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

tag_button

FMODB ID: 3JKYL

Calculation Name: 2EQ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EQ5

Chain ID: A

ChEMBL ID:

UniProt ID: O58781

Base Structure: X-ray

Registration Date: 2023-09-22

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2452883.690652
FMO2-HF: Nuclear repulsion 2372240.243553
FMO2-HF: Total energy -80643.447098
FMO2-MP2: Total energy -80882.213767


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:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-144.586-138.55918.71-12.086-12.65-0.124
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.862 / q_NPA : 0.913
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].
3A5THR00.007-0.0053.381-6.671-4.0540.016-1.364-1.2690.003
4A6ILE0-0.020-0.0155.7073.7743.7740.0000.0000.0000.000
5A7GLY00.0670.0448.689-0.369-0.3690.0000.0000.0000.000
6A8LEU0-0.084-0.05011.9841.1331.1330.0000.0000.0000.000
7A9ILE00.0390.01313.9520.4420.4420.0000.0000.0000.000
8A10ARG10.8220.91217.28216.32716.3270.0000.0000.0000.000
9A11VAL00.025-0.01020.1930.2640.2640.0000.0000.0000.000
10A12ILE00.010-0.00423.2280.5450.5450.0000.0000.0000.000
11A13THR0-0.057-0.05223.456-0.404-0.4040.0000.0000.0000.000
12A14LEU0-0.048-0.03620.8120.1380.1380.0000.0000.0000.000
13A15GLU-1-0.870-0.93822.899-11.992-11.9920.0000.0000.0000.000
14A16ASP-1-0.877-0.93521.136-14.468-14.4680.0000.0000.0000.000
15A17LYS10.8850.91815.52217.17817.1780.0000.0000.0000.000
16A18GLU-1-0.803-0.89016.074-19.076-19.0760.0000.0000.0000.000
17A19ILE0-0.005-0.00216.878-0.859-0.8590.0000.0000.0000.000
18A20LEU0-0.0050.00616.851-0.558-0.5580.0000.0000.0000.000
19A21ASN0-0.031-0.04612.919-1.694-1.6940.0000.0000.0000.000
20A22LEU0-0.027-0.00513.183-1.649-1.6490.0000.0000.0000.000
21A23HIS00.009-0.01814.181-0.014-0.0140.0000.0000.0000.000
22A24GLY00.0720.02910.812-0.754-0.7540.0000.0000.0000.000
23A25ARG10.9680.9909.12619.43319.4330.0000.0000.0000.000
24A26ILE00.0030.0139.761-1.898-1.8980.0000.0000.0000.000
25A27ILE0-0.007-0.0028.652-0.546-0.5460.0000.0000.0000.000
26A28GLU-1-0.822-0.8915.141-41.271-41.2710.0000.0000.0000.000
27A29SER0-0.060-0.0256.278-3.724-3.7240.0000.0000.0000.000
28A30ALA0-0.030-0.0088.551-0.860-0.8600.0000.0000.0000.000
29A31PHE0-0.017-0.0207.3720.8710.8710.0000.0000.0000.000
30A32PRO00.0840.0403.434-6.174-5.1660.011-0.451-0.567-0.002
31A33GLU-1-0.851-0.9041.810-82.536-81.28110.891-6.436-5.709-0.084
32A34LEU0-0.0200.0042.267-3.707-3.9637.647-3.484-3.907-0.039
33A35LYS10.8530.9382.79833.08634.4410.146-0.338-1.163-0.002
34A36VAL0-0.022-0.0264.5314.8414.889-0.001-0.013-0.0350.000
35A37VAL0-0.040-0.0088.1670.5670.5670.0000.0000.0000.000
36A38SER00.0070.01110.6991.1561.1560.0000.0000.0000.000
37A39ARG10.7940.85414.07118.31118.3110.0000.0000.0000.000
38A40CYS0-0.0200.01717.337-0.073-0.0730.0000.0000.0000.000
39A41ILE00.0040.02620.8390.0580.0580.0000.0000.0000.000
40A42GLU-1-0.777-0.86623.965-11.708-11.7080.0000.0000.0000.000
41A43ASP-1-0.883-0.95426.906-9.821-9.8210.0000.0000.0000.000
42A44GLN0-0.027-0.02428.2620.1900.1900.0000.0000.0000.000
43A45PRO00.0480.02228.256-0.384-0.3840.0000.0000.0000.000
44A46LYS10.9100.95528.9918.7218.7210.0000.0000.0000.000
45A47GLY00.0110.00927.908-0.029-0.0290.0000.0000.0000.000
46A48ILE0-0.020-0.00826.5210.3160.3160.0000.0000.0000.000
47A49TYR00.0190.01429.642-0.104-0.1040.0000.0000.0000.000
48A50ASN0-0.0010.00532.4360.0420.0420.0000.0000.0000.000
49A51GLU-1-0.772-0.87633.155-8.391-8.3910.0000.0000.0000.000
50A52GLU-1-0.909-0.93234.505-8.206-8.2060.0000.0000.0000.000
51A53THR00.0400.00131.651-0.250-0.2500.0000.0000.0000.000
52A54GLU-1-0.906-0.95029.136-10.672-10.6720.0000.0000.0000.000
53A55ARG10.8560.88930.1628.3598.3590.0000.0000.0000.000
54A56GLU-1-0.929-0.94132.129-9.611-9.6110.0000.0000.0000.000
55A57ALA00.0280.00026.791-0.158-0.1580.0000.0000.0000.000
56A58GLU-1-0.835-0.88526.853-10.729-10.7290.0000.0000.0000.000
57A59PRO00.004-0.00726.621-0.380-0.3800.0000.0000.0000.000
58A60LYS10.8020.90225.86810.11110.1110.0000.0000.0000.000
59A61ILE00.0070.00521.572-0.578-0.5780.0000.0000.0000.000
60A62ILE0-0.028-0.01521.808-0.581-0.5810.0000.0000.0000.000
61A63ARG10.8070.90222.80311.18411.1840.0000.0000.0000.000
62A64LEU00.0230.00918.062-0.319-0.3190.0000.0000.0000.000
63A65ALA0-0.006-0.00817.852-0.729-0.7290.0000.0000.0000.000
64A66LYS10.9400.96817.80911.22911.2290.0000.0000.0000.000
65A67GLU-1-0.869-0.92418.752-13.696-13.6960.0000.0000.0000.000
66A68PHE00.007-0.00113.101-0.575-0.5750.0000.0000.0000.000
67A69GLU-1-0.800-0.90114.036-16.085-16.0850.0000.0000.0000.000
68A70ARG10.8230.90315.74712.75712.7570.0000.0000.0000.000
69A71GLU-1-0.830-0.88513.564-18.151-18.1510.0000.0000.0000.000
70A72GLY0-0.027-0.00412.156-0.960-0.9600.0000.0000.0000.000
71A73VAL0-0.078-0.0209.529-1.709-1.7090.0000.0000.0000.000
72A74ASP-1-0.829-0.9196.821-30.854-30.8540.0000.0000.0000.000
73A75ALA0-0.018-0.03610.0801.5881.5880.0000.0000.0000.000
74A76ILE00.0090.01811.708-0.684-0.6840.0000.0000.0000.000
75A77ILE00.0300.01711.6390.0940.0940.0000.0000.0000.000
76A78ILE0-0.0090.00015.237-0.109-0.1090.0000.0000.0000.000
77A79SER00.0130.01016.9160.3030.3030.0000.0000.0000.000
78A80CYS0-0.027-0.01218.8700.5440.5440.0000.0000.0000.000
79A81ALA00.0550.02722.555-0.167-0.1670.0000.0000.0000.000
80A82ALA00.0200.00624.5730.2360.2360.0000.0000.0000.000
81A83ASP-1-0.775-0.86922.743-13.422-13.4220.0000.0000.0000.000
82A84PRO00.0220.01123.5270.2380.2380.0000.0000.0000.000
83A85ALA00.0930.03824.218-0.435-0.4350.0000.0000.0000.000
84A86VAL0-0.034-0.00721.071-0.218-0.2180.0000.0000.0000.000
85A87GLU-1-0.948-0.97423.231-10.654-10.6540.0000.0000.0000.000
86A88LYS10.7960.85725.83410.13510.1350.0000.0000.0000.000
87A89VAL00.0640.01420.1350.0630.0630.0000.0000.0000.000
88A90ARG10.8410.92720.24113.60613.6060.0000.0000.0000.000
89A91LYS10.9150.95622.47510.12110.1210.0000.0000.0000.000
90A92LEU0-0.072-0.02923.7200.2900.2900.0000.0000.0000.000
91A93LEU0-0.0410.00617.8280.0370.0370.0000.0000.0000.000
92A94SER0-0.056-0.02719.0940.5380.5380.0000.0000.0000.000
93A95ILE0-0.037-0.00213.650-0.473-0.4730.0000.0000.0000.000
94A96PRO0-0.051-0.02713.2690.8820.8820.0000.0000.0000.000
95A97VAL00.0350.02515.409-0.643-0.6430.0000.0000.0000.000
96A98ILE0-0.029-0.01313.4940.9400.9400.0000.0000.0000.000
97A99GLY00.0470.03517.169-0.019-0.0190.0000.0000.0000.000
98A100ALA00.0130.01419.303-0.156-0.1560.0000.0000.0000.000
99A101GLY00.0740.03620.1860.1250.1250.0000.0000.0000.000
100A102SER0-0.051-0.05822.3190.1110.1110.0000.0000.0000.000
101A103SER0-0.052-0.04618.541-0.222-0.2220.0000.0000.0000.000
102A104VAL0-0.016-0.00420.463-0.103-0.1030.0000.0000.0000.000
103A105SER0-0.014-0.01422.3890.3020.3020.0000.0000.0000.000
104A106ALA00.001-0.00222.1050.3240.3240.0000.0000.0000.000
105A107LEU0-0.025-0.02817.4970.0940.0940.0000.0000.0000.000
106A108ALA00.0290.02822.1050.0640.0640.0000.0000.0000.000
107A109LEU00.0130.00625.3360.3420.3420.0000.0000.0000.000
108A110ALA0-0.100-0.03122.9600.3230.3230.0000.0000.0000.000
109A111TYR0-0.045-0.02720.153-0.304-0.3040.0000.0000.0000.000
110A112GLY00.0080.00426.3200.3370.3370.0000.0000.0000.000
111A113ARG10.9490.97129.8409.1829.1820.0000.0000.0000.000
112A114ARG10.8130.90632.1928.9998.9990.0000.0000.0000.000
113A115VAL00.0440.03129.267-0.156-0.1560.0000.0000.0000.000
114A116GLY00.0110.02131.5210.3770.3770.0000.0000.0000.000
115A117VAL0-0.035-0.02829.612-0.443-0.4430.0000.0000.0000.000
116A118LEU00.0030.00629.4790.3510.3510.0000.0000.0000.000
117A119ASN0-0.009-0.01529.167-0.813-0.8130.0000.0000.0000.000
118A120LEU0-0.001-0.01629.0870.0660.0660.0000.0000.0000.000
119A121THR00.004-0.02031.4790.3650.3650.0000.0000.0000.000
120A122GLU-1-0.895-0.94029.785-10.288-10.2880.0000.0000.0000.000
121A123GLU-1-0.892-0.92433.779-8.700-8.7000.0000.0000.0000.000
122A124THR00.015-0.03531.408-0.431-0.4310.0000.0000.0000.000
123A125PRO0-0.0090.00728.4690.1990.1990.0000.0000.0000.000
124A126LYN00.1010.04229.3280.0030.0030.0000.0000.0000.000
125A127VAL0-0.0140.01126.1160.1230.1230.0000.0000.0000.000
126A128ILE00.0170.00626.399-0.141-0.1410.0000.0000.0000.000
127A129ARG10.8670.91329.2089.0509.0500.0000.0000.0000.000
128A130SER0-0.080-0.05230.7710.2580.2580.0000.0000.0000.000
129A131ILE0-0.057-0.01525.3460.0960.0960.0000.0000.0000.000
130A132LEU00.0150.01328.6820.0050.0050.0000.0000.0000.000
131A133GLY00.0640.05231.2960.2060.2060.0000.0000.0000.000
132A134ASN0-0.076-0.04834.653-0.129-0.1290.0000.0000.0000.000
133A135ASN0-0.039-0.02932.7090.2410.2410.0000.0000.0000.000
134A136LEU0-0.0410.00432.958-0.234-0.2340.0000.0000.0000.000
135A137ILE0-0.050-0.02634.8050.2850.2850.0000.0000.0000.000
136A138ALA0-0.014-0.01535.9620.2810.2810.0000.0000.0000.000
137A139GLU-1-0.830-0.88534.740-9.321-9.3210.0000.0000.0000.000
138A140ASP-1-0.823-0.90034.463-8.140-8.1400.0000.0000.0000.000
139A141HIS00.0000.01033.752-0.352-0.3520.0000.0000.0000.000
140A142PRO0-0.0180.00032.1160.2350.2350.0000.0000.0000.000
141A143SER00.002-0.01735.2680.0400.0400.0000.0000.0000.000
142A144GLY00.001-0.01138.6470.0220.0220.0000.0000.0000.000
143A145VAL0-0.064-0.02732.326-0.009-0.0090.0000.0000.0000.000
144A146SER0-0.0050.01134.8140.0070.0070.0000.0000.0000.000
145A147ASN0-0.016-0.01330.267-0.534-0.5340.0000.0000.0000.000
146A148THR00.0730.02925.3570.1410.1410.0000.0000.0000.000
147A149LEU0-0.015-0.01726.116-0.112-0.1120.0000.0000.0000.000
148A150ASP-1-0.783-0.88929.047-9.191-9.1910.0000.0000.0000.000
149A151LEU0-0.074-0.02727.9900.2030.2030.0000.0000.0000.000
150A152LEU0-0.033-0.01625.484-0.140-0.1400.0000.0000.0000.000
151A153THR0-0.047-0.02329.5590.2180.2180.0000.0000.0000.000
152A154ASP-1-0.848-0.93433.254-9.082-9.0820.0000.0000.0000.000
153A155TRP0-0.050-0.03335.4960.0360.0360.0000.0000.0000.000
154A156GLY00.0680.02334.0090.0440.0440.0000.0000.0000.000
155A157ARG10.9600.99329.04610.34110.3410.0000.0000.0000.000
156A158ARG10.8760.92032.5387.8607.8600.0000.0000.0000.000
157A159GLU-1-0.834-0.88935.562-8.130-8.1300.0000.0000.0000.000
158A160VAL00.0040.00629.4710.0400.0400.0000.0000.0000.000
159A161ILE00.0430.01231.381-0.068-0.0680.0000.0000.0000.000
160A162ASN0-0.033-0.02733.2330.0430.0430.0000.0000.0000.000
161A163ALA00.0020.01533.8990.1530.1530.0000.0000.0000.000
162A164ALA00.0250.01431.390-0.008-0.0080.0000.0000.0000.000
163A165LYS10.8410.89733.2658.8358.8350.0000.0000.0000.000
164A166ARG10.8230.90436.1818.5068.5060.0000.0000.0000.000
165A167LEU0-0.0100.00432.6500.1540.1540.0000.0000.0000.000
166A168LYS10.9110.95533.5639.4519.4510.0000.0000.0000.000
167A169GLU-1-0.944-0.96535.698-7.589-7.5890.0000.0000.0000.000
168A170LYS10.8030.91238.4328.4088.4080.0000.0000.0000.000
169A171GLY00.0070.00238.0690.0480.0480.0000.0000.0000.000
170A172VAL0-0.049-0.02132.625-0.067-0.0670.0000.0000.0000.000
171A173GLU-1-0.865-0.94231.641-9.454-9.4540.0000.0000.0000.000
172A174VAL0-0.010-0.00226.341-0.297-0.2970.0000.0000.0000.000
173A175ILE0-0.0080.00327.9450.3110.3110.0000.0000.0000.000
174A176ALA0-0.0010.02425.635-0.576-0.5760.0000.0000.0000.000
175A177LEU0-0.001-0.01123.5980.4720.4720.0000.0000.0000.000
176A178GLY00.0400.01324.874-0.457-0.4570.0000.0000.0000.000
177A179CYS00.0180.00925.6960.0080.0080.0000.0000.0000.000
178A180THR00.008-0.00920.459-0.060-0.0600.0000.0000.0000.000
179A181GLY00.0080.00321.185-0.550-0.5500.0000.0000.0000.000
180A182MET0-0.002-0.01323.516-0.041-0.0410.0000.0000.0000.000
181A183SER0-0.013-0.03818.1360.1930.1930.0000.0000.0000.000
182A184THR0-0.102-0.04618.921-0.678-0.6780.0000.0000.0000.000
183A185ILE0-0.044-0.01020.027-0.211-0.2110.0000.0000.0000.000
184A186GLY00.0130.02520.6200.1010.1010.0000.0000.0000.000
185A187ILE00.006-0.01021.2590.2360.2360.0000.0000.0000.000
186A188ALA00.0440.01721.7900.3550.3550.0000.0000.0000.000
187A189PRO00.0340.01920.9720.3420.3420.0000.0000.0000.000
188A190VAL0-0.0050.00423.5210.4230.4230.0000.0000.0000.000
189A191LEU0-0.013-0.00926.9020.4770.4770.0000.0000.0000.000
190A192GLU-1-0.869-0.93223.966-13.041-13.0410.0000.0000.0000.000
191A193GLU-1-0.971-0.97427.072-11.150-11.1500.0000.0000.0000.000
192A194GLU-1-0.904-0.92728.532-8.906-8.9060.0000.0000.0000.000
193A195VAL0-0.056-0.04430.2730.3680.3680.0000.0000.0000.000
194A196GLY0-0.012-0.00129.8810.2690.2690.0000.0000.0000.000
195A197ILE0-0.085-0.04029.1070.1600.1600.0000.0000.0000.000
196A198PRO00.0370.01624.174-0.110-0.1100.0000.0000.0000.000
197A199VAL0-0.0180.00524.5510.4460.4460.0000.0000.0000.000
198A200ILE0-0.029-0.03220.931-0.697-0.6970.0000.0000.0000.000
199A201ASP-1-0.728-0.84018.179-16.758-16.7580.0000.0000.0000.000
200A202PRO00.032-0.00519.202-0.767-0.7670.0000.0000.0000.000
201A203VAL0-0.022-0.00514.473-0.538-0.5380.0000.0000.0000.000
202A204ILE00.0150.01013.451-1.492-1.4920.0000.0000.0000.000
203A205ALA00.0290.01714.727-1.107-1.1070.0000.0000.0000.000
204A206SER0-0.039-0.04115.503-0.490-0.4900.0000.0000.0000.000
205A207GLY00.0370.01811.886-0.663-0.6630.0000.0000.0000.000
206A208ALA00.0340.02411.372-1.467-1.4670.0000.0000.0000.000
207A209VAL0-0.038-0.01813.069-0.065-0.0650.0000.0000.0000.000
208A210ALA0-0.012-0.01710.8980.2160.2160.0000.0000.0000.000
209A211LEU00.0120.0046.825-0.672-0.6720.0000.0000.0000.000
210A212HIS00.0110.0119.690-0.301-0.3010.0000.0000.0000.000
211A213ALA0-0.070-0.03712.6860.7890.7890.0000.0000.0000.000
212A214LEU0-0.015-0.0117.4880.8590.8590.0000.0000.0000.000
213A215LYS10.8550.9146.65731.55431.5540.0000.0000.0000.000
214A216ARG10.8420.95910.20317.30917.3090.0000.0000.0000.000
215A217ARG10.9450.96511.08919.19619.1960.0000.0000.0000.000