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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: 9GNL2

Calculation Name: 3SWY-A-Xray318

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: 2021-09-07

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 46
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -174150.864225
FMO2-HF: Nuclear repulsion 155536.597695
FMO2-HF: Total energy -18614.26653
FMO2-MP2: Total energy -18667.590972


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.
-110.269-106.13912.189-9.303-7.014-0.118
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 : 1 / q_Mulliken : 0.795 / q_NPA : 0.876
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].
3A3LEU 0-0.0020.0043.7167.8879.0260.000-0.492-0.647-0.001
4A4GLU -1-0.798-0.9091.786-112.637-110.87912.183-8.423-5.517-0.115
5A5GLU -1-0.868-0.9223.350-47.526-46.3760.006-0.381-0.775-0.002
6A6LYS 10.9190.9735.37035.48735.5700.000-0.007-0.0750.000
7A7VAL 0-0.010-0.0167.5235.0715.0710.0000.0000.0000.000
8A8GLU -1-0.865-0.9197.524-27.906-27.9060.0000.0000.0000.000
9A9GLN 0-0.033-0.0309.3932.2092.2090.0000.0000.0000.000
10A10LEU 0-0.073-0.03711.4772.8822.8820.0000.0000.0000.000
11A11GLY 00.0370.02612.5382.0282.0280.0000.0000.0000.000
12A12SER 00.0510.02613.3302.0162.0160.0000.0000.0000.000
13A13SER 0-0.031-0.02915.4191.9691.9690.0000.0000.0000.000
14A14LEU 0-0.030-0.01217.1641.4321.4320.0000.0000.0000.000
15A15ASP -1-0.850-0.91617.884-16.167-16.1670.0000.0000.0000.000
16A16THR 0-0.060-0.03719.6001.2841.2840.0000.0000.0000.000
17A17LEU 0-0.045-0.03321.5270.9550.9550.0000.0000.0000.000
18A18GLN 00.0370.02322.3951.2981.2980.0000.0000.0000.000
19A19THR 0-0.0070.00924.2490.7820.7820.0000.0000.0000.000
20A20ARG 10.8940.92625.38212.55912.5590.0000.0000.0000.000
21A21PHE 00.0160.01927.4250.4970.4970.0000.0000.0000.000
22A22ALA 00.0210.01028.9720.4660.4660.0000.0000.0000.000
23A23ARG 10.9220.96127.91211.40611.4060.0000.0000.0000.000
24A24LEU 00.0470.03132.0500.3350.3350.0000.0000.0000.000
25A25LEU 00.0020.01033.4330.3660.3660.0000.0000.0000.000
26A26ALA 0-0.006-0.00735.1220.3390.3390.0000.0000.0000.000
27A27GLU -1-0.916-0.96135.508-8.680-8.6800.0000.0000.0000.000
28A28TYR 0-0.0170.00537.8740.3210.3210.0000.0000.0000.000
29A29ASN 00.006-0.01638.5340.3460.3460.0000.0000.0000.000
30A30ALA 00.0030.01141.1130.2520.2520.0000.0000.0000.000
31A31THR 0-0.053-0.04641.9080.2600.2600.0000.0000.0000.000
32A32GLN 00.0320.02343.7520.1840.1840.0000.0000.0000.000
33A33MET 0-0.057-0.02945.5570.1670.1670.0000.0000.0000.000
34A34LYS 10.9590.98847.6956.4506.4500.0000.0000.0000.000
35A35MET 0-0.001-0.01646.0540.2040.2040.0000.0000.0000.000
36A36LYS 10.9840.99548.0686.8616.8610.0000.0000.0000.000
37A37GLN 00.0200.02451.6310.0050.0050.0000.0000.0000.000
38A38ARG 10.9030.93850.9606.3466.3460.0000.0000.0000.000
39A39LEU 00.0340.02151.8070.0900.0900.0000.0000.0000.000
40A40SER 00.0360.01755.5680.0740.0740.0000.0000.0000.000
41A41GLN 0-0.039-0.01857.5360.0670.0670.0000.0000.0000.000
42A42LEU 0-0.0090.00456.9590.0820.0820.0000.0000.0000.000
43A43GLU -1-0.926-0.96457.600-5.617-5.6170.0000.0000.0000.000
44A44SER 0-0.108-0.05861.4420.0780.0780.0000.0000.0000.000
45A45GLN 0-0.097-0.05562.5400.0570.0570.0000.0000.0000.000
46A46VAL -1-0.937-0.93863.278-4.848-4.8480.0000.0000.0000.000