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: VRL81
Calculation Name: 1VZJ-A-Xray372
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: 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.
Apendix: None
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 | 26 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -99026.232304 |
|---|---|
| FMO2-HF: Nuclear repulsion | 87090.909016 |
| FMO2-HF: Total energy | -11935.323288 |
| FMO2-MP2: Total energy | -11970.244861 |
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:3:LEU)
Summations of interaction energy for
fragment #1(A:3:LEU)
| 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. |
| -8.358 | -2.677 | 1.095 | -2.831 | -3.945 | -0.022 |
Interaction energy analysis for fragmet #1(A:3:LEU)
| 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 | 5 | GLU | -1 | -0.920 | -0.958 | 3.613 | -1.288 | 0.275 | -0.002 | -0.615 | -0.946 | 0.002 |
| 4 | A | 6 | ALA | 0 | -0.005 | -0.003 | 3.130 | -0.251 | 0.332 | 0.048 | -0.149 | -0.482 | 0.000 |
| 5 | A | 7 | GLU | -1 | -0.891 | -0.957 | 2.537 | -9.153 | -5.618 | 1.049 | -2.067 | -2.517 | -0.024 |
| 6 | A | 8 | ARG | 1 | 0.800 | 0.879 | 5.770 | 0.815 | 0.815 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 9 | GLN | 0 | -0.012 | -0.004 | 7.814 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 10 | TRP | 0 | 0.025 | 0.016 | 8.245 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 11 | LYS | 1 | 0.951 | 0.978 | 9.776 | 0.615 | 0.615 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 12 | ALA | 0 | -0.008 | -0.003 | 11.825 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 13 | GLU | -1 | -0.791 | -0.888 | 12.875 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 14 | PHE | 0 | -0.034 | -0.003 | 13.813 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 15 | HIS | 0 | 0.013 | 0.015 | 15.578 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 16 | ARG | 1 | 0.867 | 0.917 | 17.508 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 17 | TRP | 0 | 0.015 | 0.014 | 18.229 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 18 | SER | 0 | -0.002 | -0.021 | 19.253 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 19 | SER | 0 | -0.075 | -0.050 | 21.621 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 20 | TYR | 0 | 0.016 | 0.004 | 22.271 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 21 | MET | 0 | 0.005 | 0.012 | 23.170 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | VAL | 0 | -0.030 | -0.009 | 25.834 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 23 | HIS | 0 | 0.004 | -0.008 | 26.816 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 24 | TRP | 0 | -0.012 | 0.007 | 28.649 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 25 | LYS | 1 | 0.960 | 0.964 | 29.953 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 26 | ASN | 0 | -0.065 | -0.028 | 31.870 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 27 | GLN | 0 | -0.024 | -0.007 | 33.494 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 28 | PHE | 0 | -0.035 | 0.002 | 34.042 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |