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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: QY18Y

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2678469.57584
FMO2-HF: Nuclear repulsion 2591979.596943
FMO2-HF: Total energy -86489.978897
FMO2-MP2: Total energy -86743.087009


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.
-6.935-0.4572.221-2.88-5.818-0.012
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 : 0.018 / q_NPA : 0.013
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].
3A23PRO0-0.012-0.0073.826-0.1862.432-0.009-1.217-1.3920.003
4A24PHE00.020-0.0022.662-2.135-0.6000.138-0.530-1.143-0.001
5A25LEU00.000-0.0124.3801.3011.520-0.001-0.017-0.2000.000
6A26ILE00.0130.0106.6270.1680.1680.0000.0000.0000.000
7A27GLY00.0160.0149.3370.1460.1460.0000.0000.0000.000
8A28VAL0-0.022-0.02812.1840.0490.0490.0000.0000.0000.000
9A29SER00.008-0.00415.6250.0610.0610.0000.0000.0000.000
10A30GLY00.0320.01718.574-0.004-0.0040.0000.0000.0000.000
11A31GLY00.0330.00422.1990.0080.0080.0000.0000.0000.000
12A32THR00.0260.00625.477-0.013-0.0130.0000.0000.0000.000
13A33ALA0-0.009-0.01027.0160.0120.0120.0000.0000.0000.000
14A34SER00.005-0.01123.4590.0060.0060.0000.0000.0000.000
15A35GLY00.0340.01424.5290.0070.0070.0000.0000.0000.000
16A36LYS10.7870.91619.9730.3230.3230.0000.0000.0000.000
17A37SER00.0790.04519.712-0.036-0.0360.0000.0000.0000.000
18A38THR00.006-0.00821.404-0.015-0.0150.0000.0000.0000.000
19A39VAL0-0.006-0.00218.0710.0040.0040.0000.0000.0000.000
20A40CYS0-0.024-0.00416.995-0.045-0.0450.0000.0000.0000.000
21A41GLU-1-0.872-0.95318.329-0.404-0.4040.0000.0000.0000.000
22A42LYS10.7630.87121.2520.2980.2980.0000.0000.0000.000
23A43ILE00.0220.00414.8670.0050.0050.0000.0000.0000.000
24A44MET0-0.022-0.01117.202-0.047-0.0470.0000.0000.0000.000
25A45GLU-1-0.836-0.89718.988-0.279-0.2790.0000.0000.0000.000
26A46LEU0-0.033-0.01619.8170.0180.0180.0000.0000.0000.000
27A47LEU0-0.0040.01214.168-0.009-0.0090.0000.0000.0000.000
28A48GLY00.0650.03218.430-0.011-0.0110.0000.0000.0000.000
29A49GLN0-0.020-0.02616.176-0.025-0.0250.0000.0000.0000.000
30A50ASN0-0.028-0.02619.6250.0140.0140.0000.0000.0000.000
31A51GLU-1-0.944-0.95622.607-0.235-0.2350.0000.0000.0000.000
32A52VAL0-0.0110.01220.4560.0240.0240.0000.0000.0000.000
33A53GLU-1-0.796-0.88222.826-0.209-0.2090.0000.0000.0000.000
34A54GLN00.017-0.01518.295-0.046-0.0460.0000.0000.0000.000
35A55ARG10.8190.88718.7530.1450.1450.0000.0000.0000.000
36A56GLN0-0.075-0.04819.3800.0100.0100.0000.0000.0000.000
37A57ARG10.8260.94616.6650.3730.3730.0000.0000.0000.000
38A58LYS10.9420.96811.8590.7770.7770.0000.0000.0000.000
39A59VAL00.0070.01211.769-0.236-0.2360.0000.0000.0000.000
40A60VAL00.0260.00413.0250.1600.1600.0000.0000.0000.000
41A61ILE00.0070.01313.790-0.109-0.1090.0000.0000.0000.000
42A62LEU0-0.051-0.02613.6660.0580.0580.0000.0000.0000.000
43A63SER00.003-0.01916.522-0.023-0.0230.0000.0000.0000.000
44A64GLN00.0240.00218.8860.0180.0180.0000.0000.0000.000
45A65ASP-1-0.892-0.96019.896-0.257-0.2570.0000.0000.0000.000
46A66ARG10.8390.90120.3830.2940.2940.0000.0000.0000.000
47A67PHE00.0010.00017.1770.0180.0180.0000.0000.0000.000
48A68TYR0-0.045-0.02222.5370.0120.0120.0000.0000.0000.000
49A69LYS10.8420.92726.0880.1030.1030.0000.0000.0000.000
50A70VAL0-0.019-0.01128.190-0.003-0.0030.0000.0000.0000.000
51A71LEU0-0.039-0.00331.1580.0060.0060.0000.0000.0000.000
52A72THR00.039-0.00534.1260.0040.0040.0000.0000.0000.000
53A73ALA00.0440.00836.936-0.003-0.0030.0000.0000.0000.000
54A74GLU-1-0.778-0.87639.730-0.058-0.0580.0000.0000.0000.000
55A75GLN00.0810.06033.707-0.001-0.0010.0000.0000.0000.000
56A76LYS10.8860.95235.8310.0830.0830.0000.0000.0000.000
57A77ALA00.0290.00738.630-0.002-0.0020.0000.0000.0000.000
58A78LYS10.7870.87639.5910.0580.0580.0000.0000.0000.000
59A79ALA00.0250.00936.732-0.001-0.0010.0000.0000.0000.000
60A80LEU0-0.046-0.00638.586-0.004-0.0040.0000.0000.0000.000
61A81LYS10.8790.94241.4080.0590.0590.0000.0000.0000.000
62A82GLY00.0400.03139.5580.0010.0010.0000.0000.0000.000
63A83GLN0-0.028-0.01139.391-0.001-0.0010.0000.0000.0000.000
64A84TYR00.021-0.00631.3480.0070.0070.0000.0000.0000.000
65A85ASN00.0350.02032.007-0.012-0.0120.0000.0000.0000.000
66A86PHE00.010-0.00430.4260.0000.0000.0000.0000.0000.000
67A87ASP-1-0.795-0.90028.047-0.178-0.1780.0000.0000.0000.000
68A88HIS00.0570.04827.699-0.012-0.0120.0000.0000.0000.000
69A89PRO00.0550.02223.855-0.006-0.0060.0000.0000.0000.000
70A90ASP-1-0.853-0.93224.794-0.093-0.0930.0000.0000.0000.000
71A91ALA0-0.069-0.01927.3340.0090.0090.0000.0000.0000.000
72A92PHE00.002-0.00822.646-0.005-0.0050.0000.0000.0000.000
73A93ASP-1-0.827-0.90323.106-0.101-0.1010.0000.0000.0000.000
74A94ASN0-0.009-0.03120.115-0.031-0.0310.0000.0000.0000.000
75A95ASP-1-0.792-0.83518.894-0.048-0.0480.0000.0000.0000.000
76A96LEU00.0430.02718.8720.0020.0020.0000.0000.0000.000
77A97MET0-0.0340.01716.609-0.018-0.0180.0000.0000.0000.000
78A98HIS00.0290.01013.167-0.035-0.0350.0000.0000.0000.000
79A99ARG10.8140.86513.9770.0030.0030.0000.0000.0000.000
80A100THR0-0.008-0.01214.5010.0330.0330.0000.0000.0000.000
81A101LEU00.0260.01010.885-0.023-0.0230.0000.0000.0000.000
82A102LYS10.9190.9479.786-0.367-0.3670.0000.0000.0000.000
83A103ASN0-0.057-0.0449.9560.1810.1810.0000.0000.0000.000
84A104ILE00.0380.0198.3310.0550.0550.0000.0000.0000.000
85A105VAL00.0090.0034.648-0.204-0.117-0.001-0.003-0.0830.000
86A106GLU-1-0.875-0.9115.8370.8770.8770.0000.0000.0000.000
87A107GLY00.0090.0107.9520.0740.0740.0000.0000.0000.000
88A108LYS10.7840.8888.869-0.296-0.2960.0000.0000.0000.000
89A109THR0-0.012-0.01612.501-0.112-0.1120.0000.0000.0000.000
90A110VAL0-0.035-0.00713.8580.0550.0550.0000.0000.0000.000
91A111GLU-1-0.857-0.89816.611-0.140-0.1400.0000.0000.0000.000
92A112VAL0-0.014-0.00817.467-0.003-0.0030.0000.0000.0000.000
93A113PRO00.0560.02520.2030.0120.0120.0000.0000.0000.000
94A114THR00.0290.02423.193-0.035-0.0350.0000.0000.0000.000
95A115TYR0-0.026-0.02125.9540.0190.0190.0000.0000.0000.000
96A116ASP-1-0.802-0.86228.368-0.128-0.1280.0000.0000.0000.000
97A117PHE00.0540.00026.9730.0110.0110.0000.0000.0000.000
98A118VAL0-0.053-0.01032.4550.0070.0070.0000.0000.0000.000
99A119THR0-0.040-0.04735.6420.0080.0080.0000.0000.0000.000
100A120HIS10.8040.88933.5400.1120.1120.0000.0000.0000.000
101A121SER00.018-0.00132.2120.0110.0110.0000.0000.0000.000
102A122ARG10.8330.89724.8780.1250.1250.0000.0000.0000.000
103A123LEU0-0.021-0.01529.2430.0100.0100.0000.0000.0000.000
104A124PRO0-0.021-0.01629.552-0.002-0.0020.0000.0000.0000.000
105A125GLU-1-0.884-0.92228.760-0.100-0.1000.0000.0000.0000.000
106A126THR0-0.061-0.04623.231-0.016-0.0160.0000.0000.0000.000
107A127THR0-0.047-0.02421.057-0.006-0.0060.0000.0000.0000.000
108A128VAL00.0390.02918.951-0.012-0.0120.0000.0000.0000.000
109A129VAL0-0.006-0.00513.831-0.031-0.0310.0000.0000.0000.000
110A130TYR00.0500.02015.3610.0500.0500.0000.0000.0000.000
111A131PRO00.010-0.00110.898-0.105-0.1050.0000.0000.0000.000
112A132ALA00.0190.03110.779-0.008-0.0080.0000.0000.0000.000
113A133ASP-1-0.797-0.8858.297-1.237-1.2370.0000.0000.0000.000
114A134VAL0-0.0050.0037.052-1.004-1.0040.0000.0000.0000.000
115A135VAL0-0.018-0.0148.4360.4590.4590.0000.0000.0000.000
116A136LEU00.0200.0189.894-0.118-0.1180.0000.0000.0000.000
117A137PHE00.013-0.00112.2240.1580.1580.0000.0000.0000.000
118A138GLU-1-0.717-0.84313.898-0.365-0.3650.0000.0000.0000.000
119A139GLY0-0.001-0.03317.1300.0520.0520.0000.0000.0000.000
120A140ILE00.0010.01719.865-0.012-0.0120.0000.0000.0000.000
121A141LEU00.0210.01820.8490.0130.0130.0000.0000.0000.000
122A142VAL0-0.0540.00115.3510.0210.0210.0000.0000.0000.000
123A143PHE00.0140.00813.449-0.022-0.0220.0000.0000.0000.000
124A144TYR00.0010.00316.6720.0320.0320.0000.0000.0000.000
125A145SER00.002-0.00517.9840.0110.0110.0000.0000.0000.000
126A146GLN0-0.054-0.04414.568-0.025-0.0250.0000.0000.0000.000
127A147GLU-1-0.894-0.95113.582-0.064-0.0640.0000.0000.0000.000
128A148ILE0-0.032-0.00811.968-0.028-0.0280.0000.0000.0000.000
129A149ARG10.8600.93211.3840.1290.1290.0000.0000.0000.000
130A150ASP-1-0.799-0.90610.536-0.330-0.3300.0000.0000.0000.000
131A151MET0-0.060-0.0186.925-0.042-0.0420.0000.0000.0000.000
132A152PHE0-0.067-0.0226.003-0.432-0.4320.0000.0000.0000.000
133A153HIS00.0470.0282.716-3.383-1.3642.094-1.113-3.000-0.014
134A154LEU00.0200.0145.8780.3320.3320.0000.0000.0000.000
135A155ARG10.7690.8839.1810.5510.5510.0000.0000.0000.000
136A156LEU00.0480.02412.5480.1080.1080.0000.0000.0000.000
137A157PHE00.004-0.01315.4290.0200.0200.0000.0000.0000.000
138A158VAL0-0.0030.00919.0100.0230.0230.0000.0000.0000.000
139A159ASP-1-0.791-0.88721.555-0.185-0.1850.0000.0000.0000.000
140A160THR0-0.043-0.05024.7990.0010.0010.0000.0000.0000.000
141A161ASP-1-0.837-0.89728.393-0.150-0.1500.0000.0000.0000.000
142A162SER00.021-0.02031.793-0.008-0.0080.0000.0000.0000.000
143A163ASP-1-0.824-0.89432.918-0.123-0.1230.0000.0000.0000.000
144A164VAL00.0360.02232.179-0.001-0.0010.0000.0000.0000.000
145A165ARG10.8200.91927.8430.1730.1730.0000.0000.0000.000
146A166LEU00.0010.02131.883-0.003-0.0030.0000.0000.0000.000
147A167SER0-0.035-0.02635.0300.0010.0010.0000.0000.0000.000
148A168ARG10.8550.91827.9390.2040.2040.0000.0000.0000.000
149A169ARG10.8300.91831.1640.1450.1450.0000.0000.0000.000
150A170VAL00.0390.01633.4630.0020.0020.0000.0000.0000.000
151A171LEU00.0010.00536.0970.0040.0040.0000.0000.0000.000
152A172ARG10.9060.95329.0650.1790.1790.0000.0000.0000.000
153A173ASP-1-0.807-0.91334.294-0.144-0.1440.0000.0000.0000.000
154A174VAL00.0010.00336.4410.0050.0050.0000.0000.0000.000
155A175ARG10.8510.92937.1950.1270.1270.0000.0000.0000.000
156A176ARG10.9450.95236.7970.1120.1120.0000.0000.0000.000
157A177GLY00.0450.03640.3540.0010.0010.0000.0000.0000.000
158A178ARG10.7980.89534.8440.1210.1210.0000.0000.0000.000
159A179ASP-1-0.750-0.87441.279-0.077-0.0770.0000.0000.0000.000
160A180LEU00.0060.01541.961-0.004-0.0040.0000.0000.0000.000
161A181GLU-1-0.867-0.92942.801-0.071-0.0710.0000.0000.0000.000
162A182GLN0-0.028-0.01641.067-0.005-0.0050.0000.0000.0000.000
163A183ILE0-0.046-0.02037.396-0.003-0.0030.0000.0000.0000.000
164A184LEU00.0330.01238.851-0.004-0.0040.0000.0000.0000.000
165A185THR00.0080.00740.7200.0010.0010.0000.0000.0000.000
166A186GLN0-0.011-0.00235.315-0.007-0.0070.0000.0000.0000.000
167A187TYR0-0.022-0.03833.027-0.006-0.0060.0000.0000.0000.000
168A188THR0-0.033-0.02436.601-0.003-0.0030.0000.0000.0000.000
169A189THR0-0.052-0.03438.9300.0030.0030.0000.0000.0000.000
170A190PHE0-0.039-0.02234.4950.0020.0020.0000.0000.0000.000
171A191VAL0-0.0380.00231.245-0.004-0.0040.0000.0000.0000.000
172A192LYS10.8170.89531.9310.0930.0930.0000.0000.0000.000
173A193PRO00.0350.01032.909-0.005-0.0050.0000.0000.0000.000
174A194ALA00.0390.02429.735-0.001-0.0010.0000.0000.0000.000
175A195PHE0-0.018-0.01926.310-0.012-0.0120.0000.0000.0000.000
176A196GLU-1-0.826-0.90528.287-0.118-0.1180.0000.0000.0000.000
177A197GLU-1-0.928-0.95629.894-0.092-0.0920.0000.0000.0000.000
178A198PHE0-0.034-0.02325.476-0.002-0.0020.0000.0000.0000.000
179A199CYS0-0.050-0.01523.267-0.013-0.0130.0000.0000.0000.000
180A200LEU00.0220.02223.705-0.017-0.0170.0000.0000.0000.000
181A201PRO00.0220.00724.911-0.008-0.0080.0000.0000.0000.000
182A202THR0-0.078-0.05219.675-0.007-0.0070.0000.0000.0000.000
183A203LYS10.8440.91719.9510.1730.1730.0000.0000.0000.000
184A204LYS10.8660.93220.4300.1370.1370.0000.0000.0000.000
185A205TYR00.0150.00316.2320.0230.0230.0000.0000.0000.000
186A206ALA0-0.0360.00015.479-0.053-0.0530.0000.0000.0000.000
187A207ASP-1-0.763-0.85411.545-0.522-0.5220.0000.0000.0000.000
188A208VAL0-0.008-0.00614.8420.0430.0430.0000.0000.0000.000
189A209ILE0-0.014-0.00717.064-0.024-0.0240.0000.0000.0000.000
190A210ILE00.0150.00517.4570.0130.0130.0000.0000.0000.000
191A211PRO00.0130.00721.5660.0040.0040.0000.0000.0000.000
192A212ARG10.8890.91825.3560.1890.1890.0000.0000.0000.000
193A213GLY00.0400.02923.9950.0080.0080.0000.0000.0000.000
194A214VAL00.008-0.01124.142-0.003-0.0030.0000.0000.0000.000
195A215ASP-1-0.838-0.89225.133-0.193-0.1930.0000.0000.0000.000
196A216ASN0-0.023-0.00823.9500.0120.0120.0000.0000.0000.000
197A217MET00.036-0.00423.280-0.033-0.0330.0000.0000.0000.000
198A218VAL00.0060.01522.661-0.018-0.0180.0000.0000.0000.000
199A219ALA00.0150.00919.980-0.019-0.0190.0000.0000.0000.000
200A220ILE0-0.031-0.01218.437-0.047-0.0470.0000.0000.0000.000
201A221ASN00.029-0.00117.940-0.066-0.0660.0000.0000.0000.000
202A222LEU0-0.0130.01415.679-0.020-0.0200.0000.0000.0000.000
203A223ILE0-0.011-0.00912.908-0.053-0.0530.0000.0000.0000.000
204A224VAL0-0.001-0.00213.184-0.118-0.1180.0000.0000.0000.000
205A225GLN0-0.040-0.02214.236-0.042-0.0420.0000.0000.0000.000
206A226HIS00.0220.0216.8640.1550.1550.0000.0000.0000.000
207A227ILE0-0.032-0.0299.466-0.235-0.2350.0000.0000.0000.000
208A228GLN0-0.043-0.02710.437-0.094-0.0940.0000.0000.0000.000
209A229ASP-1-0.796-0.8849.956-0.584-0.5840.0000.0000.0000.000
210A230ILE0-0.048-0.0305.386-0.119-0.1190.0000.0000.0000.000
211A231LEU0-0.107-0.0587.7930.0080.0080.0000.0000.0000.000
212A232ASN0-0.075-0.03510.6200.1030.1030.0000.0000.0000.000
213A233GLY0-0.035-0.0088.2100.1070.1070.0000.0000.0000.000
214A234ASP-1-0.894-0.9369.283-0.235-0.2350.0000.0000.0000.000
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