FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: 3N2VL
Calculation Name: 1VZJ-A-Xray315
Preferred Name: Acetylcholinesterase
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 1VZJ
Chain ID: A
ChEMBL ID: CHEMBL220
UniProt ID: P22303
Base Structure: X-ray
Registration Date: 2021-09-06
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.
Apendix: None
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 | 28 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -101173.081463 |
|---|---|
| FMO2-HF: Nuclear repulsion | 89067.080252 |
| FMO2-HF: Total energy | -12106.001211 |
| FMO2-MP2: Total energy | -12141.510487 |
3D Structure
Ligand structure
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/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:2:ACE )
Summations of interaction energy for
fragment #1(A:2:ACE )
| 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. |
| 1.275 | 2.357 | -0.004 | -0.371 | -0.705 | 0 |
Interaction energy analysis for fragmet #1(A:2:ACE )
| 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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | A | 4 | ASP | -1 | -0.842 | -0.912 | 3.867 | 0.469 | 1.371 | -0.004 | -0.360 | -0.537 | 0.000 |
| 4 | A | 5 | GLU | -1 | -0.928 | -0.968 | 4.568 | 0.625 | 0.805 | 0.000 | -0.011 | -0.168 | 0.000 |
| 5 | A | 6 | ALA | 0 | 0.055 | 0.023 | 5.239 | 0.200 | 0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | GLU | -1 | -0.949 | -0.985 | 7.080 | -0.859 | -0.859 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | ARG | 1 | 0.872 | 0.933 | 8.178 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | GLN | 0 | -0.035 | -0.024 | 8.904 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | TRP | 0 | 0.055 | 0.037 | 11.222 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | LYS | 1 | 0.949 | 0.977 | 12.993 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | ALA | 0 | 0.001 | -0.005 | 14.511 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | GLU | -1 | -0.826 | -0.914 | 15.412 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | PHE | 0 | -0.030 | 0.005 | 17.293 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | HIS | 0 | 0.001 | 0.013 | 19.052 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | ARG | 1 | 0.913 | 0.954 | 19.863 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | TRP | 0 | 0.024 | 0.011 | 21.485 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | SER | 0 | 0.002 | -0.020 | 23.000 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | SER | 0 | -0.076 | -0.039 | 25.023 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | TYR | 0 | 0.003 | -0.010 | 25.616 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | MET | 0 | -0.009 | 0.000 | 27.373 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | VAL | 0 | -0.055 | -0.017 | 29.234 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | HIS | 0 | 0.004 | -0.020 | 30.294 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | TRP | 0 | 0.000 | 0.023 | 32.186 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | LYS | 1 | 0.968 | 0.961 | 33.745 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | ASN | 0 | -0.047 | -0.003 | 35.491 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | GLN | 0 | -0.025 | -0.011 | 36.901 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | PHE | 0 | -0.044 | -0.015 | 36.979 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | NME | 0 | 0.001 | 0.012 | 39.170 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |