FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: 5N45Z
Calculation Name: 1VZJ-A-Xray540
Preferred Name: Acetylcholinesterase
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1VZJ
Chain ID: A
ChEMBL ID: CHEMBL220
UniProt ID: P22303
Base Structure: X-ray
Registration Date: 2025-07-09
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 | OptHSide |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 52 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -98909.954167 |
|---|---|
| FMO2-HF: Nuclear repulsion | 86980.239446 |
| FMO2-HF: Total energy | -11929.714721 |
| FMO2-MP2: Total energy | -11964.511589 |
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. |
| -5.413 | -2.697 | 0.111 | -1.053 | -1.776 | 0.003 |
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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4 | A | 4 | ASP | -1 | -0.935 | -0.818 | 4.350 | 0.641 | 1.046 | 0.000 | -0.148 | -0.257 | 0.000 |
| 5 | A | 5 | GLU | 0 | 0.075 | -0.117 | 3.477 | -2.103 | -0.941 | -0.002 | -0.545 | -0.616 | 0.002 |
| 6 | A | 5 | GLU | -1 | -0.963 | -0.824 | 4.029 | 1.789 | 1.949 | -0.001 | -0.011 | -0.148 | 0.000 |
| 7 | A | 6 | ALA | 0 | 0.112 | -0.088 | 3.582 | -0.625 | -0.361 | 0.009 | -0.049 | -0.224 | 0.000 |
| 8 | A | 6 | ALA | 0 | -0.060 | 0.114 | 2.980 | -0.053 | 0.203 | 0.105 | -0.193 | -0.168 | 0.001 |
| 9 | A | 7 | GLU | 0 | 0.004 | -0.152 | 4.100 | 0.518 | 0.843 | -0.001 | -0.216 | -0.108 | 0.001 |
| 10 | A | 7 | GLU | -1 | -0.977 | -0.829 | 3.696 | -6.587 | -6.443 | 0.001 | 0.109 | -0.255 | -0.001 |
| 11 | A | 8 | ARG | 0 | 0.000 | -0.162 | 5.843 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 8 | ARG | 1 | 0.775 | 1.022 | 7.212 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 9 | GLN | 0 | 0.027 | -0.110 | 7.901 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 9 | GLN | 0 | -0.042 | 0.092 | 7.728 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 10 | TRP | 0 | 0.114 | -0.060 | 8.406 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 10 | TRP | 0 | -0.052 | 0.113 | 8.464 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 11 | LYS | 0 | 0.091 | -0.106 | 9.996 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 11 | LYS | 1 | 0.875 | 1.092 | 10.944 | 0.424 | 0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 12 | ALA | 0 | 0.063 | -0.119 | 12.021 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 12 | ALA | 0 | -0.060 | 0.113 | 13.210 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 13 | GLU | 0 | 0.058 | -0.130 | 12.994 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 13 | GLU | -1 | -0.916 | -0.777 | 12.918 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 14 | PHE | 0 | 0.127 | -0.078 | 14.127 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 14 | PHE | 0 | -0.097 | 0.094 | 14.389 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 15 | HIS | 0 | 0.106 | -0.057 | 15.925 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 15 | HIS | 0 | -0.087 | 0.092 | 17.407 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 16 | ARG | 0 | 0.110 | -0.086 | 17.701 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 16 | ARG | 1 | 0.766 | 1.010 | 17.447 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 17 | TRP | 0 | 0.124 | -0.075 | 18.434 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 17 | TRP | 0 | -0.083 | 0.088 | 18.549 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 18 | SER | 0 | 0.003 | -0.111 | 19.918 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 18 | SER | 0 | -0.055 | 0.058 | 19.598 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 19 | SER | 0 | 0.020 | -0.085 | 21.921 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 19 | SER | 0 | -0.058 | 0.048 | 22.613 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 20 | TYR | 0 | -0.008 | -0.122 | 23.266 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 20 | TYR | 0 | -0.046 | 0.110 | 22.797 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 21 | MET | 0 | 0.106 | -0.099 | 24.486 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 21 | MET | 0 | -0.075 | 0.119 | 23.738 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 22 | VAL | 0 | 0.039 | -0.120 | 26.180 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 22 | VAL | 0 | -0.106 | 0.097 | 26.199 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 23 | HIS | 0 | 0.064 | -0.109 | 27.873 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 23 | HIS | 0 | -0.093 | 0.091 | 27.298 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 24 | TRP | 0 | 0.103 | -0.062 | 29.005 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 24 | TRP | 0 | -0.096 | 0.076 | 28.992 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 25 | LYS | 0 | 0.125 | -0.070 | 30.348 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 25 | LYS | 1 | 0.869 | 1.052 | 30.941 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 26 | ASN | 0 | 0.081 | -0.049 | 32.265 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 26 | ASN | 0 | -0.160 | 0.033 | 32.942 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 27 | GLN | 0 | 0.065 | -0.095 | 34.093 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 27 | GLN | 0 | -0.094 | 0.076 | 34.233 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 28 | PHE | 0 | -0.032 | -0.082 | 35.313 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 28 | PHE | 0 | -0.020 | -0.017 | 34.324 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |