FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: QV1QY

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2112590.435444
FMO2-HF: Nuclear repulsion 2038937.073235
FMO2-HF: Total energy -73653.362209
FMO2-MP2: Total energy -73873.203886


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.
-36.177-30.80730.049-13.921-21.498-0.037
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 : -0.068 / q_NPA : -0.058
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].
3A4VAL0-0.030-0.0173.7790.2051.807-0.005-0.540-1.0580.001
4A5GLU-1-0.843-0.9215.136-0.164-0.088-0.001-0.003-0.0710.000
5A6LEU0-0.029-0.0128.1920.3130.3130.0000.0000.0000.000
6A7LYS10.7930.87211.4920.1610.1610.0000.0000.0000.000
7A8GLY00.0160.01414.6920.0460.0460.0000.0000.0000.000
8A9TYR0-0.117-0.08218.2810.0070.0070.0000.0000.0000.000
9A10ALA00.0110.00021.694-0.020-0.0200.0000.0000.0000.000
10A11ASN00.001-0.00823.6910.0140.0140.0000.0000.0000.000
11A12ASP-1-0.832-0.94426.904-0.146-0.1460.0000.0000.0000.000
12A13GLU-1-0.953-0.95929.176-0.176-0.1760.0000.0000.0000.000
13A14ILE00.0100.00222.580-0.013-0.0130.0000.0000.0000.000
14A15PHE0-0.042-0.04322.881-0.021-0.0210.0000.0000.0000.000
15A16GLU-1-0.845-0.91825.810-0.196-0.1960.0000.0000.0000.000
16A17LYS10.8730.94025.9020.2790.2790.0000.0000.0000.000
17A18VAL0-0.0070.00221.607-0.021-0.0210.0000.0000.0000.000
18A19ARG10.7910.87624.4400.1840.1840.0000.0000.0000.000
19A20GLU-1-0.932-0.94926.867-0.202-0.2020.0000.0000.0000.000
20A21THR0-0.138-0.07423.8540.0000.0000.0000.0000.0000.000
21A22PHE0-0.049-0.03720.663-0.038-0.0380.0000.0000.0000.000
22A23GLU-1-0.881-0.92522.324-0.279-0.2790.0000.0000.0000.000
23A24PHE00.001-0.00322.251-0.026-0.0260.0000.0000.0000.000
24A25MET0-0.071-0.01516.927-0.007-0.0070.0000.0000.0000.000
25A26ARG10.8300.90318.7500.2250.2250.0000.0000.0000.000
26A27LYS10.8830.93221.9290.1320.1320.0000.0000.0000.000
27A28GLU-1-0.793-0.87318.059-0.227-0.2270.0000.0000.0000.000
28A29ILE00.0110.00822.435-0.008-0.0080.0000.0000.0000.000
29A30HIS0-0.023-0.03516.1780.0250.0250.0000.0000.0000.000
30A31GLU-1-0.799-0.85921.4030.0070.0070.0000.0000.0000.000
31A32ASP-1-0.758-0.85417.8310.0080.0080.0000.0000.0000.000
32A33ILE0-0.0020.01120.611-0.005-0.0050.0000.0000.0000.000
33A34TYR0-0.011-0.02115.1070.0270.0270.0000.0000.0000.000
34A35TYR00.0310.00218.924-0.020-0.0200.0000.0000.0000.000
35A36GLN00.0170.01819.1890.0660.0660.0000.0000.0000.000
36A37HIS00.0060.00217.827-0.028-0.0280.0000.0000.0000.000
37A38PRO0-0.0060.00720.611-0.018-0.0180.0000.0000.0000.000
38A39CYS0-0.070-0.04521.836-0.019-0.0190.0000.0000.0000.000
39A40ARG10.8120.87313.948-0.819-0.8190.0000.0000.0000.000
40A41ASP-1-0.752-0.84020.4830.3690.3690.0000.0000.0000.000
41A42PHE00.0430.00515.4890.0450.0450.0000.0000.0000.000
42A43SER0-0.039-0.03416.1000.0390.0390.0000.0000.0000.000
43A44LYS10.8110.88417.979-0.371-0.3710.0000.0000.0000.000
44A45THR0-0.055-0.05613.979-0.007-0.0070.0000.0000.0000.000
45A46ASP-1-0.787-0.85911.3960.9370.9370.0000.0000.0000.000
46A47GLU-1-0.731-0.77211.0681.1131.1130.0000.0000.0000.000
47A48ALA00.004-0.00512.266-0.139-0.1390.0000.0000.0000.000
48A49LEU00.0200.01113.0670.0820.0820.0000.0000.0000.000
49A50ARG10.8400.93311.707-0.132-0.1320.0000.0000.0000.000
50A51ILE00.0230.02416.7570.0230.0230.0000.0000.0000.000
51A52ARG10.8230.87613.7490.0650.0650.0000.0000.0000.000
52A53ILE00.0070.01618.8120.0050.0050.0000.0000.0000.000
53A54LYS10.8000.90015.6840.0920.0920.0000.0000.0000.000
54A55ARG10.8220.87021.0390.0080.0080.0000.0000.0000.000
55A56PHE00.0390.01621.331-0.024-0.0240.0000.0000.0000.000
56A57ASN00.0090.00324.9390.0030.0030.0000.0000.0000.000
57A58GLY00.0020.01027.8270.0030.0030.0000.0000.0000.000
58A59HIS0-0.032-0.01225.0010.0210.0210.0000.0000.0000.000
59A60ASN0-0.013-0.02224.476-0.003-0.0030.0000.0000.0000.000
60A61GLU-1-0.771-0.87718.517-0.091-0.0910.0000.0000.0000.000
61A62VAL00.0200.00220.182-0.007-0.0070.0000.0000.0000.000
62A63PHE00.0300.02814.813-0.008-0.0080.0000.0000.0000.000
63A64LEU00.0000.01316.161-0.013-0.0130.0000.0000.0000.000
64A65THR0-0.040-0.06710.6730.0240.0240.0000.0000.0000.000
65A66TYR0-0.073-0.0578.7540.0130.0130.0000.0000.0000.000
66A67LYS10.8130.8858.3150.3400.3400.0000.0000.0000.000
67A68GLY00.0150.0116.967-0.021-0.0210.0000.0000.0000.000
68A69PRO0-0.006-0.0047.307-0.252-0.2520.0000.0000.0000.000
69A70LYS10.8330.9066.600-0.157-0.1570.0000.0000.0000.000
70A71ILE0-0.069-0.0362.548-0.3550.2362.515-0.566-2.5390.008
71A72ASP-1-0.720-0.8206.8000.0160.0160.0000.0000.0000.000
72A73GLU-1-0.888-0.9388.9390.3340.3340.0000.0000.0000.000
73A74LYS10.8210.89211.387-0.171-0.1710.0000.0000.0000.000
74A75SER0-0.006-0.0227.707-0.241-0.2410.0000.0000.0000.000
75A76LYN0-0.0220.0298.9610.3720.3720.0000.0000.0000.000
76A77THR00.010-0.0042.727-0.898-0.3010.575-0.270-0.9030.000
77A78ARG10.8190.8924.0460.1160.4910.000-0.050-0.3240.000
78A79LEU00.0050.0202.799-2.911-1.0200.229-0.616-1.503-0.002
79A80GLU-1-0.773-0.8793.692-0.873-0.7230.010-0.007-0.1530.000
80A81ILE0-0.029-0.0126.6580.3890.3890.0000.0000.0000.000
81A82GLU-1-0.820-0.8849.416-0.033-0.0330.0000.0000.0000.000
82A83VAL0-0.0120.00211.4330.0180.0180.0000.0000.0000.000
83A84GLU-1-0.853-0.92714.7520.0210.0210.0000.0000.0000.000
84A85ILE0-0.076-0.03917.3720.0130.0130.0000.0000.0000.000
85A86GLN0-0.055-0.04620.504-0.018-0.0180.0000.0000.0000.000
86A87GLU-1-0.945-0.96623.1640.0750.0750.0000.0000.0000.000
87A88ASP-1-0.820-0.90325.4780.1250.1250.0000.0000.0000.000
88A89VAL00.0570.01924.0680.0160.0160.0000.0000.0000.000
89A90ASP-1-0.901-0.95725.8440.1060.1060.0000.0000.0000.000
90A91LYS10.8250.89827.725-0.106-0.1060.0000.0000.0000.000
91A92TYR00.0110.01521.2790.0290.0290.0000.0000.0000.000
92A93PHE00.003-0.00423.3860.0200.0200.0000.0000.0000.000
93A94GLU-1-0.852-0.91126.0590.1530.1530.0000.0000.0000.000
94A95LEU0-0.032-0.01823.7640.0080.0080.0000.0000.0000.000
95A96LEU00.005-0.00220.4900.0190.0190.0000.0000.0000.000
96A97ASP-1-0.840-0.89624.4300.1990.1990.0000.0000.0000.000
97A98ARG10.8220.89327.579-0.153-0.1530.0000.0000.0000.000
98A99LEU0-0.055-0.02122.9990.0050.0050.0000.0000.0000.000
99A100GLY0-0.006-0.00625.3540.0200.0200.0000.0000.0000.000
100A101PHE0-0.035-0.01718.5770.0200.0200.0000.0000.0000.000
101A102LYS10.7970.88723.776-0.245-0.2450.0000.0000.0000.000
102A103GLU-1-0.786-0.87523.7750.1450.1450.0000.0000.0000.000
103A104VAL0-0.065-0.02321.466-0.006-0.0060.0000.0000.0000.000
104A105LEU0-0.020-0.03422.811-0.019-0.0190.0000.0000.0000.000
105A106LYS10.8430.91022.768-0.093-0.0930.0000.0000.0000.000
106A107VAL0-0.045-0.02320.109-0.008-0.0080.0000.0000.0000.000
107A108VAL00.0350.02822.267-0.002-0.0020.0000.0000.0000.000
108A109LYS10.8580.95417.3690.1050.1050.0000.0000.0000.000
109A110THR0-0.047-0.01023.296-0.001-0.0010.0000.0000.0000.000
110A111ARG10.7930.84213.8310.3850.3850.0000.0000.0000.000
111A112GLU-1-0.808-0.85621.064-0.189-0.1890.0000.0000.0000.000
112A113LYS10.8990.93515.2910.3290.3290.0000.0000.0000.000
113A114TYR00.003-0.01718.5780.0470.0470.0000.0000.0000.000
114A115TYR00.0310.00216.660-0.099-0.0990.0000.0000.0000.000
115A116VAL0-0.035-0.00415.9680.0400.0400.0000.0000.0000.000
116A117GLU-1-0.807-0.90414.474-0.938-0.9380.0000.0000.0000.000
117A118LYS10.9580.97712.5260.9560.9560.0000.0000.0000.000
118A119GLY0-0.023-0.01310.785-0.111-0.1110.0000.0000.0000.000
119A120VAL00.0010.03110.178-0.302-0.3020.0000.0000.0000.000
120A121THR00.0210.01112.5180.2340.2340.0000.0000.0000.000
121A122ILE00.0190.01713.845-0.087-0.0870.0000.0000.0000.000
122A123THR0-0.066-0.06615.1070.0440.0440.0000.0000.0000.000
123A124LEU00.0020.02417.8280.0010.0010.0000.0000.0000.000
124A125ASP-1-0.755-0.86418.318-0.257-0.2570.0000.0000.0000.000
125A126GLU-1-0.850-0.92021.025-0.104-0.1040.0000.0000.0000.000
126A127VAL0-0.016-0.03020.4340.0120.0120.0000.0000.0000.000
127A128GLU-1-0.876-0.94523.695-0.014-0.0140.0000.0000.0000.000
128A129GLY0-0.040-0.02625.8340.0110.0110.0000.0000.0000.000
129A130LEU0-0.114-0.06221.7370.0110.0110.0000.0000.0000.000
130A131GLY0-0.0040.00725.496-0.001-0.0010.0000.0000.0000.000
131A132LYS10.8350.94324.0170.1240.1240.0000.0000.0000.000
132A133PHE0-0.032-0.02618.7980.0160.0160.0000.0000.0000.000
133A134ILE00.0080.01217.9870.0010.0010.0000.0000.0000.000
134A135GLU-1-0.750-0.83313.126-0.390-0.3900.0000.0000.0000.000
135A136ILE0-0.020-0.01012.1490.0360.0360.0000.0000.0000.000
136A137GLU-1-0.935-0.9648.799-1.150-1.1500.0000.0000.0000.000
137A138THR0-0.001-0.0337.2760.3330.3330.0000.0000.0000.000
138A139LEU0-0.0160.0084.216-1.236-1.001-0.001-0.062-0.1720.000
139A140VAL0-0.030-0.0072.4870.0272.3560.793-1.018-2.104-0.006
140A141LYS10.8560.9231.688-2.956-13.69822.273-7.768-3.763-0.054
141A142GLU-1-0.872-0.9393.115-7.844-5.7870.123-0.800-1.381-0.006
142A143LYS10.9650.9752.706-15.045-10.2752.429-2.174-5.0250.013
143A144ASP-1-0.936-0.9773.4470.2800.0820.1480.472-0.4220.002
144A145GLU-1-0.805-0.8955.385-4.489-4.4890.0000.0000.0000.000
145A146ILE0-0.045-0.0172.929-1.736-0.0990.961-0.519-2.0800.007
146A147PRO0-0.023-0.0135.6950.1600.1600.0000.0000.0000.000
147A148GLU-1-0.877-0.9349.445-1.352-1.3520.0000.0000.0000.000
148A149ALA0-0.0020.0006.8000.1370.1370.0000.0000.0000.000
149A150VAL00.002-0.0047.6130.1700.1700.0000.0000.0000.000
150A151GLU-1-0.933-0.9579.929-0.435-0.4350.0000.0000.0000.000
151A152LYS10.7720.87111.8811.2531.2530.0000.0000.0000.000
152A153LEU0-0.007-0.0219.0100.1370.1370.0000.0000.0000.000
153A154GLU-1-0.818-0.89613.013-0.248-0.2480.0000.0000.0000.000
154A155LYS10.8580.92815.1450.5650.5650.0000.0000.0000.000
155A156ILE0-0.003-0.00214.6730.0720.0720.0000.0000.0000.000
156A157LEU00.0320.00915.2300.0720.0720.0000.0000.0000.000
157A158ARG10.8010.89018.5720.3570.3570.0000.0000.0000.000
158A159GLU-1-0.910-0.93320.815-0.333-0.3330.0000.0000.0000.000
159A160LEU0-0.044-0.01519.8900.0320.0320.0000.0000.0000.000
160A161GLY00.0150.00823.4160.0270.0270.0000.0000.0000.000
161A162VAL0-0.0320.00318.8420.0300.0300.0000.0000.0000.000
162A163GLU-1-0.923-0.96122.004-0.162-0.1620.0000.0000.0000.000
163A164LYS10.8960.94321.7440.1140.1140.0000.0000.0000.000
164A165PHE00.0470.01115.233-0.003-0.0030.0000.0000.0000.000
165A166GLU-1-0.801-0.86516.3700.0640.0640.0000.0000.0000.000
166A167ARG10.8820.92911.094-0.375-0.3750.0000.0000.0000.000
167A168ARG10.7380.85413.591-0.020-0.0200.0000.0000.0000.000
168A169SER00.031-0.02514.082-0.078-0.0780.0000.0000.0000.000
169A170TYR0-0.001-0.05315.6630.0450.0450.0000.0000.0000.000
170A171LEU00.0120.01617.3730.0080.0080.0000.0000.0000.000
171A172GLU-1-0.816-0.87915.3950.2790.2790.0000.0000.0000.000
172A173LEU00.0020.01119.163-0.002-0.0020.0000.0000.0000.000
173A174LEU0-0.033-0.03121.801-0.001-0.0010.0000.0000.0000.000
174A175LEU0-0.046-0.03120.8350.0020.0020.0000.0000.0000.000
175A176GLU-1-0.868-0.91022.2810.1160.1160.0000.0000.0000.000
176A177LYS10.8750.95025.561-0.035-0.0350.0000.0000.0000.000
177A178ARG10.9260.98927.018-0.106-0.1060.0000.0000.0000.000