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: MR25Z
Calculation Name: 1IXT-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1IXT
Chain ID: A
UniProt ID: Q9GU57
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 | 24 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -82371.323693 |
|---|---|
| FMO2-HF: Nuclear repulsion | 70815.342839 |
| FMO2-HF: Total energy | -11555.980853 |
| FMO2-MP2: Total energy | -11583.765949 |
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:SER)
Summations of interaction energy for
fragment #1(A:1:SER)
| 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. |
| -18.343 | -16.595 | -0.005 | -0.632 | -1.112 | 0.001 |
Interaction energy analysis for fragmet #1(A:1:SER)
| 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 | ASN | 0 | 0.004 | 0.002 | 3.844 | 0.487 | 1.854 | -0.010 | -0.551 | -0.806 | 0.001 |
| 22 | A | 25 | ALA | 0 | -0.004 | 0.008 | 3.401 | 3.057 | 3.350 | 0.007 | -0.075 | -0.226 | 0.000 |
| 23 | A | 26 | VAL | 0 | -0.039 | -0.021 | 5.339 | 0.641 | 0.657 | -0.001 | -0.001 | -0.013 | 0.000 |
| 24 | A | 27 | ASN | -1 | -0.916 | -0.949 | 4.688 | -42.102 | -42.030 | -0.001 | -0.005 | -0.067 | 0.000 |
| 4 | A | 4 | ASN | 0 | 0.027 | 0.012 | 5.923 | 3.040 | 3.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | SER | 0 | -0.029 | -0.034 | 9.675 | 0.699 | 0.699 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | CYS | 0 | 0.056 | 0.034 | 10.520 | -0.597 | -0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLN | 0 | -0.022 | -0.011 | 15.151 | 1.185 | 1.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | SER | 0 | -0.027 | -0.033 | 18.108 | 0.676 | 0.676 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | HIS | 0 | -0.035 | -0.045 | 14.280 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | SER | 0 | 0.039 | 0.011 | 14.069 | -1.002 | -1.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ASP | -1 | -0.852 | -0.855 | 14.240 | -17.979 | -17.979 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | CYS | 0 | -0.040 | -0.029 | 8.928 | 0.415 | 0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ALA | 0 | 0.010 | 0.005 | 6.756 | 0.547 | 0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | 0.011 | -0.016 | 6.214 | 0.629 | 0.629 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | HIS | 0 | 0.021 | 0.031 | 6.542 | 1.970 | 1.970 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ILE | 0 | 0.044 | 0.030 | 7.943 | 2.923 | 2.923 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 19 | THR | 0 | -0.052 | -0.017 | 9.481 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 20 | PHE | 0 | 0.049 | 0.014 | 11.713 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 21 | ARG | 1 | 0.899 | 0.956 | 7.072 | 33.975 | 33.975 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | GLY | 0 | 0.078 | 0.042 | 9.920 | -2.236 | -2.236 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 24 | GLY | 0 | -0.038 | -0.034 | 5.936 | -4.686 | -4.686 | 0.000 | 0.000 | 0.000 | 0.000 |