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: 6ZRMZ
Calculation Name: 1IXD-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1IXD
Chain ID: A
UniProt ID: Q9NQC7
Base Structure: SolutionNMR
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 | 104 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -644679.938649 |
|---|---|
| FMO2-HF: Nuclear repulsion | 605925.830444 |
| FMO2-HF: Total energy | -38754.108206 |
| FMO2-MP2: Total energy | -38864.587804 |
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:GLY)
Summations of interaction energy for
fragment #1(A:1:GLY)
| 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. |
| -1.656 | -1.045 | -0.004 | -0.222 | -0.385 | 0 |
Interaction energy analysis for fragmet #1(A:1:GLY)
| 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 | SER | 0 | 0.015 | 0.020 | 3.837 | -0.842 | -0.231 | -0.004 | -0.222 | -0.385 | 0.000 |
| 4 | A | 4 | GLY | 0 | 0.015 | 0.000 | 6.670 | 4.238 | 4.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | SER | 0 | 0.004 | 0.006 | 8.461 | -1.132 | -1.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | SER | 0 | 0.016 | 0.018 | 10.155 | 0.836 | 0.836 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | 0.018 | 0.006 | 7.031 | -3.188 | -3.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LEU | 0 | -0.015 | -0.023 | 7.943 | 1.309 | 1.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ALA | 0 | 0.022 | 0.033 | 7.063 | 1.611 | 1.611 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | MET | 0 | -0.011 | -0.016 | 7.566 | -2.885 | -2.885 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | PRO | 0 | 0.001 | -0.004 | 7.486 | 2.007 | 2.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.041 | -0.031 | 8.390 | 1.613 | 1.613 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | GLY | 0 | -0.013 | 0.025 | 11.401 | 1.181 | 1.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ASN | 0 | -0.003 | -0.005 | 13.730 | 1.994 | 1.994 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | SER | 0 | 0.023 | -0.013 | 13.836 | 0.997 | 0.997 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | HIS | 0 | -0.057 | -0.031 | 10.530 | -1.704 | -1.704 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLY | 0 | 0.046 | 0.024 | 12.494 | -1.231 | -1.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LEU | 0 | -0.018 | 0.004 | 15.270 | 0.597 | 0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLU | -1 | -0.837 | -0.921 | 17.838 | -16.367 | -16.367 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | VAL | 0 | -0.013 | -0.022 | 21.221 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | GLY | 0 | -0.012 | 0.006 | 24.469 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | SER | 0 | -0.045 | -0.019 | 20.070 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | LEU | 0 | 0.026 | 0.013 | 23.021 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ALA | 0 | -0.013 | -0.024 | 22.308 | -0.769 | -0.769 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | GLU | -1 | -0.803 | -0.875 | 23.206 | -11.812 | -11.812 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | VAL | 0 | 0.025 | 0.013 | 23.811 | -0.624 | -0.624 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | LYS | 1 | 0.770 | 0.869 | 22.729 | 12.647 | 12.647 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLU | -1 | -0.893 | -0.956 | 26.589 | -9.449 | -9.449 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ASN | 0 | -0.031 | -0.012 | 30.388 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | PRO | 0 | -0.003 | 0.008 | 33.669 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | PRO | 0 | -0.002 | 0.006 | 30.984 | -0.232 | -0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | PHE | 0 | 0.004 | -0.011 | 29.707 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | TYR | 0 | -0.011 | -0.023 | 25.819 | -0.181 | -0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | GLY | 0 | 0.052 | 0.014 | 28.043 | 0.446 | 0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | VAL | 0 | -0.008 | 0.010 | 26.626 | -0.493 | -0.493 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ILE | 0 | -0.002 | -0.002 | 22.379 | 0.397 | 0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | ARG | 1 | 0.866 | 0.946 | 26.670 | 9.663 | 9.663 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | TRP | 0 | 0.028 | 0.004 | 28.566 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | ILE | 0 | 0.027 | 0.020 | 22.186 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | GLY | 0 | 0.001 | 0.006 | 26.227 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | GLN | 0 | -0.008 | -0.002 | 26.033 | -0.371 | -0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | PRO | 0 | 0.011 | 0.009 | 29.490 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | PRO | 0 | 0.024 | 0.014 | 33.324 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | GLY | 0 | 0.029 | 0.014 | 34.997 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | LEU | 0 | -0.061 | -0.028 | 32.439 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | ASN | 0 | -0.006 | 0.000 | 26.457 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | GLU | -1 | -0.964 | -1.001 | 26.710 | -10.559 | -10.559 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | VAL | 0 | 0.023 | 0.010 | 22.384 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | LEU | 0 | -0.052 | -0.023 | 25.035 | -0.257 | -0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | ALA | 0 | 0.041 | 0.017 | 24.413 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | GLY | 0 | -0.001 | -0.009 | 26.519 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | LEU | 0 | -0.019 | -0.014 | 25.789 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | GLU | -1 | -0.853 | -0.923 | 29.768 | -8.763 | -8.763 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | LEU | 0 | -0.019 | 0.001 | 31.704 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | GLU | -1 | -0.893 | -0.951 | 31.978 | -9.470 | -9.470 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | ASP | -1 | -0.932 | -0.954 | 34.976 | -7.721 | -7.721 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | GLU | -1 | -0.950 | -0.982 | 37.947 | -7.371 | -7.371 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | CYS | 0 | 0.003 | 0.013 | 38.310 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | ALA | 0 | 0.017 | -0.012 | 40.374 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | GLY | 0 | -0.030 | -0.023 | 41.394 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | CYS | 0 | -0.072 | -0.003 | 36.693 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | THR | 0 | -0.009 | -0.014 | 37.616 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ASP | -1 | -0.854 | -0.938 | 39.186 | -7.629 | -7.629 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | GLY | 0 | 0.011 | 0.001 | 36.130 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | THR | 0 | -0.043 | -0.028 | 36.838 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | PHE | 0 | 0.039 | 0.008 | 33.621 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | ARG | 1 | 0.920 | 0.956 | 35.316 | 8.564 | 8.564 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | GLY | 0 | 0.040 | 0.023 | 38.991 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | THR | 0 | -0.026 | 0.003 | 36.971 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | ARG | 1 | 0.961 | 0.981 | 37.437 | 7.533 | 7.533 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | TYR | 0 | 0.000 | 0.003 | 32.911 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | PHE | 0 | 0.022 | 0.009 | 32.187 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | THR | 0 | -0.044 | -0.027 | 35.256 | 0.324 | 0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | CYS | 0 | -0.088 | -0.050 | 35.102 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | ALA | 0 | 0.033 | 0.026 | 37.774 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | LEU | 0 | 0.041 | 0.000 | 39.793 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | LYS | 1 | 0.911 | 0.962 | 41.063 | 7.113 | 7.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | LYS | 1 | 0.902 | 0.951 | 36.983 | 8.271 | 8.271 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ALA | 0 | -0.030 | 0.015 | 34.631 | -0.303 | -0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | LEU | 0 | 0.019 | 0.004 | 32.151 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | PHE | 0 | -0.031 | -0.008 | 30.802 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | VAL | 0 | 0.037 | 0.026 | 26.979 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | LYS | 1 | 0.941 | 0.968 | 24.917 | 10.409 | 10.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | LEU | 0 | 0.067 | 0.038 | 20.046 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | LYS | 1 | 0.957 | 0.969 | 19.629 | 12.093 | 12.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | SER | 0 | -0.056 | -0.028 | 20.397 | -0.185 | -0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | CYS | 0 | -0.042 | -0.001 | 21.614 | 0.595 | 0.595 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | ARG | 1 | 0.927 | 0.962 | 15.519 | 16.746 | 16.746 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | PRO | 0 | 0.017 | -0.005 | 15.972 | 0.542 | 0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | ASP | -1 | -0.857 | -0.931 | 19.290 | -12.460 | -12.460 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | SER | 0 | -0.010 | -0.019 | 20.026 | -0.423 | -0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | ARG | 1 | 0.901 | 0.966 | 21.954 | 10.818 | 10.818 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | PHE | 0 | 0.020 | 0.012 | 25.065 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | ALA | 0 | -0.034 | 0.004 | 20.419 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | SER | 0 | -0.017 | -0.014 | 22.292 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | LEU | 0 | 0.002 | -0.009 | 16.142 | -0.559 | -0.559 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | GLN | 0 | -0.020 | -0.011 | 19.920 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | PRO | 0 | 0.034 | 0.017 | 22.628 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | SER | 0 | -0.018 | -0.012 | 25.846 | 0.661 | 0.661 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | GLY | 0 | -0.003 | 0.011 | 24.556 | -0.377 | -0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | PRO | 0 | -0.035 | -0.017 | 24.753 | -0.430 | -0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | SER | 0 | 0.010 | -0.004 | 23.224 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | SER | 0 | -0.055 | -0.026 | 25.997 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | GLY | -1 | -0.916 | -0.942 | 28.508 | -9.430 | -9.430 | 0.000 | 0.000 | 0.000 | 0.000 |