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: Y95Y2
Calculation Name: 1W7Z-A-Xray547
Preferred Name:
Target Type:
Ligand Name: formic acid
Ligand 3-letter code: FMT
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1W7Z
Chain ID: A
UniProt ID: P12071
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 | 28 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -98610.966976 |
|---|---|
| FMO2-HF: Nuclear repulsion | 86086.767059 |
| FMO2-HF: Total energy | -12524.199916 |
| FMO2-MP2: Total energy | -12555.200161 |
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. |
| -35.094 | -31.217 | 2.486 | -3.391 | -2.972 | -0.045 |
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 | PRO | 0 | 0.036 | 0.014 | 3.643 | -5.557 | -4.489 | 0.002 | -0.568 | -0.502 | -0.001 |
| 18 | A | 18 | GLY | 0 | -0.008 | -0.010 | 3.590 | -5.363 | -5.357 | 0.007 | -0.036 | 0.023 | 0.000 |
| 26 | A | 29 | SER | 0 | -0.044 | -0.038 | 2.121 | -27.077 | -24.544 | 2.477 | -2.670 | -2.340 | -0.043 |
| 27 | A | 30 | PRO | 0 | 0.002 | 0.013 | 3.964 | 4.546 | 4.816 | 0.000 | -0.117 | -0.153 | -0.001 |
| 4 | A | 4 | ARG | 1 | 0.948 | 0.974 | 5.864 | 37.216 | 37.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | ILE | 0 | 0.009 | 0.007 | 7.772 | 3.793 | 3.793 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | LEU | 0 | -0.010 | -0.006 | 10.738 | -1.077 | -1.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | ILE | 0 | 0.025 | 0.019 | 11.526 | 1.957 | 1.957 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ARG | 1 | 0.934 | 0.966 | 13.335 | 16.048 | 16.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | CYS | 0 | -0.069 | -0.034 | 9.248 | -1.243 | -1.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.887 | 0.932 | 16.297 | 14.479 | 14.479 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLN | 0 | 0.012 | 0.015 | 16.343 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ASP | -1 | -0.784 | -0.899 | 11.593 | -24.347 | -24.347 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.064 | -0.037 | 12.156 | -1.342 | -1.342 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ASP | -1 | -0.783 | -0.885 | 14.652 | -17.587 | -17.587 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | CYS | 0 | -0.067 | -0.020 | 9.346 | -0.279 | -0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | LEU | 0 | 0.021 | 0.005 | 8.320 | 0.572 | 0.572 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | ALA | 0 | 0.049 | 0.012 | 7.702 | -1.434 | -1.434 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | VAL | 0 | 0.060 | 0.043 | 6.212 | 3.181 | 3.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | GLY | 0 | 0.034 | 0.029 | 11.846 | 0.519 | 0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 23 | PRO | 0 | 0.014 | -0.011 | 12.613 | 1.250 | 1.250 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 24 | ASN | 0 | -0.029 | -0.018 | 12.490 | 0.895 | 0.895 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 25 | GLY | 0 | 0.015 | 0.017 | 15.967 | 0.666 | 0.666 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 26 | PHE | 0 | -0.042 | -0.039 | 12.233 | 1.004 | 1.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 28 | GLY | 0 | 0.017 | 0.004 | 6.753 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 31 | ALA | -1 | -0.925 | -0.951 | 6.200 | -36.221 | -36.221 | 0.000 | 0.000 | 0.000 | 0.000 |