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: G7RQ1
Calculation Name: 7F9O-I-Other547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | chlorophyll b | chlorophyll a isomer | digalactosyl diacyl glycerol (dgdg) | (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol | (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | phylloquinone | iron/sulfur cluster
Ligand 3-letter code: CLA | CHL | CL0 | DGD | XAT | LUT | SQD | BCR | LMG | LHG | PQN | SF4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7F9O
Chain ID: I
Base Structure: ElectronMicroscopy
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 | 30 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -92577.652712 |
|---|---|
| FMO2-HF: Nuclear repulsion | 81178.359659 |
| FMO2-HF: Total energy | -11399.293053 |
| FMO2-MP2: Total energy | -11432.96693 |
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:3:ASN)
Summations of interaction energy for
fragment #1(A:3:ASN)
| 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. |
| 45.054 | 50.411 | 0.433 | -2.359 | -3.431 | -0.018 |
Interaction energy analysis for fragmet #1(A:3:ASN)
| 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 | 5 | PRO | 0 | 0.058 | 0.021 | 2.671 | 2.475 | 4.851 | 0.222 | -1.013 | -1.585 | -0.005 |
| 4 | A | 6 | SER | 0 | -0.001 | -0.002 | 2.896 | -3.011 | -0.530 | 0.208 | -1.282 | -1.407 | -0.013 |
| 5 | A | 7 | ILE | 0 | 0.012 | 0.021 | 3.889 | 5.005 | 5.505 | 0.003 | -0.064 | -0.439 | 0.000 |
| 6 | A | 8 | PHE | 0 | 0.041 | -0.003 | 6.856 | 3.621 | 3.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 9 | VAL | 0 | 0.020 | 0.019 | 8.135 | 3.045 | 3.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 10 | PRO | 0 | 0.027 | 0.005 | 8.641 | 2.610 | 2.610 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 11 | LEU | 0 | -0.005 | 0.004 | 10.437 | 2.113 | 2.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 12 | VAL | 0 | -0.002 | -0.008 | 12.699 | 1.680 | 1.680 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 13 | GLY | 0 | 0.007 | 0.016 | 13.793 | 1.217 | 1.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 14 | LEU | 0 | -0.022 | -0.013 | 14.632 | 1.070 | 1.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 15 | VAL | 0 | -0.005 | 0.002 | 14.961 | 1.036 | 1.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 16 | PHE | 0 | 0.017 | -0.003 | 14.871 | 0.875 | 0.875 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 17 | PRO | 0 | 0.025 | 0.017 | 18.164 | 0.965 | 0.965 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 18 | ALA | 0 | 0.025 | 0.020 | 20.693 | 0.798 | 0.798 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 19 | ILE | 0 | -0.009 | -0.011 | 19.442 | 0.712 | 0.712 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 20 | ALA | 0 | 0.007 | 0.002 | 22.999 | 0.634 | 0.634 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 21 | MET | 0 | 0.002 | -0.004 | 23.367 | 0.692 | 0.692 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 22 | THR | 0 | -0.001 | 0.005 | 25.784 | 0.668 | 0.668 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 23 | SER | 0 | -0.022 | -0.003 | 27.017 | 0.591 | 0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 24 | LEU | 0 | 0.014 | -0.005 | 28.104 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 25 | PHE | 0 | 0.008 | 0.014 | 30.694 | 0.400 | 0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 26 | LEU | 0 | 0.002 | -0.008 | 31.021 | 0.391 | 0.391 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 27 | TYR | 0 | -0.082 | -0.034 | 33.116 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 28 | VAL | 0 | 0.009 | -0.010 | 34.785 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 29 | GLN | 0 | -0.039 | -0.007 | 36.493 | 0.344 | 0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 30 | LYS | 1 | 0.900 | 0.963 | 35.928 | 8.641 | 8.641 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 31 | LYS | 1 | 0.909 | 0.945 | 39.712 | 6.773 | 6.773 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 32 | LYS | 0 | 0.082 | 0.061 | 41.278 | 0.682 | 0.682 | 0.000 | 0.000 | 0.000 | 0.000 |