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: 4Q75N
Calculation Name: 2D1K-C-Xray547
Preferred Name:
Target Type:
Ligand Name: adenosine-5'-triphosphate | 2-acetamido-2-deoxy-beta-d-glucopyranose | beta-d-mannopyranose | 4-methyl-histidine | calcium ion
Ligand 3-letter code: ATP | NAG | BMA | HIC | CA
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2D1K
Chain ID: C
UniProt ID: P68135
Base Structure: X-ray
Registration Date: 2025-10-03
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 | -77858.567208 |
|---|---|
| FMO2-HF: Nuclear repulsion | 66356.183261 |
| FMO2-HF: Total energy | -11502.383947 |
| FMO2-MP2: Total energy | -11535.433578 |
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:725:THR)
Summations of interaction energy for
fragment #1(A:725:THR)
| 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. |
| 50.707 | 52.48 | 2.905 | -1.198 | -3.477 | -0.007 |
Interaction energy analysis for fragmet #1(A:725:THR)
| 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 | 727 | GLN | 0 | 0.046 | 0.024 | 3.041 | -0.081 | 2.126 | 0.118 | -0.969 | -1.355 | -0.008 |
| 4 | A | 728 | GLY | 0 | 0.006 | 0.006 | 2.114 | 0.747 | 1.094 | 2.653 | -1.746 | -1.255 | 0.003 |
| 5 | A | 729 | GLU | -1 | -0.786 | -0.907 | 2.964 | -23.436 | -24.798 | 0.115 | 1.635 | -0.387 | -0.002 |
| 7 | A | 731 | MET | 0 | 0.057 | 0.027 | 3.675 | 3.451 | 3.726 | 0.015 | -0.059 | -0.230 | 0.000 |
| 8 | A | 732 | LEU | 0 | -0.015 | -0.015 | 3.746 | 1.964 | 2.270 | 0.004 | -0.059 | -0.250 | 0.000 |
| 6 | A | 730 | ASP | -1 | -0.911 | -0.934 | 5.968 | -22.195 | -22.195 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 733 | ASN | 0 | -0.101 | -0.045 | 7.125 | 4.913 | 4.913 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 734 | ALA | 0 | -0.001 | 0.002 | 10.285 | 2.134 | 2.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 735 | ILE | 0 | -0.028 | -0.019 | 7.340 | 1.686 | 1.686 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 736 | ARG | 1 | 0.863 | 0.919 | 8.997 | 27.369 | 27.369 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 737 | ARG | 1 | 0.928 | 0.975 | 13.200 | 20.584 | 20.584 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 738 | GLY | 0 | 0.020 | 0.037 | 14.735 | 1.116 | 1.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 739 | VAL | 0 | 0.022 | -0.004 | 15.304 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 740 | LYS | 1 | 0.925 | 0.958 | 17.877 | 11.888 | 11.888 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 741 | LEU | 0 | 0.055 | 0.040 | 18.089 | 0.305 | 0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 742 | LYS | 1 | 0.952 | 0.960 | 21.864 | 10.622 | 10.622 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 743 | LYS | 1 | 0.911 | 0.951 | 25.522 | 9.671 | 9.671 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 744 | THR | 0 | 0.062 | 0.046 | 26.819 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 745 | THR | 0 | -0.023 | -0.013 | 28.987 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 746 | THR | 0 | 0.023 | 0.003 | 28.968 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 747 | ASN | 0 | -0.015 | -0.003 | 31.089 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 748 | ASP | -1 | -0.807 | -0.887 | 31.082 | -9.430 | -9.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 749 | ARG | 1 | 0.881 | 0.930 | 32.437 | 9.015 | 9.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 750 | SER | 0 | -0.031 | -0.026 | 31.648 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 751 | ALA | 0 | -0.008 | 0.002 | 33.788 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 752 | PRO | 0 | -0.038 | -0.014 | 37.332 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 753 | ARG | 0 | 0.038 | 0.024 | 39.664 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |