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: 9L2M2
Calculation Name: 1H3O-A-Xray547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1H3O
Chain ID: A
UniProt ID: Q16514
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 | 49 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -225717.805527 |
|---|---|
| FMO2-HF: Nuclear repulsion | 206130.629023 |
| FMO2-HF: Total energy | -19587.176504 |
| FMO2-MP2: Total energy | -19645.079908 |
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:869:MET)
Summations of interaction energy for
fragment #1(A:869:MET)
| 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. |
| 17.385 | 23.114 | 17.16 | -5.952 | -16.94 | -0.06 |
Interaction energy analysis for fragmet #1(A:869:MET)
| 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 | 871 | LEU | 0 | 0.041 | 0.027 | 2.835 | 4.070 | 6.581 | 0.165 | -1.027 | -1.650 | -0.005 |
| 4 | A | 872 | LEU | 0 | 0.023 | 0.000 | 2.543 | -13.506 | -11.206 | 1.472 | -1.802 | -1.969 | -0.023 |
| 5 | A | 873 | GLN | 0 | 0.091 | 0.027 | 2.588 | -4.403 | -2.544 | 4.647 | -2.139 | -4.368 | -0.007 |
| 6 | A | 874 | ALA | 0 | 0.033 | 0.022 | 3.860 | 4.364 | 2.707 | 0.036 | 1.918 | -0.297 | 0.001 |
| 8 | A | 876 | LEU | 0 | 0.013 | 0.021 | 3.613 | 1.353 | 1.887 | 0.169 | -0.139 | -0.564 | 0.000 |
| 29 | A | 897 | VAL | 0 | -0.013 | -0.010 | 2.869 | -1.419 | -0.560 | 0.600 | -0.269 | -1.191 | -0.002 |
| 30 | A | 898 | SER | 0 | 0.003 | -0.017 | 2.303 | -7.579 | -5.269 | 2.841 | -1.967 | -3.185 | -0.014 |
| 31 | A | 899 | TYR | 0 | 0.020 | 0.019 | 2.964 | 0.687 | -0.907 | 0.133 | 1.792 | -0.331 | -0.001 |
| 33 | A | 901 | SER | 0 | -0.008 | 0.002 | 1.767 | -1.336 | -2.875 | 7.097 | -2.265 | -3.293 | -0.009 |
| 34 | A | 902 | HIS | 0 | 0.024 | 0.016 | 4.699 | -2.730 | -2.584 | 0.000 | -0.054 | -0.092 | 0.000 |
| 7 | A | 875 | PRO | 0 | -0.022 | -0.022 | 7.382 | 2.265 | 2.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 877 | GLN | 0 | 0.030 | 0.008 | 5.735 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 878 | ARG | 1 | 0.952 | 0.971 | 7.310 | 22.406 | 22.406 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 879 | ARG | 1 | 0.999 | 1.000 | 10.168 | 20.934 | 20.934 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 880 | ILE | 0 | 0.022 | 0.013 | 7.141 | 1.089 | 1.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 881 | LEU | 0 | 0.028 | 0.017 | 10.853 | 1.150 | 1.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 882 | GLU | -1 | -0.937 | -0.951 | 13.045 | -14.157 | -14.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 883 | ILE | 0 | 0.048 | 0.008 | 13.293 | 0.990 | 0.990 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 884 | GLY | 0 | 0.026 | 0.022 | 15.008 | 0.760 | 0.760 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 885 | LYS | 1 | 1.006 | 1.000 | 16.365 | 13.976 | 13.976 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 886 | LYS | 1 | 0.789 | 0.895 | 18.806 | 14.024 | 14.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 887 | HIS | 1 | 0.824 | 0.892 | 18.815 | 13.246 | 13.246 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 888 | GLY | 0 | 0.061 | 0.042 | 20.822 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 889 | ILE | 0 | -0.029 | 0.006 | 15.075 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 890 | THR | 0 | -0.029 | -0.018 | 17.843 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 891 | GLU | -1 | -0.937 | -0.965 | 14.522 | -14.408 | -14.408 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 892 | LEU | 0 | -0.055 | -0.038 | 8.155 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 893 | HIS | 0 | 0.015 | 0.000 | 10.312 | 0.789 | 0.789 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 894 | PRO | 0 | 0.031 | 0.007 | 7.389 | -1.269 | -1.269 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 895 | ASP | -1 | -0.844 | -0.910 | 5.222 | -26.482 | -26.482 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 896 | VAL | 0 | 0.037 | 0.019 | 5.668 | -2.422 | -2.422 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 900 | VAL | 0 | 0.046 | 0.015 | 6.740 | 0.630 | 0.630 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 903 | ALA | 0 | 0.038 | 0.020 | 6.326 | 2.061 | 2.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 904 | THR | 0 | -0.067 | -0.051 | 7.146 | 2.409 | 2.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 905 | GLN | 0 | -0.026 | -0.007 | 6.668 | 0.929 | 0.929 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 906 | GLN | 0 | -0.003 | -0.012 | 8.592 | 3.503 | 3.503 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 907 | ARG | 1 | 0.887 | 0.947 | 11.746 | 18.327 | 18.327 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 908 | LEU | 0 | -0.007 | -0.013 | 10.049 | 1.438 | 1.438 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 909 | GLN | 0 | -0.021 | -0.001 | 12.634 | -1.036 | -1.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 910 | ASN | 0 | 0.082 | 0.040 | 14.286 | 1.376 | 1.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 911 | LEU | 0 | -0.087 | -0.043 | 16.047 | 0.961 | 0.961 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 912 | VAL | 0 | 0.014 | 0.002 | 15.438 | 0.649 | 0.649 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 913 | GLU | -1 | -0.858 | -0.913 | 17.369 | -17.117 | -17.117 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 914 | LYS | 1 | 0.805 | 0.881 | 20.180 | 13.805 | 13.805 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 915 | ILE | 0 | -0.079 | -0.035 | 19.978 | 0.520 | 0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 916 | SER | 0 | -0.089 | -0.056 | 21.379 | 0.253 | 0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 917 | GLU | -2 | -1.794 | -1.854 | 23.699 | -23.950 | -23.950 | 0.000 | 0.000 | 0.000 | 0.000 |