Manual

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: R9518

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 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 -2667828.525606
FMO2-HF: Nuclear repulsion 2581339.043735
FMO2-HF: Total energy -86489.481871
FMO2-MP2: Total energy -86742.594856


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.
-6.782-1.0271.929-2.633-5.05-0.006
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 : 0.017 / q_NPA : 0.011
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].
3A23PRO0-0.037-0.0103.829-0.6972.037-0.021-1.285-1.4290.003
4A24PHE00.0420.0042.953-1.807-0.7310.038-0.350-0.764-0.001
5A25LEU0-0.001-0.0164.5281.2901.462-0.001-0.013-0.1580.000
6A26ILE00.0110.0046.8470.1180.1180.0000.0000.0000.000
7A27GLY00.0170.0199.7750.1420.1420.0000.0000.0000.000
8A28VAL0-0.002-0.00912.5720.0560.0560.0000.0000.0000.000
9A29SER00.013-0.00916.0180.0520.0520.0000.0000.0000.000
10A30GLY00.0290.01819.010-0.001-0.0010.0000.0000.0000.000
11A31GLY00.0510.01022.6560.0060.0060.0000.0000.0000.000
12A32THR00.012-0.00625.485-0.017-0.0170.0000.0000.0000.000
13A33ALA00.002-0.00927.0000.0130.0130.0000.0000.0000.000
14A34SER00.0350.01623.5620.0080.0080.0000.0000.0000.000
15A35GLY00.0580.03024.9160.0100.0100.0000.0000.0000.000
16A36LYS10.8410.92820.1260.3350.3350.0000.0000.0000.000
17A37SER00.0480.02520.124-0.036-0.0360.0000.0000.0000.000
18A38THR00.006-0.00922.092-0.010-0.0100.0000.0000.0000.000
19A39VAL00.0020.00618.5730.0010.0010.0000.0000.0000.000
20A40CYS0-0.012-0.00117.395-0.043-0.0430.0000.0000.0000.000
21A41GLU-1-0.897-0.95418.771-0.438-0.4380.0000.0000.0000.000
22A42LYS10.7670.87121.6650.3240.3240.0000.0000.0000.000
23A43ILE00.007-0.01015.3180.0050.0050.0000.0000.0000.000
24A44MET0-0.0030.00317.343-0.051-0.0510.0000.0000.0000.000
25A45GLU-1-0.842-0.89619.105-0.307-0.3070.0000.0000.0000.000
26A46LEU0-0.034-0.02020.3240.0200.0200.0000.0000.0000.000
27A47LEU0-0.017-0.00814.378-0.003-0.0030.0000.0000.0000.000
28A48GLY00.0450.03718.721-0.003-0.0030.0000.0000.0000.000
29A49GLN00.033-0.00316.393-0.031-0.0310.0000.0000.0000.000
30A50ASN0-0.037-0.02219.8120.0080.0080.0000.0000.0000.000
31A51GLU-1-0.955-0.95822.760-0.256-0.2560.0000.0000.0000.000
32A52VAL0-0.0140.00520.5980.0200.0200.0000.0000.0000.000
33A53GLU-1-0.802-0.89622.845-0.248-0.2480.0000.0000.0000.000
34A54GLN00.0360.00219.345-0.046-0.0460.0000.0000.0000.000
35A55ARG10.8480.90619.2730.1790.1790.0000.0000.0000.000
36A56GLN0-0.074-0.03319.066-0.015-0.0150.0000.0000.0000.000
37A57ARG10.8260.94316.9870.4310.4310.0000.0000.0000.000
38A58LYS10.9430.97012.2260.8450.8450.0000.0000.0000.000
39A59VAL00.0000.00912.196-0.243-0.2430.0000.0000.0000.000
40A60VAL00.0380.01213.1130.1640.1640.0000.0000.0000.000
41A61ILE0-0.0020.00613.980-0.110-0.1100.0000.0000.0000.000
42A62LEU0-0.064-0.03214.4080.0730.0730.0000.0000.0000.000
43A63SER00.023-0.00316.668-0.029-0.0290.0000.0000.0000.000
44A64GLN00.0340.00019.1040.0160.0160.0000.0000.0000.000
45A65ASP-1-0.941-0.97020.116-0.272-0.2720.0000.0000.0000.000
46A66ARG10.8520.90820.5520.3430.3430.0000.0000.0000.000
47A67PHE0-0.010-0.01217.6420.0210.0210.0000.0000.0000.000
48A68TYR0-0.043-0.00922.8660.0140.0140.0000.0000.0000.000
49A69LYS10.8630.94026.2650.1130.1130.0000.0000.0000.000
50A70VAL0-0.010-0.00528.224-0.003-0.0030.0000.0000.0000.000
51A71LEU0-0.055-0.01331.2880.0070.0070.0000.0000.0000.000
52A72THR00.0470.00034.1840.0050.0050.0000.0000.0000.000
53A73ALA00.034-0.00137.013-0.003-0.0030.0000.0000.0000.000
54A74GLU-1-0.806-0.89640.086-0.064-0.0640.0000.0000.0000.000
55A75GLN00.0870.06633.579-0.001-0.0010.0000.0000.0000.000
56A76LYS10.9150.96437.1430.0930.0930.0000.0000.0000.000
57A77ALA00.002-0.00438.768-0.002-0.0020.0000.0000.0000.000
58A78LYS10.8320.89839.4370.0640.0640.0000.0000.0000.000
59A79ALA00.0000.00537.017-0.002-0.0020.0000.0000.0000.000
60A80LEU0-0.056-0.01538.853-0.003-0.0030.0000.0000.0000.000
61A81LYS10.9270.97141.9030.0640.0640.0000.0000.0000.000
62A82GLY00.0320.01939.9960.0020.0020.0000.0000.0000.000
63A83GLN0-0.060-0.03739.952-0.002-0.0020.0000.0000.0000.000
64A84TYR00.003-0.00631.2330.0080.0080.0000.0000.0000.000
65A85ASN00.0260.01032.277-0.014-0.0140.0000.0000.0000.000
66A86PHE0-0.001-0.00630.3520.0010.0010.0000.0000.0000.000
67A87ASP-1-0.841-0.93328.267-0.192-0.1920.0000.0000.0000.000
68A88HIS00.0500.05028.024-0.012-0.0120.0000.0000.0000.000
69A89PRO00.0810.03723.993-0.008-0.0080.0000.0000.0000.000
70A90ASP-1-0.883-0.94124.981-0.101-0.1010.0000.0000.0000.000
71A91ALA0-0.100-0.03627.5460.0070.0070.0000.0000.0000.000
72A92PHE0-0.003-0.01722.711-0.008-0.0080.0000.0000.0000.000
73A93ASP-1-0.838-0.91823.521-0.117-0.1170.0000.0000.0000.000
74A94ASN0-0.003-0.02420.328-0.038-0.0380.0000.0000.0000.000
75A95ASP-1-0.797-0.84519.001-0.068-0.0680.0000.0000.0000.000
76A96LEU00.0490.03018.901-0.002-0.0020.0000.0000.0000.000
77A97MET0-0.0240.01716.491-0.028-0.0280.0000.0000.0000.000
78A98HIS00.0300.00113.211-0.051-0.0510.0000.0000.0000.000
79A99ARG10.8260.87513.8530.0140.0140.0000.0000.0000.000
80A100THR00.002-0.00714.4260.0200.0200.0000.0000.0000.000
81A101LEU00.0240.00411.034-0.038-0.0380.0000.0000.0000.000
82A102LYS10.9180.9499.981-0.384-0.3840.0000.0000.0000.000
83A103ASN0-0.080-0.05510.1700.1700.1700.0000.0000.0000.000
84A104ILE00.0280.0158.7570.0260.0260.0000.0000.0000.000
85A105VAL00.0200.0094.619-0.241-0.159-0.001-0.002-0.0780.000
86A106GLU-1-0.881-0.9105.6520.4860.4860.0000.0000.0000.000
87A107GLY0-0.0020.0097.9430.1180.1180.0000.0000.0000.000
88A108LYS10.8090.9018.956-0.115-0.1150.0000.0000.0000.000
89A109THR0-0.006-0.01412.563-0.113-0.1130.0000.0000.0000.000
90A110VAL0-0.039-0.00514.0150.0560.0560.0000.0000.0000.000
91A111GLU-1-0.859-0.89816.783-0.170-0.1700.0000.0000.0000.000
92A112VAL0-0.022-0.01617.857-0.004-0.0040.0000.0000.0000.000
93A113PRO00.0620.03920.7960.0150.0150.0000.0000.0000.000
94A114THR00.0420.03223.665-0.039-0.0390.0000.0000.0000.000
95A115TYR00.0060.00926.4290.0230.0230.0000.0000.0000.000
96A116ASP-1-0.815-0.88228.536-0.144-0.1440.0000.0000.0000.000
97A117PHE00.030-0.01227.2170.0130.0130.0000.0000.0000.000
98A118VAL0-0.048-0.01932.7520.0080.0080.0000.0000.0000.000
99A119THR0-0.059-0.04835.9660.0100.0100.0000.0000.0000.000
100A120HIS10.8650.92533.6080.1290.1290.0000.0000.0000.000
101A121SER00.0280.02032.8420.0090.0090.0000.0000.0000.000
102A122ARG10.8230.89025.2510.1450.1450.0000.0000.0000.000
103A123LEU0-0.016-0.02129.7180.0110.0110.0000.0000.0000.000
104A124PRO0-0.015-0.00929.977-0.003-0.0030.0000.0000.0000.000
105A125GLU-1-0.897-0.92929.018-0.121-0.1210.0000.0000.0000.000
106A126THR0-0.086-0.06123.692-0.014-0.0140.0000.0000.0000.000
107A127THR0-0.046-0.03221.147-0.005-0.0050.0000.0000.0000.000
108A128VAL00.0460.02219.680-0.010-0.0100.0000.0000.0000.000
109A129VAL0-0.024-0.01514.518-0.024-0.0240.0000.0000.0000.000
110A130TYR00.0280.00215.9040.0380.0380.0000.0000.0000.000
111A131PRO0-0.014-0.01010.947-0.089-0.0890.0000.0000.0000.000
112A132ALA00.0230.02710.7910.0640.0640.0000.0000.0000.000
113A133ASP-1-0.837-0.9128.340-1.516-1.5160.0000.0000.0000.000
114A134VAL00.0040.0037.265-0.901-0.9010.0000.0000.0000.000
115A135VAL00.0000.0018.5860.4350.4350.0000.0000.0000.000
116A136LEU00.0090.01310.070-0.117-0.1170.0000.0000.0000.000
117A137PHE00.007-0.00612.4850.1510.1510.0000.0000.0000.000
118A138GLU-1-0.748-0.85713.975-0.384-0.3840.0000.0000.0000.000
119A139GLY00.024-0.01317.3230.0410.0410.0000.0000.0000.000
120A140ILE0-0.030-0.00219.945-0.014-0.0140.0000.0000.0000.000
121A141LEU00.0250.01121.0710.0100.0100.0000.0000.0000.000
122A142VAL0-0.0320.00915.5380.0260.0260.0000.0000.0000.000
123A143PHE00.0010.00513.587-0.028-0.0280.0000.0000.0000.000
124A144TYR0-0.0170.00017.0520.0360.0360.0000.0000.0000.000
125A145SER00.002-0.00317.6350.0150.0150.0000.0000.0000.000
126A146GLN0-0.042-0.04314.159-0.040-0.0400.0000.0000.0000.000
127A147GLU-1-0.903-0.93513.538-0.031-0.0310.0000.0000.0000.000
128A148ILE0-0.006-0.00511.817-0.031-0.0310.0000.0000.0000.000
129A149ARG10.8920.95111.2180.1210.1210.0000.0000.0000.000
130A150ASP-1-0.858-0.94710.010-0.314-0.3140.0000.0000.0000.000
131A151MET0-0.070-0.0247.038-0.056-0.0560.0000.0000.0000.000
132A152PHE0-0.067-0.0266.320-0.413-0.4130.0000.0000.0000.000
133A153HIS00.0290.0322.392-2.410-0.7191.914-0.983-2.621-0.008
134A154LEU00.0050.0066.2280.3850.3850.0000.0000.0000.000
135A155ARG10.8120.9049.6190.5220.5220.0000.0000.0000.000
136A156LEU00.0230.01312.8480.1020.1020.0000.0000.0000.000
137A157PHE00.0380.00115.8380.0180.0180.0000.0000.0000.000
138A158VAL0-0.036-0.00319.3520.0160.0160.0000.0000.0000.000
139A159ASP-1-0.836-0.91722.082-0.198-0.1980.0000.0000.0000.000
140A160THR0-0.028-0.04225.2430.0050.0050.0000.0000.0000.000
141A161ASP-1-0.844-0.90528.475-0.162-0.1620.0000.0000.0000.000
142A162SER00.007-0.03631.823-0.009-0.0090.0000.0000.0000.000
143A163ASP-1-0.841-0.90833.010-0.138-0.1380.0000.0000.0000.000
144A164VAL00.0290.02032.262-0.001-0.0010.0000.0000.0000.000
145A165ARG10.8400.94227.9610.1880.1880.0000.0000.0000.000
146A166LEU0-0.0020.00631.973-0.003-0.0030.0000.0000.0000.000
147A167SER0-0.005-0.00535.0370.0030.0030.0000.0000.0000.000
148A168ARG10.8540.92528.2000.2220.2220.0000.0000.0000.000
149A169ARG10.8910.94631.6320.1600.1600.0000.0000.0000.000
150A170VAL00.0280.01233.6710.0020.0020.0000.0000.0000.000
151A171LEU00.0120.00936.5710.0040.0040.0000.0000.0000.000
152A172ARG10.8790.93229.2880.1990.1990.0000.0000.0000.000
153A173ASP-1-0.827-0.91434.564-0.161-0.1610.0000.0000.0000.000
154A174VAL00.0280.02436.8450.0060.0060.0000.0000.0000.000
155A175ARG10.8560.92937.3490.1420.1420.0000.0000.0000.000
156A176ARG10.9370.95337.1760.1270.1270.0000.0000.0000.000
157A177GLY00.0280.02540.7490.0010.0010.0000.0000.0000.000
158A178ARG10.8160.90235.1600.1340.1340.0000.0000.0000.000
159A179ASP-1-0.771-0.89141.426-0.086-0.0860.0000.0000.0000.000
160A180LEU00.0090.01442.311-0.003-0.0030.0000.0000.0000.000
161A181GLU-1-0.854-0.92642.898-0.079-0.0790.0000.0000.0000.000
162A182GLN0-0.016-0.00441.501-0.004-0.0040.0000.0000.0000.000
163A183ILE0-0.053-0.02237.578-0.004-0.0040.0000.0000.0000.000
164A184LEU00.0170.00738.976-0.005-0.0050.0000.0000.0000.000
165A185THR00.0150.00540.6660.0000.0000.0000.0000.0000.000
166A186GLN0-0.012-0.00235.647-0.007-0.0070.0000.0000.0000.000
167A187TYR00.026-0.00533.111-0.008-0.0080.0000.0000.0000.000
168A188THR0-0.037-0.02736.723-0.003-0.0030.0000.0000.0000.000
169A189THR0-0.047-0.01939.1950.0040.0040.0000.0000.0000.000
170A190PHE0-0.022-0.01934.9880.0020.0020.0000.0000.0000.000
171A191VAL0-0.048-0.00131.383-0.005-0.0050.0000.0000.0000.000
172A192LYS10.8070.88732.2070.1030.1030.0000.0000.0000.000
173A193PRO00.0330.01233.104-0.005-0.0050.0000.0000.0000.000
174A194ALA00.0510.03830.2080.0000.0000.0000.0000.0000.000
175A195PHE0-0.019-0.01826.323-0.012-0.0120.0000.0000.0000.000
176A196GLU-1-0.831-0.91528.341-0.129-0.1290.0000.0000.0000.000
177A197GLU-1-0.928-0.94929.865-0.099-0.0990.0000.0000.0000.000
178A198PHE0-0.024-0.02325.680-0.002-0.0020.0000.0000.0000.000
179A199CYS0-0.065-0.02823.280-0.014-0.0140.0000.0000.0000.000
180A200LEU00.0160.01623.797-0.020-0.0200.0000.0000.0000.000
181A201PRO00.0280.01225.023-0.010-0.0100.0000.0000.0000.000
182A202THR0-0.093-0.06219.967-0.010-0.0100.0000.0000.0000.000
183A203LYS10.8630.92420.0130.1780.1780.0000.0000.0000.000
184A204LYS10.8990.96320.6580.1270.1270.0000.0000.0000.000
185A205TYR00.001-0.01016.3810.0210.0210.0000.0000.0000.000
186A206ALA0-0.055-0.00415.937-0.050-0.0500.0000.0000.0000.000
187A207ASP-1-0.769-0.86612.206-0.547-0.5470.0000.0000.0000.000
188A208VAL00.000-0.00415.3430.0500.0500.0000.0000.0000.000
189A209ILE0-0.015-0.00917.692-0.026-0.0260.0000.0000.0000.000
190A210ILE0-0.005-0.00717.8760.0150.0150.0000.0000.0000.000
191A211PRO00.0180.01621.9810.0050.0050.0000.0000.0000.000
192A212ARG10.9020.92925.6920.2050.2050.0000.0000.0000.000
193A213GLY00.0220.00224.5640.0080.0080.0000.0000.0000.000
194A214VAL00.017-0.00424.838-0.011-0.0110.0000.0000.0000.000
195A215ASP-1-0.863-0.90725.894-0.211-0.2110.0000.0000.0000.000
196A216ASN0-0.022-0.00824.2560.0120.0120.0000.0000.0000.000
197A217MET00.0500.01223.625-0.036-0.0360.0000.0000.0000.000
198A218VAL00.0200.01422.870-0.023-0.0230.0000.0000.0000.000
199A219ALA00.0020.00720.473-0.021-0.0210.0000.0000.0000.000
200A220ILE0-0.013-0.00118.810-0.047-0.0470.0000.0000.0000.000
201A221ASN00.0370.00118.066-0.074-0.0740.0000.0000.0000.000
202A222LEU0-0.0010.02716.106-0.023-0.0230.0000.0000.0000.000
203A223ILE0-0.012-0.01113.177-0.057-0.0570.0000.0000.0000.000
204A224VAL0-0.006-0.00613.432-0.126-0.1260.0000.0000.0000.000
205A225GLN0-0.051-0.03514.518-0.038-0.0380.0000.0000.0000.000
206A226HIS00.0210.0257.3150.1400.1400.0000.0000.0000.000
207A227ILE0-0.034-0.0389.917-0.199-0.1990.0000.0000.0000.000
208A228GLN0-0.030-0.02210.695-0.112-0.1120.0000.0000.0000.000
209A229ASP-1-0.784-0.86910.403-0.621-0.6210.0000.0000.0000.000
210A230ILE0-0.052-0.0235.646-0.107-0.1070.0000.0000.0000.000
211A231LEU0-0.103-0.0608.068-0.022-0.0220.0000.0000.0000.000
212A232ASN0-0.069-0.02310.6180.1010.1010.0000.0000.0000.000
213A233GLY0-0.046-0.0108.4790.1210.1210.0000.0000.0000.000
214A234ASP-1-0.913-0.9589.557-0.266-0.2660.0000.0000.0000.000
215A235ILE0-0.091-0.0415.590-0.213-0.2130.0000.0000.0000.000