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: KG3N3

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2112541.065275
FMO2-HF: Nuclear repulsion 2038887.217767
FMO2-HF: Total energy -73653.847508
FMO2-MP2: Total energy -73873.628163


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.
-40.453-26.93717.217-9.576-21.153-0.027
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 : -0.041 / 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].
3A4VAL0-0.034-0.0183.681-0.2561.1900.000-0.492-0.9540.002
4A5GLU-1-0.803-0.8935.1450.1300.217-0.001-0.003-0.0830.000
5A6LEU0-0.012-0.0188.2630.2370.2370.0000.0000.0000.000
6A7LYS10.7830.87811.4520.1200.1200.0000.0000.0000.000
7A8GLY00.0410.02314.9590.0280.0280.0000.0000.0000.000
8A9TYR0-0.091-0.06418.5510.0060.0060.0000.0000.0000.000
9A10ALA0-0.0020.00422.007-0.021-0.0210.0000.0000.0000.000
10A11ASN0-0.029-0.02824.0280.0120.0120.0000.0000.0000.000
11A12ASP-1-0.805-0.93127.055-0.119-0.1190.0000.0000.0000.000
12A13GLU-1-0.896-0.92629.263-0.154-0.1540.0000.0000.0000.000
13A14ILE00.0150.00422.925-0.014-0.0140.0000.0000.0000.000
14A15PHE0-0.034-0.03123.594-0.021-0.0210.0000.0000.0000.000
15A16GLU-1-0.855-0.91826.247-0.166-0.1660.0000.0000.0000.000
16A17LYS10.8300.91126.0190.2520.2520.0000.0000.0000.000
17A18VAL0-0.0150.00121.848-0.022-0.0220.0000.0000.0000.000
18A19ARG10.7860.86324.6200.1520.1520.0000.0000.0000.000
19A20GLU-1-0.929-0.95127.169-0.188-0.1880.0000.0000.0000.000
20A21THR0-0.124-0.07024.032-0.001-0.0010.0000.0000.0000.000
21A22PHE0-0.034-0.03120.954-0.039-0.0390.0000.0000.0000.000
22A23GLU-1-0.865-0.92022.596-0.251-0.2510.0000.0000.0000.000
23A24PHE0-0.009-0.00722.397-0.021-0.0210.0000.0000.0000.000
24A25MET0-0.068-0.01717.001-0.009-0.0090.0000.0000.0000.000
25A26ARG10.7670.85918.6120.1410.1410.0000.0000.0000.000
26A27LYS10.8600.92322.4560.0960.0960.0000.0000.0000.000
27A28GLU-1-0.772-0.86018.065-0.135-0.1350.0000.0000.0000.000
28A29ILE00.006-0.00222.456-0.008-0.0080.0000.0000.0000.000
29A30HIS0-0.043-0.03616.4110.0350.0350.0000.0000.0000.000
30A31GLU-1-0.802-0.86921.6010.0520.0520.0000.0000.0000.000
31A32ASP-1-0.756-0.82817.7730.0980.0980.0000.0000.0000.000
32A33ILE0-0.004-0.00520.259-0.014-0.0140.0000.0000.0000.000
33A34TYR0-0.006-0.02215.3640.0390.0390.0000.0000.0000.000
34A35TYR00.0230.00019.213-0.028-0.0280.0000.0000.0000.000
35A36GLN00.0210.00719.2640.0790.0790.0000.0000.0000.000
36A37HIS00.0290.01218.380-0.026-0.0260.0000.0000.0000.000
37A38PRO0-0.0150.00120.870-0.021-0.0210.0000.0000.0000.000
38A39CYS0-0.070-0.04222.344-0.025-0.0250.0000.0000.0000.000
39A40ARG10.8120.87314.105-0.854-0.8540.0000.0000.0000.000
40A41ASP-1-0.739-0.82420.6330.4010.4010.0000.0000.0000.000
41A42PHE00.0390.01215.7580.0330.0330.0000.0000.0000.000
42A43SER0-0.041-0.04016.4650.0340.0340.0000.0000.0000.000
43A44LYS10.7670.86018.766-0.416-0.4160.0000.0000.0000.000
44A45THR0-0.044-0.05614.023-0.017-0.0170.0000.0000.0000.000
45A46ASP-1-0.775-0.85211.6390.8790.8790.0000.0000.0000.000
46A47GLU-1-0.739-0.77811.5001.1601.1600.0000.0000.0000.000
47A48ALA00.012-0.00212.651-0.140-0.1400.0000.0000.0000.000
48A49LEU00.0010.01113.4000.0940.0940.0000.0000.0000.000
49A50ARG10.8240.89911.692-0.309-0.3090.0000.0000.0000.000
50A51ILE00.0260.03016.8360.0380.0380.0000.0000.0000.000
51A52ARG10.8570.88913.827-0.065-0.0650.0000.0000.0000.000
52A53ILE00.0160.02218.8890.0030.0030.0000.0000.0000.000
53A54LYS10.8290.91815.745-0.035-0.0350.0000.0000.0000.000
54A55ARG10.8070.86621.190-0.048-0.0480.0000.0000.0000.000
55A56PHE00.0440.01822.094-0.022-0.0220.0000.0000.0000.000
56A57ASN0-0.010-0.01625.3710.0040.0040.0000.0000.0000.000
57A58GLY00.0050.01128.4350.0010.0010.0000.0000.0000.000
58A59HIS0-0.0080.00225.3730.0210.0210.0000.0000.0000.000
59A60ASN0-0.007-0.01924.8030.0000.0000.0000.0000.0000.000
60A61GLU-1-0.720-0.82118.542-0.010-0.0100.0000.0000.0000.000
61A62VAL00.005-0.01320.431-0.007-0.0070.0000.0000.0000.000
62A63PHE00.0180.02015.230-0.003-0.0030.0000.0000.0000.000
63A64LEU00.0120.01016.377-0.026-0.0260.0000.0000.0000.000
64A65THR0-0.019-0.04810.9010.0220.0220.0000.0000.0000.000
65A66TYR0-0.080-0.0578.917-0.004-0.0040.0000.0000.0000.000
66A67LYS10.7830.8788.0210.2530.2530.0000.0000.0000.000
67A68GLY00.0400.0177.732-0.099-0.0990.0000.0000.0000.000
68A69PRO0-0.012-0.0117.825-0.218-0.2180.0000.0000.0000.000
69A70LYS10.8030.8996.971-0.210-0.2100.0000.0000.0000.000
70A71ILE0-0.090-0.0452.555-0.1160.0243.316-0.628-2.8280.007
71A72ASP-1-0.760-0.8516.7040.2340.2340.0000.0000.0000.000
72A73GLU-1-0.882-0.9418.8350.2390.2390.0000.0000.0000.000
73A74LYS10.8490.92211.259-0.159-0.1590.0000.0000.0000.000
74A75SER0-0.048-0.0367.974-0.184-0.1840.0000.0000.0000.000
75A76LYN0-0.0080.0229.3640.2980.2980.0000.0000.0000.000
76A77THR00.0180.0053.029-0.656-0.1250.136-0.125-0.5410.000
77A78ARG10.8270.9034.4990.0260.313-0.001-0.033-0.2540.000
78A79LEU0-0.0010.0173.116-3.154-1.0770.137-0.834-1.379-0.006
79A80GLU-1-0.805-0.9013.994-0.660-0.5230.002-0.027-0.1120.000
80A81ILE0-0.011-0.0096.5930.5440.5440.0000.0000.0000.000
81A82GLU-1-0.818-0.8709.3250.1040.1040.0000.0000.0000.000
82A83VAL0-0.023-0.00811.6090.0280.0280.0000.0000.0000.000
83A84GLU-1-0.850-0.92314.9970.0950.0950.0000.0000.0000.000
84A85ILE0-0.064-0.03017.8040.0020.0020.0000.0000.0000.000
85A86GLN0-0.069-0.05420.966-0.023-0.0230.0000.0000.0000.000
86A87GLU-1-0.940-0.96323.3200.1100.1100.0000.0000.0000.000
87A88ASP-1-0.812-0.90725.5650.1680.1680.0000.0000.0000.000
88A89VAL00.0270.01924.1660.0140.0140.0000.0000.0000.000
89A90ASP-1-0.894-0.94725.8320.1510.1510.0000.0000.0000.000
90A91LYS10.8370.89228.097-0.141-0.1410.0000.0000.0000.000
91A92TYR00.0000.00621.4340.0310.0310.0000.0000.0000.000
92A93PHE00.005-0.00223.4880.0230.0230.0000.0000.0000.000
93A94GLU-1-0.841-0.89825.8780.1860.1860.0000.0000.0000.000
94A95LEU0-0.023-0.00823.5180.0080.0080.0000.0000.0000.000
95A96LEU00.001-0.00320.4040.0200.0200.0000.0000.0000.000
96A97ASP-1-0.861-0.91724.4700.2320.2320.0000.0000.0000.000
97A98ARG10.8070.87127.709-0.185-0.1850.0000.0000.0000.000
98A99LEU0-0.053-0.01723.2460.0010.0010.0000.0000.0000.000
99A100GLY0-0.002-0.00125.6640.0210.0210.0000.0000.0000.000
100A101PHE0-0.013-0.00418.9120.0160.0160.0000.0000.0000.000
101A102LYS10.7830.88324.106-0.286-0.2860.0000.0000.0000.000
102A103GLU-1-0.795-0.87323.9890.1930.1930.0000.0000.0000.000
103A104VAL0-0.052-0.02021.519-0.009-0.0090.0000.0000.0000.000
104A105LEU0-0.033-0.03422.908-0.022-0.0220.0000.0000.0000.000
105A106LYS10.8420.91322.947-0.133-0.1330.0000.0000.0000.000
106A107VAL0-0.039-0.02820.767-0.008-0.0080.0000.0000.0000.000
107A108VAL00.0180.02422.0780.0000.0000.0000.0000.0000.000
108A109LYS10.8580.93817.8010.0030.0030.0000.0000.0000.000
109A110THR0-0.056-0.02123.616-0.001-0.0010.0000.0000.0000.000
110A111ARG10.7990.85214.1340.2700.2700.0000.0000.0000.000
111A112GLU-1-0.795-0.84621.241-0.154-0.1540.0000.0000.0000.000
112A113LYS10.8820.93415.1880.2400.2400.0000.0000.0000.000
113A114TYR00.002-0.02218.8640.0380.0380.0000.0000.0000.000
114A115TYR00.0230.00316.773-0.094-0.0940.0000.0000.0000.000
115A116VAL0-0.0270.00116.4700.0400.0400.0000.0000.0000.000
116A117GLU-1-0.788-0.89114.776-0.979-0.9790.0000.0000.0000.000
117A118LYS10.9240.95612.5251.0811.0810.0000.0000.0000.000
118A119GLY0-0.022-0.01511.087-0.108-0.1080.0000.0000.0000.000
119A120VAL0-0.0100.03210.453-0.275-0.2750.0000.0000.0000.000
120A121THR0-0.019-0.02112.7470.1680.1680.0000.0000.0000.000
121A122ILE00.0090.00914.119-0.074-0.0740.0000.0000.0000.000
122A123THR0-0.063-0.06415.1440.0370.0370.0000.0000.0000.000
123A124LEU00.0010.03018.0330.0010.0010.0000.0000.0000.000
124A125ASP-1-0.764-0.86118.769-0.171-0.1710.0000.0000.0000.000
125A126GLU-1-0.846-0.92621.460-0.073-0.0730.0000.0000.0000.000
126A127VAL0-0.008-0.01621.0800.0140.0140.0000.0000.0000.000
127A128GLU-1-0.897-0.95324.3680.0200.0200.0000.0000.0000.000
128A129GLY0-0.028-0.01826.4670.0140.0140.0000.0000.0000.000
129A130LEU0-0.118-0.06622.1190.0090.0090.0000.0000.0000.000
130A131GLY0-0.0110.01225.987-0.006-0.0060.0000.0000.0000.000
131A132LYS10.8250.92324.5120.1000.1000.0000.0000.0000.000
132A133PHE0-0.029-0.03219.1820.0130.0130.0000.0000.0000.000
133A134ILE00.0040.00818.3390.0020.0020.0000.0000.0000.000
134A135GLU-1-0.762-0.84213.130-0.278-0.2780.0000.0000.0000.000
135A136ILE0-0.027-0.01512.1800.0180.0180.0000.0000.0000.000
136A137GLU-1-0.850-0.9049.498-0.740-0.7400.0000.0000.0000.000
137A138THR0-0.007-0.0377.1620.1560.1560.0000.0000.0000.000
138A139LEU0-0.0110.0014.469-0.769-0.608-0.001-0.036-0.1240.000
139A140VAL0-0.036-0.0042.3650.3691.6341.626-0.835-2.057-0.005
140A141LYS10.8320.9071.913-6.104-7.2047.422-3.455-2.866-0.038
141A142GLU-1-0.865-0.9372.541-9.095-6.8890.596-0.839-1.962-0.009
142A143LYS10.9390.9612.708-14.410-9.6173.109-2.242-5.6600.013
143A144ASP-1-0.918-0.9713.614-0.470-0.6170.1330.461-0.4460.002
144A145GLU-1-0.787-0.8835.102-5.300-5.3000.0000.0000.0000.000
145A146ILE0-0.042-0.0113.007-1.676-0.0430.743-0.488-1.8870.007
146A147PRO00.002-0.0055.7590.0780.0780.0000.0000.0000.000
147A148GLU-1-0.889-0.9359.582-1.431-1.4310.0000.0000.0000.000
148A149ALA0-0.010-0.0056.8150.1340.1340.0000.0000.0000.000
149A150VAL0-0.005-0.0087.6020.1970.1970.0000.0000.0000.000
150A151GLU-1-0.922-0.96010.103-0.432-0.4320.0000.0000.0000.000
151A152LYS10.7760.87511.8131.2681.2680.0000.0000.0000.000
152A153LEU00.005-0.0119.3150.1310.1310.0000.0000.0000.000
153A154GLU-1-0.823-0.89513.265-0.240-0.2400.0000.0000.0000.000
154A155LYS10.8750.93215.2890.5340.5340.0000.0000.0000.000
155A156ILE0-0.0050.00114.7780.0700.0700.0000.0000.0000.000
156A157LEU00.0340.01215.3540.0680.0680.0000.0000.0000.000
157A158ARG10.7540.85818.6800.3430.3430.0000.0000.0000.000
158A159GLU-1-0.886-0.93021.174-0.324-0.3240.0000.0000.0000.000
159A160LEU0-0.0360.00120.1230.0340.0340.0000.0000.0000.000
160A161GLY00.0240.00622.9390.0320.0320.0000.0000.0000.000
161A162VAL0-0.023-0.00218.9620.0310.0310.0000.0000.0000.000
162A163GLU-1-0.930-0.95621.633-0.141-0.1410.0000.0000.0000.000
163A164LYS10.8790.94721.8630.0770.0770.0000.0000.0000.000
164A165PHE00.0610.01115.2120.0050.0050.0000.0000.0000.000
165A166GLU-1-0.793-0.85316.4550.0830.0830.0000.0000.0000.000
166A167ARG10.8730.92211.152-0.325-0.3250.0000.0000.0000.000
167A168ARG10.7410.85013.915-0.023-0.0230.0000.0000.0000.000
168A169SER00.031-0.03314.369-0.070-0.0700.0000.0000.0000.000
169A170TYR0-0.007-0.05615.9880.0330.0330.0000.0000.0000.000
170A171LEU00.0200.02117.5790.0000.0000.0000.0000.0000.000
171A172GLU-1-0.805-0.87615.4160.3120.3120.0000.0000.0000.000
172A173LEU00.0040.01119.285-0.006-0.0060.0000.0000.0000.000
173A174LEU00.0270.01521.971-0.011-0.0110.0000.0000.0000.000
174A175LEU0-0.020-0.01021.198-0.002-0.0020.0000.0000.0000.000
175A176GLU-1-0.869-0.92422.7500.1160.1160.0000.0000.0000.000
176A177LYS10.8150.91825.033-0.081-0.0810.0000.0000.0000.000
177A178ARG10.9090.97927.628-0.135-0.1350.0000.0000.0000.000