FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: R85R8

Calculation Name: 2EEN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EEN

Chain ID: A

ChEMBL ID:

UniProt ID: O59483

Base Structure: X-ray

Registration Date: 2023-09-21

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2112525.267938
FMO2-HF: Nuclear repulsion 2038873.365839
FMO2-HF: Total energy -73651.902099
FMO2-MP2: Total energy -73871.764131


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:2:TYR)


Summations of interaction energy for fragment #1(A:2:TYR)
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.
-34.576-29.36426.778-13.616-18.373-0.046
Interaction energy analysis for fragmet #1(A:2:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.061
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].
3A4VAL0-0.054-0.0293.7800.1551.720-0.006-0.526-1.0330.001
4A5GLU-1-0.888-0.9445.090-0.321-0.250-0.001-0.003-0.0670.000
5A6LEU0-0.070-0.0268.1460.3130.3130.0000.0000.0000.000
6A7LYS10.8370.92711.4510.2010.2010.0000.0000.0000.000
7A8GLY00.0100.00814.6490.0430.0430.0000.0000.0000.000
8A9TYR0-0.124-0.06918.2390.0130.0130.0000.0000.0000.000
9A10ALA00.0180.00121.652-0.021-0.0210.0000.0000.0000.000
10A11ASN0-0.014-0.00923.6450.0200.0200.0000.0000.0000.000
11A12ASP-1-0.845-0.94326.855-0.151-0.1510.0000.0000.0000.000
12A13GLU-1-0.953-0.96428.704-0.199-0.1990.0000.0000.0000.000
13A14ILE0-0.003-0.00422.456-0.012-0.0120.0000.0000.0000.000
14A15PHE0-0.059-0.05322.603-0.020-0.0200.0000.0000.0000.000
15A16GLU-1-0.891-0.96325.760-0.211-0.2110.0000.0000.0000.000
16A17LYS10.9270.98526.0450.2940.2940.0000.0000.0000.000
17A18VAL0-0.0190.00121.603-0.021-0.0210.0000.0000.0000.000
18A19ARG10.8320.92024.3900.1940.1940.0000.0000.0000.000
19A20GLU-1-0.911-0.93126.867-0.211-0.2110.0000.0000.0000.000
20A21THR0-0.142-0.07523.6690.0000.0000.0000.0000.0000.000
21A22PHE0-0.053-0.04220.749-0.037-0.0370.0000.0000.0000.000
22A23GLU-1-0.892-0.92822.226-0.291-0.2910.0000.0000.0000.000
23A24PHE00.002-0.00322.209-0.025-0.0250.0000.0000.0000.000
24A25MET0-0.071-0.01516.902-0.006-0.0060.0000.0000.0000.000
25A26ARG10.8550.90018.5290.2270.2270.0000.0000.0000.000
26A27LYS10.9941.00321.9030.1170.1170.0000.0000.0000.000
27A28GLU-1-0.801-0.89318.218-0.213-0.2130.0000.0000.0000.000
28A29ILE00.0130.01322.408-0.010-0.0100.0000.0000.0000.000
29A30HIS0-0.062-0.05716.3740.0150.0150.0000.0000.0000.000
30A31GLU-1-0.804-0.87621.3780.0160.0160.0000.0000.0000.000
31A32ASP-1-0.788-0.88318.0410.0390.0390.0000.0000.0000.000
32A33ILE00.0080.01220.590-0.008-0.0080.0000.0000.0000.000
33A34TYR00.0210.00814.7660.0280.0280.0000.0000.0000.000
34A35TYR00.0330.00418.797-0.027-0.0270.0000.0000.0000.000
35A36GLN00.0140.02419.0670.0740.0740.0000.0000.0000.000
36A37HIS0-0.002-0.00117.313-0.039-0.0390.0000.0000.0000.000
37A38PRO0-0.010-0.00120.284-0.025-0.0250.0000.0000.0000.000
38A39CYS0-0.065-0.04321.574-0.019-0.0190.0000.0000.0000.000
39A40ARG10.8110.88713.917-0.915-0.9150.0000.0000.0000.000
40A41ASP-1-0.788-0.86320.1660.3940.3940.0000.0000.0000.000
41A42PHE00.030-0.00115.2800.0480.0480.0000.0000.0000.000
42A43SER0-0.049-0.04915.7560.0390.0390.0000.0000.0000.000
43A44LYS10.8750.92917.653-0.401-0.4010.0000.0000.0000.000
44A45THR0-0.067-0.06713.760-0.017-0.0170.0000.0000.0000.000
45A46ASP-1-0.777-0.86911.1450.9740.9740.0000.0000.0000.000
46A47GLU-1-0.727-0.76210.8211.2401.2400.0000.0000.0000.000
47A48ALA0-0.002-0.01012.120-0.166-0.1660.0000.0000.0000.000
48A49LEU00.0220.01312.9660.1040.1040.0000.0000.0000.000
49A50ARG10.9020.94611.955-0.179-0.1790.0000.0000.0000.000
50A51ILE00.0100.03216.7420.0320.0320.0000.0000.0000.000
51A52ARG10.8180.88313.8590.0370.0370.0000.0000.0000.000
52A53ILE0-0.0070.01518.7920.0060.0060.0000.0000.0000.000
53A54LYS10.8480.92815.0070.0980.0980.0000.0000.0000.000
54A55ARG10.8280.89121.016-0.003-0.0030.0000.0000.0000.000
55A56PHE00.0240.00520.699-0.028-0.0280.0000.0000.0000.000
56A57ASN0-0.0030.00024.9150.0010.0010.0000.0000.0000.000
57A58GLY0-0.0060.00727.8030.0030.0030.0000.0000.0000.000
58A59HIS0-0.020-0.00724.8920.0210.0210.0000.0000.0000.000
59A60ASN0-0.008-0.02124.457-0.009-0.0090.0000.0000.0000.000
60A61GLU-1-0.835-0.91518.898-0.052-0.0520.0000.0000.0000.000
61A62VAL00.017-0.00120.209-0.009-0.0090.0000.0000.0000.000
62A63PHE00.0260.03114.877-0.004-0.0040.0000.0000.0000.000
63A64LEU0-0.0130.00816.126-0.019-0.0190.0000.0000.0000.000
64A65THR0-0.052-0.07710.5280.0430.0430.0000.0000.0000.000
65A66TYR0-0.066-0.0698.415-0.007-0.0070.0000.0000.0000.000
66A67LYS10.8710.9308.2080.2080.2080.0000.0000.0000.000
67A68GLY00.0200.0116.625-0.051-0.0510.0000.0000.0000.000
68A69PRO0-0.0060.0006.993-0.321-0.3210.0000.0000.0000.000
69A70LYS10.8110.8996.280-0.149-0.1490.0000.0000.0000.000
70A71ILE0-0.066-0.0362.652-0.6170.4451.482-0.479-2.0650.007
71A72ASP-1-0.749-0.8406.661-0.239-0.2390.0000.0000.0000.000
72A73GLU-1-0.964-1.0148.7930.3020.3020.0000.0000.0000.000
73A74LYS10.9300.96411.3870.0750.0750.0000.0000.0000.000
74A75SER00.013-0.0017.695-0.233-0.2330.0000.0000.0000.000
75A76LYN0-0.031-0.0048.9360.3770.3770.0000.0000.0000.000
76A77THR00.0300.0212.621-0.951-0.3130.578-0.276-0.9400.000
77A78ARG10.8200.9063.8920.0520.4990.002-0.065-0.3840.000
78A79LEU00.0170.0272.561-3.407-1.1190.478-0.859-1.907-0.003
79A80GLU-1-0.831-0.9333.667-1.251-1.0950.0230.017-0.1960.000
80A81ILE0-0.029-0.0126.6570.4590.4590.0000.0000.0000.000
81A82GLU-1-0.863-0.8999.4140.0030.0030.0000.0000.0000.000
82A83VAL0-0.025-0.00411.4230.0180.0180.0000.0000.0000.000
83A84GLU-1-0.906-0.96214.7430.0560.0560.0000.0000.0000.000
84A85ILE0-0.093-0.04617.3600.0150.0150.0000.0000.0000.000
85A86GLN00.008-0.01220.615-0.045-0.0450.0000.0000.0000.000
86A87GLU-1-0.945-0.96623.1510.1020.1020.0000.0000.0000.000
87A88ASP-1-0.916-0.96525.4670.1560.1560.0000.0000.0000.000
88A89VAL00.0530.01323.9620.0180.0180.0000.0000.0000.000
89A90ASP-1-0.899-0.95725.8310.1320.1320.0000.0000.0000.000
90A91LYS10.9410.97627.598-0.141-0.1410.0000.0000.0000.000
91A92TYR00.0080.01220.8750.0150.0150.0000.0000.0000.000
92A93PHE00.010-0.00423.7750.0230.0230.0000.0000.0000.000
93A94GLU-1-0.955-0.97226.0480.1770.1770.0000.0000.0000.000
94A95LEU0-0.034-0.01723.7720.0090.0090.0000.0000.0000.000
95A96LEU00.003-0.00620.4400.0220.0220.0000.0000.0000.000
96A97ASP-1-0.852-0.91624.2850.2210.2210.0000.0000.0000.000
97A98ARG10.8900.92927.429-0.184-0.1840.0000.0000.0000.000
98A99LEU0-0.053-0.02122.9030.0030.0030.0000.0000.0000.000
99A100GLY0-0.024-0.01925.0670.0200.0200.0000.0000.0000.000
100A101PHE0-0.037-0.01818.4630.0200.0200.0000.0000.0000.000
101A102LYS10.8580.94623.463-0.280-0.2800.0000.0000.0000.000
102A103GLU-1-0.807-0.87923.6560.1680.1680.0000.0000.0000.000
103A104VAL0-0.058-0.02021.290-0.009-0.0090.0000.0000.0000.000
104A105LEU0-0.022-0.03622.602-0.023-0.0230.0000.0000.0000.000
105A106LYS10.8550.90922.597-0.104-0.1040.0000.0000.0000.000
106A107VAL0-0.044-0.02119.966-0.011-0.0110.0000.0000.0000.000
107A108VAL00.0510.03722.244-0.001-0.0010.0000.0000.0000.000
108A109LYS10.8970.96917.2020.1200.1200.0000.0000.0000.000
109A110THR0-0.057-0.01523.2700.0010.0010.0000.0000.0000.000
110A111ARG10.8550.89414.0530.3850.3850.0000.0000.0000.000
111A112GLU-1-0.891-0.91721.036-0.202-0.2020.0000.0000.0000.000
112A113LYS10.9050.95415.3640.3300.3300.0000.0000.0000.000
113A114TYR00.005-0.01918.5860.0490.0490.0000.0000.0000.000
114A115TYR00.0360.00416.743-0.102-0.1020.0000.0000.0000.000
115A116VAL0-0.030-0.00215.9290.0430.0430.0000.0000.0000.000
116A117GLU-1-0.835-0.92914.435-0.951-0.9510.0000.0000.0000.000
117A118LYS10.9520.97312.6580.9210.9210.0000.0000.0000.000
118A119GLY0-0.039-0.02110.746-0.111-0.1110.0000.0000.0000.000
119A120VAL00.0060.02210.139-0.301-0.3010.0000.0000.0000.000
120A121THR00.003-0.00212.4830.2580.2580.0000.0000.0000.000
121A122ILE00.0340.02713.845-0.092-0.0920.0000.0000.0000.000
122A123THR0-0.027-0.03015.3680.0490.0490.0000.0000.0000.000
123A124LEU0-0.0200.00817.777-0.001-0.0010.0000.0000.0000.000
124A125ASP-1-0.748-0.84517.474-0.293-0.2930.0000.0000.0000.000
125A126GLU-1-0.849-0.90720.977-0.109-0.1090.0000.0000.0000.000
126A127VAL0-0.015-0.03120.4510.0140.0140.0000.0000.0000.000
127A128GLU-1-0.877-0.94923.653-0.007-0.0070.0000.0000.0000.000
128A129GLY0-0.036-0.02325.7970.0120.0120.0000.0000.0000.000
129A130LEU0-0.112-0.05821.6820.0100.0100.0000.0000.0000.000
130A131GLY00.0040.01025.466-0.003-0.0030.0000.0000.0000.000
131A132LYS10.8330.92023.9450.1290.1290.0000.0000.0000.000
132A133PHE0-0.017-0.01118.7170.0160.0160.0000.0000.0000.000
133A134ILE00.0030.00717.7910.0070.0070.0000.0000.0000.000
134A135GLU-1-0.861-0.93513.041-0.441-0.4410.0000.0000.0000.000
135A136ILE0-0.007-0.01012.0290.0480.0480.0000.0000.0000.000
136A137GLU-1-0.915-0.9548.585-1.337-1.3370.0000.0000.0000.000
137A138THR00.009-0.0167.2160.3280.3280.0000.0000.0000.000
138A139LEU0-0.0150.0144.176-1.268-0.9710.000-0.082-0.2150.000
139A140VAL0-0.019-0.0012.4620.1682.4821.001-1.110-2.206-0.006
140A141LYS10.9150.9631.690-3.364-14.23722.185-7.634-3.678-0.053
141A142GLU-1-0.919-0.9833.291-7.722-5.8620.065-0.761-1.163-0.006
142A143LYS10.9490.9713.054-11.692-7.9290.574-1.405-2.9320.009
143A144ASP-1-0.924-0.9733.969-0.358-0.1430.037-0.039-0.2130.001
144A145GLU-1-0.836-0.9055.754-4.011-4.0110.0000.0000.0000.000
145A146ILE0-0.036-0.0143.015-1.3740.0350.360-0.394-1.3740.004
146A147PRO0-0.020-0.0125.7260.1520.1520.0000.0000.0000.000
147A148GLU-1-0.876-0.9329.475-1.366-1.3660.0000.0000.0000.000
148A149ALA0-0.0020.0026.8820.1420.1420.0000.0000.0000.000
149A150VAL0-0.002-0.0047.7030.1780.1780.0000.0000.0000.000
150A151GLU-1-0.924-0.9589.995-0.533-0.5330.0000.0000.0000.000
151A152LYS10.8030.90111.9541.3061.3060.0000.0000.0000.000
152A153LEU0-0.002-0.0199.2340.1480.1480.0000.0000.0000.000
153A154GLU-1-0.888-0.95213.097-0.330-0.3300.0000.0000.0000.000
154A155LYS10.9370.96915.2200.6360.6360.0000.0000.0000.000
155A156ILE00.0000.00214.8690.0750.0750.0000.0000.0000.000
156A157LEU00.0340.00915.0970.0800.0800.0000.0000.0000.000
157A158ARG10.8670.93918.5760.3960.3960.0000.0000.0000.000
158A159GLU-1-0.970-0.97120.904-0.347-0.3470.0000.0000.0000.000
159A160LEU0-0.060-0.03119.9430.0350.0350.0000.0000.0000.000
160A161GLY00.0180.00923.4410.0290.0290.0000.0000.0000.000
161A162VAL0-0.0310.00418.8950.0310.0310.0000.0000.0000.000
162A163GLU-1-0.957-0.97821.966-0.192-0.1920.0000.0000.0000.000
163A164LYS10.8940.94821.7390.1330.1330.0000.0000.0000.000
164A165PHE00.0610.01315.4870.0010.0010.0000.0000.0000.000
165A166GLU-1-0.792-0.86216.3410.0370.0370.0000.0000.0000.000
166A167ARG10.8680.93310.670-0.300-0.3000.0000.0000.0000.000
167A168ARG10.7420.84313.5150.0010.0010.0000.0000.0000.000
168A169SER00.0290.00313.909-0.071-0.0710.0000.0000.0000.000
169A170TYR00.036-0.03115.5250.0430.0430.0000.0000.0000.000
170A171LEU00.0070.01317.1780.0080.0080.0000.0000.0000.000
171A172GLU-1-0.840-0.92815.4580.2790.2790.0000.0000.0000.000
172A173LEU00.0070.01519.182-0.003-0.0030.0000.0000.0000.000
173A174LEU0-0.042-0.03421.592-0.001-0.0010.0000.0000.0000.000
174A175LEU0-0.052-0.03420.7520.0020.0020.0000.0000.0000.000
175A176GLU-1-0.858-0.90522.0070.1010.1010.0000.0000.0000.000
176A177LYS10.8850.95125.361-0.026-0.0260.0000.0000.0000.000
177A178ARG10.9250.99126.673-0.116-0.1160.0000.0000.0000.000