.0000.0000.0000.0000.0000.000
183A190GLU-1-0.828-0.88625.5480.0170.0170.0000.0000.0000.000
184A191ARG10.7400.82527.532-0.038-0.0380.0000.0000.0000.000
185A192ILE00.0020.01727.755-0.005-0.0050.0000.0000.0000.000
186A193ASP-1-0.794-0.88531.4770.0270.0270.0000.0000.0000.000
187A194SER0-0.034-0.05232.7170.0000.0000.0000.0000.0000.000
188A195THR0-0.078-0.05533.7520.0010.0010.0000.0000.0000.000
189A196GLN0-0.083-0.03434.862-0.005-0.0050.0000.0000.0000.000
190A197PHE0-0.009-0.01427.009-0.001-0.0010.0000.0000.0000.000
191A198HIS0-0.064-0.00927.3490.0070.0070.0000.0000.0000.000
192A199VAL0-0.018-0.01722.8700.0010.0010.0000.0000.0000.000
193A200ASP-1-0.783-0.87122.609-0.011-0.0110.0000.0000.0000.000
194A201VAL00.003-0.01018.5390.0050.0050.0000.0000.0000.000
195A202SER0-0.0180.00016.527-0.009-0.0090.0000.0000.0000.000
196A203ILE0-0.0080.00814.2030.0250.0250.0000.0000.0000.000
197A204SER0-0.002-0.02010.876-0.004-0.0040.0000.0000.0000.000