FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 7G81K

Calculation Name: 2V1Y-A-Xray372

Preferred Name: PI3-kinase p85-alpha subunit

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2V1Y

Chain ID: A

ChEMBL ID: CHEMBL2506

UniProt ID: P27986

Base Structure: X-ray

Registration Date: 2023-06-21

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 90
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -690535.737452
FMO2-HF: Nuclear repulsion 652799.456254
FMO2-HF: Total energy -37736.281198
FMO2-MP2: Total energy -37844.73224


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:16:MET)


Summations of interaction energy for fragment #1(A:16:MET)
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.
-13.267-6.4779.47-3.566-12.697-0.014
Interaction energy analysis for fragmet #1(A:16:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.012
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].
3A18PRO0-0.019-0.0143.333-1.843-0.1560.038-0.862-0.8630.000
4A19ARG10.8420.8915.5850.0810.0810.0000.0000.0000.000
5A20ILE0-0.042-0.0232.830-2.039-0.4891.167-0.533-2.184-0.003
6A21LEU00.0310.0115.5580.1010.1010.0000.0000.0000.000
7A22VAL00.005-0.0065.432-0.218-0.2180.0000.0000.0000.000
8A23GLU-1-0.950-0.9727.888-0.271-0.2710.0000.0000.0000.000
9A24CYS0-0.0160.00310.384-0.148-0.1480.0000.0000.0000.000
10A25LEU0-0.001-0.00912.5680.0650.0650.0000.0000.0000.000
11A26LEU00.0440.01815.485-0.013-0.0130.0000.0000.0000.000
12A27PRO00.0100.00718.142-0.001-0.0010.0000.0000.0000.000
13A28ASN0-0.018-0.01920.935-0.001-0.0010.0000.0000.0000.000
14A29GLY0-0.024-0.01821.7650.0150.0150.0000.0000.0000.000
15A30MET0-0.054-0.01220.6830.0020.0020.0000.0000.0000.000
16A31ILE00.0050.00714.594-0.025-0.0250.0000.0000.0000.000
17A32VAL00.0170.00314.9610.0360.0360.0000.0000.0000.000
18A33THR0-0.022-0.00511.965-0.044-0.0440.0000.0000.0000.000
19A34LEU00.0470.02111.2610.0420.0420.0000.0000.0000.000
20A35GLU-1-0.824-0.8698.9420.2620.2620.0000.0000.0000.000
21A36CYS0-0.0180.0036.740-0.119-0.1190.0000.0000.0000.000
22A37LEU00.0390.0186.2850.1590.1590.0000.0000.0000.000
23A38ARG10.9330.9632.348-1.633-0.0552.606-1.219-2.9650.001
24A39GLU-1-0.937-0.9834.2350.8051.1180.0020.024-0.3390.000
25A40ALA0-0.0200.0047.297-0.382-0.3820.0000.0000.0000.000
26A41THR00.0140.0047.9020.0190.0190.0000.0000.0000.000
27A42LEU00.0480.0277.4560.0230.0230.0000.0000.0000.000
28A43ILE00.0360.02010.1870.0160.0160.0000.0000.0000.000
29A44THR0-0.044-0.02112.6140.0280.0280.0000.0000.0000.000
30A45ILE00.0460.0207.2630.0070.0070.0000.0000.0000.000
31A46LYS10.8810.95211.5780.1480.1480.0000.0000.0000.000
32A47HIS00.0200.00914.0680.0070.0070.0000.0000.0000.000
33A48GLU-1-0.942-0.98313.1580.1390.1390.0000.0000.0000.000
34A49LEU0-0.028-0.01113.478-0.008-0.0080.0000.0000.0000.000
35A50PHE00.0270.00715.418-0.006-0.0060.0000.0000.0000.000
36A51LYS10.8200.92618.625-0.029-0.0290.0000.0000.0000.000
37A52GLU-1-0.894-0.95316.8240.0050.0050.0000.0000.0000.000
38A53ALA00.0270.00419.231-0.002-0.0020.0000.0000.0000.000
39A54ARG10.9310.96020.6020.0420.0420.0000.0000.0000.000
40A55LYS10.8660.95421.151-0.006-0.0060.0000.0000.0000.000
41A56TYR0-0.028-0.00118.733-0.004-0.0040.0000.0000.0000.000
42A57PRO0-0.004-0.01523.7330.0030.0030.0000.0000.0000.000
43A58LEU00.0340.00624.943-0.008-0.0080.0000.0000.0000.000
44A59HIS00.0370.03924.720-0.010-0.0100.0000.0000.0000.000
45A60GLN0-0.015-0.01725.688-0.004-0.0040.0000.0000.0000.000
46A61LEU0-0.049-0.02626.5900.0020.0020.0000.0000.0000.000
47A62LEU0-0.061-0.01021.441-0.011-0.0110.0000.0000.0000.000
48A63GLN00.0340.01924.4480.0190.0190.0000.0000.0000.000
49A64ASP-1-0.810-0.89623.682-0.084-0.0840.0000.0000.0000.000
50A65GLU-1-0.880-0.95218.595-0.079-0.0790.0000.0000.0000.000
51A66SER0-0.121-0.09519.137-0.026-0.0260.0000.0000.0000.000
52A67SER0-0.037-0.01120.995-0.006-0.0060.0000.0000.0000.000
53A68TYR0-0.036-0.01717.956-0.006-0.0060.0000.0000.0000.000
54A69ILE00.0280.02715.1680.0050.0050.0000.0000.0000.000
55A70PHE0-0.010-0.00810.714-0.014-0.0140.0000.0000.0000.000
56A71VAL0-0.005-0.00512.550-0.001-0.0010.0000.0000.0000.000
57A72SER0-0.038-0.0258.065-0.069-0.0690.0000.0000.0000.000
58A73VAL0-0.0020.0069.5790.1750.1750.0000.0000.0000.000
59A74THR00.0610.0408.403-0.320-0.3200.0000.0000.0000.000
60A75GLN0-0.049-0.0466.232-0.298-0.2980.0000.0000.0000.000
61A76GLU-1-0.937-0.9769.630-0.729-0.7290.0000.0000.0000.000
62A77ALA0-0.035-0.01312.3230.0920.0920.0000.0000.0000.000
63A78GLU-1-0.901-0.92913.385-0.375-0.3750.0000.0000.0000.000
64A79ARG10.8960.94712.8670.3050.3050.0000.0000.0000.000
65A80GLU-1-0.858-0.94511.059-0.759-0.7590.0000.0000.0000.000
66A81GLU-1-0.918-0.97012.488-0.406-0.4060.0000.0000.0000.000
67A82PHE0-0.035-0.0278.3070.0080.0080.0000.0000.0000.000
68A83PHE00.0630.01312.8130.0410.0410.0000.0000.0000.000
69A84ASP-1-0.881-0.91113.853-0.169-0.1690.0000.0000.0000.000
70A85GLU-1-0.896-0.97012.338-0.300-0.3000.0000.0000.0000.000
71A86THR0-0.067-0.05312.6470.0600.0600.0000.0000.0000.000
72A87ARG10.9050.9679.2480.7670.7670.0000.0000.0000.000
73A88ARG10.8840.9397.606-0.458-0.4580.0000.0000.0000.000
74A89LEU00.0340.0202.396-1.448-0.5211.370-0.414-1.883-0.001
75A90CYS0-0.042-0.0492.668-5.852-3.9284.218-2.986-3.157-0.010
76A91ASP-1-0.869-0.9193.7780.402-1.8790.0002.564-0.284-0.001
77A92LEU0-0.052-0.0284.165-0.0730.041-0.001-0.007-0.1060.000
78A93ARG10.8830.9614.6131.1731.243-0.001-0.002-0.0670.000
79A94LEU00.0140.0143.147-0.0370.5400.072-0.103-0.5470.000
80A95PHE0-0.015-0.0024.962-0.346-0.279-0.0010.000-0.0670.000
81A96GLN0-0.046-0.0346.3700.3890.3890.0000.0000.0000.000
82A97PRO00.0110.0133.729-0.708-0.4810.001-0.026-0.2020.000
83A98PHE00.0220.0094.9760.5910.628-0.001-0.002-0.0330.000
84A99LEU00.0000.0046.864-0.279-0.2790.0000.0000.0000.000
85A100LYS10.9400.9739.9330.5050.5050.0000.0000.0000.000
86A101VAL0-0.0070.00413.591-0.025-0.0250.0000.0000.0000.000
87A102ILE0-0.063-0.03515.7210.0300.0300.0000.0000.0000.000
88A103GLU-1-0.899-0.94918.638-0.155-0.1550.0000.0000.0000.000
89A104PRO0-0.009-0.00719.2770.0010.0010.0000.0000.0000.000
90A105VAL0-0.040-0.00221.5790.0100.0100.0000.0000.0000.000