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: 2NG1R

Calculation Name: 1B34-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B34

Chain ID: B

ChEMBL ID:

UniProt ID: P62314

Base Structure: X-ray

Registration Date: 2023-09-23

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 74
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -467574.744417
FMO2-HF: Nuclear repulsion 437492.77537
FMO2-HF: Total energy -30081.969047
FMO2-MP2: Total energy -30167.254134


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(B:26:THR)


Summations of interaction energy for fragment #1(B:26:THR)
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.
-9.965-7.31610.733-4.837-8.5450.003
Interaction energy analysis for fragmet #1(B:26:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.027
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].
3B28PRO00.0580.0313.501-0.9410.4940.024-0.497-0.9620.001
4B29LEU00.0210.0002.170-0.2330.2183.157-1.084-2.524-0.002
5B30SER00.006-0.0121.888-2.561-1.6307.506-3.642-4.7940.004
6B31VAL00.0390.0173.282-0.536-0.7040.0460.386-0.2650.000
7B32LEU00.0490.0375.8790.0680.0680.0000.0000.0000.000
8B33THR0-0.062-0.0025.296-0.336-0.3360.0000.0000.0000.000
9B34GLN00.006-0.0017.236-0.606-0.6060.0000.0000.0000.000
10B35SER0-0.050-0.0489.219-0.303-0.3030.0000.0000.0000.000
11B36VAL0-0.014-0.00810.792-0.107-0.1070.0000.0000.0000.000
12B37LYS10.9270.98011.649-0.842-0.8420.0000.0000.0000.000
13B38ASN00.002-0.00513.166-0.055-0.0550.0000.0000.0000.000
14B39ASN00.0380.03015.260-0.059-0.0590.0000.0000.0000.000
15B40THR00.0080.03313.723-0.067-0.0670.0000.0000.0000.000
16B41GLN0-0.083-0.05015.0190.0230.0230.0000.0000.0000.000
17B42VAL00.0160.01411.366-0.047-0.0470.0000.0000.0000.000
18B43LEU00.0260.00614.3770.0230.0230.0000.0000.0000.000
19B44ILE00.0090.00113.078-0.082-0.0820.0000.0000.0000.000
20B45ASN00.0010.00214.0400.0540.0540.0000.0000.0000.000
21B46CYS0-0.024-0.02614.412-0.015-0.0150.0000.0000.0000.000
22B47ARG11.0100.99615.6020.1320.1320.0000.0000.0000.000
23B48ASN0-0.011-0.00418.223-0.007-0.0070.0000.0000.0000.000
24B49ASN00.0600.04020.535-0.007-0.0070.0000.0000.0000.000
25B50LYS10.9110.96920.1610.0510.0510.0000.0000.0000.000
26B51LYS10.9280.95418.7790.2200.2200.0000.0000.0000.000
27B52LEU00.0250.02717.7170.0280.0280.0000.0000.0000.000
28B53LEU0-0.0190.00717.534-0.018-0.0180.0000.0000.0000.000
29B54GLY00.0630.02917.6100.0100.0100.0000.0000.0000.000
30B55ARG10.8500.91516.610-0.171-0.1710.0000.0000.0000.000
31B56VAL00.0280.01111.608-0.016-0.0160.0000.0000.0000.000
32B57LYS10.9260.98914.703-0.351-0.3510.0000.0000.0000.000
33B58ALA00.0290.00514.0080.0860.0860.0000.0000.0000.000
34B59PHE0-0.017-0.0136.689-0.080-0.0800.0000.0000.0000.000
35B60ASP-1-0.731-0.84610.3550.9470.9470.0000.0000.0000.000
36B61ARG10.9440.9454.806-3.730-3.7300.0000.0000.0000.000
37B62HIS00.0150.0127.418-0.053-0.0530.0000.0000.0000.000
38B63CYS0-0.056-0.0237.274-0.217-0.2170.0000.0000.0000.000
39B64ASN00.0080.0089.689-0.234-0.2340.0000.0000.0000.000
40B65MET0-0.040-0.01410.5740.1340.1340.0000.0000.0000.000
41B66VAL0-0.0050.00514.341-0.078-0.0780.0000.0000.0000.000
42B67LEU0-0.019-0.02414.8430.0400.0400.0000.0000.0000.000
43B68GLU-1-0.850-0.93818.3110.2610.2610.0000.0000.0000.000
44B69ASN0-0.082-0.04920.708-0.023-0.0230.0000.0000.0000.000
45B70VAL0-0.009-0.02319.956-0.014-0.0140.0000.0000.0000.000
46B71LYS10.9280.98022.147-0.029-0.0290.0000.0000.0000.000
47B72GLU-1-0.860-0.93422.4400.0150.0150.0000.0000.0000.000
48B73MET00.0180.00421.547-0.011-0.0110.0000.0000.0000.000
49B93ASP-1-0.929-0.96528.127-0.013-0.0130.0000.0000.0000.000
50B94ARG10.8790.92826.895-0.037-0.0370.0000.0000.0000.000
51B95TYR0-0.015-0.00525.9480.0030.0030.0000.0000.0000.000
52B96ILE00.001-0.00924.2350.0060.0060.0000.0000.0000.000
53B97SER0-0.0060.01924.5690.0160.0160.0000.0000.0000.000
54B98LYS10.9900.97423.043-0.182-0.1820.0000.0000.0000.000
55B99MET00.0050.02020.081-0.015-0.0150.0000.0000.0000.000
56B100PHE00.0150.01517.2920.0400.0400.0000.0000.0000.000
57B101LEU0-0.012-0.00814.740-0.044-0.0440.0000.0000.0000.000
58B102ARG10.9300.93915.930-0.131-0.1310.0000.0000.0000.000
59B103GLY00.0510.01412.335-0.052-0.0520.0000.0000.0000.000
60B104ASP-1-0.866-0.91512.6110.0490.0490.0000.0000.0000.000
61B105SER0-0.040-0.02614.525-0.067-0.0670.0000.0000.0000.000
62B106VAL0-0.040-0.02710.401-0.070-0.0700.0000.0000.0000.000
63B107ILE0-0.0220.00311.806-0.029-0.0290.0000.0000.0000.000
64B108VAL00.0290.00510.072-0.164-0.1640.0000.0000.0000.000
65B109VAL0-0.035-0.0058.9220.1670.1670.0000.0000.0000.000
66B110LEU00.0060.0019.897-0.221-0.2210.0000.0000.0000.000
67B111ARG10.9650.9769.8520.4600.4600.0000.0000.0000.000
68B112ASN0-0.0040.00112.988-0.085-0.0850.0000.0000.0000.000
69B113PRO0-0.028-0.00815.6010.0550.0550.0000.0000.0000.000
70B114LEU00.0430.01517.959-0.023-0.0230.0000.0000.0000.000
71B115ILE0-0.018-0.01018.2650.0160.0160.0000.0000.0000.000
72B116ALA00.0170.01722.322-0.002-0.0020.0000.0000.0000.000
73B117GLY00.0120.00225.004-0.010-0.0100.0000.0000.0000.000
74B118LYS10.9961.00424.6300.1050.1050.0000.0000.0000.000