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: 3N24L

Calculation Name: 1NO1-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NO1

Chain ID: A

ChEMBL ID:

UniProt ID: Q38151

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 68
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -410394.969553
FMO2-HF: Nuclear repulsion 383311.92384
FMO2-HF: Total energy -27083.045713
FMO2-MP2: Total energy -27162.529889


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:1:HCS )


Summations of interaction energy for fragment #1(A:1:HCS )
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.
-31.275-21.42620.286-11.639-18.499-0.085
Interaction energy analysis for fragmet #1(A:1:HCS )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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].
3A3GLU -1-0.787-0.9053.597-0.6061.1830.012-1.010-0.7920.004
4A4LYS 10.9020.9686.074-0.895-0.8950.0000.0000.0000.000
5A5ASP -1-0.843-0.9462.2310.8452.0061.894-1.049-2.006-0.004
6A6VAL 00.0030.0063.2310.3591.6080.420-0.378-1.2910.002
7A7VAL 0-0.059-0.0384.724-1.292-1.2280.0080.024-0.0960.000
8A8GLN 0-0.049-0.0236.718-0.715-0.7150.0000.0000.0000.000
9A9ILE 00.0700.0493.520-1.086-0.6220.059-0.101-0.4230.000
10A10LEU 0-0.026-0.0246.768-0.599-0.5990.0000.0000.0000.000
11A11LYS 10.9230.9669.359-0.765-0.7650.0000.0000.0000.000
12A12ALA 00.0740.04610.067-0.149-0.1490.0000.0000.0000.000
13A13VAL 0-0.028-0.0079.866-0.164-0.1640.0000.0000.0000.000
14A14SER 0-0.047-0.03612.515-0.091-0.0910.0000.0000.0000.000
15A15GLU -1-0.933-0.96814.4200.5470.5470.0000.0000.0000.000
16A16PHE 00.0080.00413.592-0.064-0.0640.0000.0000.0000.000
17A17TYR 0-0.097-0.04315.376-0.056-0.0560.0000.0000.0000.000
18A18PRO 00.0460.01318.682-0.014-0.0140.0000.0000.0000.000
19A19GLY 0-0.031-0.01821.054-0.022-0.0220.0000.0000.0000.000
20A20ARG 10.8940.94920.672-0.074-0.0740.0000.0000.0000.000
21A21PHE 00.0230.00812.220-0.024-0.0240.0000.0000.0000.000
22A22GLN 0-0.043-0.02217.6580.0560.0560.0000.0000.0000.000
23A23PRO 0-0.033-0.01314.229-0.030-0.0300.0000.0000.0000.000
24A24ASP -1-0.882-0.93017.2760.0160.0160.0000.0000.0000.000
25A25ASP -1-0.853-0.91917.7960.0330.0330.0000.0000.0000.000
26A26LEU 00.0180.00412.628-0.018-0.0180.0000.0000.0000.000
27A27LYS 10.9520.97711.607-0.105-0.1050.0000.0000.0000.000
28A28GLY 00.0410.00613.210-0.035-0.0350.0000.0000.0000.000
29A29THR 0-0.009-0.01010.849-0.101-0.1010.0000.0000.0000.000
30A30VAL 0-0.018-0.0038.194-0.087-0.0870.0000.0000.0000.000
31A31LYS 10.8240.9068.4370.2520.2520.0000.0000.0000.000
32A32ALA 0-0.031-0.0249.739-0.220-0.2200.0000.0000.0000.000
33A33TRP 00.0610.0156.561-0.202-0.2020.0000.0000.0000.000
34A34HIS 0-0.026-0.0113.6420.0130.3520.001-0.067-0.2730.000
35A35ARG 10.9150.9625.866-0.054-0.0540.0000.0000.0000.000
36A36VAL 00.0120.0266.8810.0690.0690.0000.0000.0000.000
37A37LEU 00.003-0.0362.075-0.765-0.2842.314-0.799-1.995-0.006
38A38ALA 0-0.0320.0152.229-8.599-7.3313.281-1.895-2.654-0.017
39A39GLU -1-0.921-0.9622.771-1.931-0.8850.590-0.431-1.206-0.008
40A40TYR 0-0.043-0.0193.4201.3972.4170.019-0.303-0.7360.000
41A41GLU -1-0.851-0.9191.854-15.859-16.78910.815-5.167-4.718-0.053
42A42LEU 0-0.017-0.0222.9340.4182.2810.839-0.804-1.899-0.003
43A43GLU -1-0.976-0.9983.9740.2990.0200.0210.396-0.1380.000
44A44GLU -1-0.913-0.9526.998-0.490-0.4900.0000.0000.0000.000
45A45ILE 0-0.019-0.0163.811-0.341-0.0270.013-0.055-0.2720.000
46A46MET 0-0.003-0.0086.4630.0070.0070.0000.0000.0000.000
47A47ASN 00.0060.0128.342-0.091-0.0910.0000.0000.0000.000
48A48ASN 00.0220.0039.1630.0570.0570.0000.0000.0000.000
49A49LEU 0-0.052-0.0259.386-0.035-0.0350.0000.0000.0000.000
50A50THR 0-0.0080.00011.164-0.041-0.0410.0000.0000.0000.000
51A51ASP -1-0.855-0.93214.154-0.031-0.0310.0000.0000.0000.000
52A52TYR 0-0.025-0.00713.645-0.033-0.0330.0000.0000.0000.000
53A53ALA 00.0290.01415.461-0.015-0.0150.0000.0000.0000.000
54A54LYS 10.7730.89317.165-0.062-0.0620.0000.0000.0000.000
55A55VAL 0-0.046-0.02119.544-0.007-0.0070.0000.0000.0000.000
56A56ASN 0-0.0250.00517.953-0.027-0.0270.0000.0000.0000.000
57A57LYS 10.9460.96620.2490.0270.0270.0000.0000.0000.000
58A58PHE 0-0.041-0.02920.1990.0160.0160.0000.0000.0000.000
59A59PRO 00.0490.02415.856-0.006-0.0060.0000.0000.0000.000
60A60PRO 00.0050.03611.984-0.026-0.0260.0000.0000.0000.000
61A61THR 0-0.036-0.03212.808-0.011-0.0110.0000.0000.0000.000
62A62VAL 00.0370.0126.7780.0230.0230.0000.0000.0000.000
63A63SER 0-0.008-0.0119.162-0.137-0.1370.0000.0000.0000.000
64A64ASP -1-0.873-0.94611.610-0.289-0.2890.0000.0000.0000.000
65A65LEU 0-0.0070.0007.6190.0740.0740.0000.0000.0000.000
66A66LEU 0-0.0070.0066.955-0.040-0.0400.0000.0000.0000.000
67A67LYS 10.8770.9619.4390.4510.4510.0000.0000.0000.000
68A68NME 00.0260.01912.6610.0700.0700.0000.0000.0000.000