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: 3KM5L
Calculation Name: 1D1H-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1D1H
Chain ID: A
UniProt ID: P56852
Base Structure: SolutionNMR
Registration Date: 2025-09-02
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 | 32 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -148342.666138 |
|---|---|
| FMO2-HF: Nuclear repulsion | 132520.774771 |
| FMO2-HF: Total energy | -15821.891366 |
| FMO2-MP2: Total energy | -15863.051195 |
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:1:GLU)
Summations of interaction energy for
fragment #1(A:1:GLU)
| 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. |
| -70.23 | -75.272 | 25.394 | -10.43 | -9.924 | 0.104 |
Interaction energy analysis for fragmet #1(A:1:GLU)
| 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 | 3 | ARG | 1 | 0.819 | 0.911 | 1.789 | -53.335 | -58.838 | 25.393 | -10.276 | -9.615 | 0.104 |
| 14 | A | 14 | ASP | -1 | -0.839 | -0.917 | 3.549 | -23.279 | -22.890 | 0.003 | -0.069 | -0.324 | 0.000 |
| 15 | A | 15 | CYS | 0 | -0.051 | 0.003 | 4.116 | -2.990 | -2.918 | -0.002 | -0.085 | 0.015 | 0.000 |
| 4 | A | 4 | TYR | 0 | 0.115 | 0.018 | 5.544 | -0.981 | -0.981 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | LEU | 0 | 0.022 | 0.013 | 8.694 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | PHE | 0 | -0.014 | -0.007 | 11.868 | 0.683 | 0.683 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | -0.004 | 0.006 | 7.758 | 1.008 | 1.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLY | 0 | 0.006 | -0.009 | 8.368 | -1.584 | -1.584 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | CYS | 0 | -0.098 | -0.044 | 6.138 | 0.811 | 0.811 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.896 | 0.939 | 6.553 | 3.406 | 3.406 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | THR | 0 | 0.019 | 0.001 | 7.417 | 2.052 | 2.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | THR | 0 | 0.075 | 0.018 | 7.753 | -1.359 | -1.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.013 | 0.005 | 6.369 | 1.103 | 1.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | LYS | 1 | 0.985 | 0.986 | 7.929 | 3.882 | 3.882 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | HIS | 0 | 0.055 | 0.032 | 11.235 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LEU | 0 | -0.044 | -0.001 | 9.974 | 0.594 | 0.594 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | GLY | 0 | 0.066 | 0.044 | 11.107 | -1.021 | -1.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | LYS | 1 | 0.826 | 0.911 | 11.329 | 2.750 | 2.750 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 23 | PHE | 0 | 0.009 | -0.001 | 14.584 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 24 | ARG | 1 | 0.938 | 0.957 | 15.774 | 1.678 | 1.678 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 25 | ASP | -1 | -0.842 | -0.921 | 15.724 | -1.054 | -1.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 26 | LYS | 1 | 0.882 | 0.950 | 11.587 | 1.328 | 1.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 27 | TYR | 0 | -0.001 | 0.014 | 10.787 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 29 | ALA | 0 | 0.041 | 0.011 | 10.852 | 0.878 | 0.878 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 30 | TRP | 0 | 0.022 | -0.014 | 13.459 | -0.647 | -0.647 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 31 | ASP | -1 | -0.845 | -0.925 | 15.421 | -2.466 | -2.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 32 | PHE | 0 | -0.035 | -0.012 | 15.759 | -0.396 | -0.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 33 | THR | 0 | -0.010 | 0.002 | 17.834 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 34 | PHE | 0 | -0.029 | -0.018 | 21.529 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 35 | SER | -1 | -0.938 | -0.951 | 21.962 | -1.118 | -1.118 | 0.000 | 0.000 | 0.000 | 0.000 |