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: PLQV9

Calculation Name: 4FKG-A-Xray47

Preferred Name: Cyclin-dependent kinase 2

Target Type: SINGLE PROTEIN

Ligand Name: 4-[(5-cyclopropyl-1h-pyrazol-3-yl)carbamoyl]benzoic acid

ligand 3-letter code: 4CK

PDB ID: 4FKG

Chain ID: A

ChEMBL ID: CHEMBL301

UniProt ID: P24941

Base Structure: X-ray

Registration Date: 2019-02-28

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHL
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20170908
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 299
LigandResidueName LIG
LigandFragmentNumber 299
LigandCharge LIG=-1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4480359.569263
FMO2-HF: Nuclear repulsion 4361907.535337
FMO2-HF: Total energy -118452.033926
FMO2-MP2: Total energy -118802.104936


3D Structure
Snapshot
 
Ligand structure

LIG

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.
-189.812-169.99253.367-21.749-51.4380.005


Interactive mode: IFIE and PIEDA for fragment #299(X:299:LIG)


Summations of interaction energy for fragment #299(X:299:LIG)
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.
-189.812-169.99253.367-21.749-51.438-0.005
Interaction energy analysis for fragmet #299(X:299:LIG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -1.005 / q_NPA : -1.014
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].
1X1MET10.8550.91713.450-14.578-14.5780.0000.0000.0000.000
2X2GLU-1-0.842-0.91917.19512.28412.2840.0000.0000.0000.000
3X3ASN00.0180.00015.350-0.258-0.2580.0000.0000.0000.000
4X4PHE00.0380.03710.9220.5890.5890.0000.0000.0000.000
5X5GLN0-0.008-0.00713.133-1.221-1.2210.0000.0000.0000.000
6X6LYS10.8990.93410.972-20.663-20.6630.0000.0000.0000.000
7X7VAL0-0.071-0.0577.882-1.374-1.3740.0000.0000.0000.000
8X8GLU-1-0.790-0.8406.05636.44236.4420.0000.0000.0000.000
9X9LYS10.7920.8807.305-26.736-26.7360.0000.0000.0000.000
10X10ILE0-0.006-0.0122.562-1.0812.9884.853-2.222-6.7010.020
11X11GLY00.0200.0123.0131.3322.9540.236-0.608-1.249-0.005
12X12GLU-1-0.858-0.9215.54821.46621.492-0.001-0.003-0.0210.000
13X13GLY00.0070.0117.3770.0640.0640.0000.0000.0000.000
14X14THR0-0.073-0.0637.868-0.565-0.5650.0000.0000.0000.000
15X15TYR00.0260.0097.050-1.398-1.3980.0000.0000.0000.000
16X16GLY00.0420.0227.947-1.216-1.2160.0000.0000.0000.000
17X17VAL0-0.0020.0137.4841.4011.4010.0000.0000.0000.000
18X18VAL0-0.013-0.0212.626-2.706-1.5250.246-0.288-1.1380.000
19X19TYR0-0.007-0.0095.8451.4671.4670.0000.0000.0000.000
20X20LYS10.9971.0143.240-72.190-69.6370.044-1.320-1.2770.011
21X21ALA0-0.004-0.0236.614-3.485-3.4850.0000.0000.0000.000
22X22ARG10.9360.9698.988-23.461-23.4610.0000.0000.0000.000
23X23ASN00.0560.02511.762-1.463-1.4630.0000.0000.0000.000
24X24LYS10.8860.94413.485-13.746-13.7460.0000.0000.0000.000
25X25LEU00.0060.00317.211-0.267-0.2670.0000.0000.0000.000
26X26THR00.0210.00214.962-0.272-0.2720.0000.0000.0000.000
27X27GLY00.0240.03215.7710.1400.1400.0000.0000.0000.000
28X28GLU-1-0.923-0.96111.28019.30319.3030.0000.0000.0000.000
29X29VAL0-0.063-0.0397.6260.3190.3190.0000.0000.0000.000
30X30VAL00.0100.0055.807-1.222-1.2220.0000.0000.0000.000
31X31ALA0-0.0040.0172.3301.8763.5821.426-0.843-2.2900.003
32X32LEU0-0.034-0.0294.143-4.786-4.4720.000-0.053-0.2600.000
33X33LYS10.9030.9502.036-25.325-25.3703.319-0.788-2.4860.009
34X34LYS10.9210.9726.065-18.082-18.0820.0000.0000.0000.000
35X35ILE00.0410.0268.8190.6040.6040.0000.0000.0000.000
36X36ARG10.7720.85211.467-15.336-15.3360.0000.0000.0000.000
37X37LEU0-0.034-0.00813.671-0.455-0.4550.0000.0000.0000.000
38X38ASP-1-0.741-0.87616.41312.87712.8770.0000.0000.0000.000
39X39THR0-0.063-0.04119.866-0.550-0.5500.0000.0000.0000.000
40X40GLU-1-0.944-0.95621.94410.49810.4980.0000.0000.0000.000
41X41THR0-0.068-0.04223.936-0.437-0.4370.0000.0000.0000.000
42X42GLU-1-0.947-0.96523.4609.4539.4530.0000.0000.0000.000
43X43GLY00.0330.03319.7250.4040.4040.0000.0000.0000.000
44X44VAL0-0.062-0.01514.648-0.116-0.1160.0000.0000.0000.000
45X45PRO00.0770.02518.036-0.175-0.1750.0000.0000.0000.000
46X46SER00.014-0.00619.1930.2910.2910.0000.0000.0000.000
47X47THR00.0220.01020.0460.1910.1910.0000.0000.0000.000
48X48ALA00.0250.01716.984-0.059-0.0590.0000.0000.0000.000
49X49ILE00.0040.00315.1770.2820.2820.0000.0000.0000.000
50X50ARG10.9861.00015.649-9.696-9.6960.0000.0000.0000.000
51X51GLU-1-0.783-0.88514.94910.62310.6230.0000.0000.0000.000
52X52ILE00.0160.00910.2040.3150.3150.0000.0000.0000.000
53X53SER0-0.055-0.03911.9320.3050.3050.0000.0000.0000.000
54X54LEU00.0010.01514.391-0.043-0.0430.0000.0000.0000.000
55X55LEU0-0.019-0.0148.0100.0570.0570.0000.0000.0000.000
56X56LYS10.9180.96510.027-12.504-12.5040.0000.0000.0000.000
57X57GLU-1-0.967-0.97211.04910.80310.8030.0000.0000.0000.000
58X58LEU0-0.0120.00911.293-0.173-0.1730.0000.0000.0000.000
59X59ASN0-0.024-0.02811.6381.0201.0200.0000.0000.0000.000
60X60HIS00.0470.01611.639-0.011-0.0110.0000.0000.0000.000
61X61PRO00.0180.01010.7360.6330.6330.0000.0000.0000.000
62X62ASN0-0.014-0.01610.1510.1430.1430.0000.0000.0000.000
63X63ILE0-0.029-0.0167.5340.1780.1780.0000.0000.0000.000
64X64VAL0-0.066-0.0322.227-1.605-0.7812.863-0.763-2.9240.000
65X65LYS10.8650.9254.926-14.579-14.457-0.001-0.003-0.1180.000
66X66LEU0-0.042-0.0135.9270.4250.4250.0000.0000.0000.000
67X67LEU0-0.011-0.0236.662-0.564-0.5640.0000.0000.0000.000
68X68ASP-1-0.872-0.9388.73113.92213.9220.0000.0000.0000.000
69X69VAL0-0.084-0.0479.2810.4540.4540.0000.0000.0000.000
70X70ILE00.0090.00311.500-0.084-0.0840.0000.0000.0000.000
71X71HIS00.0140.00913.8250.7590.7590.0000.0000.0000.000
72X72THR00.0500.03416.549-0.410-0.4100.0000.0000.0000.000
73X73GLU-1-0.962-0.99218.64812.79412.7940.0000.0000.0000.000
74X74ASN00.0240.03219.498-0.132-0.1320.0000.0000.0000.000
75X75LYS10.8330.88516.492-11.803-11.8030.0000.0000.0000.000
76X76LEU0-0.026-0.01211.7910.4160.4160.0000.0000.0000.000
77X77TYR0-0.052-0.0309.3660.5330.5330.0000.0000.0000.000
78X78LEU0-0.014-0.0276.309-0.953-0.9530.0000.0000.0000.000
79X79VAL0-0.031-0.0105.8401.6461.6460.0000.0000.0000.000
80X80PHE00.0540.0222.476-4.096-2.4383.179-1.052-3.785-0.011
81X81GLU-1-0.737-0.8443.70120.79721.3360.001-0.205-0.334-0.001
82X82PHE0-0.040-0.0322.061-17.535-13.48911.377-5.334-10.089-0.017
83X83LEU00.0290.0092.097-9.559-10.5987.337-1.606-4.6920.022
84X84HIS0-0.0040.0001.808-10.178-13.10114.966-5.453-6.590-0.045
85X85GLN00.0330.0133.9051.9942.5590.0030.260-0.8290.001
86X86ASP-1-0.790-0.8794.98033.43033.841-0.001-0.013-0.3970.000
87X87LEU00.0420.0076.642-0.419-0.4190.0000.0000.0000.000
88X88LYS10.9520.9858.997-21.210-21.2100.0000.0000.0000.000
89X89LYS10.9080.9523.260-44.371-43.8340.016-0.107-0.4470.001
90X90PHE0-0.0190.0048.871-0.811-0.8110.0000.0000.0000.000
91X91MET00.020-0.01111.487-1.616-1.6160.0000.0000.0000.000
92X92ASP-1-0.982-0.99111.75021.10621.1060.0000.0000.0000.000
93X93ALA0-0.0070.00212.203-1.098-1.0980.0000.0000.0000.000
94X94SER0-0.030-0.01614.105-1.009-1.0090.0000.0000.0000.000
95X95ALA00.0090.00217.079-1.131-1.1310.0000.0000.0000.000
96X96LEU0-0.068-0.04718.955-0.875-0.8750.0000.0000.0000.000
97X97THR00.0020.00619.028-0.425-0.4250.0000.0000.0000.000
98X98GLY0-0.066-0.02120.813-0.677-0.6770.0000.0000.0000.000
99X99ILE00.0390.02317.1140.5260.5260.0000.0000.0000.000
100X100PRO00.0540.03020.672-0.680-0.6800.0000.0000.0000.000
101X101LEU00.0700.03922.1570.3430.3430.0000.0000.0000.000
102X102PRO00.018-0.01123.3700.1540.1540.0000.0000.0000.000
103X103LEU00.0130.02217.0570.0440.0440.0000.0000.0000.000
104X104ILE00.0280.00719.1300.4090.4090.0000.0000.0000.000
105X105LYS10.8760.95519.382-10.143-10.1430.0000.0000.0000.000
106X106SER00.0680.04319.049-0.153-0.1530.0000.0000.0000.000
107X107TYR0-0.008-0.02512.758-0.225-0.2250.0000.0000.0000.000
108X108LEU00.0000.00615.4180.2560.2560.0000.0000.0000.000
109X109PHE00.009-0.00317.469-0.142-0.1420.0000.0000.0000.000
110X110GLN0-0.070-0.04414.1700.3400.3400.0000.0000.0000.000
111X111LEU00.0170.01711.522-0.099-0.0990.0000.0000.0000.000
112X112LEU0-0.021-0.02613.681-0.174-0.1740.0000.0000.0000.000
113X113GLN0-0.016-0.00115.889-0.214-0.2140.0000.0000.0000.000
114X114GLY00.0420.02312.116-0.300-0.3000.0000.0000.0000.000
115X115LEU0-0.022-0.01113.007-0.326-0.3260.0000.0000.0000.000
116X116ALA00.0320.02014.417-0.371-0.3710.0000.0000.0000.000
117X117PHE00.0030.01714.741-0.464-0.4640.0000.0000.0000.000
118X118CYS0-0.009-0.00313.823-0.049-0.0490.0000.0000.0000.000
119X119HIS00.032-0.01516.255-0.653-0.6530.0000.0000.0000.000
120X120SER0-0.122-0.09118.473-0.480-0.4800.0000.0000.0000.000
121X121HIS0-0.0220.01418.801-0.445-0.4450.0000.0000.0000.000
122X122ARG10.8930.93720.763-8.886-8.8860.0000.0000.0000.000
123X123VAL0-0.0160.00914.4760.0780.0780.0000.0000.0000.000
124X124LEU0-0.022-0.02815.6250.0400.0400.0000.0000.0000.000
125X125HIS0-0.057-0.0327.571-0.698-0.6980.0000.0000.0000.000
126X126ARG10.8830.92912.718-11.476-11.4760.0000.0000.0000.000
127X127ASP-1-0.803-0.88510.52416.98416.9840.0000.0000.0000.000
128X128LEU00.0200.02810.3011.0501.0500.0000.0000.0000.000
129X129LYS10.8750.9429.702-19.053-19.0530.0000.0000.0000.000
130X130PRO00.0210.0109.8660.9690.9690.0000.0000.0000.000
131X131GLN00.0580.0267.7550.4140.4140.0000.0000.0000.000
132X132ASN0-0.081-0.0374.9822.4572.4570.0000.0000.0000.000
133X133LEU00.0260.0056.088-1.936-1.9360.0000.0000.0000.000
134X134LEU00.0020.0102.484-2.8160.0102.504-0.942-4.3880.008
135X135ILE0-0.031-0.0376.258-3.158-3.1580.0000.0000.0000.000
136X136ASN0-0.007-0.0067.3372.5962.5960.0000.0000.0000.000
137X137THR00.030-0.0019.961-0.853-0.8530.0000.0000.0000.000
138X138GLU-1-0.892-0.93112.75416.39516.3950.0000.0000.0000.000
139X139GLY0-0.0030.01514.040-1.056-1.0560.0000.0000.0000.000
140X140ALA0-0.055-0.03312.474-1.009-1.0090.0000.0000.0000.000
141X141ILE00.0230.0179.8761.5191.5190.0000.0000.0000.000
142X142LYS10.8520.9476.223-20.428-20.4280.0000.0000.0000.000
143X143LEU0-0.018-0.0046.5831.2321.2320.0000.0000.0000.000
144X144ALA00.0230.0162.393-1.253-0.7800.999-0.341-1.131-0.001
145X145ASP-1-0.877-0.9413.66722.79823.1530.001-0.065-0.2920.000
146X146PHE00.0060.0035.535-0.852-0.8520.0000.0000.0000.000
147X147GLY00.0520.0228.361-0.064-0.0640.0000.0000.0000.000
148X148LEU00.0250.0176.730-0.217-0.2170.0000.0000.0000.000
149X149ALA00.0140.01811.081-0.235-0.2350.0000.0000.0000.000
150X150ARG10.8140.87813.946-10.747-10.7470.0000.0000.0000.000
151X151ALA0-0.0030.01513.020-0.341-0.3410.0000.0000.0000.000
152X152PHE0-0.028-0.04110.845-0.052-0.0520.0000.0000.0000.000
153X153GLY00.0260.04715.103-0.021-0.0210.0000.0000.0000.000
154X154VAL0-0.028-0.02513.4490.5410.5410.0000.0000.0000.000
155X155PRO0-0.026-0.00714.680-0.483-0.4830.0000.0000.0000.000
156X156VAL00.020-0.01716.6320.4900.4900.0000.0000.0000.000
157X157ARG10.9040.96317.998-11.680-11.6800.0000.0000.0000.000
158X158THR00.0670.06013.715-0.320-0.3200.0000.0000.0000.000
159X159TYR00.018-0.00210.595-0.456-0.4560.0000.0000.0000.000
160X160THR00.010-0.00315.393-0.378-0.3780.0000.0000.0000.000
161X161HIS00.0320.02617.619-0.206-0.2060.0000.0000.0000.000
162X162GLU-1-0.917-0.94016.40816.17716.1770.0000.0000.0000.000
163X163VAL0-0.024-0.02618.285-0.161-0.1610.0000.0000.0000.000
164X164VAL00.0050.01314.2680.6090.6090.0000.0000.0000.000
165X165THR00.0300.00114.781-0.799-0.7990.0000.0000.0000.000
166X166LEU00.0180.00017.094-0.024-0.0240.0000.0000.0000.000
167X167TRP0-0.090-0.03616.0230.1650.1650.0000.0000.0000.000
168X168TYR00.0810.04315.073-0.083-0.0830.0000.0000.0000.000
169X169ARG10.8820.97817.933-12.616-12.6160.0000.0000.0000.000
170X170ALA0-0.0040.00019.607-0.296-0.2960.0000.0000.0000.000
171X171PRO00.0220.00822.110-0.035-0.0350.0000.0000.0000.000
172X172GLU-1-0.726-0.85323.9209.5679.5670.0000.0000.0000.000
173X173ILE0-0.068-0.04220.920-0.113-0.1130.0000.0000.0000.000
174X174LEU0-0.0040.00823.2740.0290.0290.0000.0000.0000.000
175X175LEU00.0160.02126.006-0.150-0.1500.0000.0000.0000.000
176X176GLY00.0690.05727.235-0.257-0.2570.0000.0000.0000.000
177X177CYS0-0.091-0.07627.286-0.272-0.2720.0000.0000.0000.000
178X178LYS10.9230.96026.982-7.438-7.4380.0000.0000.0000.000
179X179TYR0-0.0030.00326.8320.0040.0040.0000.0000.0000.000
180X180TYR00.0090.00019.5300.2420.2420.0000.0000.0000.000
181X181SER00.0550.02322.580-0.084-0.0840.0000.0000.0000.000
182X182THR00.0420.01418.9830.2110.2110.0000.0000.0000.000
183X183ALA00.0180.00119.3740.3960.3960.0000.0000.0000.000
184X184VAL00.0000.00617.5700.0730.0730.0000.0000.0000.000
185X185ASP-1-0.668-0.81415.19513.10213.1020.0000.0000.0000.000
186X186ILE0-0.066-0.00616.9830.4380.4380.0000.0000.0000.000
187X187TRP00.0840.03919.763-0.108-0.1080.0000.0000.0000.000
188X188SER0-0.019-0.02715.5260.1900.1900.0000.0000.0000.000
189X189LEU0-0.035-0.02515.6940.5160.5160.0000.0000.0000.000
190X190GLY00.039-0.00117.4560.1170.1170.0000.0000.0000.000
191X191CYS0-0.089-0.03618.823-0.089-0.0890.0000.0000.0000.000
192X192ILE00.0100.01213.6370.2410.2410.0000.0000.0000.000
193X193PHE0-0.013-0.01817.7490.1410.1410.0000.0000.0000.000
194X194ALA00.013-0.00120.054-0.169-0.1690.0000.0000.0000.000
195X195GLU-1-0.903-0.92517.23616.07916.0790.0000.0000.0000.000
196X196MET0-0.013-0.01316.513-0.019-0.0190.0000.0000.0000.000
197X197VAL0-0.050-0.01420.219-0.058-0.0580.0000.0000.0000.000
198X198THR0-0.074-0.06022.827-0.393-0.3930.0000.0000.0000.000
199X199ARG10.9210.97220.569-13.222-13.2220.0000.0000.0000.000
200X200ARG10.9690.99220.161-11.633-11.6330.0000.0000.0000.000
201X201ALA00.0310.01718.999-0.245-0.2450.0000.0000.0000.000
202X202LEU00.0060.01620.698-0.473-0.4730.0000.0000.0000.000
203X203PHE0-0.007-0.01622.787-0.523-0.5230.0000.0000.0000.000
204X204PRO0-0.016-0.00522.4880.2710.2710.0000.0000.0000.000
205X205GLY00.0280.00523.482-0.436-0.4360.0000.0000.0000.000
206X206ASP-1-0.944-0.96722.82012.94612.9460.0000.0000.0000.000
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