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: P2LRP

Calculation Name: 3FMM-A-Xray9

Preferred Name: MAP kinase p38 alpha

Target Type: SINGLE PROTEIN

Ligand Name: 6-(2,4-difluorophenoxy)-n-[(1r)-1-methyl-2-(methylsulfonyl)ethyl]-1h-pyrazolo[3,4-d]pyrimidin-3-amine

ligand 3-letter code: XI2

PDB ID: 3FMM

Chain ID: A

ChEMBL ID: CHEMBL260

UniProt ID: Q16539

Base Structure: X-ray

Registration Date: 2017-05-08

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:MMFF94x
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Homology modeling
Water No
Procedure Auto-FMO protocol ver. 1.20170327
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 347
LigandResidueName XI2
LigandFragmentNumber 347
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5754845.606818
FMO2-HF: Nuclear repulsion 5614219.561861
FMO2-HF: Total energy -140626.044957
FMO2-MP2: Total energy -141035.572267


3D Structure
Snapshot
 
Ligand structure

XI2

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.
-131.837-101.87287.384-39.730-77.6180.045


Interactive mode: IFIE and PIEDA for fragment #347(A:361:XI2)


Summations of interaction energy for fragment #347(A:361:XI2)
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.
-131.837-101.87287.384-39.73-77.618-0.045
Interaction energy analysis for fragmet #347(A:361:XI2)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.019
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].
1A6PRO10.8500.90115.266-0.129-0.1290.0000.0000.0000.000
2A7THR00.0800.06018.3500.0260.0260.0000.0000.0000.000
3A8PHE00.0180.01313.068-0.035-0.0350.0000.0000.0000.000
4A9TYR0-0.036-0.03014.3120.0110.0110.0000.0000.0000.000
5A10ARG10.9480.97216.001-0.611-0.6110.0000.0000.0000.000
6A11GLN00.0590.02614.760-0.112-0.1120.0000.0000.0000.000
7A12GLU-1-0.989-0.97615.8161.2941.2940.0000.0000.0000.000
8A13LEU0-0.001-0.00611.0120.0120.0120.0000.0000.0000.000
9A14ASN00.0250.0159.423-0.241-0.2410.0000.0000.0000.000
10A15LYS10.9350.95413.379-1.576-1.5760.0000.0000.0000.000
11A16THR00.0050.02612.834-0.194-0.1940.0000.0000.0000.000
12A17ILE00.030-0.00515.3400.0520.0520.0000.0000.0000.000
13A18TRP0-0.049-0.0366.425-0.141-0.1410.0000.0000.0000.000
14A19GLU-1-0.910-0.96413.1010.5140.5140.0000.0000.0000.000
15A20VAL00.0100.0059.7770.0140.0140.0000.0000.0000.000
16A21PRO0-0.033-0.01111.136-0.061-0.0610.0000.0000.0000.000
17A22GLU-1-0.867-0.95213.5830.1550.1550.0000.0000.0000.000
18A23ARG10.7730.87712.0470.3960.3960.0000.0000.0000.000
19A24TYR0-0.045-0.0339.034-0.150-0.1500.0000.0000.0000.000
20A25GLN00.0230.01012.1670.1900.1900.0000.0000.0000.000
21A26ASN0-0.025-0.02112.2320.0130.0130.0000.0000.0000.000
22A27LEU00.0020.0109.722-0.001-0.0010.0000.0000.0000.000
23A28SER0-0.019-0.0127.7200.1400.1400.0000.0000.0000.000
24A29PRO00.0150.0056.9080.3240.3240.0000.0000.0000.000
25A30VAL00.0030.0062.606-3.249-1.1841.640-0.956-2.7490.010
26A31GLY00.0580.0073.4800.5141.7350.149-0.372-0.9980.002
27A32SER0-0.066-0.0253.780-4.120-3.7410.036-0.130-0.2850.002
28A33GLY00.0020.0047.036-1.219-1.2190.0000.0000.0000.000
29A34ALA0-0.025-0.0106.096-0.415-0.4150.0000.0000.0000.000
30A35TYR00.005-0.0102.505-14.527-8.4278.957-3.561-11.497-0.012
31A36GLY0-0.0150.0104.7671.7951.932-0.001-0.015-0.1220.000
32A37SER0-0.054-0.0397.2110.3220.3220.0000.0000.0000.000
33A38VAL00.0340.0112.670-4.899-1.3820.944-1.416-3.0450.014
34A39CYS0-0.058-0.0095.029-0.559-0.368-0.001-0.011-0.1790.000
35A40ALA00.0370.0374.309-0.482-0.330-0.001-0.014-0.1360.000
36A41ALA00.012-0.0016.1990.3130.3130.0000.0000.0000.000
37A42PHE0-0.010-0.0039.362-0.483-0.4830.0000.0000.0000.000
38A43ASP-1-0.703-0.80410.178-0.373-0.3730.0000.0000.0000.000
39A44THR0-0.041-0.04112.144-0.083-0.0830.0000.0000.0000.000
40A45LYS10.8770.93714.5070.1860.1860.0000.0000.0000.000
41A46THR00.021-0.01212.143-0.042-0.0420.0000.0000.0000.000
42A47GLY0-0.0140.00814.513-0.051-0.0510.0000.0000.0000.000
43A48LEU00.0100.0148.980-0.145-0.1450.0000.0000.0000.000
44A49ARG10.9480.9747.8122.3982.3980.0000.0000.0000.000
45A50VAL00.010-0.0025.417-0.526-0.5260.0000.0000.0000.000
46A51ALA0-0.007-0.0082.732-2.1270.4232.267-1.376-3.4400.010
47A52VAL0-0.004-0.0072.682-6.242-3.6990.692-1.247-1.987-0.012
48A53LYS10.8560.9052.379-7.997-4.0103.879-2.424-5.4410.020
49A54LYS10.8820.9574.055-3.305-2.9540.008-0.075-0.2830.001
50A55LEU0-0.008-0.0087.2660.4930.4930.0000.0000.0000.000
51A56SER0-0.029-0.0209.625-0.331-0.3310.0000.0000.0000.000
52A57ARG10.9070.95012.613-1.281-1.2810.0000.0000.0000.000
53A58PRO00.0610.04212.427-0.039-0.0390.0000.0000.0000.000
54A59PHE00.0510.01014.035-0.096-0.0960.0000.0000.0000.000
55A60GLN00.0040.00717.239-0.130-0.1300.0000.0000.0000.000
56A61SER00.002-0.03819.682-0.067-0.0670.0000.0000.0000.000
57A62ILE00.0830.03419.8430.0280.0280.0000.0000.0000.000
58A63ILE00.0200.01617.946-0.009-0.0090.0000.0000.0000.000
59A64HIS00.0000.02215.579-0.044-0.0440.0000.0000.0000.000
60A65ALA00.0530.03614.9390.0490.0490.0000.0000.0000.000
61A66LYS10.8580.93915.391-0.191-0.1910.0000.0000.0000.000
62A67ARG10.9280.9669.450-1.600-1.6000.0000.0000.0000.000
63A68THR0-0.028-0.02010.8160.0650.0650.0000.0000.0000.000
64A69TYR00.0230.02010.425-0.072-0.0720.0000.0000.0000.000
65A70ARG10.7970.85611.219-0.278-0.2780.0000.0000.0000.000
66A71GLU-1-0.817-0.8845.0631.6351.757-0.001-0.004-0.1170.000
67A72LEU0-0.0160.0006.754-0.341-0.3410.0000.0000.0000.000
68A73ARG10.8680.9238.259-0.013-0.0130.0000.0000.0000.000
69A74LEU0-0.037-0.0097.982-0.096-0.0960.0000.0000.0000.000
70A75LEU0-0.008-0.0172.374-2.102-0.9891.433-0.597-1.949-0.005
71A76LYS10.7760.8565.8540.1200.1200.0000.0000.0000.000
72A77HIS0-0.053-0.0208.938-0.053-0.0530.0000.0000.0000.000
73A78MET0-0.077-0.0167.5390.0060.0060.0000.0000.0000.000
74A79LYS10.9490.9688.9160.5330.5330.0000.0000.0000.000
75A80HIS00.0990.04810.809-0.036-0.0360.0000.0000.0000.000
76A81GLU-1-0.827-0.89611.027-1.718-1.7180.0000.0000.0000.000
77A82ASN0-0.016-0.01010.576-0.119-0.1190.0000.0000.0000.000
78A83VAL0-0.036-0.0157.847-0.095-0.0950.0000.0000.0000.000
79A84ILE0-0.047-0.0162.637-2.003-0.4021.051-0.509-2.1440.001
80A85GLY00.0940.0465.4130.0560.0560.0000.0000.0000.000
81A86LEU0-0.074-0.0322.733-1.214-0.1380.361-0.432-1.0060.004
82A87LEU0-0.005-0.0015.055-0.242-0.121-0.001-0.003-0.1170.000
83A88ASP-1-0.845-0.9145.540-0.025-0.0250.0000.0000.0000.000
84A89VAL0-0.0220.0055.1890.3310.389-0.001-0.003-0.0540.000
85A90PHE0-0.0040.0007.261-0.082-0.0820.0000.0000.0000.000
86A91THR00.011-0.01310.2170.1510.1510.0000.0000.0000.000
87A92PRO0-0.005-0.00213.053-0.078-0.0780.0000.0000.0000.000
88A93ALA0-0.0390.00115.902-0.042-0.0420.0000.0000.0000.000
89A94ARG10.9390.95718.032-0.300-0.3000.0000.0000.0000.000
90A95SER00.0130.00820.809-0.030-0.0300.0000.0000.0000.000
91A96LEU00.0760.03619.6570.0460.0460.0000.0000.0000.000
92A97GLU-1-0.929-0.98820.8710.2960.2960.0000.0000.0000.000
93A98GLU-1-0.922-0.94720.9350.3900.3900.0000.0000.0000.000
94A99PHE0-0.109-0.03513.0320.0720.0720.0000.0000.0000.000
95A100ASN0-0.016-0.03416.719-0.018-0.0180.0000.0000.0000.000
96A101ASP-1-0.920-0.94512.4751.2701.2700.0000.0000.0000.000
97A102VAL00.006-0.0117.657-0.148-0.1480.0000.0000.0000.000
98A103TYR00.0130.0096.8120.4670.4670.0000.0000.0000.000
99A104LEU00.0160.0042.363-2.284-0.6932.117-1.352-2.3550.013
100A105VAL00.0160.0172.395-6.542-4.2672.414-1.715-2.974-0.015
101A106THR00.0100.0032.307-3.5970.2905.692-2.300-7.2790.007
102A107HIS00.1040.0404.127-0.911-0.1080.004-0.337-0.470-0.001
103A108LEU0-0.058-0.0201.780-17.648-19.42214.373-5.443-7.156-0.040
104A109MET00.004-0.0051.754-5.757-18.61626.882-7.913-6.1100.039
105A110GLY00.0430.0211.858-26.240-26.1729.980-4.369-5.679-0.065
106A111ALA0-0.024-0.0152.488-2.6640.3281.191-1.658-2.526-0.013
107A112ASP-1-0.819-0.8882.529-7.587-6.1570.685-0.271-1.843-0.011
108A113LEU00.0630.0213.9761.5101.6760.009-0.026-0.1480.000
109A114ASN0-0.001-0.0017.1880.6530.6530.0000.0000.0000.000
110A115ASN0-0.029-0.0144.6991.1501.225-0.001-0.001-0.0740.000
111A116ILE0-0.028-0.0077.3470.5240.5240.0000.0000.0000.000
112A117VAL00.0230.00810.0680.3800.3800.0000.0000.0000.000
113A118LYS10.8830.95711.6211.2621.2620.0000.0000.0000.000
114A119CYS0-0.064-0.03714.0600.1150.1150.0000.0000.0000.000
115A120GLN0-0.045-0.01516.342-0.020-0.0200.0000.0000.0000.000
116A121LYS10.9280.96517.8810.3990.3990.0000.0000.0000.000
117A122LEU00.0330.02814.064-0.018-0.0180.0000.0000.0000.000
118A123THR0-0.036-0.02618.7550.0970.0970.0000.0000.0000.000
119A124ASP-1-0.763-0.89720.057-0.763-0.7630.0000.0000.0000.000
120A125ASP-1-0.847-0.91221.050-1.013-1.0130.0000.0000.0000.000
121A126HIS00.0730.04115.9440.0200.0200.0000.0000.0000.000
122A127VAL0-0.044-0.02216.390-0.144-0.1440.0000.0000.0000.000
123A128GLN0-0.0020.00817.676-0.077-0.0770.0000.0000.0000.000
124A129PHE00.0690.04314.379-0.015-0.0150.0000.0000.0000.000
125A130LEU0-0.007-0.01010.878-0.115-0.1150.0000.0000.0000.000
126A131ILE0-0.021-0.02814.010-0.062-0.0620.0000.0000.0000.000
127A132TYR0-0.017-0.01516.338-0.011-0.0110.0000.0000.0000.000
128A133GLN00.0160.00512.629-0.104-0.1040.0000.0000.0000.000
129A134ILE0-0.035-0.01111.977-0.004-0.0040.0000.0000.0000.000
130A135LEU0-0.003-0.00714.2050.0940.0940.0000.0000.0000.000
131A136ARG10.8150.91316.0271.3541.3540.0000.0000.0000.000
132A137GLY00.0130.00213.8050.0510.0510.0000.0000.0000.000
133A138LEU0-0.039-0.03714.1800.0870.0870.0000.0000.0000.000
134A139LYS10.8600.92815.8850.8110.8110.0000.0000.0000.000
135A140TYR00.0440.03611.9420.0580.0580.0000.0000.0000.000
136A141ILE00.0230.01210.7280.0900.0900.0000.0000.0000.000
137A142HIS0-0.101-0.07714.3550.1070.1070.0000.0000.0000.000
138A143SER0-0.074-0.02717.5530.0810.0810.0000.0000.0000.000
139A144ALA00.0240.01615.2290.0480.0480.0000.0000.0000.000
140A145ASP-1-0.936-0.97017.300-0.319-0.3190.0000.0000.0000.000
141A146ILE0-0.055-0.01112.0450.0640.0640.0000.0000.0000.000
142A147ILE0-0.037-0.02915.513-0.036-0.0360.0000.0000.0000.000
143A148HIS0-0.022-0.0258.9000.1940.1940.0000.0000.0000.000
144A149ARG10.9170.93712.7500.3090.3090.0000.0000.0000.000
145A150ASP-1-0.772-0.86212.3120.1530.1530.0000.0000.0000.000
146A151LEU00.0520.05311.101-0.010-0.0100.0000.0000.0000.000
147A152LYS10.8960.9339.9740.1330.1330.0000.0000.0000.000
148A153PRO00.0720.0399.346-0.285-0.2850.0000.0000.0000.000
149A154SER00.006-0.0086.073-0.585-0.5850.0000.0000.0000.000
150A155ASN0-0.050-0.0234.928-0.919-0.848-0.001-0.006-0.0640.000
151A156LEU00.0240.0246.2260.1600.1600.0000.0000.0000.000
152A157ALA00.0120.0032.726-1.814-1.0760.407-0.226-0.9200.001
153A158VAL0-0.008-0.0113.8081.8722.0830.0030.017-0.2310.000
154A159ASN0-0.058-0.0285.426-2.128-2.1280.0000.0000.0000.000
155A160GLU-1-0.920-0.9817.780-3.785-3.7850.0000.0000.0000.000
156A161ASP-1-0.892-0.92610.591-1.729-1.7290.0000.0000.0000.000
157A162CYS0-0.100-0.06610.6430.3080.3080.0000.0000.0000.000
158A163GLU-1-0.854-0.90110.747-2.236-2.2360.0000.0000.0000.000
159A164LEU0-0.030-0.0198.100-0.744-0.7440.0000.0000.0000.000
160A165LYS10.8610.9185.5023.5813.5810.0000.0000.0000.000
161A166ILE0-0.015-0.0086.787-0.509-0.5090.0000.0000.0000.000
162A167LEU00.010-0.0022.307-3.753-0.8512.219-0.980-4.1410.005
163A168ASP-1-0.941-0.9684.3732.2152.320-0.001-0.005-0.0990.000
164A169PHE0-0.017-0.0025.8630.3560.3560.0000.0000.0000.000
165A170GLY00.0330.0158.7660.0340.0340.0000.0000.0000.000
166A171LEU0-0.053-0.0307.6490.1780.1780.0000.0000.0000.000
167A172ALA00.006-0.00310.9750.0660.0660.0000.0000.0000.000
168A173ARG10.6800.80313.0540.2890.2890.0000.0000.0000.000
169A174HIS0-0.046-0.00511.759-0.182-0.1820.0000.0000.0000.000
170A175THR0-0.057-0.02216.228-0.102-0.1020.0000.0000.0000.000
171A176ASP-1-0.876-0.95019.7910.3090.3090.0000.0000.0000.000
172A177ASP-1-0.963-0.96421.9230.5790.5790.0000.0000.0000.000
173A178GLU-1-0.800-0.89516.3881.0031.0030.0000.0000.0000.000
174A179MET0-0.0600.00918.275-0.086-0.0860.0000.0000.0000.000
175A180THR0-0.031-0.02120.318-0.100-0.1000.0000.0000.0000.000
176A181GLY00.0220.01522.0060.0330.0330.0000.0000.0000.000
177A182TYR0-0.009-0.00220.969-0.052-0.0520.0000.0000.0000.000
178A183VAL00.0130.01717.3690.0340.0340.0000.0000.0000.000
179A184ALA00.0690.01913.629-0.053-0.0530.0000.0000.0000.000
180A185THR0-0.077-0.08213.647-0.154-0.1540.0000.0000.0000.000
181A186ARG10.8740.91215.356-0.129-0.1290.0000.0000.0000.000
182A187TRP0-0.0320.01116.550-0.061-0.0610.0000.0000.0000.000
183A188TYR0-0.071-0.07014.131-0.027-0.0270.0000.0000.0000.000
184A189ARG10.8770.94116.906-0.019-0.0190.0000.0000.0000.000
185A190ALA00.0660.03219.7180.0090.0090.0000.0000.0000.000
186A191PRO00.0130.01022.8850.0440.0440.0000.0000.0000.000
187A192GLU-1-0.753-0.86824.742-0.207-0.2070.0000.0000.0000.000
188A193ILE0-0.0110.00419.2490.0290.0290.0000.0000.0000.000
189A194MET0-0.070-0.01523.2720.0430.0430.0000.0000.0000.000
190A195LEU0-0.007-0.01524.3100.0410.0410.0000.0000.0000.000
191A196ASN0-0.046-0.01324.830-0.008-0.0080.0000.0000.0000.000
192A197TRP0-0.004-0.00927.147-0.003-0.0030.0000.0000.0000.000
193A198MET0-0.019-0.02227.754-0.002-0.0020.0000.0000.0000.000
194A199HIS00.0050.01023.8540.0180.0180.0000.0000.0000.000
195A200TYR00.0270.02919.239-0.022-0.0220.0000.0000.0000.000
196A201ASN00.0750.03922.674-0.025-0.0250.0000.0000.0000.000
197A202GLN00.0750.01219.556-0.003-0.0030.0000.0000.0000.000
198A203THR00.0200.00319.994-0.047-0.0470.0000.0000.0000.000
199A204VAL0-0.050-0.02118.533-0.012-0.0120.0000.0000.0000.000
200A205ASP-1-0.703-0.83716.036-0.636-0.6360.0000.0000.0000.000
201A206ILE0-0.026-0.00618.278-0.084-0.0840.0000.0000.0000.000
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