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: XV31P

Calculation Name: 3FLY-A-Xray12

Preferred Name: MAP kinase p38 alpha

Target Type: SINGLE PROTEIN

Ligand Name: 6-(2,4-difluorophenoxy)-8-methyl-2-[(1-methylethyl)amino]pyrido[2,3-d]pyrimidin-7(8h)-one

ligand 3-letter code: FLY

PDB ID: 3FLY

Chain ID: A

ChEMBL ID: CHEMBL260

UniProt ID: Q16539

Base Structure: X-ray

Registration Date: 2017-08-22

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Homology modeling
Water No
Procedure Auto-FMO protocol ver. 1.20160629
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 347
LigandResidueName FLY
LigandFragmentNumber 347
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5755304.723218
FMO2-HF: Nuclear repulsion 5615128.477651
FMO2-HF: Total energy -140176.245568
FMO2-MP2: Total energy -140585.232152


3D Structure
Snapshot
 
Ligand structure

FLY

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.
-94.588-63.60158.946-27.816-62.121-0.008


Interactive mode: IFIE and PIEDA for fragment #347(A:361:FLY)


Summations of interaction energy for fragment #347(A:361:FLY)
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.
-94.588-63.60158.946-27.816-62.1210.008
Interaction energy analysis for fragmet #347(A:361:FLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.003
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].
1A6PRO10.8520.90215.231-0.169-0.1690.0000.0000.0000.000
2A7THR00.0840.05718.4120.0430.0430.0000.0000.0000.000
3A8PHE00.0220.01913.112-0.038-0.0380.0000.0000.0000.000
4A9TYR0-0.039-0.03014.358-0.006-0.0060.0000.0000.0000.000
5A10ARG10.9340.96716.016-0.474-0.4740.0000.0000.0000.000
6A11GLN00.0590.02214.876-0.052-0.0520.0000.0000.0000.000
7A12GLU-1-0.962-0.96315.6940.7660.7660.0000.0000.0000.000
8A13LEU00.018-0.00311.309-0.071-0.0710.0000.0000.0000.000
9A14ASN00.0100.0089.888-0.386-0.3860.0000.0000.0000.000
10A15LYS10.9160.96513.927-0.591-0.5910.0000.0000.0000.000
11A16THR0-0.002-0.00913.6070.0390.0390.0000.0000.0000.000
12A17ILE00.0220.00415.330-0.038-0.0380.0000.0000.0000.000
13A18TRP0-0.020-0.0226.651-0.022-0.0220.0000.0000.0000.000
14A19GLU-1-0.909-0.96413.2050.3920.3920.0000.0000.0000.000
15A20VAL00.0090.0089.9090.0780.0780.0000.0000.0000.000
16A21PRO0-0.029-0.01011.156-0.077-0.0770.0000.0000.0000.000
17A22GLU-1-0.862-0.95313.6500.0230.0230.0000.0000.0000.000
18A23ARG10.7780.89111.9570.2530.2530.0000.0000.0000.000
19A24TYR0-0.043-0.0218.969-0.148-0.1480.0000.0000.0000.000
20A25GLN00.0220.01112.2490.1070.1070.0000.0000.0000.000
21A26ASN0-0.016-0.02113.228-0.015-0.0150.0000.0000.0000.000
22A27LEU0-0.0040.01210.162-0.087-0.0870.0000.0000.0000.000
23A28SER0-0.015-0.0139.9170.0760.0760.0000.0000.0000.000
24A29PRO0-0.006-0.0069.0030.0720.0720.0000.0000.0000.000
25A30VAL00.0010.0014.210-0.775-0.4490.000-0.020-0.3050.000
26A31GLY00.0070.0195.391-0.860-0.8600.0000.0000.0000.000
27A32SER0-0.052-0.0385.4291.0561.0560.0000.0000.0000.000
28A33GLY00.1010.0552.752-2.0740.8041.205-1.614-2.4690.005
29A34ALA00.0240.0163.324-7.166-7.4900.0350.932-0.6440.004
30A35TYR00.034-0.0045.606-0.545-0.468-0.001-0.002-0.0750.000
31A36GLY00.0370.0177.102-1.249-1.2490.0000.0000.0000.000
32A37SER0-0.0330.0016.2751.5531.5530.0000.0000.0000.000
33A38VAL00.0560.0212.669-4.154-0.1831.244-1.621-3.5940.015
34A39CYS0-0.054-0.0074.843-2.041-1.841-0.001-0.012-0.1880.000
35A40ALA00.0290.0295.992-0.067-0.0670.0000.0000.0000.000
36A41ALA00.0000.0008.0240.1800.1800.0000.0000.0000.000
37A42PHE0-0.010-0.0059.625-0.267-0.2670.0000.0000.0000.000
38A43ASP-1-0.703-0.81110.188-0.327-0.3270.0000.0000.0000.000
39A44THR0-0.035-0.04912.151-0.031-0.0310.0000.0000.0000.000
40A45LYS10.8770.93714.4160.1480.1480.0000.0000.0000.000
41A46THR00.009-0.01212.091-0.021-0.0210.0000.0000.0000.000
42A47GLY0-0.0100.00714.845-0.028-0.0280.0000.0000.0000.000
43A48LEU0-0.0030.0139.383-0.109-0.1090.0000.0000.0000.000
44A49ARG10.9500.9737.9761.8701.8700.0000.0000.0000.000
45A50VAL00.007-0.0035.787-0.158-0.1580.0000.0000.0000.000
46A51ALA00.002-0.0052.630-1.8910.2561.208-1.210-2.1440.008
47A52VAL0-0.007-0.0132.830-4.993-2.9700.358-0.926-1.455-0.009
48A53LYS10.8220.8992.364-16.648-12.0033.374-2.412-5.6070.023
49A54LYS10.8660.9614.106-3.165-2.8940.004-0.061-0.2140.000
50A55LEU00.0010.0017.2290.5420.5420.0000.0000.0000.000
51A56SER0-0.037-0.0159.445-0.502-0.5020.0000.0000.0000.000
52A57ARG10.9280.94312.469-1.527-1.5270.0000.0000.0000.000
53A58PRO00.0660.05012.3600.0020.0020.0000.0000.0000.000
54A59PHE00.0640.01113.865-0.060-0.0600.0000.0000.0000.000
55A60GLN0-0.038-0.01317.698-0.008-0.0080.0000.0000.0000.000
56A61SER00.000-0.00919.528-0.099-0.0990.0000.0000.0000.000
57A62ILE00.0950.04419.5000.0780.0780.0000.0000.0000.000
58A63ILE00.0160.02017.2410.0270.0270.0000.0000.0000.000
59A64HIS0-0.018-0.01615.5450.0750.0750.0000.0000.0000.000
60A65ALA00.0500.02914.7030.1420.1420.0000.0000.0000.000
61A66LYS10.8570.94015.106-0.689-0.6890.0000.0000.0000.000
62A67ARG10.8510.93911.371-2.729-2.7290.0000.0000.0000.000
63A68THR0-0.037-0.01810.5660.2860.2860.0000.0000.0000.000
64A69TYR00.0290.01910.151-0.042-0.0420.0000.0000.0000.000
65A70ARG10.8080.88211.034-1.235-1.2350.0000.0000.0000.000
66A71GLU-1-0.827-0.9124.5865.0755.2950.000-0.012-0.2080.000
67A72LEU0-0.016-0.0016.532-0.446-0.4460.0000.0000.0000.000
68A73ARG10.8750.9308.018-0.608-0.6080.0000.0000.0000.000
69A74LEU0-0.032-0.0107.797-0.135-0.1350.0000.0000.0000.000
70A75LEU0-0.013-0.0152.351-1.967-1.0081.742-0.596-2.105-0.001
71A76LYS10.7850.8765.719-0.332-0.3320.0000.0000.0000.000
72A77HIS0-0.061-0.0228.712-0.056-0.0560.0000.0000.0000.000
73A78MET0-0.078-0.0137.6010.0360.0360.0000.0000.0000.000
74A79LYS10.9520.9719.0720.1250.1250.0000.0000.0000.000
75A80HIS00.0930.04711.0470.0150.0150.0000.0000.0000.000
76A81GLU-1-0.828-0.90311.407-0.898-0.8980.0000.0000.0000.000
77A82ASN0-0.020-0.01611.536-0.069-0.0690.0000.0000.0000.000
78A83VAL0-0.038-0.0178.0890.0790.0790.0000.0000.0000.000
79A84ILE0-0.057-0.0102.456-1.087-1.8745.677-1.194-3.6960.001
80A85GLY00.0810.0395.9010.2360.2360.0000.0000.0000.000
81A86LEU0-0.074-0.0202.734-1.777-0.6270.395-0.444-1.1010.004
82A87LEU0-0.006-0.0064.628-0.151-0.053-0.001-0.006-0.0910.000
83A88ASP-1-0.834-0.9185.2000.1150.1150.0000.0000.0000.000
84A89VAL0-0.0130.0044.9390.4090.495-0.001-0.003-0.0820.000
85A90PHE0-0.018-0.0047.093-0.140-0.1400.0000.0000.0000.000
86A91THR00.010-0.02010.1470.1800.1800.0000.0000.0000.000
87A92PRO0-0.011-0.00212.988-0.084-0.0840.0000.0000.0000.000
88A93ALA0-0.0430.00415.876-0.061-0.0610.0000.0000.0000.000
89A94ARG10.9370.96517.881-0.313-0.3130.0000.0000.0000.000
90A95SER00.0060.00420.661-0.028-0.0280.0000.0000.0000.000
91A96LEU00.0670.02819.6160.0510.0510.0000.0000.0000.000
92A97GLU-1-0.930-0.97120.9330.4290.4290.0000.0000.0000.000
93A98GLU-1-0.931-0.96420.7860.4520.4520.0000.0000.0000.000
94A99PHE0-0.062-0.01913.1440.0710.0710.0000.0000.0000.000
95A100ASN0-0.048-0.04517.0000.0320.0320.0000.0000.0000.000
96A101ASP-1-0.931-0.96012.4391.4351.4350.0000.0000.0000.000
97A102VAL00.024-0.0017.824-0.177-0.1770.0000.0000.0000.000
98A103TYR00.0040.0026.8290.5120.5120.0000.0000.0000.000
99A104LEU00.0200.0072.418-2.590-0.6371.645-1.287-2.3120.012
100A105VAL00.0000.0102.498-6.086-3.5951.954-1.620-2.825-0.013
101A106THR00.009-0.0052.148-4.375-0.9977.255-2.770-7.8630.008
102A107HIS00.0940.0404.103-0.927-0.1070.007-0.096-0.7310.000
103A108LEU0-0.058-0.0332.363-8.618-4.4772.213-2.532-3.822-0.015
104A109MET0-0.001-0.0071.938-8.433-14.00318.679-5.061-8.0490.041
105A110GLY00.0360.0221.913-15.741-16.8229.147-3.262-4.804-0.058
106A111ALA0-0.012-0.0082.678-3.636-1.7741.187-0.988-2.061-0.012
107A112ASP-1-0.805-0.8972.679-3.694-2.6161.294-0.372-2.000-0.007
108A113LEU00.0330.0043.8160.1440.2210.0200.035-0.1320.000
109A114ASN0-0.046-0.0266.6690.3690.3690.0000.0000.0000.000
110A115ASN0-0.039-0.0244.670-0.716-0.560-0.001-0.002-0.1530.000
111A116ILE00.0060.0067.5070.2250.2250.0000.0000.0000.000
112A117VAL00.0380.02410.1210.1880.1880.0000.0000.0000.000
113A118LYS10.9100.97311.6021.5011.5010.0000.0000.0000.000
114A119CYS0-0.082-0.04713.2450.1030.1030.0000.0000.0000.000
115A120GLN0-0.066-0.02915.8270.0400.0400.0000.0000.0000.000
116A121LYS10.9340.97016.9580.3280.3280.0000.0000.0000.000
117A122LEU00.0190.02813.319-0.038-0.0380.0000.0000.0000.000
118A123THR0-0.020-0.01717.9720.0780.0780.0000.0000.0000.000
119A124ASP-1-0.737-0.86519.487-0.416-0.4160.0000.0000.0000.000
120A125ASP-1-0.865-0.92821.007-0.470-0.4700.0000.0000.0000.000
121A126HIS00.0200.00915.7610.0080.0080.0000.0000.0000.000
122A127VAL0-0.034-0.01716.159-0.051-0.0510.0000.0000.0000.000
123A128GLN00.0020.01417.520-0.006-0.0060.0000.0000.0000.000
124A129PHE00.0550.03514.4090.0280.0280.0000.0000.0000.000
125A130LEU0-0.004-0.00510.870-0.027-0.0270.0000.0000.0000.000
126A131ILE0-0.018-0.02614.2170.0220.0220.0000.0000.0000.000
127A132TYR0-0.026-0.02716.5170.0230.0230.0000.0000.0000.000
128A133GLN00.0240.00912.883-0.016-0.0160.0000.0000.0000.000
129A134ILE0-0.030-0.00412.1530.0210.0210.0000.0000.0000.000
130A135LEU0-0.004-0.01114.4970.0780.0780.0000.0000.0000.000
131A136ARG10.8070.90717.0660.6430.6430.0000.0000.0000.000
132A137GLY00.009-0.00114.0470.0190.0190.0000.0000.0000.000
133A138LEU0-0.043-0.03714.1440.0650.0650.0000.0000.0000.000
134A139LYS10.8760.93816.0350.3040.3040.0000.0000.0000.000
135A140TYR00.0410.03212.0450.0340.0340.0000.0000.0000.000
136A141ILE00.0250.01810.8280.0610.0610.0000.0000.0000.000
137A142HIS0-0.097-0.07114.4720.0400.0400.0000.0000.0000.000
138A143SER0-0.065-0.02917.6640.0340.0340.0000.0000.0000.000
139A144ALA00.0130.01115.2070.0110.0110.0000.0000.0000.000
140A145ASP-1-0.953-0.98317.2080.1410.1410.0000.0000.0000.000
141A146ILE0-0.059-0.01111.8170.0880.0880.0000.0000.0000.000
142A147ILE0-0.050-0.03415.061-0.047-0.0470.0000.0000.0000.000
143A148HIS0-0.038-0.0368.7360.0180.0180.0000.0000.0000.000
144A149ARG10.8830.92312.334-0.424-0.4240.0000.0000.0000.000
145A150ASP-1-0.903-0.96710.5951.6181.6180.0000.0000.0000.000
146A151LEU00.0530.04210.8190.1280.1280.0000.0000.0000.000
147A152LYS10.9020.9518.404-1.451-1.4510.0000.0000.0000.000
148A153PRO00.0270.0119.297-0.030-0.0300.0000.0000.0000.000
149A154SER00.0480.0185.985-0.267-0.2670.0000.0000.0000.000
150A155ASN0-0.105-0.0344.545-0.0410.163-0.001-0.011-0.1910.000
151A156LEU0-0.032-0.0096.1880.0140.0140.0000.0000.0000.000
152A157ALA00.0260.0173.029-1.067-0.3290.111-0.156-0.6930.001
153A158VAL0-0.023-0.0124.3140.4000.5420.000-0.015-0.1280.000
154A159ASN0-0.058-0.0275.565-0.868-0.8680.0000.0000.0000.000
155A160GLU-1-0.923-0.9857.832-2.481-2.4810.0000.0000.0000.000
156A161ASP-1-0.919-0.93610.721-1.017-1.0170.0000.0000.0000.000
157A162CYS0-0.098-0.07110.6130.1630.1630.0000.0000.0000.000
158A163GLU-1-0.827-0.88911.199-1.097-1.0970.0000.0000.0000.000
159A164LEU0-0.048-0.0278.621-0.252-0.2520.0000.0000.0000.000
160A165LYS10.8620.9256.4551.6931.6930.0000.0000.0000.000
161A166ILE0-0.013-0.0057.5060.0140.0140.0000.0000.0000.000
162A167LEU00.018-0.0073.177-2.759-0.5580.198-0.431-1.9690.001
163A168ASP-1-0.891-0.9364.28610.58611.0430.000-0.047-0.4100.000
164A169PHE0-0.008-0.0025.8670.0730.0730.0000.0000.0000.000
165A170GLY00.0310.0058.5160.0180.0180.0000.0000.0000.000
166A171LEU0-0.086-0.0406.5500.0830.0830.0000.0000.0000.000
167A172ALA00.0630.02710.032-0.127-0.1270.0000.0000.0000.000
168A173ARG10.7160.85311.919-1.091-1.0910.0000.0000.0000.000
169A174HIS00.0460.0259.7880.0970.0970.0000.0000.0000.000
170A175THR0-0.028-0.02114.078-0.301-0.3010.0000.0000.0000.000
171A176ASP-1-0.835-0.92317.2770.6690.6690.0000.0000.0000.000
172A177ASP-1-0.938-0.95319.0390.6800.6800.0000.0000.0000.000
173A178GLU-1-0.777-0.88013.7571.7211.7210.0000.0000.0000.000
174A179MET0-0.0540.01116.155-0.020-0.0200.0000.0000.0000.000
175A180THR0-0.038-0.02518.254-0.128-0.1280.0000.0000.0000.000
176A181GLY00.0190.01620.2170.0050.0050.0000.0000.0000.000
177A182TYR0-0.011-0.00320.2020.0050.0050.0000.0000.0000.000
178A183VAL00.0060.01315.993-0.032-0.0320.0000.0000.0000.000
179A184ALA00.0660.01612.9750.0110.0110.0000.0000.0000.000
180A185THR0-0.102-0.08711.848-0.035-0.0350.0000.0000.0000.000
181A186ARG10.8300.89013.837-0.287-0.2870.0000.0000.0000.000
182A187TRP0-0.041-0.00515.972-0.053-0.0530.0000.0000.0000.000
183A188TYR0-0.042-0.06013.970-0.042-0.0420.0000.0000.0000.000
184A189ARG10.9290.98715.240-0.789-0.7890.0000.0000.0000.000
185A190ALA00.0510.02618.482-0.047-0.0470.0000.0000.0000.000
186A191PRO00.0110.00621.7260.0490.0490.0000.0000.0000.000
187A192GLU-1-0.743-0.86424.4930.2140.2140.0000.0000.0000.000
188A193ILE0-0.0070.00218.9270.0240.0240.0000.0000.0000.000
189A194MET0-0.079-0.01421.7790.0460.0460.0000.0000.0000.000
190A195LEU0-0.019-0.02322.6430.0180.0180.0000.0000.0000.000
191A196ASN0-0.044-0.01324.0560.0020.0020.0000.0000.0000.000
192A197TRP0-0.004-0.00626.485-0.023-0.0230.0000.0000.0000.000
193A198MET0-0.002-0.01927.427-0.024-0.0240.0000.0000.0000.000
194A199HIS00.0100.01623.4570.0460.0460.0000.0000.0000.000
195A200TYR00.0210.01718.551-0.006-0.0060.0000.0000.0000.000
196A201ASN00.0730.05221.7770.0040.0040.0000.0000.0000.000
197A202GLN00.0730.01219.2250.0080.0080.0000.0000.0000.000
198A203THR0-0.004-0.02219.878-0.007-0.0070.0000.0000.0000.000
199A204VAL0-0.047-0.02518.237-0.022-0.0220.0000.0000.0000.000
200A205ASP-1-0.691-0.83315.8780.2890.2890.0000.0000.0000.000
201A206ILE0-0.0140.00118.023-0.052-0.0520.0000.0000.0000.000
202A207TRP0-0.0050.00219.993-0.046-0.0460.0000.0000.0000.000
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