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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: YVY72

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 OptHSide
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 -2045995.658144
FMO2-HF: Nuclear repulsion 1973484.517647
FMO2-HF: Total energy -72511.140497
FMO2-MP2: Total energy -72724.658159


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.
-14.295-2.5818.14-5.687-14.165-0.03
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 : -0.041 / q_NPA : -0.022
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-1-0.739-0.8573.150-4.911-2.9820.132-0.998-1.064-0.002
4A118LEU00.0030.0055.5910.4490.4490.0000.0000.0000.000
5A119ALA0-0.074-0.0626.8250.3370.3370.0000.0000.0000.000
6A120GLU-1-0.881-0.9336.974-1.474-1.4740.0000.0000.0000.000
7A121GLN0-0.062-0.0132.9000.0041.1310.377-0.429-1.075-0.003
8A122PHE0-0.003-0.0077.2770.2410.2410.0000.0000.0000.000
9A123ALA0-0.006-0.00210.901-0.085-0.0850.0000.0000.0000.000
10A124PRO00.000-0.04514.1570.0400.0400.0000.0000.0000.000
11A125PRO0-0.0360.02817.303-0.002-0.0020.0000.0000.0000.000
12A126ASP-1-0.892-0.92114.191-0.219-0.2190.0000.0000.0000.000
13A127ILE0-0.005-0.02915.270-0.035-0.0350.0000.0000.0000.000
14A128ALA0-0.024-0.01211.145-0.021-0.0210.0000.0000.0000.000
15A129PRO00.0330.0316.9450.0630.0630.0000.0000.0000.000
16A130PRO00.0930.0328.3830.0870.0870.0000.0000.0000.000
17A131LEU0-0.0190.0033.123-0.3940.0550.087-0.091-0.4450.000
18A132LEU00.0150.0086.7300.0740.0740.0000.0000.0000.000
19A133ILE00.0160.0078.0820.0350.0350.0000.0000.0000.000
20A134LYS10.8800.9459.187-0.230-0.2300.0000.0000.0000.000
21A135LEU0-0.014-0.0126.2290.0090.0090.0000.0000.0000.000
22A136VAL0-0.037-0.01410.652-0.007-0.0070.0000.0000.0000.000
23A137GLU-1-0.896-0.95613.043-0.034-0.0340.0000.0000.0000.000
24A138ALA0-0.030-0.01113.9630.0050.0050.0000.0000.0000.000
25A139ILE0-0.021-0.00811.587-0.004-0.0040.0000.0000.0000.000
26A140GLU-1-0.817-0.87715.771-0.098-0.0980.0000.0000.0000.000
27A141LYS10.8300.92117.593-0.043-0.0430.0000.0000.0000.000
28A142LYS10.8150.88917.260-0.101-0.1010.0000.0000.0000.000
29A143GLY00.0080.00119.4240.0040.0040.0000.0000.0000.000
30A144LEU0-0.0020.01020.355-0.009-0.0090.0000.0000.0000.000
31A145GLU-1-0.893-0.94822.278-0.020-0.0200.0000.0000.0000.000
32A146CYM-1-0.809-0.83921.2890.0140.0140.0000.0000.0000.000
33A147SER0-0.018-0.01422.595-0.006-0.0060.0000.0000.0000.000
34A148THR0-0.056-0.05922.2540.0000.0000.0000.0000.0000.000
35A149LEU00.0440.01815.9170.0030.0030.0000.0000.0000.000
36A150TYR0-0.012-0.01112.345-0.020-0.0200.0000.0000.0000.000
37A151ARG10.8530.92416.5730.0310.0310.0000.0000.0000.000
38A152THR0-0.020-0.00118.0780.0070.0070.0000.0000.0000.000
39A153GLN0-0.090-0.03714.418-0.016-0.0160.0000.0000.0000.000
40A154SER0-0.070-0.05314.3500.0100.0100.0000.0000.0000.000
41A155SER00.017-0.01016.948-0.009-0.0090.0000.0000.0000.000
42A156SER0-0.028-0.01813.4120.0020.0020.0000.0000.0000.000
43A157ASN00.0290.02914.106-0.038-0.0380.0000.0000.0000.000
44A158LEU00.045-0.0069.4070.0440.0440.0000.0000.0000.000
45A159ALA0-0.048-0.0169.186-0.019-0.0190.0000.0000.0000.000
46A160GLU-1-0.816-0.89510.3050.4470.4470.0000.0000.0000.000
47A161LEU0-0.016-0.0208.2260.0540.0540.0000.0000.0000.000
48A162ARG10.8030.8535.319-0.874-0.8740.0000.0000.0000.000
49A163GLN0-0.037-0.0175.8390.3530.3530.0000.0000.0000.000
50A164LEU00.0130.0097.889-0.046-0.0460.0000.0000.0000.000
51A165LEU0-0.063-0.0062.212-1.404-0.4181.364-0.500-1.850-0.001
52A166ASP-1-0.844-0.9513.6550.4981.0090.019-0.201-0.329-0.001
53A167CYS0-0.0190.0174.541-0.108-0.010-0.001-0.006-0.0910.000
54A168ASP-1-0.965-0.9956.2510.3150.3150.0000.0000.0000.000
55A169THR0-0.052-0.0649.9210.0540.0540.0000.0000.0000.000
56A170PRO0-0.0280.0269.9370.0770.0770.0000.0000.0000.000
57A171SER0-0.023-0.0048.554-0.035-0.0350.0000.0000.0000.000
58A172VAL0-0.0080.00010.576-0.047-0.0470.0000.0000.0000.000
59A173ASP-1-0.828-0.89512.5430.1650.1650.0000.0000.0000.000
60A174LEU00.031-0.0099.452-0.016-0.0160.0000.0000.0000.000
61A175GLU-1-0.769-0.90313.5560.0500.0500.0000.0000.0000.000
62A176MET0-0.070-0.02116.917-0.013-0.0130.0000.0000.0000.000
63A177ILE0-0.050-0.01013.0030.0040.0040.0000.0000.0000.000
64A178ASP-1-0.772-0.89816.2010.0870.0870.0000.0000.0000.000
65A179VAL00.0300.00815.9160.0130.0130.0000.0000.0000.000
66A180HIS10.8720.92715.372-0.058-0.0580.0000.0000.0000.000
67A181VAL00.0440.02512.589-0.003-0.0030.0000.0000.0000.000
68A182LEU0-0.0120.00611.2880.0350.0350.0000.0000.0000.000
69A183ALA0-0.012-0.01110.473-0.011-0.0110.0000.0000.0000.000
70A184ASP-1-0.763-0.86011.0700.0510.0510.0000.0000.0000.000
71A185ALA00.0020.0047.555-0.014-0.0140.0000.0000.0000.000
72A186PHE0-0.019-0.0126.0440.0340.0340.0000.0000.0000.000
73A187LYS10.9120.9516.859-0.042-0.0420.0000.0000.0000.000
74A188ARG10.8440.9205.183-0.063-0.0630.0000.0000.0000.000
75A189TYR00.035-0.0082.316-1.916-1.0543.642-1.214-3.290-0.003
76A190LEU00.0000.0002.975-1.575-1.0050.2890.021-0.879-0.006
77A191LEU0-0.043-0.0175.682-0.326-0.3260.0000.0000.0000.000
78A192ASP-1-0.752-0.8312.538-0.6500.5330.626-0.398-1.4100.001
79A193LEU0-0.0360.0082.647-6.829-3.6661.539-1.734-2.967-0.015
80A194PRO00.0220.0442.9880.9251.6690.067-0.134-0.6770.000
81A195ASN0-0.047-0.0295.2390.9631.055-0.001-0.003-0.0880.000
82A196PRO0-0.025-0.0197.599-0.268-0.2680.0000.0000.0000.000
83A197VAL00.0380.0098.5670.0220.0220.0000.0000.0000.000
84A198ILE0-0.023-0.00510.4710.0770.0770.0000.0000.0000.000
85A199PRO00.0270.01812.6770.0020.0020.0000.0000.0000.000
86A200ALA00.0610.01013.7610.0910.0910.0000.0000.0000.000
87A201ALA00.0110.00615.7410.0630.0630.0000.0000.0000.000
88A202VAL00.0320.02317.3260.0460.0460.0000.0000.0000.000
89A203TYR00.0260.00617.2850.0460.0460.0000.0000.0000.000
90A204SER00.007-0.00219.1850.0430.0430.0000.0000.0000.000
91A205GLU-1-0.928-0.96321.523-0.245-0.2450.0000.0000.0000.000
92A206MET0-0.068-0.01421.3390.0250.0250.0000.0000.0000.000
93A207ILE0-0.0070.01022.5570.0240.0240.0000.0000.0000.000
94A208SER0-0.007-0.00625.2270.0140.0140.0000.0000.0000.000
95A209LEU00.0070.00427.0100.0130.0130.0000.0000.0000.000
96A210ALA0-0.044-0.00627.5810.0100.0100.0000.0000.0000.000
97A211PRO0-0.025-0.01929.3770.0090.0090.0000.0000.0000.000
98A212GLU-1-0.970-0.98232.308-0.143-0.1430.0000.0000.0000.000
99A213VAL0-0.092-0.03129.3720.0020.0020.0000.0000.0000.000
100A214GLN00.000-0.00832.682-0.001-0.0010.0000.0000.0000.000
101A215SER0-0.069-0.06333.5790.0060.0060.0000.0000.0000.000
102A216SER00.0480.00829.365-0.008-0.0080.0000.0000.0000.000
103A217GLU-1-0.862-0.92729.264-0.168-0.1680.0000.0000.0000.000
104A218GLU-1-0.820-0.87229.398-0.139-0.1390.0000.0000.0000.000
105A219TYR00.005-0.01025.096-0.015-0.0150.0000.0000.0000.000
106A220ILE00.0270.00124.595-0.022-0.0220.0000.0000.0000.000
107A221GLN0-0.074-0.06124.740-0.030-0.0300.0000.0000.0000.000
108A222LEU00.0040.01225.610-0.011-0.0110.0000.0000.0000.000
109A223LEU00.0540.03118.713-0.021-0.0210.0000.0000.0000.000
110A224LYS10.8640.92721.3250.1740.1740.0000.0000.0000.000
111A225LYS10.9320.96722.4030.1820.1820.0000.0000.0000.000
112A226LEU00.0170.00721.378-0.011-0.0110.0000.0000.0000.000
113A227ILE0-0.036-0.01414.870-0.021-0.0210.0000.0000.0000.000
114A228ARG10.8980.95518.3700.2410.2410.0000.0000.0000.000
115A229SER00.0080.01820.6980.0280.0280.0000.0000.0000.000
116A230PRO00.026-0.01220.491-0.027-0.0270.0000.0000.0000.000
117A231SER0-0.055-0.01819.9240.0070.0070.0000.0000.0000.000
118A232ILE0-0.0370.00015.116-0.060-0.0600.0000.0000.0000.000
119A233PRO00.0180.01313.1610.0420.0420.0000.0000.0000.000
120A234HIS00.0510.00815.123-0.042-0.0420.0000.0000.0000.000
121A235GLN00.0490.02110.8140.0730.0730.0000.0000.0000.000
122A236TYR0-0.047-0.0299.4860.0330.0330.0000.0000.0000.000
123A237TRP00.0350.01512.7610.0420.0420.0000.0000.0000.000
124A238LEU0-0.037-0.01014.1700.0370.0370.0000.0000.0000.000
125A239THR00.014-0.0098.4000.0310.0310.0000.0000.0000.000
126A240LEU00.002-0.00511.6930.0470.0470.0000.0000.0000.000
127A241GLN0-0.039-0.03513.8170.0720.0720.0000.0000.0000.000
128A242TYR00.0210.02611.6000.0420.0420.0000.0000.0000.000
129A243LEU0-0.017-0.0259.5780.0510.0510.0000.0000.0000.000
130A244LEU0-0.0020.01113.7940.0380.0380.0000.0000.0000.000
131A245LYS10.9290.96417.3650.2420.2420.0000.0000.0000.000
132A246HIS10.8080.90413.8480.1510.1510.0000.0000.0000.000
133A247PHE0-0.001-0.02213.2640.0260.0260.0000.0000.0000.000
134A248PHE00.0530.02918.4380.0190.0190.0000.0000.0000.000
135A249LYS10.8940.93719.8980.1030.1030.0000.0000.0000.000
136A250LEU0-0.019-0.01617.1350.0140.0140.0000.0000.0000.000
137A251SER0-0.0300.01021.5780.0100.0100.0000.0000.0000.000
138A252GLN0-0.044-0.03324.2630.0130.0130.0000.0000.0000.000
139A253THR0-0.054-0.02425.1110.0090.0090.0000.0000.0000.000
140A254SER0-0.0010.01026.0380.0060.0060.0000.0000.0000.000
141A255SER0-0.049-0.02426.9550.0030.0030.0000.0000.0000.000
142A256LYS10.8820.93327.6960.0240.0240.0000.0000.0000.000
143A257ASN00.0300.00422.850-0.001-0.0010.0000.0000.0000.000
144A258LEU0-0.017-0.01524.239-0.001-0.0010.0000.0000.0000.000
145A259LEU0-0.066-0.02819.462-0.006-0.0060.0000.0000.0000.000
146A260ASN00.0640.04123.357-0.013-0.0130.0000.0000.0000.000
147A261ALA00.0510.00522.616-0.006-0.0060.0000.0000.0000.000
148A262ARG10.7060.80922.4610.1180.1180.0000.0000.0000.000
149A263VAL00.0240.02321.563-0.009-0.0090.0000.0000.0000.000
150A264LEU0-0.007-0.01417.765-0.007-0.0070.0000.0000.0000.000
151A265SER0-0.027-0.01217.881-0.033-0.0330.0000.0000.0000.000
152A266GLU-1-0.827-0.92218.591-0.141-0.1410.0000.0000.0000.000
153A267ILE0-0.072-0.01815.379-0.006-0.0060.0000.0000.0000.000
154A268PHE00.000-0.03211.553-0.012-0.0120.0000.0000.0000.000
155A269SER00.0270.02613.677-0.068-0.0680.0000.0000.0000.000
156A270PRO00.0170.00715.081-0.052-0.0520.0000.0000.0000.000
157A271MET0-0.059-0.0359.763-0.044-0.0440.0000.0000.0000.000
158A272LEU0-0.033-0.01310.137-0.142-0.1420.0000.0000.0000.000
159A273PHE00.0270.00611.966-0.078-0.0780.0000.0000.0000.000
160A274ARG10.7890.8825.9161.8541.8540.0000.0000.0000.000
161A275PHE00.0100.00113.1610.0270.0270.0000.0000.0000.000
162A276SER0-0.0100.01215.9910.0030.0030.0000.0000.0000.000
163A277ALA0-0.024-0.03117.7290.0270.0270.0000.0000.0000.000
164A278ALA00.0070.02520.6520.0080.0080.0000.0000.0000.000
165A279SER00.0370.01422.4960.0090.0090.0000.0000.0000.000
166A280SER00.0460.01625.179-0.012-0.0120.0000.0000.0000.000
167A281ASP-1-0.803-0.88326.698-0.135-0.1350.0000.0000.0000.000
168A282ASN0-0.0010.00124.327-0.012-0.0120.0000.0000.0000.000
169A283THR0-0.039-0.02721.347-0.021-0.0210.0000.0000.0000.000
170A284GLU-1-0.810-0.88523.024-0.148-0.1480.0000.0000.0000.000
171A285ASN0-0.056-0.04825.3860.0020.0020.0000.0000.0000.000
172A286LEU0-0.015-0.00619.947-0.007-0.0070.0000.0000.0000.000
173A287ILE00.0080.01320.400-0.015-0.0150.0000.0000.0000.000
174A288LYS10.8820.94421.9250.1320.1320.0000.0000.0000.000
175A289VAL00.0070.00521.6740.0030.0030.0000.0000.0000.000
176A290ILE0-0.017-0.00717.417-0.002-0.0020.0000.0000.0000.000
177A291GLU-1-0.792-0.88420.722-0.127-0.1270.0000.0000.0000.000
178A292ILE0-0.013-0.00923.1410.0110.0110.0000.0000.0000.000
179A293LEU0-0.005-0.00120.2560.0050.0050.0000.0000.0000.000
180A294ILE0-0.0230.00018.8140.0040.0040.0000.0000.0000.000
181A295SER0-0.059-0.04021.9130.0130.0130.0000.0000.0000.000
182A296THR0-0.048-0.03525.1620.0070.0070.0000.0000.0000.000
183A297GLU-1-0.837-0.91020.813-0.210-0.2100.0000.0000.0000.000
184A298TRP0-0.099-0.03024.2940.0100.0100.0000.0000.0000.000