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: Q5JJY
Calculation Name: 1CLV-I-Xray547
Preferred Name: Alpha-amylase
Target Type: SINGLE PROTEIN
Ligand Name: pyroglutamic acid | calcium ion | chloride ion
Ligand 3-letter code: PCA | CA | CL
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1CLV
Chain ID: I
ChEMBL ID: CHEMBL3580521
UniProt ID: P56634
Base Structure: X-ray
Registration Date: 2025-10-06
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 29 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -122908.853677 |
|---|---|
| FMO2-HF: Nuclear repulsion | 108509.578734 |
| FMO2-HF: Total energy | -14399.274944 |
| FMO2-MP2: Total energy | -14434.873006 |
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(I:501:CYS)
Summations of interaction energy for
fragment #1(I:501:CYS)
| 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. |
| -28.03 | -22.484 | 11.937 | -6.329 | -11.152 | -0.031 |
Interaction energy analysis for fragmet #1(I:501:CYS)
| 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 | I | 503 | PRO | 0 | 0.030 | 0.008 | 1.880 | -10.421 | -13.431 | 11.232 | -2.707 | -5.514 | -0.034 |
| 4 | I | 504 | LYS | 1 | 0.937 | 0.969 | 3.730 | 26.729 | 26.760 | 0.013 | 0.252 | -0.295 | 0.000 |
| 8 | I | 508 | CYS | 0 | -0.015 | -0.002 | 5.174 | -3.085 | -3.044 | -0.003 | -0.012 | -0.026 | 0.000 |
| 15 | I | 515 | VAL | 0 | -0.075 | -0.039 | 3.208 | -4.777 | -4.337 | 0.046 | -0.137 | -0.350 | -0.001 |
| 16 | I | 516 | PRO | 0 | -0.003 | 0.011 | 2.737 | -6.627 | -1.763 | 0.656 | -2.515 | -3.006 | 0.000 |
| 19 | I | 520 | PRO | 0 | -0.079 | -0.038 | 3.840 | -3.319 | -1.400 | -0.010 | -0.860 | -1.048 | 0.004 |
| 20 | I | 521 | TYR | 0 | -0.013 | -0.010 | 3.584 | 4.736 | 5.639 | 0.003 | -0.246 | -0.660 | 0.000 |
| 21 | I | 522 | THR | 0 | 0.026 | 0.007 | 4.186 | -3.053 | -2.768 | 0.002 | -0.102 | -0.184 | 0.000 |
| 29 | I | 532 | SER | -1 | -0.823 | -0.920 | 5.833 | -26.581 | -26.508 | -0.002 | -0.002 | -0.069 | 0.000 |
| 5 | I | 505 | TRP | 0 | -0.014 | -0.009 | 5.810 | 1.968 | 1.968 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | I | 506 | ASN | 0 | -0.044 | -0.011 | 6.722 | 2.438 | 2.438 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | I | 507 | ARG | 1 | 0.870 | 0.926 | 7.610 | 22.387 | 22.387 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | I | 509 | GLY | 0 | 0.050 | 0.018 | 7.232 | 3.694 | 3.694 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | I | 510 | PRO | 0 | 0.053 | 0.029 | 5.609 | 1.139 | 1.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | I | 511 | LYS | 1 | 0.893 | 0.948 | 8.256 | 18.039 | 18.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | I | 512 | MET | 0 | -0.079 | -0.033 | 11.484 | 2.179 | 2.179 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | I | 513 | ASP | -1 | -0.859 | -0.940 | 8.367 | -34.344 | -34.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | I | 514 | GLY | 0 | 0.007 | 0.022 | 8.913 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | I | 524 | THR | 0 | -0.026 | -0.020 | 6.316 | 2.973 | 2.973 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | I | 525 | SER | 0 | 0.007 | -0.010 | 9.359 | 2.297 | 2.297 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | I | 526 | ASP | -1 | -0.846 | -0.919 | 9.509 | -22.469 | -22.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | I | 527 | TYR | 0 | -0.024 | -0.010 | 11.067 | -0.904 | -0.904 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | I | 528 | TYR | 0 | 0.016 | -0.008 | 11.847 | -0.992 | -0.992 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | I | 529 | GLY | 0 | 0.026 | 0.019 | 10.360 | 1.803 | 1.803 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | I | 530 | ASN | 0 | -0.032 | -0.010 | 8.406 | -1.460 | -1.460 | 0.000 | 0.000 | 0.000 | 0.000 |