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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: Z6Y2N

Calculation Name: 2JEO-A-Xray372

Preferred Name: Uridine-cytidine kinase 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2JEO

Chain ID: A

ChEMBL ID: CHEMBL5682

UniProt ID: Q9HA47

Base Structure: X-ray

Registration Date: 2023-06-21

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2665144.725732
FMO2-HF: Nuclear repulsion 2578656.466383
FMO2-HF: Total energy -86488.259349
FMO2-MP2: Total energy -86741.324908


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:21:MET)


Summations of interaction energy for fragment #1(A:21:MET)
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.
-3.104-0.435.951-2.964-5.659-0.008
Interaction energy analysis for fragmet #1(A:21:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.025
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].
3A23PRO0-0.0230.0023.829-0.2541.683-0.020-0.834-1.082-0.001
4A24PHE00.0430.0033.050-2.260-1.1420.033-0.443-0.708-0.002
5A25LEU00.005-0.0284.5971.3281.481-0.001-0.011-0.1410.000
6A26ILE00.0070.0046.8970.0150.0150.0000.0000.0000.000
7A27GLY00.0170.0179.9300.1770.1770.0000.0000.0000.000
8A28VAL0-0.003-0.00712.6980.0560.0560.0000.0000.0000.000
9A29SER00.0210.00916.1680.0630.0630.0000.0000.0000.000
10A30GLY00.0250.01019.1500.0070.0070.0000.0000.0000.000
11A31GLY00.0550.01022.8140.0070.0070.0000.0000.0000.000
12A32THR00.009-0.00825.612-0.012-0.0120.0000.0000.0000.000
13A33ALA0-0.006-0.01227.1010.0140.0140.0000.0000.0000.000
14A34SER00.0450.02123.7100.0160.0160.0000.0000.0000.000
15A35GLY00.0630.03725.0790.0120.0120.0000.0000.0000.000
16A36LYS10.8540.94620.2340.3910.3910.0000.0000.0000.000
17A37SER00.0270.01120.252-0.031-0.0310.0000.0000.0000.000
18A38THR00.0450.01422.188-0.005-0.0050.0000.0000.0000.000
19A39VAL0-0.0130.00118.8700.0100.0100.0000.0000.0000.000
20A40CYS0-0.0050.00417.480-0.034-0.0340.0000.0000.0000.000
21A41GLU-1-0.899-0.95318.887-0.378-0.3780.0000.0000.0000.000
22A42LYS10.8340.92021.7510.2850.2850.0000.0000.0000.000
23A43ILE0-0.005-0.01015.2610.0160.0160.0000.0000.0000.000
24A44MET0-0.030-0.01017.267-0.022-0.0220.0000.0000.0000.000
25A45GLU-1-0.888-0.93619.015-0.233-0.2330.0000.0000.0000.000
26A46LEU0-0.040-0.02520.2930.0250.0250.0000.0000.0000.000
27A47LEU0-0.020-0.01014.1980.0090.0090.0000.0000.0000.000
28A48GLY00.0410.03818.5800.0190.0190.0000.0000.0000.000
29A49GLN00.0440.01016.194-0.021-0.0210.0000.0000.0000.000
30A50ASN0-0.036-0.02419.6610.0050.0050.0000.0000.0000.000
31A51GLU-1-0.956-0.96022.635-0.172-0.1720.0000.0000.0000.000
32A52VAL0-0.0150.00720.4240.0260.0260.0000.0000.0000.000
33A53GLU-1-0.896-0.95322.761-0.168-0.1680.0000.0000.0000.000
34A54GLN00.006-0.01218.920-0.058-0.0580.0000.0000.0000.000
35A55ARG10.9180.94919.2410.0900.0900.0000.0000.0000.000
36A56GLN0-0.040-0.01719.307-0.002-0.0020.0000.0000.0000.000
37A57ARG10.8640.95517.0050.3750.3750.0000.0000.0000.000
38A58LYS10.9870.99712.6380.1980.1980.0000.0000.0000.000
39A59VAL00.0040.01012.055-0.197-0.1970.0000.0000.0000.000
40A60VAL00.0520.02013.0680.1300.1300.0000.0000.0000.000
41A61ILE0-0.018-0.00413.955-0.116-0.1160.0000.0000.0000.000
42A62LEU0-0.051-0.02314.1120.0720.0720.0000.0000.0000.000
43A63SER00.0370.01816.601-0.039-0.0390.0000.0000.0000.000
44A64GLN00.0450.00019.1910.0130.0130.0000.0000.0000.000
45A65ASP-1-0.941-0.96820.067-0.307-0.3070.0000.0000.0000.000
46A66ARG10.8850.93920.3070.3690.3690.0000.0000.0000.000
47A67PHE0-0.019-0.01818.0280.0230.0230.0000.0000.0000.000
48A68TYR0-0.048-0.00423.0090.0080.0080.0000.0000.0000.000
49A69LYS10.8840.95726.4380.1940.1940.0000.0000.0000.000
50A70VAL0-0.015-0.00428.3720.0010.0010.0000.0000.0000.000
51A71LEU0-0.048-0.01231.4310.0050.0050.0000.0000.0000.000
52A72THR00.0450.01434.3320.0080.0080.0000.0000.0000.000
53A73ALA00.037-0.00237.146-0.003-0.0030.0000.0000.0000.000
54A74GLU-1-0.905-0.96440.450-0.093-0.0930.0000.0000.0000.000
55A75GLN00.0440.03033.855-0.003-0.0030.0000.0000.0000.000
56A76LYS10.9590.99037.5390.1170.1170.0000.0000.0000.000
57A77ALA00.006-0.00338.934-0.001-0.0010.0000.0000.0000.000
58A78LYS10.9520.98139.4600.1090.1090.0000.0000.0000.000
59A79ALA00.0000.00637.182-0.001-0.0010.0000.0000.0000.000
60A80LEU0-0.059-0.02138.964-0.002-0.0020.0000.0000.0000.000
61A81LYS10.9230.97141.8970.0910.0910.0000.0000.0000.000
62A82GLY00.0450.02839.9780.0010.0010.0000.0000.0000.000
63A83GLN0-0.057-0.03740.008-0.004-0.0040.0000.0000.0000.000
64A84TYR00.000-0.01531.9060.0010.0010.0000.0000.0000.000
65A85ASN00.0310.01532.672-0.012-0.0120.0000.0000.0000.000
66A86PHE0-0.004-0.00830.277-0.001-0.0010.0000.0000.0000.000
67A87ASP-1-0.845-0.93528.352-0.254-0.2540.0000.0000.0000.000
68A88HIS00.0370.03728.219-0.018-0.0180.0000.0000.0000.000
69A89PRO00.0700.02924.204-0.006-0.0060.0000.0000.0000.000
70A90ASP-1-0.908-0.94225.137-0.195-0.1950.0000.0000.0000.000
71A91ALA0-0.081-0.04727.6920.0120.0120.0000.0000.0000.000
72A92PHE0-0.015-0.02122.858-0.003-0.0030.0000.0000.0000.000
73A93ASP-1-0.878-0.95623.623-0.202-0.2020.0000.0000.0000.000
74A94ASN0-0.011-0.02820.364-0.048-0.0480.0000.0000.0000.000
75A95ASP-1-0.825-0.88419.113-0.212-0.2120.0000.0000.0000.000
76A96LEU00.0330.02118.982-0.014-0.0140.0000.0000.0000.000
77A97MET0-0.0270.01316.672-0.035-0.0350.0000.0000.0000.000
78A98HIS00.0520.00613.792-0.087-0.0870.0000.0000.0000.000
79A99ARG10.8400.90913.9340.1210.1210.0000.0000.0000.000
80A100THR0-0.013-0.01114.6770.0150.0150.0000.0000.0000.000
81A101LEU00.0270.00110.737-0.033-0.0330.0000.0000.0000.000
82A102LYS10.9320.97510.159-0.069-0.0690.0000.0000.0000.000
83A103ASN0-0.045-0.02210.3990.1190.1190.0000.0000.0000.000
84A104ILE00.0140.0099.0410.0300.0300.0000.0000.0000.000
85A105VAL00.0100.0054.976-0.135-0.1350.0000.0000.0000.000
86A106GLU-1-0.950-0.9785.8860.0200.0200.0000.0000.0000.000
87A107GLY0-0.0020.0098.2180.1870.1870.0000.0000.0000.000
88A108LYS10.8770.9419.1760.1270.1270.0000.0000.0000.000
89A109THR0-0.006-0.01112.807-0.099-0.0990.0000.0000.0000.000
90A110VAL0-0.041-0.00514.4340.0370.0370.0000.0000.0000.000
91A111GLU-1-0.912-0.95117.173-0.167-0.1670.0000.0000.0000.000
92A112VAL0-0.014-0.01118.009-0.017-0.0170.0000.0000.0000.000
93A113PRO00.0500.03021.1990.0260.0260.0000.0000.0000.000
94A114THR00.0620.03223.757-0.037-0.0370.0000.0000.0000.000
95A115TYR0-0.0070.00226.4590.0220.0220.0000.0000.0000.000
96A116ASP-1-0.845-0.93628.448-0.161-0.1610.0000.0000.0000.000
97A117PHE00.010-0.01927.4180.0120.0120.0000.0000.0000.000
98A118VAL0-0.052-0.01232.6870.0060.0060.0000.0000.0000.000
99A119THR0-0.014-0.00935.9160.0070.0070.0000.0000.0000.000
100A120HIS10.8760.93833.5270.1600.1600.0000.0000.0000.000
101A121SER0-0.028-0.00533.0150.0060.0060.0000.0000.0000.000
102A122ARG10.9050.95325.6920.1970.1970.0000.0000.0000.000
103A123LEU0-0.013-0.01829.8910.0120.0120.0000.0000.0000.000
104A124PRO0-0.031-0.01430.343-0.004-0.0040.0000.0000.0000.000
105A125GLU-1-0.899-0.93329.438-0.121-0.1210.0000.0000.0000.000
106A126THR0-0.054-0.01924.106-0.014-0.0140.0000.0000.0000.000
107A127THR0-0.061-0.04421.6110.0040.0040.0000.0000.0000.000
108A128VAL00.0430.02120.085-0.019-0.0190.0000.0000.0000.000
109A129VAL0-0.011-0.00414.950-0.010-0.0100.0000.0000.0000.000
110A130TYR00.021-0.00316.3050.0220.0220.0000.0000.0000.000
111A131PRO0-0.015-0.01011.366-0.081-0.0810.0000.0000.0000.000
112A132ALA00.0270.02711.0640.0930.0930.0000.0000.0000.000
113A133ASP-1-0.909-0.9658.328-0.824-0.8240.0000.0000.0000.000
114A134VAL0-0.019-0.0097.127-0.814-0.8140.0000.0000.0000.000
115A135VAL00.0020.0008.5890.3900.3900.0000.0000.0000.000
116A136LEU00.0050.00710.108-0.162-0.1620.0000.0000.0000.000
117A137PHE00.007-0.00912.4330.1600.1600.0000.0000.0000.000
118A138GLU-1-0.794-0.91113.987-0.461-0.4610.0000.0000.0000.000
119A139GLY00.032-0.00617.3770.0470.0470.0000.0000.0000.000
120A140ILE0-0.054-0.02620.025-0.022-0.0220.0000.0000.0000.000
121A141LEU00.0130.00421.1980.0040.0040.0000.0000.0000.000
122A142VAL0-0.0160.01715.5150.0160.0160.0000.0000.0000.000
123A143PHE0-0.0080.00513.744-0.054-0.0540.0000.0000.0000.000
124A144TYR00.0000.00517.2460.0240.0240.0000.0000.0000.000
125A145SER0-0.004-0.00817.5120.0100.0100.0000.0000.0000.000
126A146GLN00.007-0.01714.426-0.036-0.0360.0000.0000.0000.000
127A147GLU-1-0.907-0.93213.616-0.342-0.3420.0000.0000.0000.000
128A148ILE0-0.001-0.00211.915-0.066-0.0660.0000.0000.0000.000
129A149ARG10.8720.93611.3820.3640.3640.0000.0000.0000.000
130A150ASP-1-0.918-0.9749.562-0.775-0.7750.0000.0000.0000.000
131A151MET0-0.080-0.0347.167-0.158-0.1580.0000.0000.0000.000
132A152PHE0-0.076-0.0296.522-0.388-0.3880.0000.0000.0000.000
133A153HIS00.0370.0582.169-0.448-0.9825.939-1.676-3.728-0.005
134A154LEU00.0200.0106.4980.3550.3550.0000.0000.0000.000
135A155ARG10.8720.9439.9061.0091.0090.0000.0000.0000.000
136A156LEU00.0260.01613.0870.1210.1210.0000.0000.0000.000
137A157PHE00.0400.00716.0810.0240.0240.0000.0000.0000.000
138A158VAL0-0.038-0.00719.5760.0220.0220.0000.0000.0000.000
139A159ASP-1-0.931-0.97322.301-0.278-0.2780.0000.0000.0000.000
140A160THR0-0.032-0.05125.4760.0110.0110.0000.0000.0000.000
141A161ASP-1-0.826-0.89428.692-0.212-0.2120.0000.0000.0000.000
142A162SER0-0.013-0.04632.036-0.007-0.0070.0000.0000.0000.000
143A163ASP-1-0.842-0.90733.186-0.172-0.1720.0000.0000.0000.000
144A164VAL00.0290.01432.2120.0030.0030.0000.0000.0000.000
145A165ARG10.8210.92928.0450.2480.2480.0000.0000.0000.000
146A166LEU0-0.0010.00332.1280.0000.0000.0000.0000.0000.000
147A167SER00.0290.01935.1700.0040.0040.0000.0000.0000.000
148A168ARG10.8710.94328.5570.2510.2510.0000.0000.0000.000
149A169ARG10.9140.95531.2500.2080.2080.0000.0000.0000.000
150A170VAL00.0190.00833.7660.0040.0040.0000.0000.0000.000
151A171LEU00.0180.00136.8450.0060.0060.0000.0000.0000.000
152A172ARG10.8350.89929.4140.2300.2300.0000.0000.0000.000
153A173ASP-1-0.814-0.90134.447-0.186-0.1860.0000.0000.0000.000
154A174VAL00.0260.02336.8860.0060.0060.0000.0000.0000.000
155A175ARG10.9000.96037.2430.1520.1520.0000.0000.0000.000
156A176ARG10.9330.95536.7220.1350.1350.0000.0000.0000.000
157A177GLY00.0310.02440.4860.0020.0020.0000.0000.0000.000
158A178ARG10.7930.89535.0450.1540.1540.0000.0000.0000.000
159A179ASP-1-0.788-0.89441.292-0.102-0.1020.0000.0000.0000.000
160A180LEU00.0290.01042.506-0.005-0.0050.0000.0000.0000.000
161A181GLU-1-0.860-0.92642.959-0.100-0.1000.0000.0000.0000.000
162A182GLN0-0.009-0.01041.895-0.007-0.0070.0000.0000.0000.000
163A183ILE0-0.062-0.01937.612-0.006-0.0060.0000.0000.0000.000
164A184LEU00.0100.00339.035-0.008-0.0080.0000.0000.0000.000
165A185THR00.0280.01740.742-0.002-0.0020.0000.0000.0000.000
166A186GLN0-0.0170.00035.418-0.011-0.0110.0000.0000.0000.000
167A187TYR00.026-0.00133.327-0.012-0.0120.0000.0000.0000.000
168A188THR0-0.030-0.01436.806-0.006-0.0060.0000.0000.0000.000
169A189THR0-0.051-0.03639.2790.0020.0020.0000.0000.0000.000
170A190PHE0-0.013-0.01435.0690.0010.0010.0000.0000.0000.000
171A191VAL0-0.048-0.00231.419-0.008-0.0080.0000.0000.0000.000
172A192LYS10.8670.93432.2900.1550.1550.0000.0000.0000.000
173A193PRO00.0330.01133.214-0.010-0.0100.0000.0000.0000.000
174A194ALA00.0520.03730.336-0.004-0.0040.0000.0000.0000.000
175A195PHE0-0.009-0.01626.677-0.019-0.0190.0000.0000.0000.000
176A196GLU-1-0.889-0.96128.463-0.199-0.1990.0000.0000.0000.000
177A197GLU-1-0.944-0.95329.928-0.185-0.1850.0000.0000.0000.000
178A198PHE0-0.007-0.01625.839-0.010-0.0100.0000.0000.0000.000
179A199CYS0-0.056-0.01623.406-0.022-0.0220.0000.0000.0000.000
180A200LEU00.0060.02323.939-0.031-0.0310.0000.0000.0000.000
181A201PRO00.0280.01225.207-0.020-0.0200.0000.0000.0000.000
182A202THR0-0.089-0.07520.165-0.024-0.0240.0000.0000.0000.000
183A203LYS10.9590.97820.1960.2600.2600.0000.0000.0000.000
184A204LYS10.9010.96120.6140.2880.2880.0000.0000.0000.000
185A205TYR0-0.030-0.01616.1300.0160.0160.0000.0000.0000.000
186A206ALA0-0.041-0.00715.916-0.087-0.0870.0000.0000.0000.000
187A207ASP-1-0.811-0.89212.344-0.998-0.9980.0000.0000.0000.000
188A208VAL0-0.011-0.00715.5340.0790.0790.0000.0000.0000.000
189A209ILE0-0.024-0.01817.927-0.016-0.0160.0000.0000.0000.000
190A210ILE00.000-0.00618.0710.0270.0270.0000.0000.0000.000
191A211PRO00.0040.01422.1860.0080.0080.0000.0000.0000.000
192A212ARG10.9930.98225.8610.2420.2420.0000.0000.0000.000
193A213GLY00.0240.00024.7740.0080.0080.0000.0000.0000.000
194A214VAL00.015-0.00524.881-0.011-0.0110.0000.0000.0000.000
195A215ASP-1-0.946-0.96925.927-0.207-0.2070.0000.0000.0000.000
196A216ASN0-0.057-0.01424.1650.0190.0190.0000.0000.0000.000
197A217MET00.0730.02423.643-0.035-0.0350.0000.0000.0000.000
198A218VAL00.0070.00922.853-0.015-0.0150.0000.0000.0000.000
199A219ALA00.0030.00520.498-0.019-0.0190.0000.0000.0000.000
200A220ILE0-0.002-0.00318.828-0.049-0.0490.0000.0000.0000.000
201A221ASN00.0420.00618.042-0.056-0.0560.0000.0000.0000.000
202A222LEU0-0.0150.02016.236-0.003-0.0030.0000.0000.0000.000
203A223ILE0-0.014-0.01213.144-0.047-0.0470.0000.0000.0000.000
204A224VAL00.005-0.00213.390-0.091-0.0910.0000.0000.0000.000
205A225GLN0-0.016-0.01114.415-0.014-0.0140.0000.0000.0000.000
206A226HIS00.0270.0237.7320.1790.1790.0000.0000.0000.000
207A227ILE0-0.031-0.0299.814-0.087-0.0870.0000.0000.0000.000
208A228GLN0-0.029-0.02410.5350.0090.0090.0000.0000.0000.000
209A229ASP-1-0.823-0.89810.351-0.230-0.2300.0000.0000.0000.000
210A230ILE0-0.052-0.0225.5940.0870.0870.0000.0000.0000.000
211A231LEU0-0.087-0.0547.8740.2410.2410.0000.0000.0000.000
212A232ASN0-0.046-0.01710.5110.1030.1030.0000.0000.0000.000
213A233GLY0-0.036-0.0028.9490.1060.1060.0000.0000.0000.000
214A234ASP-1-0.946-0.97210.0290.2680.2680.0000.0000.0000.000
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