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: RM428
Calculation Name: 4OWF-G-Xray547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4OWF
Chain ID: G
UniProt ID: O88522
Base Structure: X-ray
Registration Date: 2025-10-04
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 | 29 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -105069.006955 |
|---|---|
| FMO2-HF: Nuclear repulsion | 92774.041213 |
| FMO2-HF: Total energy | -12294.965741 |
| FMO2-MP2: Total energy | -12327.489735 |
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:351:ARG)
Summations of interaction energy for
fragment #1(A:351:ARG)
| 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. |
| -46.362 | -37.601 | 3.338 | -4.688 | -7.409 | -0.034 |
Interaction energy analysis for fragmet #1(A:351:ARG)
| 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 | 353 | ARG | 1 | 0.860 | 0.914 | 3.070 | 38.375 | 41.025 | 0.109 | -1.336 | -1.423 | -0.006 |
| 4 | A | 354 | TRP | 0 | -0.009 | -0.007 | 4.748 | 0.407 | 0.533 | -0.001 | -0.011 | -0.113 | 0.000 |
| 15 | A | 365 | ALA | 0 | -0.008 | -0.010 | 2.186 | -5.992 | -5.957 | 1.449 | -0.465 | -1.019 | -0.004 |
| 16 | A | 366 | ALA | 0 | -0.057 | -0.035 | 2.718 | -29.623 | -25.737 | 1.262 | -2.284 | -2.864 | -0.024 |
| 17 | A | 367 | ALA | 0 | -0.021 | 0.010 | 4.419 | 2.263 | 2.388 | -0.001 | -0.020 | -0.103 | 0.000 |
| 18 | A | 368 | VAL | 0 | -0.009 | -0.015 | 3.866 | -9.321 | -9.072 | -0.001 | -0.030 | -0.218 | 0.000 |
| 27 | A | 377 | ARG | 1 | 0.897 | 0.957 | 3.169 | 93.307 | 94.997 | 0.521 | -0.542 | -1.669 | 0.000 |
| 5 | A | 355 | ALA | 0 | 0.077 | 0.050 | 7.181 | 2.728 | 2.728 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 356 | CYS | 0 | -0.056 | -0.024 | 10.968 | -0.861 | -0.861 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 357 | GLN | 0 | 0.009 | -0.009 | 12.168 | 4.494 | 4.494 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 358 | SER | 0 | -0.018 | -0.002 | 14.755 | 2.118 | 2.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 359 | CYS | 0 | 0.010 | 0.003 | 16.188 | 0.784 | 0.784 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 360 | THR | 0 | -0.031 | -0.013 | 15.360 | 1.227 | 1.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 361 | PHE | 0 | 0.043 | 0.018 | 13.100 | -0.865 | -0.865 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 362 | GLU | -1 | -0.894 | -0.947 | 9.952 | -51.402 | -51.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 363 | ASN | 0 | 0.045 | 0.027 | 8.442 | 3.497 | 3.497 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 364 | GLU | -1 | -0.759 | -0.881 | 7.369 | -61.077 | -61.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 369 | LEU | 0 | 0.016 | 0.013 | 5.408 | 1.032 | 1.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 370 | CYS | 0 | -0.097 | -0.034 | 9.028 | -1.677 | -1.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 371 | SER | 0 | -0.004 | -0.027 | 11.276 | 2.196 | 2.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 372 | ILE | 0 | -0.002 | 0.005 | 13.164 | 1.968 | 1.968 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 373 | CYS | 0 | -0.007 | -0.010 | 15.168 | 0.615 | 0.615 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 374 | GLU | -1 | -0.885 | -0.932 | 13.191 | -32.303 | -32.303 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 375 | ARG | 1 | 0.820 | 0.877 | 12.723 | 35.021 | 35.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 376 | PRO | 0 | 0.023 | -0.006 | 8.667 | -2.944 | -2.944 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 378 | LEU | 0 | -0.092 | -0.050 | 5.264 | -3.458 | -3.458 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 379 | ALA | -1 | -0.775 | -0.832 | 9.161 | -36.871 | -36.871 | 0.000 | 0.000 | 0.000 | 0.000 |