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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: 22VMR

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 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 46
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -174141.292063
FMO2-HF: Nuclear repulsion 155526.89641
FMO2-HF: Total energy -18614.395654
FMO2-MP2: Total energy -18667.710528


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.
-12.454-14.49815.962-7.73-6.186-0.05
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 : 0.044 / q_NPA : 0.016
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].
3A3LEU0-0.038-0.0193.674-0.8521.505-0.005-1.311-1.0410.007
4A4GLU-1-0.833-0.9241.779-14.176-19.58615.961-6.150-4.401-0.056
5A5GLU-1-0.869-0.9223.298-1.526-0.5910.007-0.264-0.677-0.001
6A6LYS10.9040.9645.2672.7542.828-0.001-0.005-0.0670.000
7A7VAL0-0.016-0.0207.5450.6840.6840.0000.0000.0000.000
8A8GLU-1-0.864-0.9177.442-0.889-0.8890.0000.0000.0000.000
9A9GLN0-0.039-0.0339.2960.2310.2310.0000.0000.0000.000
10A10LEU0-0.077-0.04011.3760.2730.2730.0000.0000.0000.000
11A11GLY00.0340.02512.4220.1700.1700.0000.0000.0000.000
12A12SER00.0510.02613.2480.1560.1560.0000.0000.0000.000
13A13SER0-0.032-0.03015.3180.1360.1360.0000.0000.0000.000
14A14LEU0-0.032-0.01317.0520.0910.0910.0000.0000.0000.000
15A15ASP-1-0.850-0.91617.803-0.434-0.4340.0000.0000.0000.000
16A16THR0-0.061-0.03819.5200.0760.0760.0000.0000.0000.000
17A17LEU0-0.046-0.03421.4240.0500.0500.0000.0000.0000.000
18A18GLN00.0370.02322.2880.0620.0620.0000.0000.0000.000
19A19THR0-0.0070.00924.1640.0390.0390.0000.0000.0000.000
20A20ARG10.8940.92625.2940.2950.2950.0000.0000.0000.000
21A21PHE00.0160.01927.3200.0200.0200.0000.0000.0000.000
22A22ALA00.0190.00928.8700.0180.0180.0000.0000.0000.000
23A23ARG10.9250.96227.8460.2240.2240.0000.0000.0000.000
24A24LEU00.0460.03131.9490.0120.0120.0000.0000.0000.000
25A25LEU00.0020.01033.3270.0130.0130.0000.0000.0000.000
26A26ALA0-0.006-0.00735.0210.0110.0110.0000.0000.0000.000
27A27GLU-1-0.916-0.96035.420-0.140-0.1400.0000.0000.0000.000
28A28TYR0-0.0180.00437.7700.0100.0100.0000.0000.0000.000
29A29ASN00.006-0.01638.4250.0090.0090.0000.0000.0000.000
30A30ALA00.0040.01241.0130.0070.0070.0000.0000.0000.000
31A31THR0-0.053-0.04541.8060.0070.0070.0000.0000.0000.000
32A32GLN00.0340.02443.6410.0050.0050.0000.0000.0000.000
33A33MET0-0.057-0.02945.4490.0040.0040.0000.0000.0000.000
34A34LYS10.9600.98847.5950.0790.0790.0000.0000.0000.000
35A35MET00.001-0.01545.9510.0060.0060.0000.0000.0000.000
36A36LYS10.9870.99647.9510.0950.0950.0000.0000.0000.000
37A37GLN00.0210.02551.5200.0000.0000.0000.0000.0000.000
38A38ARG10.9070.94050.8650.0780.0780.0000.0000.0000.000
39A39LEU00.0350.02251.6910.0020.0020.0000.0000.0000.000
40A40SER00.0360.01755.4580.0020.0020.0000.0000.0000.000
41A41GLN0-0.028-0.01257.4400.0020.0020.0000.0000.0000.000
42A42LEU00.0000.01156.8550.0020.0020.0000.0000.0000.000
43A43GLU-1-0.931-0.97057.482-0.065-0.0650.0000.0000.0000.000
44A44SER0-0.100-0.05461.3290.0020.0020.0000.0000.0000.000
45A45GLN0-0.052-0.02662.4410.0010.0010.0000.0000.0000.000
46A46VAL0-0.0220.01363.1600.0020.0020.0000.0000.0000.000