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About

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: 6614Z

Calculation Name: 3SWY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SWY

Chain ID: A

ChEMBL ID:

UniProt ID: Q16281

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptHSide
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 46
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -173988.73626
FMO2-HF: Nuclear repulsion 155374.167129
FMO2-HF: Total energy -18614.569131
FMO2-MP2: Total energy -18667.864992


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-11.806-13.52815.234-7.363-6.148-0.051
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / 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].
3A3LEU0-0.038-0.0153.674-0.5751.688-0.005-1.248-1.0100.006
4A4GLU-1-0.829-0.9251.807-14.581-19.41515.235-5.907-4.493-0.056
5A5GLU-1-0.881-0.9323.391-0.961-0.1890.005-0.202-0.575-0.001
6A6LYS10.9060.9685.2772.7682.845-0.001-0.006-0.0700.000
7A7VAL0-0.010-0.0187.5520.6760.6760.0000.0000.0000.000
8A8GLU-1-0.862-0.9147.483-0.772-0.7720.0000.0000.0000.000
9A9GLN0-0.017-0.0189.3080.3200.3200.0000.0000.0000.000
10A10LEU0-0.070-0.02811.3870.2780.2780.0000.0000.0000.000
11A11GLY00.0420.02712.4370.1700.1700.0000.0000.0000.000
12A12SER00.0580.02613.0270.1450.1450.0000.0000.0000.000
13A13SER0-0.063-0.04815.2310.1350.1350.0000.0000.0000.000
14A14LEU0-0.026-0.01517.0660.0910.0910.0000.0000.0000.000
15A15ASP-1-0.850-0.91417.771-0.424-0.4240.0000.0000.0000.000
16A16THR0-0.074-0.04719.3480.0740.0740.0000.0000.0000.000
17A17LEU0-0.046-0.03221.4370.0490.0490.0000.0000.0000.000
18A18GLN00.0410.02322.4960.0580.0580.0000.0000.0000.000
19A19THR0-0.030-0.00623.9800.0400.0400.0000.0000.0000.000
20A20ARG10.9110.93725.3520.2970.2970.0000.0000.0000.000
21A21PHE00.0080.01527.3340.0200.0200.0000.0000.0000.000
22A22ALA00.0200.00928.8830.0180.0180.0000.0000.0000.000
23A23ARG10.9260.96527.6950.2200.2200.0000.0000.0000.000
24A24LEU00.0460.03231.9620.0120.0120.0000.0000.0000.000
25A25LEU00.0060.00933.3400.0130.0130.0000.0000.0000.000
26A26ALA0-0.006-0.00635.0330.0110.0110.0000.0000.0000.000
27A27GLU-1-0.903-0.95635.136-0.142-0.1420.0000.0000.0000.000
28A28TYR0-0.0060.01437.7820.0110.0110.0000.0000.0000.000
29A29ASN0-0.002-0.02238.5510.0090.0090.0000.0000.0000.000
30A30ALA00.0040.01541.0270.0070.0070.0000.0000.0000.000
31A31THR0-0.050-0.04941.7420.0070.0070.0000.0000.0000.000
32A32GLN00.0100.00743.7250.0100.0100.0000.0000.0000.000
33A33MET0-0.047-0.02045.4620.0040.0040.0000.0000.0000.000
34A34LYS10.9740.99147.6060.0780.0780.0000.0000.0000.000
35A35MET00.002-0.00946.4330.0060.0060.0000.0000.0000.000
36A36LYS10.9820.99547.5090.0950.0950.0000.0000.0000.000
37A37GLN0-0.0120.00151.5330.0010.0010.0000.0000.0000.000
38A38ARG10.9160.94650.6480.0780.0780.0000.0000.0000.000
39A39LEU00.0220.01551.6610.0020.0020.0000.0000.0000.000
40A40SER00.0490.02655.4700.0020.0020.0000.0000.0000.000
41A41GLN0-0.028-0.00457.4950.0020.0020.0000.0000.0000.000
42A42LEU00.0070.01256.8630.0020.0020.0000.0000.0000.000
43A43GLU-1-0.917-0.96757.708-0.065-0.0650.0000.0000.0000.000
44A44SER0-0.110-0.05861.3420.0020.0020.0000.0000.0000.000
45A45GLN0-0.056-0.02762.2750.0010.0010.0000.0000.0000.000
46A46VAL0-0.0160.01763.1820.0020.0020.0000.0000.0000.000