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: 3QZ6L

Calculation Name: 2JEU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JEU

Chain ID: A

ChEMBL ID:

UniProt ID: P03122

Base Structure: X-ray

Registration Date: 2023-03-13

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2078426.138207
FMO2-HF: Nuclear repulsion 1998276.393835
FMO2-HF: Total energy -80149.744372
FMO2-MP2: Total energy -80379.530838


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:3:THR)


Summations of interaction energy for fragment #1(A:3:THR)
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.
-31.393-27.08115.177-9.854-9.635-0.089
Interaction energy analysis for fragmet #1(A:3:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.010
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].
3A5CYS00.0200.0013.330-1.971-0.034-0.007-0.840-1.0900.003
4A6GLU-1-0.769-0.8741.978-29.178-27.22813.120-8.387-6.683-0.094
5A7ARG10.9570.9662.2560.2160.5662.065-0.623-1.7920.002
6A8LEU0-0.036-0.0055.3780.7130.788-0.001-0.004-0.0700.000
7A9HIS00.0530.0297.7110.2940.2940.0000.0000.0000.000
8A10VAL00.0230.0167.6150.2880.2880.0000.0000.0000.000
9A11ALA0-0.038-0.0059.4070.2810.2810.0000.0000.0000.000
10A12GLN0-0.037-0.04211.2190.0130.0130.0000.0000.0000.000
11A13GLU-1-0.859-0.91512.877-0.719-0.7190.0000.0000.0000.000
12A14THR0-0.035-0.03712.8360.1060.1060.0000.0000.0000.000
13A15GLN0-0.101-0.07914.2840.1370.1370.0000.0000.0000.000
14A16MET0-0.014-0.00317.6390.0430.0430.0000.0000.0000.000
15A17GLN0-0.009-0.00617.1350.0640.0640.0000.0000.0000.000
16A18LEU0-0.042-0.02918.2990.0450.0450.0000.0000.0000.000
17A19ILE0-0.051-0.03621.2960.0370.0370.0000.0000.0000.000
18A20GLU-1-0.922-0.96123.323-0.335-0.3350.0000.0000.0000.000
19A21LYS10.8000.90922.6930.2820.2820.0000.0000.0000.000
20A22SER0-0.028-0.01625.8090.0230.0230.0000.0000.0000.000
21A23SER0-0.062-0.06425.3530.0120.0120.0000.0000.0000.000
22A24ASP-1-0.804-0.90327.442-0.114-0.1140.0000.0000.0000.000
23A25LYS10.9160.96626.0030.1910.1910.0000.0000.0000.000
24A26LEU00.0870.04425.801-0.012-0.0120.0000.0000.0000.000
25A27GLN0-0.018-0.02022.585-0.012-0.0120.0000.0000.0000.000
26A28ASP-1-0.780-0.85821.180-0.255-0.2550.0000.0000.0000.000
27A29HIS00.005-0.00520.888-0.029-0.0290.0000.0000.0000.000
28A30ILE0-0.0010.00819.0400.0100.0100.0000.0000.0000.000
29A31LEU0-0.0190.00914.9050.0160.0160.0000.0000.0000.000
30A32TYR00.0540.02416.296-0.018-0.0180.0000.0000.0000.000
31A33TRP00.0370.00817.148-0.011-0.0110.0000.0000.0000.000
32A34THR0-0.026-0.02412.9550.0490.0490.0000.0000.0000.000
33A35ALA0-0.0180.00712.5730.0360.0360.0000.0000.0000.000
34A36VAL00.0520.04012.946-0.006-0.0060.0000.0000.0000.000
35A37ARG10.9280.95913.676-0.125-0.1250.0000.0000.0000.000
36A38THR0-0.067-0.0268.2270.1370.1370.0000.0000.0000.000
37A39GLU-1-0.796-0.87810.155-0.266-0.2660.0000.0000.0000.000
38A40ASN0-0.051-0.05011.5920.1010.1010.0000.0000.0000.000
39A41THR0-0.007-0.01210.9900.0880.0880.0000.0000.0000.000
40A42LEU0-0.054-0.0225.4100.2270.2270.0000.0000.0000.000
41A43LEU00.0230.0149.5180.1900.1900.0000.0000.0000.000
42A44TYR00.005-0.00712.5290.0420.0420.0000.0000.0000.000
43A45ALA0-0.020-0.02510.3440.0300.0300.0000.0000.0000.000
44A46ALA0-0.008-0.00210.8430.1160.1160.0000.0000.0000.000
45A47ARG10.9120.95312.163-0.242-0.2420.0000.0000.0000.000
46A48LYS10.8550.94215.302-0.390-0.3900.0000.0000.0000.000
47A49LYS10.9190.9689.386-1.526-1.5260.0000.0000.0000.000
48A50GLY00.0000.00714.8450.0010.0010.0000.0000.0000.000
49A51VAL0-0.0180.00111.219-0.043-0.0430.0000.0000.0000.000
50A52THR0-0.004-0.01314.551-0.053-0.0530.0000.0000.0000.000
51A53VAL0-0.012-0.00614.348-0.068-0.0680.0000.0000.0000.000
52A54LEU00.0390.0287.5370.1220.1220.0000.0000.0000.000
53A55GLY00.0510.0359.806-0.133-0.1330.0000.0000.0000.000
54A56HIS0-0.025-0.02410.9560.1150.1150.0000.0000.0000.000
55A57CYS0-0.025-0.01013.7710.0130.0130.0000.0000.0000.000
56A58ARG10.9870.98314.7500.1630.1630.0000.0000.0000.000
57A59VAL00.0090.01713.538-0.040-0.0400.0000.0000.0000.000
58A60PRO00.0240.01416.3040.0320.0320.0000.0000.0000.000
59A61HIS00.1150.04318.6590.0580.0580.0000.0000.0000.000
60A62SER00.0050.00918.565-0.001-0.0010.0000.0000.0000.000
61A63VAL00.0500.01019.5900.0050.0050.0000.0000.0000.000
62A64VAL00.0120.01021.034-0.012-0.0120.0000.0000.0000.000
63A65CYS0-0.065-0.02016.053-0.019-0.0190.0000.0000.0000.000
64A66GLN00.023-0.00517.850-0.016-0.0160.0000.0000.0000.000
65A67GLU-1-0.826-0.89919.2540.1130.1130.0000.0000.0000.000
66A68ARG10.9951.01218.8690.0320.0320.0000.0000.0000.000
67A69ALA00.0040.00716.138-0.019-0.0190.0000.0000.0000.000
68A70LYS10.8600.90917.651-0.157-0.1570.0000.0000.0000.000
69A71GLN0-0.0110.00120.794-0.017-0.0170.0000.0000.0000.000
70A72ALA00.0250.00917.729-0.010-0.0100.0000.0000.0000.000
71A73ILE0-0.071-0.04016.926-0.003-0.0030.0000.0000.0000.000
72A74GLU-1-0.759-0.82619.5290.0460.0460.0000.0000.0000.000
73A75MET00.0010.02521.875-0.001-0.0010.0000.0000.0000.000
74A76GLN00.0370.02916.1420.0190.0190.0000.0000.0000.000
75A77LEU0-0.039-0.03019.386-0.005-0.0050.0000.0000.0000.000
76A78SER00.0110.00122.421-0.002-0.0020.0000.0000.0000.000
77A79LEU00.0390.02423.028-0.005-0.0050.0000.0000.0000.000
78A80GLN0-0.027-0.01318.997-0.016-0.0160.0000.0000.0000.000
79A81GLU-1-0.848-0.88823.8870.0500.0500.0000.0000.0000.000
80A82LEU00.0130.02127.130-0.002-0.0020.0000.0000.0000.000
81A83SER0-0.039-0.02525.722-0.004-0.0040.0000.0000.0000.000
82A84LYS10.8950.96024.226-0.031-0.0310.0000.0000.0000.000
83A85THR0-0.042-0.02629.4960.0040.0040.0000.0000.0000.000
84A86GLU-1-0.855-0.93832.842-0.026-0.0260.0000.0000.0000.000
85A87PHE00.009-0.00533.545-0.004-0.0040.0000.0000.0000.000
86A88GLY0-0.078-0.02730.502-0.007-0.0070.0000.0000.0000.000
87A89ASP-1-0.895-0.93530.387-0.067-0.0670.0000.0000.0000.000
88A90GLU-1-0.897-0.93233.023-0.054-0.0540.0000.0000.0000.000
89A91PRO00.0070.01632.256-0.005-0.0050.0000.0000.0000.000
90A92TRP0-0.028-0.03129.1010.0110.0110.0000.0000.0000.000
91A93SER00.0550.01229.309-0.014-0.0140.0000.0000.0000.000
92A94LEU00.0320.00823.8550.0100.0100.0000.0000.0000.000
93A95LEU0-0.0100.00527.4060.0080.0080.0000.0000.0000.000
94A96ASP-1-0.789-0.86430.316-0.070-0.0700.0000.0000.0000.000
95A97THR0-0.040-0.01524.7220.0140.0140.0000.0000.0000.000
96A98SER0-0.003-0.01125.861-0.001-0.0010.0000.0000.0000.000
97A99TRP00.058-0.00525.2350.0140.0140.0000.0000.0000.000
98A100ASP-1-0.881-0.94227.209-0.043-0.0430.0000.0000.0000.000
99A101ARG10.8040.90230.4960.0700.0700.0000.0000.0000.000
100A102TYR0-0.049-0.04228.1840.0050.0050.0000.0000.0000.000
101A103MET0-0.032-0.02429.3630.0100.0100.0000.0000.0000.000
102A104SER0-0.053-0.01632.1440.0050.0050.0000.0000.0000.000
103A105GLU-1-0.769-0.85635.4290.0100.0100.0000.0000.0000.000
104A106PRO0-0.058-0.03238.397-0.005-0.0050.0000.0000.0000.000
105A107LYS10.8590.89234.249-0.015-0.0150.0000.0000.0000.000
106A108ARG10.8350.88527.851-0.048-0.0480.0000.0000.0000.000
107A109CYS0-0.0510.00732.2900.0020.0020.0000.0000.0000.000
108A110PHE00.0470.01826.852-0.005-0.0050.0000.0000.0000.000
109A111LYS10.8670.93832.7550.0200.0200.0000.0000.0000.000
110A112LYS10.8260.92233.4190.0570.0570.0000.0000.0000.000
111A113GLY00.0270.02636.8250.0040.0040.0000.0000.0000.000
112A114ALA0-0.022-0.01239.1470.0050.0050.0000.0000.0000.000
113A115ARG10.8620.90241.1500.0260.0260.0000.0000.0000.000
114A116VAL0-0.006-0.00244.1450.0020.0020.0000.0000.0000.000
115A117VAL0-0.0270.00346.1670.0010.0010.0000.0000.0000.000
116A118GLU-1-0.821-0.89448.712-0.029-0.0290.0000.0000.0000.000
117A119VAL0-0.016-0.01050.6650.0010.0010.0000.0000.0000.000
118A120GLU-1-0.898-0.93552.924-0.018-0.0180.0000.0000.0000.000
119A121PHE00.0350.00251.7340.0020.0020.0000.0000.0000.000
120A122ASP-1-0.783-0.88657.398-0.007-0.0070.0000.0000.0000.000
121A123GLY0-0.0040.01360.3760.0000.0000.0000.0000.0000.000
122A124ASN0-0.063-0.03359.407-0.002-0.0020.0000.0000.0000.000
123A125ALA00.0900.04958.1760.0000.0000.0000.0000.0000.000
124A126SER0-0.061-0.03256.411-0.001-0.0010.0000.0000.0000.000
125A127ASN0-0.090-0.03954.199-0.001-0.0010.0000.0000.0000.000
126A128THR00.0290.00451.8910.0020.0020.0000.0000.0000.000
127A129ASN0-0.033-0.01048.485-0.002-0.0020.0000.0000.0000.000
128A130TRP0-0.074-0.05345.964-0.002-0.0020.0000.0000.0000.000
129A131TYR0-0.040-0.04244.4490.0000.0000.0000.0000.0000.000
130A132THR0-0.001-0.00839.898-0.002-0.0020.0000.0000.0000.000
131A133VAL0-0.0220.01242.1960.0030.0030.0000.0000.0000.000
132A134TYR00.015-0.01237.008-0.007-0.0070.0000.0000.0000.000
133A135SER00.006-0.00441.2220.0030.0030.0000.0000.0000.000
134A136ASN0-0.028-0.01539.0930.0050.0050.0000.0000.0000.000
135A137LEU0-0.002-0.01137.510-0.003-0.0030.0000.0000.0000.000
136A138TYR0-0.024-0.04533.9040.0020.0020.0000.0000.0000.000
137A139MET0-0.004-0.01134.1210.0020.0020.0000.0000.0000.000
138A140ARG10.8590.92127.796-0.051-0.0510.0000.0000.0000.000
139A141THR0-0.013-0.01333.7740.0020.0020.0000.0000.0000.000
140A142GLU-1-0.910-0.95835.3970.0610.0610.0000.0000.0000.000
141A143ASP-1-0.982-0.97836.7540.0320.0320.0000.0000.0000.000
142A144GLY0-0.020-0.00633.898-0.004-0.0040.0000.0000.0000.000
143A145TRP0-0.066-0.07528.796-0.005-0.0050.0000.0000.0000.000
144A146GLN00.0310.02734.582-0.004-0.0040.0000.0000.0000.000
145A147LEU0-0.034-0.01337.8320.0000.0000.0000.0000.0000.000
146A148ALA00.0160.02039.6740.0030.0030.0000.0000.0000.000
147A149LYS10.9160.95941.5540.0220.0220.0000.0000.0000.000
148A150ALA00.0370.01942.6870.0040.0040.0000.0000.0000.000
149A151GLY0-0.040-0.02444.819-0.003-0.0030.0000.0000.0000.000
150A152ALA00.0250.01847.6250.0020.0020.0000.0000.0000.000
151A153ASP-1-0.791-0.86850.125-0.006-0.0060.0000.0000.0000.000
152A154GLY00.0640.01653.3560.0000.0000.0000.0000.0000.000
153A155THR0-0.0310.01153.5900.0010.0010.0000.0000.0000.000
154A156GLY00.018-0.01850.4250.0020.0020.0000.0000.0000.000
155A157LEU0-0.0260.01644.717-0.002-0.0020.0000.0000.0000.000
156A158TYR0-0.007-0.02146.6790.0030.0030.0000.0000.0000.000
157A159TYR00.016-0.01041.555-0.003-0.0030.0000.0000.0000.000
158A160CYS0-0.041-0.01545.4370.0030.0030.0000.0000.0000.000
159A161THR00.0580.02142.680-0.002-0.0020.0000.0000.0000.000
160A162MET0-0.036-0.02345.2230.0000.0000.0000.0000.0000.000
161A163ALA00.0360.02244.8730.0010.0010.0000.0000.0000.000
162A164GLY00.006-0.01147.0090.0020.0020.0000.0000.0000.000
163A165ALA0-0.044-0.00550.120-0.002-0.0020.0000.0000.0000.000
164A166GLY00.0150.00151.2320.0010.0010.0000.0000.0000.000
165A167ARG10.8560.92949.4450.0060.0060.0000.0000.0000.000
166A168ILE00.0240.01544.7070.0020.0020.0000.0000.0000.000
167A169TYR0-0.077-0.07346.167-0.001-0.0010.0000.0000.0000.000
168A170TYR0-0.012-0.00542.1100.0030.0030.0000.0000.0000.000
169A171SER0-0.024-0.00644.3650.0010.0010.0000.0000.0000.000
170A172ARG10.9840.99646.389-0.010-0.0100.0000.0000.0000.000
171A173PHE00.0710.03448.7930.0010.0010.0000.0000.0000.000
172A174GLY00.0590.03852.0860.0000.0000.0000.0000.0000.000
173A175ASP-1-0.877-0.95750.4620.0090.0090.0000.0000.0000.000
174A176GLU-1-0.822-0.87447.120-0.003-0.0030.0000.0000.0000.000
175A177ALA00.0140.00651.000-0.001-0.0010.0000.0000.0000.000
176A178ALA0-0.0350.00953.6640.0000.0000.0000.0000.0000.000
177A179ARG10.7720.87846.605-0.002-0.0020.0000.0000.0000.000
178A180PHE0-0.025-0.01746.9570.0000.0000.0000.0000.0000.000
179A181SER0-0.072-0.02653.167-0.001-0.0010.0000.0000.0000.000
180A182THR0-0.055-0.04356.8130.0010.0010.0000.0000.0000.000
181A183THR0-0.061-0.05560.1520.0010.0010.0000.0000.0000.000
182A184GLY0-0.0090.01658.9370.0010.0010.0000.0000.0000.000
183A185HIS00.007-0.02459.0760.0000.0000.0000.0000.0000.000
184A186TYR0-0.020-0.01655.5170.0000.0000.0000.0000.0000.000
185A187SER0-0.045-0.01457.4640.0000.0000.0000.0000.0000.000
186A188VAL00.001-0.01552.502-0.001-0.0010.0000.0000.0000.000
187A189ARG10.9260.96254.3930.0260.0260.0000.0000.0000.000
188A190ASP-1-0.840-0.90150.522-0.025-0.0250.0000.0000.0000.000
189A191GLN0-0.035-0.04250.921-0.002-0.0020.0000.0000.0000.000
190A192ASP-1-0.914-0.94353.774-0.027-0.0270.0000.0000.0000.000
191A193ARG10.9210.96155.3700.0210.0210.0000.0000.0000.000
192A194VAL00.0290.02156.439-0.001-0.0010.0000.0000.0000.000
193A195TYR0-0.039-0.01054.2010.0020.0020.0000.0000.0000.000
194A196ALA00.0480.00958.574-0.001-0.0010.0000.0000.0000.000
195A197GLY0-0.0270.00058.7590.0010.0010.0000.0000.0000.000
196A198VAL0-0.003-0.00859.750-0.001-0.0010.0000.0000.0000.000
197A199SER0-0.0420.00356.6430.0010.0010.0000.0000.0000.000