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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: ZY4ZN

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 OptAll
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 -174133.570956
FMO2-HF: Nuclear repulsion 155518.902321
FMO2-HF: Total energy -18614.668635
FMO2-MP2: Total energy -18667.980607


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.
-10.431-11.27113.197-6.49-5.868-0.045
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].
3A3LEU0-0.041-0.0063.8000.1292.276-0.006-1.178-0.9630.004
4A4GLU-1-0.828-0.9221.866-14.497-18.26913.201-5.129-4.301-0.049
5A5GLU-1-0.889-0.9453.573-0.5500.1560.003-0.177-0.5320.000
6A6LYS10.9360.9775.3872.6902.769-0.001-0.006-0.0720.000
7A7VAL0-0.021-0.0167.4660.7000.7000.0000.0000.0000.000
8A8GLU-1-0.872-0.9267.515-0.706-0.7060.0000.0000.0000.000
9A9GLN0-0.026-0.0078.8370.4860.4860.0000.0000.0000.000
10A10LEU0-0.046-0.01411.4410.2760.2760.0000.0000.0000.000
11A11GLY00.0230.01812.4790.1660.1660.0000.0000.0000.000
12A12SER00.0560.01612.9590.1440.1440.0000.0000.0000.000
13A13SER0-0.048-0.03115.2530.1350.1350.0000.0000.0000.000
14A14LEU0-0.030-0.01017.0000.0900.0900.0000.0000.0000.000
15A15ASP-1-0.851-0.92317.458-0.414-0.4140.0000.0000.0000.000
16A16THR0-0.061-0.03219.0790.0770.0770.0000.0000.0000.000
17A17LEU0-0.042-0.02621.2710.0470.0470.0000.0000.0000.000
18A18GLN00.0230.00922.4580.0550.0550.0000.0000.0000.000
19A19THR0-0.038-0.02723.4190.0410.0410.0000.0000.0000.000
20A20ARG10.8960.93724.7280.3020.3020.0000.0000.0000.000
21A21PHE00.0120.00927.2030.0210.0210.0000.0000.0000.000
22A22ALA00.0250.00928.6170.0180.0180.0000.0000.0000.000
23A23ARG10.9100.97127.5410.2120.2120.0000.0000.0000.000
24A24LEU00.0790.04231.8130.0120.0120.0000.0000.0000.000
25A25LEU00.0060.00933.1120.0120.0120.0000.0000.0000.000
26A26ALA00.0050.00634.9300.0110.0110.0000.0000.0000.000
27A27GLU-1-0.908-0.96834.384-0.144-0.1440.0000.0000.0000.000
28A28TYR00.0140.02637.4810.0110.0110.0000.0000.0000.000
29A29ASN0-0.027-0.02338.2520.0120.0120.0000.0000.0000.000
30A30ALA00.0220.01540.9030.0070.0070.0000.0000.0000.000
31A31THR0-0.049-0.04641.3680.0060.0060.0000.0000.0000.000
32A32GLN0-0.005-0.00243.2730.0110.0110.0000.0000.0000.000
33A33MET0-0.031-0.01945.0260.0040.0040.0000.0000.0000.000
34A34LYS10.9500.98147.0430.0760.0760.0000.0000.0000.000
35A35MET00.003-0.00946.5340.0060.0060.0000.0000.0000.000
36A36LYS10.9790.99147.2330.0950.0950.0000.0000.0000.000
37A37GLN0-0.014-0.00151.3620.0010.0010.0000.0000.0000.000
38A38ARG10.9050.94550.2220.0780.0780.0000.0000.0000.000
39A39LEU00.0100.01151.1860.0020.0020.0000.0000.0000.000
40A40SER00.0590.00955.0880.0020.0020.0000.0000.0000.000
41A41GLN0-0.047-0.00957.1540.0020.0020.0000.0000.0000.000
42A42LEU00.0060.02056.8520.0020.0020.0000.0000.0000.000
43A43GLU-1-0.874-0.93757.143-0.065-0.0650.0000.0000.0000.000
44A44SER0-0.115-0.05960.8530.0020.0020.0000.0000.0000.000
45A45GLN0-0.050-0.02462.1950.0020.0020.0000.0000.0000.000
46A46VAL0-0.030-0.00162.7510.0020.0020.0000.0000.0000.000