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: X6Z4Z

Calculation Name: 4FKQ-A-Xray47

Preferred Name: Cyclin-dependent kinase 2

Target Type: SINGLE PROTEIN

Ligand Name: 4-[(2z)-2-(7-oxidanylidene-3,6-dihydropyrrolo[3,2-e]benzotriazol-8-ylidene)hydrazinyl]benzenesulfonamide

ligand 3-letter code: 42K

PDB ID: 4FKQ

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
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4499555.113457
FMO2-HF: Nuclear repulsion 4380488.572498
FMO2-HF: Total energy -119066.540959
FMO2-MP2: Total energy -119417.301897


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.
-125.246-105.64785.544-37.586-67.5560.139


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.
-125.246-105.64785.544-37.586-67.556-0.139
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 : 0 / q_Mulliken : -0.140 / q_NPA : -0.117
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].
1X1MET10.8380.90612.3800.2870.2870.0000.0000.0000.000
2X2GLU-1-0.814-0.91517.342-0.301-0.3010.0000.0000.0000.000
3X3ASN00.0700.05015.6340.1450.1450.0000.0000.0000.000
4X4PHE00.0160.01310.7350.0110.0110.0000.0000.0000.000
5X5GLN0-0.021-0.01212.9940.1330.1330.0000.0000.0000.000
6X6LYS10.9530.98011.339-0.957-0.9570.0000.0000.0000.000
7X7VAL0-0.037-0.0129.822-0.100-0.1000.0000.0000.0000.000
8X8GLU-1-0.819-0.9038.1693.3163.3160.0000.0000.0000.000
9X9LYS10.8340.8917.415-4.041-4.0410.0000.0000.0000.000
10X10ILE0-0.017-0.0172.601-4.380-0.2403.621-1.747-6.0140.016
11X11GLY00.0270.0183.172-1.6360.5321.389-0.975-2.583-0.006
12X12GLU-1-0.882-0.9374.7901.8192.1000.000-0.027-0.2540.000
13X13GLY00.0020.0036.3750.2340.2340.0000.0000.0000.000
14X14THR0-0.005-0.0107.336-0.331-0.3310.0000.0000.0000.000
15X15TYR00.0450.0377.625-0.039-0.0390.0000.0000.0000.000
16X16GLY0-0.028-0.0148.752-0.099-0.0990.0000.0000.0000.000
17X17VAL0-0.017-0.0057.7550.3930.3930.0000.0000.0000.000
18X18VAL00.001-0.0112.732-5.630-2.3961.906-1.226-3.9140.013
19X19TYR0-0.036-0.0125.9660.3140.540-0.001-0.007-0.2180.000
20X20LYS10.9781.0155.645-3.206-3.2060.0000.0000.0000.000
21X21ALA0-0.044-0.0516.784-0.512-0.5120.0000.0000.0000.000
22X22ARG10.9440.9608.928-0.711-0.7110.0000.0000.0000.000
23X23ASN00.0500.02711.624-0.079-0.0790.0000.0000.0000.000
24X24LYS10.8460.90913.1790.1330.1330.0000.0000.0000.000
25X25LEU00.0160.02016.4720.0460.0460.0000.0000.0000.000
26X26THR0-0.010-0.01215.1790.0330.0330.0000.0000.0000.000
27X27GLY0-0.0050.01715.4180.0590.0590.0000.0000.0000.000
28X28GLU-1-0.888-0.93411.580-0.306-0.3060.0000.0000.0000.000
29X29VAL0-0.051-0.0256.902-0.022-0.0220.0000.0000.0000.000
30X30VAL0-0.009-0.0065.917-0.260-0.2600.0000.0000.0000.000
31X31ALA0-0.0060.0022.8690.6112.0620.326-0.503-1.2750.004
32X32LEU0-0.062-0.0294.971-2.209-1.941-0.001-0.009-0.2570.000
33X33LYS10.8650.9282.8328.57110.2030.041-0.644-1.0290.002
34X34LYS10.9090.9597.093-0.333-0.3330.0000.0000.0000.000
35X35ILE00.0060.0037.154-0.074-0.0740.0000.0000.0000.000
36X36ARG10.9340.98410.886-0.052-0.0520.0000.0000.0000.000
37X37LEU0-0.006-0.02213.204-0.146-0.1460.0000.0000.0000.000
38X38ASP-1-0.897-0.93715.647-0.388-0.3880.0000.0000.0000.000
39X39THR0-0.082-0.06619.151-0.070-0.0700.0000.0000.0000.000
40X40GLU-1-0.872-0.91921.812-0.263-0.2630.0000.0000.0000.000
41X41THR0-0.049-0.02123.8490.0250.0250.0000.0000.0000.000
42X42GLU-1-0.928-0.97523.569-0.262-0.2620.0000.0000.0000.000
43X43GLY0-0.030-0.01920.1240.0320.0320.0000.0000.0000.000
44X44VAL0-0.0080.01714.991-0.014-0.0140.0000.0000.0000.000
45X45PRO00.0910.05618.227-0.031-0.0310.0000.0000.0000.000
46X46SER00.0410.00418.315-0.116-0.1160.0000.0000.0000.000
47X47THR0-0.004-0.01118.527-0.116-0.1160.0000.0000.0000.000
48X48ALA00.0300.02014.578-0.067-0.0670.0000.0000.0000.000
49X49ILE00.0130.00013.963-0.266-0.2660.0000.0000.0000.000
50X50ARG10.8630.93815.0140.8460.8460.0000.0000.0000.000
51X51GLU-1-0.746-0.84314.465-1.558-1.5580.0000.0000.0000.000
52X52ILE00.0260.0189.436-0.236-0.2360.0000.0000.0000.000
53X53SER0-0.032-0.02411.824-0.244-0.2440.0000.0000.0000.000
54X54LEU00.0770.05614.2770.0270.0270.0000.0000.0000.000
55X55LEU0-0.039-0.0318.940-0.077-0.0770.0000.0000.0000.000
56X56LYS10.8800.9489.7921.5061.5060.0000.0000.0000.000
57X57GLU-1-0.935-0.96411.368-1.407-1.4070.0000.0000.0000.000
58X58LEU0-0.0270.0089.4390.1900.1900.0000.0000.0000.000
59X59ASN0-0.023-0.04110.901-0.450-0.4500.0000.0000.0000.000
60X60HIS00.0320.00611.2100.1780.1780.0000.0000.0000.000
61X61PRO00.0750.04211.077-0.331-0.3310.0000.0000.0000.000
62X62ASN0-0.050-0.03711.211-0.008-0.0080.0000.0000.0000.000
63X63ILE0-0.056-0.0287.527-0.072-0.0720.0000.0000.0000.000
64X64VAL0-0.040-0.0082.441-1.494-0.0880.972-0.486-1.8910.001
65X65LYS10.8960.9654.3450.8161.1230.000-0.036-0.2700.000
66X66LEU00.0300.0205.107-1.462-1.400-0.001-0.008-0.0530.000
67X67LEU0-0.057-0.0316.3141.2021.2020.0000.0000.0000.000
68X68ASP-1-0.873-0.9638.827-1.001-1.0010.0000.0000.0000.000
69X69VAL0-0.043-0.0179.465-0.558-0.5580.0000.0000.0000.000
70X70ILE0-0.0100.00111.8460.3030.3030.0000.0000.0000.000
71X71HIS00.012-0.02514.146-0.049-0.0490.0000.0000.0000.000
72X72THR00.0410.02116.7230.0440.0440.0000.0000.0000.000
73X73GLU-1-0.846-0.91219.743-0.100-0.1000.0000.0000.0000.000
74X74ASN00.0260.02819.764-0.005-0.0050.0000.0000.0000.000
75X75LYS10.8140.90717.3580.0970.0970.0000.0000.0000.000
76X76LEU0-0.009-0.00112.016-0.027-0.0270.0000.0000.0000.000
77X77TYR0-0.040-0.03110.6840.3430.3430.0000.0000.0000.000
78X78LEU00.0280.0066.350-0.161-0.1610.0000.0000.0000.000
79X79VAL0-0.003-0.0066.7870.3320.3320.0000.0000.0000.000
80X80PHE00.007-0.0062.484-6.113-3.2415.271-1.872-6.270-0.019
81X81GLU-1-0.819-0.9034.194-2.223-1.3170.000-0.373-0.533-0.001
82X82PHE0-0.012-0.0251.789-21.059-21.01112.394-6.089-6.353-0.029
83X83LEU00.013-0.0051.926-7.729-9.8527.223-1.794-3.3060.026
84X84HIS0-0.037-0.0132.060-7.755-6.5457.375-3.304-5.281-0.030
85X85GLN00.0610.0282.513-3.558-0.5022.927-1.360-4.623-0.005
86X86ASP-1-0.812-0.8951.693-34.823-40.19719.225-7.342-6.509-0.072
87X87LEU00.0540.0134.0490.4600.6700.000-0.006-0.2040.000
88X88LYS10.8510.9266.2831.2851.2850.0000.0000.0000.000
89X89LYS11.0051.0112.342-1.997-0.6221.004-0.584-1.7950.004
90X90PHE0-0.019-0.0094.7451.4921.583-0.001-0.006-0.0840.000
91X91MET0-0.016-0.0037.4910.4210.4210.0000.0000.0000.000
92X92ASP-1-0.971-0.9767.4010.7360.7360.0000.0000.0000.000
93X93ALA0-0.025-0.0107.3350.2870.2870.0000.0000.0000.000
94X94SER0-0.017-0.0129.2800.2120.2120.0000.0000.0000.000
95X95ALA0-0.0080.00112.513-0.086-0.0860.0000.0000.0000.000
96X96LEU0-0.012-0.00114.598-0.031-0.0310.0000.0000.0000.000
97X97THR0-0.032-0.02114.713-0.030-0.0300.0000.0000.0000.000
98X98GLY0-0.044-0.01915.707-0.043-0.0430.0000.0000.0000.000
99X99ILE00.0420.00912.873-0.023-0.0230.0000.0000.0000.000
100X100PRO00.0210.02016.342-0.016-0.0160.0000.0000.0000.000
101X101LEU00.0850.01618.973-0.046-0.0460.0000.0000.0000.000
102X102PRO00.0520.01221.052-0.052-0.0520.0000.0000.0000.000
103X103LEU0-0.0060.01514.033-0.027-0.0270.0000.0000.0000.000
104X104ILE00.000-0.00916.808-0.094-0.0940.0000.0000.0000.000
105X105LYS10.9531.00817.9230.2100.2100.0000.0000.0000.000
106X106SER0-0.0120.00418.179-0.090-0.0900.0000.0000.0000.000
107X107TYR00.037-0.00111.247-0.063-0.0630.0000.0000.0000.000
108X108LEU00.002-0.00816.413-0.136-0.1360.0000.0000.0000.000
109X109PHE00.0300.02318.745-0.091-0.0910.0000.0000.0000.000
110X110GLN0-0.037-0.03615.496-0.126-0.1260.0000.0000.0000.000
111X111LEU00.0060.01212.645-0.172-0.1720.0000.0000.0000.000
112X112LEU0-0.0080.00615.295-0.146-0.1460.0000.0000.0000.000
113X113GLN00.000-0.00616.822-0.113-0.1130.0000.0000.0000.000
114X114GLY00.0100.02113.010-0.038-0.0380.0000.0000.0000.000
115X115LEU00.0000.00313.569-0.120-0.1200.0000.0000.0000.000
116X116ALA00.001-0.00114.6160.0190.0190.0000.0000.0000.000
117X117PHE0-0.015-0.00613.9880.0810.0810.0000.0000.0000.000
118X118CYS00.0010.01912.094-0.104-0.1040.0000.0000.0000.000
119X119HIS0-0.039-0.05714.4390.1600.1600.0000.0000.0000.000
120X120SER0-0.071-0.03617.5960.1310.1310.0000.0000.0000.000
121X121HIS0-0.0070.01514.5680.1680.1680.0000.0000.0000.000
122X122ARG10.8710.94117.7550.9400.9400.0000.0000.0000.000
123X123VAL00.0300.03112.588-0.032-0.0320.0000.0000.0000.000
124X124LEU0-0.068-0.04114.2540.0300.0300.0000.0000.0000.000
125X125HIS0-0.037-0.0136.324-0.061-0.0610.0000.0000.0000.000
126X126ARG10.9060.93410.2861.4591.4590.0000.0000.0000.000
127X127ASP-1-0.883-0.9447.571-1.993-1.9930.0000.0000.0000.000
128X128LEU0-0.0280.0138.243-0.255-0.2550.0000.0000.0000.000
129X129LYS10.9410.9656.2681.2361.2360.0000.0000.0000.000
130X130PRO00.0470.0288.451-0.093-0.0930.0000.0000.0000.000
131X131GLN00.029-0.0026.033-0.691-0.6910.0000.0000.0000.000
132X132ASN0-0.062-0.0354.2761.1381.7090.003-0.113-0.4610.000
133X133LEU00.0010.0175.137-1.130-0.891-0.001-0.009-0.2300.000
134X134LEU00.0080.0032.777-4.721-1.2732.792-1.129-5.1120.005
135X135ILE00.0210.0176.5070.1000.1000.0000.0000.0000.000
136X136ASN0-0.046-0.0437.7540.4580.4580.0000.0000.0000.000
137X137THR00.0550.02110.277-0.076-0.0760.0000.0000.0000.000
138X138GLU-1-0.920-0.94312.770-0.048-0.0480.0000.0000.0000.000
139X139GLY0-0.0100.00414.662-0.041-0.0410.0000.0000.0000.000
140X140ALA0-0.057-0.04613.388-0.110-0.1100.0000.0000.0000.000
141X141ILE0-0.011-0.00210.6370.0420.0420.0000.0000.0000.000
142X142LYS10.8800.9567.2431.9181.9180.0000.0000.0000.000
143X143LEU00.0290.0228.3720.0960.0960.0000.0000.0000.000
144X144ALA00.0190.0042.835-2.085-0.9061.753-0.825-2.1070.011
145X145ASP-1-0.803-0.8771.708-33.943-37.42417.251-7.323-6.446-0.059
146X146PHE00.0190.0163.2522.6832.7500.0760.238-0.3810.000
147X147GLY00.0490.0236.596-0.282-0.2820.0000.0000.0000.000
148X148LEU0-0.010-0.0104.2560.4960.6260.000-0.027-0.1030.000
149X149ALA00.0360.0278.2260.5260.5260.0000.0000.0000.000
150X150ARG10.7440.83410.5941.9091.9090.0000.0000.0000.000
151X151ALA0-0.0160.00010.7300.2340.2340.0000.0000.0000.000
152X152PHE0-0.047-0.0238.1180.1580.1580.0000.0000.0000.000
153X153GLY00.0290.03012.5760.2520.2520.0000.0000.0000.000
154X154VAL0-0.036-0.03512.221-0.209-0.2090.0000.0000.0000.000
155X155PRO00.0100.01412.4160.1360.1360.0000.0000.0000.000
156X156VAL00.0700.02315.128-0.020-0.0200.0000.0000.0000.000
157X157ARG10.8910.92717.3030.1800.1800.0000.0000.0000.000
158X158THR0-0.034-0.02512.910-0.092-0.0920.0000.0000.0000.000
159X159TYR00.010-0.00915.0760.0090.0090.0000.0000.0000.000
160X160THR0-0.047-0.04116.721-0.022-0.0220.0000.0000.0000.000
161X161HIS00.0220.03118.5760.0450.0450.0000.0000.0000.000
162X162GLU-1-0.851-0.89616.1560.5520.5520.0000.0000.0000.000
163X163VAL00.0170.02216.737-0.097-0.0970.0000.0000.0000.000
164X164VAL0-0.004-0.00311.9340.0700.0700.0000.0000.0000.000
165X165THR0-0.038-0.01812.837-0.038-0.0380.0000.0000.0000.000
166X166LEU00.0480.01814.358-0.155-0.1550.0000.0000.0000.000
167X167TRP0-0.071-0.02016.203-0.087-0.0870.0000.0000.0000.000
168X168TYR00.0210.00112.394-0.004-0.0040.0000.0000.0000.000
169X169ARG10.8710.94713.8190.7830.7830.0000.0000.0000.000
170X170ALA00.0760.04817.7000.0750.0750.0000.0000.0000.000
171X171PRO00.0370.01220.4680.0010.0010.0000.0000.0000.000
172X172GLU-1-0.762-0.85822.406-0.700-0.7000.0000.0000.0000.000
173X173ILE0-0.054-0.02717.4910.0010.0010.0000.0000.0000.000
174X174LEU0-0.021-0.00820.4810.0260.0260.0000.0000.0000.000
175X175LEU0-0.031-0.00123.5630.0420.0420.0000.0000.0000.000
176X176GLY00.0890.03924.7420.0180.0180.0000.0000.0000.000
177X177CYS0-0.035-0.00323.455-0.031-0.0310.0000.0000.0000.000
178X178LYS10.9350.95019.2980.8050.8050.0000.0000.0000.000
179X179TYR0-0.012-0.01021.166-0.091-0.0910.0000.0000.0000.000
180X180TYR00.0520.02317.108-0.019-0.0190.0000.0000.0000.000
181X181SER00.0390.02021.221-0.078-0.0780.0000.0000.0000.000
182X182THR00.0570.00617.502-0.024-0.0240.0000.0000.0000.000
183X183ALA0-0.006-0.00718.889-0.054-0.0540.0000.0000.0000.000
184X184VAL00.0110.00216.3540.0250.0250.0000.0000.0000.000
185X185ASP-1-0.697-0.84713.739-1.856-1.8560.0000.0000.0000.000
186X186ILE0-0.080-0.01916.007-0.018-0.0180.0000.0000.0000.000
187X187TRP00.0750.03218.8470.0630.0630.0000.0000.0000.000
188X188SER0-0.022-0.01814.2920.0180.0180.0000.0000.0000.000
189X189LEU0-0.015-0.01115.1600.0150.0150.0000.0000.0000.000
190X190GLY00.0230.01016.6100.0600.0600.0000.0000.0000.000
191X191CYS0-0.069-0.04517.3150.0860.0860.0000.0000.0000.000
192X192ILE00.0300.02712.4590.0460.0460.0000.0000.0000.000
193X193PHE0-0.046-0.02416.4990.0550.0550.0000.0000.0000.000
194X194ALA00.0250.01018.7890.0590.0590.0000.0000.0000.000
195X195GLU-1-0.863-0.91913.468-0.635-0.6350.0000.0000.0000.000
196X196MET0-0.021-0.02013.9430.0490.0490.0000.0000.0000.000
197X197VAL0-0.024-0.00215.9840.0600.0600.0000.0000.0000.000
198X198THR0-0.040-0.02818.4420.0570.0570.0000.0000.0000.000
199X199ARG10.8990.95814.2710.0340.0340.0000.0000.0000.000
200X200ARG10.9430.96715.9810.1490.1490.0000.0000.0000.000
201X201ALA00.0340.02717.756-0.052-0.0520.0000.0000.0000.000
202X202LEU00.0400.03618.7110.0420.0420.0000.0000.0000.000
203X203PHE00.003-0.01321.1390.0430.0430.0000.0000.0000.000
204X204PRO0-0.034-0.01620.621-0.034-0.0340.0000.0000.0000.000
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