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: 4GLGN
Calculation Name: 4V9G-A-Xray547
Preferred Name:
Target Type:
Ligand Name: bacteriochlorophyll a | bacteriopheophytin a | ubiquinone-10 | spheroidene | phosphate ion | fe (ii) ion
Ligand 3-letter code: BCL | BPH | U10 | SPO | PO4 | FE2
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4V9G
Chain ID: A
UniProt ID: P0C0X9
Base Structure: X-ray
Registration Date: 2025-10-06
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 | 57 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -220024.511896 |
|---|---|
| FMO2-HF: Nuclear repulsion | 197547.261064 |
| FMO2-HF: Total energy | -22477.250832 |
| FMO2-MP2: Total energy | -22542.026475 |
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:2:ALA)
Summations of interaction energy for
fragment #1(A:2:ALA)
| 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. |
| 60.862 | 64.414 | 6.878 | -5.155 | -5.272 | -0.066 |
Interaction energy analysis for fragmet #1(A:2:ALA)
| 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 | 4 | LYS | 1 | 0.962 | 0.978 | 3.732 | 35.915 | 38.004 | -0.029 | -1.185 | -0.875 | -0.005 |
| 9 | A | 10 | HIS | 0 | -0.040 | -0.007 | 2.134 | -41.051 | -40.110 | 6.910 | -3.873 | -3.977 | -0.061 |
| 10 | A | 11 | LEU | 0 | -0.030 | -0.022 | 3.890 | 7.032 | 7.159 | 0.000 | -0.039 | -0.087 | 0.000 |
| 12 | A | 13 | THR | 0 | -0.002 | 0.006 | 4.793 | -3.286 | -3.237 | -0.001 | -0.002 | -0.046 | 0.000 |
| 15 | A | 16 | LYS | 1 | 0.931 | 0.958 | 4.117 | 33.195 | 33.382 | -0.001 | -0.027 | -0.159 | 0.000 |
| 16 | A | 17 | THR | 0 | 0.037 | 0.013 | 3.831 | -3.622 | -3.463 | -0.001 | -0.029 | -0.128 | 0.000 |
| 4 | A | 5 | THR | 0 | 0.019 | 0.009 | 6.408 | 6.633 | 6.633 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | ILE | 0 | -0.029 | 0.002 | 8.918 | 1.699 | 1.699 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | PHE | 0 | 0.006 | -0.001 | 8.736 | 2.135 | 2.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | ASN | 0 | -0.010 | -0.007 | 7.436 | 1.359 | 1.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | ASP | -1 | -0.848 | -0.937 | 4.834 | -45.286 | -45.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | ASN | 0 | 0.039 | 0.011 | 6.225 | 5.201 | 5.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | ASN | 0 | 0.037 | 0.027 | 7.853 | 2.742 | 2.742 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | PRO | 0 | 0.010 | 0.012 | 7.727 | 0.553 | 0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | ASN | 0 | -0.007 | -0.012 | 6.178 | 2.372 | 2.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LEU | 0 | 0.029 | 0.025 | 9.642 | 2.641 | 2.641 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ARG | 1 | 0.912 | 0.952 | 10.266 | 21.436 | 21.436 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | LEU | 0 | 0.039 | 0.031 | 6.631 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | TRP | 0 | 0.056 | 0.014 | 10.597 | 1.244 | 1.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | VAL | 0 | -0.034 | 0.001 | 13.658 | 1.078 | 1.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | ALA | 0 | -0.029 | -0.024 | 14.048 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | PHE | 0 | 0.033 | 0.013 | 12.680 | 0.737 | 0.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | GLN | 0 | 0.038 | 0.018 | 12.145 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | MET | 0 | -0.022 | -0.017 | 16.650 | 0.661 | 0.661 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | MET | 0 | 0.036 | 0.031 | 19.435 | 0.727 | 0.727 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | LYS | 1 | 0.975 | 0.976 | 21.171 | 14.290 | 14.290 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | GLY | 0 | -0.030 | -0.007 | 23.646 | 0.498 | 0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | ALA | 0 | 0.018 | -0.003 | 25.127 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | GLY | 0 | 0.005 | 0.004 | 26.524 | 0.361 | 0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | TRP | 0 | 0.010 | 0.018 | 28.329 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | ALA | 0 | -0.029 | -0.010 | 29.744 | 0.397 | 0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | GLY | 0 | 0.036 | 0.021 | 31.575 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | GLY | 0 | 0.024 | 0.009 | 34.260 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | VAL | 0 | 0.018 | 0.009 | 34.197 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | PHE | 0 | 0.005 | -0.009 | 31.453 | 0.182 | 0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | PHE | 0 | -0.013 | 0.008 | 35.834 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | GLY | 0 | 0.041 | 0.011 | 38.449 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | THR | 0 | -0.030 | -0.025 | 38.933 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | LEU | 0 | -0.025 | -0.023 | 37.851 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | LEU | 0 | 0.000 | 0.009 | 41.813 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LEU | 0 | 0.020 | -0.001 | 44.451 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | ILE | 0 | -0.034 | 0.004 | 43.597 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | GLY | 0 | 0.025 | 0.007 | 43.114 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | PHE | 0 | 0.022 | 0.002 | 44.031 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | PHE | 0 | 0.037 | 0.021 | 46.832 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | ARG | 1 | 0.878 | 0.923 | 47.206 | 6.411 | 6.411 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | VAL | 0 | 0.022 | 0.035 | 45.369 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | VAL | 0 | 0.017 | 0.008 | 48.018 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | GLY | 0 | -0.048 | -0.010 | 51.484 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | ARG | 1 | 0.925 | 0.956 | 48.823 | 6.400 | 6.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | MET | 0 | 0.002 | -0.012 | 52.688 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | LEU | 0 | 0.054 | 0.024 | 55.404 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | PRO | 0 | -0.054 | -0.018 | 55.917 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | ILE | 0 | -0.059 | -0.019 | 56.350 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | GLN | -1 | -0.918 | -0.946 | 59.929 | -4.984 | -4.984 | 0.000 | 0.000 | 0.000 | 0.000 |