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: VQRZ1

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 OptAll
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 -2055107.447752
FMO2-HF: Nuclear repulsion 1982595.310888
FMO2-HF: Total energy -72512.136865
FMO2-MP2: Total energy -72725.634008


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.
-15.925-4.714.246-6.565-18.906-0.043
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 : -0.045 / q_NPA : -0.026
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-1-0.742-0.8522.761-4.994-2.6560.575-1.338-1.575-0.009
4A118LEU0-0.002-0.0045.3630.2870.2870.0000.0000.0000.000
5A119ALA0-0.054-0.0436.9900.2420.2420.0000.0000.0000.000
6A120GLU-1-0.899-0.9396.693-1.243-1.2430.0000.0000.0000.000
7A121GLN0-0.028-0.0062.368-0.2711.0331.347-0.777-1.874-0.003
8A122PHE0-0.0090.0007.1310.2220.2220.0000.0000.0000.000
9A123ALA00.0340.01610.687-0.069-0.0690.0000.0000.0000.000
10A124PRO00.0030.01414.0490.0410.0410.0000.0000.0000.000
11A125PRO0-0.041-0.03417.3330.0070.0070.0000.0000.0000.000
12A126ASP-1-0.911-0.92513.784-0.180-0.1800.0000.0000.0000.000
13A127ILE0-0.007-0.03415.079-0.032-0.0320.0000.0000.0000.000
14A128ALA0-0.005-0.01110.799-0.016-0.0160.0000.0000.0000.000
15A129PRO00.0190.0256.3790.0440.0440.0000.0000.0000.000
16A130PRO00.0600.0248.1560.0870.0870.0000.0000.0000.000
17A131LEU0-0.0020.0172.765-0.470-0.0410.558-0.132-0.8540.000
18A132LEU00.0180.0066.2970.0510.0510.0000.0000.0000.000
19A133ILE00.0100.0037.7140.0200.0200.0000.0000.0000.000
20A134LYS10.8920.9499.278-0.204-0.2040.0000.0000.0000.000
21A135LEU00.0000.0025.977-0.001-0.0010.0000.0000.0000.000
22A136VAL0-0.043-0.02410.306-0.012-0.0120.0000.0000.0000.000
23A137GLU-1-0.873-0.94312.669-0.009-0.0090.0000.0000.0000.000
24A138ALA0-0.0220.00013.4510.0010.0010.0000.0000.0000.000
25A139ILE0-0.044-0.02811.348-0.003-0.0030.0000.0000.0000.000
26A140GLU-1-0.795-0.86615.414-0.081-0.0810.0000.0000.0000.000
27A141LYS10.8290.90716.969-0.026-0.0260.0000.0000.0000.000
28A142LYS10.8060.91716.934-0.072-0.0720.0000.0000.0000.000
29A143GLY00.0260.00919.2840.0030.0030.0000.0000.0000.000
30A144LEU0-0.009-0.00120.255-0.009-0.0090.0000.0000.0000.000
31A145GLU-1-0.882-0.93421.733-0.022-0.0220.0000.0000.0000.000
32A146CYM-1-0.817-0.82321.096-0.007-0.0070.0000.0000.0000.000
33A147SER00.0250.01422.598-0.006-0.0060.0000.0000.0000.000
34A148THR0-0.122-0.11322.2890.0000.0000.0000.0000.0000.000
35A149LEU00.0750.04515.796-0.001-0.0010.0000.0000.0000.000
36A150TYR00.0020.01211.965-0.013-0.0130.0000.0000.0000.000
37A151ARG10.7950.88516.3720.0480.0480.0000.0000.0000.000
38A152THR00.005-0.00318.1450.0090.0090.0000.0000.0000.000
39A153GLN0-0.087-0.04614.731-0.016-0.0160.0000.0000.0000.000
40A154SER0-0.049-0.03814.5980.0140.0140.0000.0000.0000.000
41A155SER0-0.005-0.01517.232-0.009-0.0090.0000.0000.0000.000
42A156SER0-0.009-0.00413.8210.0050.0050.0000.0000.0000.000
43A157ASN00.0130.01013.966-0.041-0.0410.0000.0000.0000.000
44A158LEU0-0.042-0.0419.0840.0430.0430.0000.0000.0000.000
45A159ALA00.0240.01010.1020.0230.0230.0000.0000.0000.000
46A160GLU-1-0.845-0.89810.6170.3440.3440.0000.0000.0000.000
47A161LEU00.023-0.0018.4340.0420.0420.0000.0000.0000.000
48A162ARG10.8080.8585.258-0.295-0.2950.0000.0000.0000.000
49A163GLN0-0.013-0.0086.2500.2930.2930.0000.0000.0000.000
50A164LEU0-0.027-0.0087.890-0.053-0.0530.0000.0000.0000.000
51A165LEU0-0.074-0.0342.361-1.616-0.5721.639-0.421-2.262-0.001
52A166ASP-1-0.872-0.9523.5980.3010.8960.031-0.237-0.389-0.001
53A167CYS00.0240.0425.4540.0320.0320.0000.0000.0000.000
54A168ASP-1-0.935-0.9746.3660.2390.2390.0000.0000.0000.000
55A169THR0-0.071-0.01010.139-0.007-0.0070.0000.0000.0000.000
56A170PRO0-0.034-0.0509.6240.1290.1290.0000.0000.0000.000
57A171SER0-0.025-0.0078.642-0.045-0.0450.0000.0000.0000.000
58A172VAL00.0110.01510.600-0.044-0.0440.0000.0000.0000.000
59A173ASP-1-0.847-0.92712.3550.1380.1380.0000.0000.0000.000
60A174LEU00.0360.0099.221-0.016-0.0160.0000.0000.0000.000
61A175GLU-1-0.797-0.92413.2880.0310.0310.0000.0000.0000.000
62A176MET0-0.068-0.02616.660-0.009-0.0090.0000.0000.0000.000
63A177ILE0-0.049-0.00312.736-0.001-0.0010.0000.0000.0000.000
64A178ASP-1-0.776-0.90415.9500.0490.0490.0000.0000.0000.000
65A179VAL00.0520.02215.6040.0090.0090.0000.0000.0000.000
66A180HIS10.8550.92215.331-0.032-0.0320.0000.0000.0000.000
67A181VAL00.0270.00912.618-0.008-0.0080.0000.0000.0000.000
68A182LEU0-0.0140.00111.2450.0140.0140.0000.0000.0000.000
69A183ALA00.005-0.00210.447-0.010-0.0100.0000.0000.0000.000
70A184ASP-1-0.722-0.83810.920-0.020-0.0200.0000.0000.0000.000
71A185ALA00.0120.0127.516-0.031-0.0310.0000.0000.0000.000
72A186PHE00.0020.0025.9420.0190.0190.0000.0000.0000.000
73A187LYS10.8330.9056.941-0.014-0.0140.0000.0000.0000.000
74A188ARG10.8500.9175.5080.2570.2570.0000.0000.0000.000
75A189TYR00.037-0.0212.278-1.798-1.1394.399-1.330-3.728-0.003
76A190LEU00.009-0.0012.834-1.464-1.0490.4670.137-1.020-0.008
77A191LEU0-0.062-0.0195.463-0.202-0.2020.0000.0000.0000.000
78A192ASP-1-0.748-0.8302.607-1.628-0.1390.800-0.561-1.7280.002
79A193LEU0-0.0250.0112.332-7.812-4.7574.397-2.524-4.928-0.020
80A194PRO00.0020.0273.1881.3631.2600.0330.618-0.5480.000
81A195ASN0-0.058-0.0345.7310.7810.7810.0000.0000.0000.000
82A196PRO0-0.020-0.0107.132-0.251-0.2510.0000.0000.0000.000
83A197VAL00.026-0.0068.0370.0290.0290.0000.0000.0000.000
84A198ILE0-0.011-0.00110.0910.0770.0770.0000.0000.0000.000
85A199PRO00.0070.00812.3060.0180.0180.0000.0000.0000.000
86A200ALA00.0670.02413.7160.0730.0730.0000.0000.0000.000
87A201ALA00.0120.01415.6640.0510.0510.0000.0000.0000.000
88A202VAL00.0360.02217.0890.0370.0370.0000.0000.0000.000
89A203TYR00.0210.00516.8590.0340.0340.0000.0000.0000.000
90A204SER00.0410.01218.8100.0340.0340.0000.0000.0000.000
91A205GLU-1-0.941-0.95621.510-0.205-0.2050.0000.0000.0000.000
92A206MET0-0.044-0.00820.8030.0210.0210.0000.0000.0000.000
93A207ILE0-0.0240.00921.9580.0180.0180.0000.0000.0000.000
94A208SER0-0.068-0.05524.6240.0180.0180.0000.0000.0000.000
95A209LEU00.0400.01326.7400.0110.0110.0000.0000.0000.000
96A210ALA0-0.0130.00527.1600.0090.0090.0000.0000.0000.000
97A211PRO0-0.063-0.04028.9840.0080.0080.0000.0000.0000.000
98A212GLU-1-0.956-0.97031.912-0.119-0.1190.0000.0000.0000.000
99A213VAL0-0.080-0.02729.2550.0030.0030.0000.0000.0000.000
100A214GLN0-0.014-0.01732.581-0.002-0.0020.0000.0000.0000.000
101A215SER0-0.067-0.07133.2550.0040.0040.0000.0000.0000.000
102A216SER00.0520.01128.598-0.007-0.0070.0000.0000.0000.000
103A217GLU-1-0.815-0.91328.474-0.146-0.1460.0000.0000.0000.000
104A218GLU-1-0.822-0.86928.758-0.115-0.1150.0000.0000.0000.000
105A219TYR00.000-0.01024.756-0.011-0.0110.0000.0000.0000.000
106A220ILE00.0230.00323.799-0.017-0.0170.0000.0000.0000.000
107A221GLN0-0.079-0.05824.240-0.023-0.0230.0000.0000.0000.000
108A222LEU0-0.0020.01525.048-0.008-0.0080.0000.0000.0000.000
109A223LEU00.0570.02518.104-0.015-0.0150.0000.0000.0000.000
110A224LYS10.8390.92020.9940.1370.1370.0000.0000.0000.000
111A225LYS10.9430.98922.5050.1570.1570.0000.0000.0000.000
112A226LEU00.0180.00521.118-0.009-0.0090.0000.0000.0000.000
113A227ILE0-0.033-0.01414.650-0.019-0.0190.0000.0000.0000.000
114A228ARG10.8570.92517.8520.2020.2020.0000.0000.0000.000
115A229SER00.0320.02720.5150.0280.0280.0000.0000.0000.000
116A230PRO00.003-0.01820.312-0.025-0.0250.0000.0000.0000.000
117A231SER0-0.043-0.01019.4980.0100.0100.0000.0000.0000.000
118A232ILE0-0.033-0.00715.201-0.049-0.0490.0000.0000.0000.000
119A233PRO00.0060.01013.0850.0330.0330.0000.0000.0000.000
120A234HIS00.0640.02314.718-0.044-0.0440.0000.0000.0000.000
121A235GLN00.0430.01710.6910.0620.0620.0000.0000.0000.000
122A236TYR0-0.044-0.0289.4750.0240.0240.0000.0000.0000.000
123A237TRP00.0270.00712.2810.0330.0330.0000.0000.0000.000
124A238LEU0-0.035-0.01113.7050.0310.0310.0000.0000.0000.000
125A239THR00.027-0.0087.8760.0190.0190.0000.0000.0000.000
126A240LEU0-0.009-0.00611.0970.0400.0400.0000.0000.0000.000
127A241GLN0-0.034-0.02113.4430.0580.0580.0000.0000.0000.000
128A242TYR00.0330.02011.1980.0370.0370.0000.0000.0000.000
129A243LEU0-0.022-0.0109.1430.0390.0390.0000.0000.0000.000
130A244LEU00.0060.00513.2890.0320.0320.0000.0000.0000.000
131A245LYS10.8840.95316.9420.1940.1940.0000.0000.0000.000
132A246HIS10.8010.88913.4790.1290.1290.0000.0000.0000.000
133A247PHE00.000-0.01512.8230.0190.0190.0000.0000.0000.000
134A248PHE00.0610.03018.0930.0160.0160.0000.0000.0000.000
135A249LYS10.8690.92419.2540.0880.0880.0000.0000.0000.000
136A250LEU00.0040.00116.7940.0120.0120.0000.0000.0000.000
137A251SER0-0.036-0.00821.0690.0090.0090.0000.0000.0000.000
138A252GLN0-0.049-0.02923.7070.0100.0100.0000.0000.0000.000
139A253THR0-0.017-0.00424.4080.0080.0080.0000.0000.0000.000
140A254SER00.0090.00425.4890.0030.0030.0000.0000.0000.000
141A255SER0-0.064-0.03126.3680.0020.0020.0000.0000.0000.000
142A256LYS10.8410.92227.1930.0260.0260.0000.0000.0000.000
143A257ASN00.0570.00422.279-0.002-0.0020.0000.0000.0000.000
144A258LEU0-0.030-0.01423.479-0.003-0.0030.0000.0000.0000.000
145A259LEU0-0.051-0.01218.723-0.006-0.0060.0000.0000.0000.000
146A260ASN00.0600.02622.506-0.011-0.0110.0000.0000.0000.000
147A261ALA00.0610.01122.331-0.006-0.0060.0000.0000.0000.000
148A262ARG10.7100.83322.1300.1070.1070.0000.0000.0000.000
149A263VAL00.0470.01421.134-0.011-0.0110.0000.0000.0000.000
150A264LEU0-0.050-0.01717.381-0.009-0.0090.0000.0000.0000.000
151A265SER00.006-0.00817.556-0.028-0.0280.0000.0000.0000.000
152A266GLU-1-0.837-0.91718.315-0.134-0.1340.0000.0000.0000.000
153A267ILE0-0.051-0.01714.891-0.008-0.0080.0000.0000.0000.000
154A268PHE00.008-0.01011.390-0.018-0.0180.0000.0000.0000.000
155A269SER00.0100.01013.478-0.059-0.0590.0000.0000.0000.000
156A270PRO0-0.006-0.01214.829-0.041-0.0410.0000.0000.0000.000
157A271MET0-0.057-0.0219.562-0.035-0.0350.0000.0000.0000.000
158A272LEU0-0.026-0.01610.125-0.116-0.1160.0000.0000.0000.000
159A273PHE00.030-0.00311.886-0.065-0.0650.0000.0000.0000.000
160A274ARG10.7960.8965.3751.7601.7600.0000.0000.0000.000
161A275PHE00.0170.00812.9050.0230.0230.0000.0000.0000.000
162A276SER0-0.015-0.00215.5750.0070.0070.0000.0000.0000.000
163A277ALA0-0.025-0.02517.5590.0260.0260.0000.0000.0000.000
164A278ALA0-0.0150.01720.7250.0100.0100.0000.0000.0000.000
165A279SER00.016-0.00722.4780.0070.0070.0000.0000.0000.000
166A280SER00.0210.00325.072-0.011-0.0110.0000.0000.0000.000
167A281ASP-1-0.773-0.85326.455-0.128-0.1280.0000.0000.0000.000
168A282ASN00.010-0.00224.113-0.011-0.0110.0000.0000.0000.000
169A283THR0-0.033-0.02321.050-0.017-0.0170.0000.0000.0000.000
170A284GLU-1-0.795-0.87822.625-0.131-0.1310.0000.0000.0000.000
171A285ASN0-0.049-0.03724.9920.0010.0010.0000.0000.0000.000
172A286LEU0-0.001-0.00119.750-0.005-0.0050.0000.0000.0000.000
173A287ILE00.0040.00520.163-0.012-0.0120.0000.0000.0000.000
174A288LYS10.8450.92121.6290.1190.1190.0000.0000.0000.000
175A289VAL00.001-0.00321.0660.0040.0040.0000.0000.0000.000
176A290ILE0-0.005-0.00117.1130.0000.0000.0000.0000.0000.000
177A291GLU-1-0.791-0.87520.292-0.114-0.1140.0000.0000.0000.000
178A292ILE00.0100.00422.9130.0090.0090.0000.0000.0000.000
179A293LEU0-0.0050.02019.7680.0050.0050.0000.0000.0000.000
180A294ILE0-0.014-0.00718.2920.0060.0060.0000.0000.0000.000
181A295SER0-0.101-0.06521.5030.0130.0130.0000.0000.0000.000
182A296THR0-0.032-0.03424.4330.0070.0070.0000.0000.0000.000
183A297GLU-1-0.851-0.91720.430-0.172-0.1720.0000.0000.0000.000
184A298TRP0-0.069-0.02223.8730.0100.0100.0000.0000.0000.000