FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 8J19Y

Calculation Name: 3KU7-A-Xray313

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3KU7

Chain ID: A

ChEMBL ID:
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UniProt ID: O25099

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 66
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -354573.313044
FMO2-HF: Nuclear repulsion 328679.215375
FMO2-HF: Total energy -25894.097669
FMO2-MP2: Total energy -25969.72359


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:12:ACE )


Summations of interaction energy for fragment #1(A:12:ACE )
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.
1.7432.627-0.006-0.42-0.4580
Interaction energy analysis for fragmet #1(A:12:ACE )
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 : 0.002
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].
3A14ALA 0-0.017-0.0033.8421.0881.894-0.006-0.408-0.3920.000
4A15THR 0-0.017-0.0345.9680.1150.1150.0000.0000.0000.000
5A16ALA 00.0180.0334.0910.1400.2180.000-0.012-0.0660.000
6A17THR 0-0.030-0.0125.4260.2970.2970.0000.0000.0000.000
7A18ASP -1-0.871-0.9237.700-0.009-0.0090.0000.0000.0000.000
8A19ARG 10.9050.9525.392-0.198-0.1980.0000.0000.0000.000
9A20LEU 00.0060.01112.069-0.057-0.0570.0000.0000.0000.000
10A21LYS 10.8710.93814.940-0.061-0.0610.0000.0000.0000.000
11A22LEU 00.0000.00617.081-0.019-0.0190.0000.0000.0000.000
12A23ILE 00.0170.00820.0580.0070.0070.0000.0000.0000.000
13A24LEU 0-0.018-0.00922.743-0.007-0.0070.0000.0000.0000.000
14A25ALA 0-0.0140.00726.2460.0020.0020.0000.0000.0000.000
15A26LYS 10.8390.92728.227-0.039-0.0390.0000.0000.0000.000
16A27GLU -1-0.892-0.93631.6870.0160.0160.0000.0000.0000.000
17A28ARG 10.9730.98832.064-0.034-0.0340.0000.0000.0000.000
18A29THR 0-0.031-0.02133.7060.0020.0020.0000.0000.0000.000
19A30LEU 00.004-0.00436.0020.0010.0010.0000.0000.0000.000
20A31ASN 00.0050.00736.9890.0040.0040.0000.0000.0000.000
21A32LEU 0-0.015-0.01134.5920.0020.0020.0000.0000.0000.000
22A33PRO 00.0550.01636.0410.0030.0030.0000.0000.0000.000
23A34TYR 00.0470.02634.5650.0020.0020.0000.0000.0000.000
24A35MET 00.0440.03529.3640.0020.0020.0000.0000.0000.000
25A36GLU -1-0.853-0.93329.0670.0840.0840.0000.0000.0000.000
26A37GLU -1-0.924-0.97130.3050.0580.0580.0000.0000.0000.000
27A38MET 00.0180.00631.2350.0010.0010.0000.0000.0000.000
28A39ARG 10.8520.94925.053-0.087-0.0870.0000.0000.0000.000
29A40LYS 10.9260.94926.921-0.075-0.0750.0000.0000.0000.000
30A41GLU -1-0.867-0.92927.7290.0590.0590.0000.0000.0000.000
31A42ILE 0-0.020-0.00325.1380.0010.0010.0000.0000.0000.000
32A43ILE 0-0.024-0.02022.0850.0040.0040.0000.0000.0000.000
33A44ALA 00.0110.01124.3120.0060.0060.0000.0000.0000.000
34A45VAL 0-0.016-0.01526.4890.0010.0010.0000.0000.0000.000
35A46ILE 00.0360.01920.624-0.001-0.0010.0000.0000.0000.000
36A47GLN 0-0.017-0.01421.347-0.006-0.0060.0000.0000.0000.000
37A48LYS 10.8950.98923.043-0.059-0.0590.0000.0000.0000.000
38A49TYR 0-0.050-0.05224.737-0.004-0.0040.0000.0000.0000.000
39A50THR 0-0.025-0.02519.2370.0030.0030.0000.0000.0000.000
40A51LYS 10.8680.93819.781-0.075-0.0750.0000.0000.0000.000
41A52SER 0-0.006-0.00516.1400.0100.0100.0000.0000.0000.000
42A53SER 0-0.019-0.01917.232-0.012-0.0120.0000.0000.0000.000
43A54ASP -1-0.936-0.93512.2410.4940.4940.0000.0000.0000.000
44A55ILE 00.004-0.02215.456-0.012-0.0120.0000.0000.0000.000
45A56HIS 0-0.0050.00013.719-0.018-0.0180.0000.0000.0000.000
46A57PHE 00.0090.00016.874-0.020-0.0200.0000.0000.0000.000
47A58LYS 10.9350.99014.939-0.176-0.1760.0000.0000.0000.000
48A59THR 00.010-0.01621.011-0.006-0.0060.0000.0000.0000.000
49A60LEU 00.0050.01423.852-0.005-0.0050.0000.0000.0000.000
50A61ASP -1-0.810-0.89920.5840.0400.0400.0000.0000.0000.000
51A62SER 0-0.085-0.03921.624-0.003-0.0030.0000.0000.0000.000
52A63ASN 0-0.051-0.03323.452-0.010-0.0100.0000.0000.0000.000
53A64GLN 00.0080.00125.8620.0000.0000.0000.0000.0000.000
54A65SER 0-0.016-0.01329.5770.0030.0030.0000.0000.0000.000
55A66VAL 0-0.0080.00128.8310.0010.0010.0000.0000.0000.000
56A67GLU -1-0.942-0.98327.9500.0460.0460.0000.0000.0000.000
57A68THR 00.006-0.02922.543-0.004-0.0040.0000.0000.0000.000
58A69ILE 0-0.0060.01323.6350.0070.0070.0000.0000.0000.000
59A70GLU -1-0.907-0.95018.0160.0770.0770.0000.0000.0000.000
60A71VAL 00.023-0.01118.8350.0130.0130.0000.0000.0000.000
61A72GLU -1-0.910-0.96313.2910.1560.1560.0000.0000.0000.000
62A73ILE 00.005-0.00515.1320.0210.0210.0000.0000.0000.000
63A74ILE 00.0320.02410.239-0.014-0.0140.0000.0000.0000.000
64A75LEU 0-0.040-0.02512.850-0.027-0.0270.0000.0000.0000.000
65A76PRO 0-0.032-0.02113.0350.0490.0490.0000.0000.0000.000
66A77NME 00.0190.03012.861-0.034-0.0340.0000.0000.0000.000