FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LNQR9

Calculation Name: 3CUQ-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CUQ

Chain ID: D

ChEMBL ID:

UniProt ID: Q96H20

Base Structure: X-ray

Registration Date: 2023-09-22

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 97
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -781988.080495
FMO2-HF: Nuclear repulsion 741057.722543
FMO2-HF: Total energy -40930.357952
FMO2-MP2: Total energy -41048.956635


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(D:5:PHE)


Summations of interaction energy for fragment #1(D:5:PHE)
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.
-20.232-16.74313.313-6.171-10.630.058
Interaction energy analysis for fragmet #1(D:5:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.015
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].
3D7TRP0-0.028-0.0183.849-0.4580.757-0.005-0.446-0.7640.002
4D8PRO00.0580.0345.8380.3500.3500.0000.0000.0000.000
5D9TRP00.0320.0008.180-0.078-0.0780.0000.0000.0000.000
6D10GLN00.0430.02011.409-0.031-0.0310.0000.0000.0000.000
7D11TYR0-0.024-0.0369.049-0.014-0.0140.0000.0000.0000.000
8D12ARG10.9440.9669.7070.6220.6220.0000.0000.0000.000
9D13PHE00.0050.00013.8260.0330.0330.0000.0000.0000.000
10D14PRO00.0490.01016.4360.0140.0140.0000.0000.0000.000
11D15PRO0-0.011-0.01118.5830.0040.0040.0000.0000.0000.000
12D16PHE0-0.0030.01411.1570.0260.0260.0000.0000.0000.000
13D17PHE0-0.003-0.00812.4800.0230.0230.0000.0000.0000.000
14D18THR0-0.0090.00117.4120.0040.0040.0000.0000.0000.000
15D19LEU0-0.0120.03220.6330.0070.0070.0000.0000.0000.000
16D20GLN00.009-0.02421.164-0.002-0.0020.0000.0000.0000.000
17D21PRO00.0280.01223.5090.0110.0110.0000.0000.0000.000
18D22ASN00.0340.03726.3210.0100.0100.0000.0000.0000.000
19D23VAL00.0610.01725.3610.0020.0020.0000.0000.0000.000
20D24ASP-1-0.817-0.90024.9440.0560.0560.0000.0000.0000.000
21D25THR0-0.086-0.05421.9440.0080.0080.0000.0000.0000.000
22D26ARG10.9250.95120.923-0.026-0.0260.0000.0000.0000.000
23D27GLN00.0310.03620.1470.0060.0060.0000.0000.0000.000
24D28LYS10.9820.98717.257-0.058-0.0580.0000.0000.0000.000
25D29GLN0-0.056-0.03116.4670.0310.0310.0000.0000.0000.000
26D30LEU00.023-0.01115.5440.0170.0170.0000.0000.0000.000
27D31ALA0-0.017-0.00315.5130.0340.0340.0000.0000.0000.000
28D32ALA0-0.021-0.01312.2460.0780.0780.0000.0000.0000.000
29D33TRP0-0.006-0.00710.6270.0800.0800.0000.0000.0000.000
30D34CYS0-0.027-0.00210.9460.0300.0300.0000.0000.0000.000
31D35SER0-0.042-0.0399.2770.1820.1820.0000.0000.0000.000
32D36LEU00.0210.0205.4160.4070.4070.0000.0000.0000.000
33D37VAL00.0210.0116.1150.2070.2070.0000.0000.0000.000
34D38LEU00.0080.0078.055-0.069-0.0690.0000.0000.0000.000
35D39SER0-0.049-0.0093.7801.3861.8930.063-0.205-0.3650.000
36D40PHE00.027-0.0023.129-1.2800.1220.143-0.587-0.959-0.004
37D41CYS0-0.038-0.0154.266-0.706-0.638-0.001-0.001-0.0650.000
38D42ARG10.9160.9792.055-20.683-20.80813.110-4.844-8.1410.060
39D43LEU0-0.061-0.0373.677-0.0580.3450.004-0.087-0.3190.000
40D44HIS00.0330.0075.2250.1280.147-0.001-0.001-0.0170.000
41D45LYS10.8930.9767.589-0.805-0.8050.0000.0000.0000.000
42D46GLN0-0.004-0.0169.4720.0230.0230.0000.0000.0000.000
43D47SER0-0.001-0.01010.8050.0020.0020.0000.0000.0000.000
44D48SER0-0.077-0.05212.9560.0050.0050.0000.0000.0000.000
45D49MET0-0.0100.01912.325-0.039-0.0390.0000.0000.0000.000
46D50THR00.0680.04817.5050.0150.0150.0000.0000.0000.000
47D51VAL0-0.017-0.01618.128-0.011-0.0110.0000.0000.0000.000
48D52MET00.047-0.01918.787-0.015-0.0150.0000.0000.0000.000
49D53GLU-1-0.923-0.96016.557-0.064-0.0640.0000.0000.0000.000
50D54ALA00.0200.00714.047-0.036-0.0360.0000.0000.0000.000
51D55GLN0-0.045-0.00414.631-0.030-0.0300.0000.0000.0000.000
52D56GLU-1-0.897-0.94616.577-0.212-0.2120.0000.0000.0000.000
53D57SER00.0050.01210.976-0.082-0.0820.0000.0000.0000.000
54D58PRO00.0560.0098.7230.0040.0040.0000.0000.0000.000
55D59LEU0-0.0530.0167.814-0.094-0.0940.0000.0000.0000.000
56D60PHE00.018-0.0068.9190.0990.0990.0000.0000.0000.000
57D61ASN0-0.035-0.01812.2560.0360.0360.0000.0000.0000.000
58D62ASN00.0090.01912.600-0.067-0.0670.0000.0000.0000.000
59D63VAL00.0390.01213.8240.0450.0450.0000.0000.0000.000
60D64LYS10.9210.96315.4360.3710.3710.0000.0000.0000.000
61D65LEU0-0.0350.00215.3740.0330.0330.0000.0000.0000.000
62D66GLN00.025-0.00517.6220.0210.0210.0000.0000.0000.000
63D67ARG10.9010.95218.0970.1480.1480.0000.0000.0000.000
64D68LYS11.0451.03316.5110.1200.1200.0000.0000.0000.000
65D69LEU0-0.010-0.00414.6190.0220.0220.0000.0000.0000.000
66D70PRO0-0.0040.00917.5490.0020.0020.0000.0000.0000.000
67D71VAL00.0940.03020.3760.0100.0100.0000.0000.0000.000
68D72GLU-1-0.933-0.96421.641-0.001-0.0010.0000.0000.0000.000
69D73SER0-0.011-0.02519.8460.0130.0130.0000.0000.0000.000
70D74ILE0-0.0280.00416.3440.0160.0160.0000.0000.0000.000
71D75GLN00.034-0.00118.6690.0310.0310.0000.0000.0000.000
72D76ILE0-0.049-0.00521.0140.0130.0130.0000.0000.0000.000
73D77VAL00.000-0.00714.4160.0170.0170.0000.0000.0000.000
74D78LEU00.0340.01315.8800.0340.0340.0000.0000.0000.000
75D79GLU-1-0.850-0.89618.3100.1260.1260.0000.0000.0000.000
76D80GLU-1-0.965-1.00418.4710.1390.1390.0000.0000.0000.000
77D81LEU0-0.021-0.01213.0100.0320.0320.0000.0000.0000.000
78D82ARG10.8820.93617.149-0.103-0.1030.0000.0000.0000.000
79D83LYS10.8480.94319.958-0.114-0.1140.0000.0000.0000.000
80D84LYS10.9510.97915.431-0.352-0.3520.0000.0000.0000.000
81D85GLY00.0000.00518.9000.0250.0250.0000.0000.0000.000
82D86ASN0-0.008-0.03913.116-0.005-0.0050.0000.0000.0000.000
83D87LEU0-0.010-0.01315.719-0.006-0.0060.0000.0000.0000.000
84D88GLU-1-0.922-0.94318.4280.1490.1490.0000.0000.0000.000
85D89TRP0-0.048-0.00821.238-0.008-0.0080.0000.0000.0000.000
86D90LEU00.0150.00821.5450.0020.0020.0000.0000.0000.000
87D91ASP-1-0.842-0.92425.1210.0420.0420.0000.0000.0000.000
88D92LYS10.9320.94727.970-0.062-0.0620.0000.0000.0000.000
89D93SER0-0.0080.00829.893-0.001-0.0010.0000.0000.0000.000
90D94LYS10.8880.95925.748-0.058-0.0580.0000.0000.0000.000
91D95SER0-0.004-0.03224.682-0.010-0.0100.0000.0000.0000.000
92D96SER00.0490.03021.588-0.002-0.0020.0000.0000.0000.000
93D97PHE0-0.044-0.02415.0430.0090.0090.0000.0000.0000.000
94D98LEU00.0500.03317.283-0.005-0.0050.0000.0000.0000.000
95D99ILE0-0.021-0.00411.3440.0110.0110.0000.0000.0000.000
96D100MET0-0.0020.00813.6650.0010.0010.0000.0000.0000.000
97D101TRP00.0230.0246.6940.0410.0410.0000.0000.0000.000