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: 5J3QZ

Calculation Name: 1PBW-A-Xray372

Preferred Name: PI3-kinase p85-alpha subunit

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1PBW

Chain ID: A

ChEMBL ID: CHEMBL2506

UniProt ID: P27986

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptH
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 184
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2047615.275057
FMO2-HF: Nuclear repulsion 1975105.788798
FMO2-HF: Total energy -72509.486259
FMO2-MP2: Total energy -72723.0919


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:115:LEU)


Summations of interaction energy for fragment #1(A:115:LEU)
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.
-14.097-2.9279.301-5.933-14.537-0.032
Interaction energy analysis for fragmet #1(A:115:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / 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].
3A117ASP-1-0.734-0.8463.292-4.579-2.6590.117-0.998-1.038-0.001
4A118LEU00.0100.0045.8590.5460.5460.0000.0000.0000.000
5A119ALA0-0.081-0.0606.9410.3500.3500.0000.0000.0000.000
6A120GLU-1-0.908-0.9577.110-1.502-1.5020.0000.0000.0000.000
7A121GLN0-0.068-0.0232.9050.0971.1980.401-0.434-1.068-0.003
8A122PHE0-0.015-0.0197.1890.2450.2450.0000.0000.0000.000
9A123ALA00.0040.00910.829-0.101-0.1010.0000.0000.0000.000
10A124PRO0-0.020-0.03914.1240.0450.0450.0000.0000.0000.000
11A125PRO00.0060.03717.283-0.007-0.0070.0000.0000.0000.000
12A126ASP-1-0.925-0.94514.014-0.160-0.1600.0000.0000.0000.000
13A127ILE0-0.005-0.02615.057-0.040-0.0400.0000.0000.0000.000
14A128ALA0-0.019-0.01311.300-0.026-0.0260.0000.0000.0000.000
15A129PRO00.0400.0376.7890.0580.0580.0000.0000.0000.000
16A130PRO00.0980.0338.1010.1060.1060.0000.0000.0000.000
17A131LEU0-0.028-0.0093.174-0.4290.0260.100-0.097-0.4580.000
18A132LEU00.0200.0136.7090.0610.0610.0000.0000.0000.000
19A133ILE00.0170.0128.0920.0110.0110.0000.0000.0000.000
20A134LYS10.9700.9939.317-0.296-0.2960.0000.0000.0000.000
21A135LEU0-0.014-0.0116.414-0.016-0.0160.0000.0000.0000.000
22A136VAL0-0.040-0.01310.506-0.024-0.0240.0000.0000.0000.000
23A137GLU-1-0.883-0.95013.2570.0200.0200.0000.0000.0000.000
24A138ALA0-0.046-0.01513.734-0.004-0.0040.0000.0000.0000.000
25A139ILE00.0020.00111.880-0.015-0.0150.0000.0000.0000.000
26A140GLU-1-0.846-0.91715.987-0.053-0.0530.0000.0000.0000.000
27A141LYS10.8820.95417.082-0.127-0.1270.0000.0000.0000.000
28A142LYS10.8430.93917.335-0.166-0.1660.0000.0000.0000.000
29A143GLY00.0160.00319.6830.0020.0020.0000.0000.0000.000
30A144LEU00.0050.01320.629-0.011-0.0110.0000.0000.0000.000
31A145GLU-1-0.947-0.98822.5260.0050.0050.0000.0000.0000.000
32A146CYM-1-0.826-0.88121.4870.0530.0530.0000.0000.0000.000
33A147SER0-0.027-0.01622.695-0.005-0.0050.0000.0000.0000.000
34A148THR0-0.023-0.02122.1150.0000.0000.0000.0000.0000.000
35A149LEU00.0300.01516.5100.0050.0050.0000.0000.0000.000
36A150TYR0-0.0120.00812.735-0.031-0.0310.0000.0000.0000.000
37A151ARG10.8650.92116.520-0.003-0.0030.0000.0000.0000.000
38A152THR0-0.0060.00317.9700.0030.0030.0000.0000.0000.000
39A153GLN0-0.106-0.03213.787-0.013-0.0130.0000.0000.0000.000
40A154SER0-0.073-0.04114.5470.0060.0060.0000.0000.0000.000
41A155SER00.008-0.01116.990-0.013-0.0130.0000.0000.0000.000
42A156SER00.0040.01513.533-0.001-0.0010.0000.0000.0000.000
43A157ASN00.0530.02913.924-0.076-0.0760.0000.0000.0000.000
44A158LEU00.046-0.0059.4120.0540.0540.0000.0000.0000.000
45A159ALA0-0.073-0.0299.250-0.039-0.0390.0000.0000.0000.000
46A160GLU-1-0.867-0.93610.4500.5680.5680.0000.0000.0000.000
47A161LEU0-0.021-0.0248.3330.0730.0730.0000.0000.0000.000
48A162ARG10.8470.9085.763-1.220-1.2200.0000.0000.0000.000
49A163GLN0-0.0090.0026.1130.4230.4230.0000.0000.0000.000
50A164LEU00.0300.0097.891-0.057-0.0570.0000.0000.0000.000
51A165LEU0-0.069-0.0032.190-1.068-0.4501.395-0.493-1.5200.000
52A166ASP-1-0.917-0.9983.8900.9491.2750.006-0.098-0.2340.000
53A167CYS0-0.0290.0225.051-0.020-0.0200.0000.0000.0000.000
54A168ASP-1-0.984-1.0086.3710.3850.3850.0000.0000.0000.000
55A169THR0-0.054-0.06310.1060.0160.0160.0000.0000.0000.000
56A170PRO0-0.0500.0249.9900.0740.0740.0000.0000.0000.000
57A171SER00.005-0.0058.952-0.059-0.0590.0000.0000.0000.000
58A172VAL00.0040.01510.854-0.067-0.0670.0000.0000.0000.000
59A173ASP-1-0.816-0.89212.6850.2510.2510.0000.0000.0000.000
60A174LEU00.018-0.0219.575-0.031-0.0310.0000.0000.0000.000
61A175GLU-1-0.891-0.98013.4890.1080.1080.0000.0000.0000.000
62A176MET0-0.066-0.02516.894-0.022-0.0220.0000.0000.0000.000
63A177ILE0-0.061-0.01612.9320.0030.0030.0000.0000.0000.000
64A178ASP-1-0.834-0.92616.0730.1410.1410.0000.0000.0000.000
65A179VAL00.0760.02215.9190.0220.0220.0000.0000.0000.000
66A180HIS10.8740.92515.621-0.098-0.0980.0000.0000.0000.000
67A181VAL00.0640.03412.632-0.003-0.0030.0000.0000.0000.000
68A182LEU0-0.0050.00911.3570.0510.0510.0000.0000.0000.000
69A183ALA0-0.011-0.00610.7210.0000.0000.0000.0000.0000.000
70A184ASP-1-0.750-0.86611.0980.1270.1270.0000.0000.0000.000
71A185ALA0-0.001-0.0027.556-0.010-0.0100.0000.0000.0000.000
72A186PHE0-0.031-0.0196.1880.0560.0560.0000.0000.0000.000
73A187LYS10.8980.9296.815-0.059-0.0590.0000.0000.0000.000
74A188ARG10.7970.9195.048-0.226-0.2260.0000.0000.0000.000
75A189TYR00.0480.0112.163-2.440-0.8212.504-1.327-2.797-0.002
76A190LEU0-0.004-0.0043.176-1.297-0.8330.3920.182-1.038-0.007
77A191LEU0-0.064-0.0385.667-0.348-0.3480.0000.0000.0000.000
78A192ASP-1-0.769-0.8872.491-0.3690.3921.789-0.625-1.9250.001
79A193LEU0-0.052-0.0052.575-7.875-4.7652.517-1.980-3.648-0.020
80A194PRO00.0370.0483.0131.0841.7920.081-0.061-0.7270.000
81A195ASN0-0.038-0.0135.3260.9741.062-0.001-0.002-0.0840.000
82A196PRO0-0.028-0.0217.601-0.254-0.2540.0000.0000.0000.000
83A197VAL00.0340.0098.1660.0290.0290.0000.0000.0000.000
84A198ILE0-0.019-0.00310.1440.0800.0800.0000.0000.0000.000
85A199PRO00.0180.00812.738-0.008-0.0080.0000.0000.0000.000
86A200ALA00.0650.01813.7620.1000.1000.0000.0000.0000.000
87A201ALA00.0100.00315.7000.0700.0700.0000.0000.0000.000
88A202VAL00.0400.02617.2130.0520.0520.0000.0000.0000.000
89A203TYR00.0180.00116.9250.0530.0530.0000.0000.0000.000
90A204SER0-0.014-0.00618.9030.0540.0540.0000.0000.0000.000
91A205GLU-1-0.887-0.95421.324-0.257-0.2570.0000.0000.0000.000
92A206MET0-0.071-0.00821.0240.0260.0260.0000.0000.0000.000
93A207ILE0-0.027-0.00522.1940.0270.0270.0000.0000.0000.000
94A208SER0-0.052-0.02924.9460.0240.0240.0000.0000.0000.000
95A209LEU00.0720.03426.9980.0140.0140.0000.0000.0000.000
96A210ALA0-0.046-0.00927.3990.0120.0120.0000.0000.0000.000
97A211PRO0-0.043-0.02629.1530.0110.0110.0000.0000.0000.000
98A212GLU-1-0.961-0.97832.053-0.157-0.1570.0000.0000.0000.000
99A213VAL0-0.110-0.03929.2480.0030.0030.0000.0000.0000.000
100A214GLN00.0490.03432.5110.0010.0010.0000.0000.0000.000
101A215SER0-0.085-0.06733.4020.0060.0060.0000.0000.0000.000
102A216SER00.003-0.01029.857-0.013-0.0130.0000.0000.0000.000
103A217GLU-1-0.815-0.91228.994-0.161-0.1610.0000.0000.0000.000
104A218GLU-1-0.828-0.89429.101-0.145-0.1450.0000.0000.0000.000
105A219TYR00.003-0.01325.229-0.015-0.0150.0000.0000.0000.000
106A220ILE00.0160.00124.236-0.024-0.0240.0000.0000.0000.000
107A221GLN0-0.113-0.08624.449-0.029-0.0290.0000.0000.0000.000
108A222LEU0-0.0040.01025.306-0.012-0.0120.0000.0000.0000.000
109A223LEU00.0610.03218.468-0.024-0.0240.0000.0000.0000.000
110A224LYS10.9090.95621.0250.1780.1780.0000.0000.0000.000
111A225LYS10.9220.96122.1760.1910.1910.0000.0000.0000.000
112A226LEU00.0220.00421.350-0.013-0.0130.0000.0000.0000.000
113A227ILE0-0.032-0.01114.511-0.024-0.0240.0000.0000.0000.000
114A228ARG10.8810.94918.2030.2410.2410.0000.0000.0000.000
115A229SER0-0.0090.01620.6450.0270.0270.0000.0000.0000.000
116A230PRO00.057-0.00120.351-0.026-0.0260.0000.0000.0000.000
117A231SER0-0.059-0.01619.6180.0080.0080.0000.0000.0000.000
118A232ILE0-0.043-0.00914.757-0.072-0.0720.0000.0000.0000.000
119A233PRO00.0150.01413.1740.0550.0550.0000.0000.0000.000
120A234HIS00.0640.01315.194-0.043-0.0430.0000.0000.0000.000
121A235GLN00.0430.01610.8600.0630.0630.0000.0000.0000.000
122A236TYR0-0.059-0.0479.243-0.004-0.0040.0000.0000.0000.000
123A237TRP00.0330.01112.6040.0500.0500.0000.0000.0000.000
124A238LEU0-0.045-0.01414.2170.0400.0400.0000.0000.0000.000
125A239THR00.0360.0088.2920.0520.0520.0000.0000.0000.000
126A240LEU0-0.004-0.00811.6540.0510.0510.0000.0000.0000.000
127A241GLN0-0.016-0.02113.6590.0710.0710.0000.0000.0000.000
128A242TYR00.0010.01611.9660.0460.0460.0000.0000.0000.000
129A243LEU0-0.003-0.0169.5640.0510.0510.0000.0000.0000.000
130A244LEU0-0.0100.00713.7270.0360.0360.0000.0000.0000.000
131A245LYS11.0081.00417.2500.2160.2160.0000.0000.0000.000
132A246HIS10.8170.89714.1550.0880.0880.0000.0000.0000.000
133A247PHE00.002-0.02513.1220.0250.0250.0000.0000.0000.000
134A248PHE00.0530.03218.3490.0180.0180.0000.0000.0000.000
135A249LYS10.9410.98620.1990.0570.0570.0000.0000.0000.000
136A250LEU0-0.016-0.01517.2490.0130.0130.0000.0000.0000.000
137A251SER0-0.047-0.00621.6210.0090.0090.0000.0000.0000.000
138A252GLN0-0.011-0.01724.1840.0100.0100.0000.0000.0000.000
139A253THR0-0.047-0.01525.2630.0080.0080.0000.0000.0000.000
140A254SER00.007-0.00625.8370.0070.0070.0000.0000.0000.000
141A255SER0-0.082-0.03327.0010.0040.0040.0000.0000.0000.000
142A256LYS10.9250.97227.9340.0050.0050.0000.0000.0000.000
143A257ASN00.0310.01122.947-0.003-0.0030.0000.0000.0000.000
144A258LEU0-0.023-0.01324.2600.0010.0010.0000.0000.0000.000
145A259LEU0-0.042-0.01419.552-0.008-0.0080.0000.0000.0000.000
146A260ASN00.0640.04923.318-0.012-0.0120.0000.0000.0000.000
147A261ALA00.0600.00722.413-0.005-0.0050.0000.0000.0000.000
148A262ARG10.7300.84422.2620.1110.1110.0000.0000.0000.000
149A263VAL00.0240.01921.427-0.010-0.0100.0000.0000.0000.000
150A264LEU0-0.002-0.01017.567-0.007-0.0070.0000.0000.0000.000
151A265SER0-0.026-0.01417.795-0.032-0.0320.0000.0000.0000.000
152A266GLU-1-0.866-0.95018.683-0.131-0.1310.0000.0000.0000.000
153A267ILE0-0.055-0.00814.985-0.007-0.0070.0000.0000.0000.000
154A268PHE0-0.016-0.04111.654-0.010-0.0100.0000.0000.0000.000
155A269SER00.0290.02913.740-0.071-0.0710.0000.0000.0000.000
156A270PRO00.009-0.00515.050-0.058-0.0580.0000.0000.0000.000
157A271MET0-0.053-0.0319.727-0.044-0.0440.0000.0000.0000.000
158A272LEU0-0.044-0.01810.039-0.147-0.1470.0000.0000.0000.000
159A273PHE00.0320.01011.917-0.086-0.0860.0000.0000.0000.000
160A274ARG10.8070.9025.7911.9121.9120.0000.0000.0000.000
161A275PHE00.0010.00312.9030.0220.0220.0000.0000.0000.000
162A276SER0-0.0010.01015.4470.0070.0070.0000.0000.0000.000
163A277ALA0-0.017-0.02417.3880.0310.0310.0000.0000.0000.000
164A278ALA00.0110.02420.3340.0090.0090.0000.0000.0000.000
165A279SER00.0530.02622.2220.0120.0120.0000.0000.0000.000
166A280SER00.0510.01224.982-0.012-0.0120.0000.0000.0000.000
167A281ASP-1-0.832-0.91326.563-0.131-0.1310.0000.0000.0000.000
168A282ASN0-0.033-0.01024.110-0.008-0.0080.0000.0000.0000.000
169A283THR0-0.053-0.02621.440-0.022-0.0220.0000.0000.0000.000
170A284GLU-1-0.804-0.88722.935-0.144-0.1440.0000.0000.0000.000
171A285ASN0-0.018-0.01925.3430.0080.0080.0000.0000.0000.000
172A286LEU0-0.032-0.01919.740-0.006-0.0060.0000.0000.0000.000
173A287ILE00.0260.02320.519-0.013-0.0130.0000.0000.0000.000
174A288LYS10.9240.98421.9250.1290.1290.0000.0000.0000.000
175A289VAL00.0030.00721.4720.0050.0050.0000.0000.0000.000
176A290ILE0-0.013-0.00717.1340.0000.0000.0000.0000.0000.000
177A291GLU-1-0.825-0.92620.460-0.114-0.1140.0000.0000.0000.000
178A292ILE0-0.029-0.01422.8890.0130.0130.0000.0000.0000.000
179A293LEU0-0.003-0.01519.9720.0050.0050.0000.0000.0000.000
180A294ILE0-0.0170.00718.8020.0060.0060.0000.0000.0000.000
181A295SER0-0.062-0.03821.7380.0140.0140.0000.0000.0000.000
182A296THR0-0.055-0.03125.0010.0070.0070.0000.0000.0000.000
183A297GLU-1-0.886-0.94120.805-0.187-0.1870.0000.0000.0000.000
184A298TRP0-0.120-0.04224.2200.0120.0120.0000.0000.0000.000