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: ZLQRN
Calculation Name: 7DR0-I-Other547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | chlorophyll a isomer | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | phylloquinone | iron/sulfur cluster
Ligand 3-letter code: CLA | CL0 | BCR | LMG | LHG | PQN | SF4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7DR0
Chain ID: I
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-05
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 | -90304.326472 |
|---|---|
| FMO2-HF: Nuclear repulsion | 78736.852673 |
| FMO2-HF: Total energy | -11567.473799 |
| FMO2-MP2: Total energy | -11600.389447 |
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:4:ASN)
Summations of interaction energy for
fragment #1(A:4: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. |
| 3.553 | 7.919 | 1.015 | -1.876 | -3.505 | 0 |
Interaction energy analysis for fragmet #1(A:4: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 | 6 | PRO | 0 | 0.059 | 0.024 | 2.528 | 0.332 | 3.034 | 0.322 | -1.202 | -1.822 | -0.005 |
| 4 | A | 7 | SER | 0 | 0.004 | -0.001 | 3.686 | 7.528 | 8.047 | 0.005 | -0.171 | -0.353 | 0.000 |
| 5 | A | 8 | ILE | 0 | -0.014 | 0.009 | 2.775 | 3.215 | 4.360 | 0.688 | -0.503 | -1.330 | 0.005 |
| 6 | A | 9 | LEU | 0 | 0.026 | -0.001 | 6.416 | 3.769 | 3.769 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 10 | VAL | 0 | 0.018 | 0.012 | 8.632 | 2.708 | 2.708 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 11 | PRO | 0 | 0.013 | 0.016 | 9.093 | 2.360 | 2.360 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 12 | MET | 0 | 0.010 | 0.010 | 10.797 | 1.895 | 1.895 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 13 | VAL | 0 | 0.004 | -0.014 | 12.615 | 1.547 | 1.547 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 14 | GLY | 0 | 0.005 | 0.013 | 14.344 | 1.111 | 1.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 15 | ILE | 0 | -0.026 | -0.017 | 14.946 | 0.917 | 0.917 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 16 | VAL | 0 | -0.009 | -0.004 | 14.077 | 0.967 | 0.967 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 17 | LEU | 0 | 0.012 | -0.002 | 15.084 | 0.835 | 0.835 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 18 | PRO | 0 | -0.001 | 0.005 | 18.090 | 0.857 | 0.857 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 19 | ALA | 0 | 0.047 | 0.024 | 20.413 | 0.715 | 0.715 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 20 | ILE | 0 | -0.021 | -0.009 | 18.388 | 0.567 | 0.567 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 21 | VAL | 0 | 0.001 | -0.004 | 22.308 | 0.553 | 0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 22 | MET | 0 | -0.013 | -0.009 | 24.284 | 0.499 | 0.499 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 23 | ALA | 0 | 0.003 | 0.011 | 25.577 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 24 | LEU | 0 | -0.026 | -0.019 | 24.606 | 0.360 | 0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 25 | LEU | 0 | -0.010 | -0.009 | 27.755 | 0.339 | 0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 26 | PHE | 0 | -0.021 | -0.004 | 29.993 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 27 | VAL | 0 | -0.003 | -0.009 | 31.233 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 28 | TYR | 0 | -0.055 | -0.024 | 32.422 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 29 | ILE | 0 | -0.055 | -0.023 | 33.358 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 30 | GLU | -1 | -0.972 | -0.986 | 35.901 | -8.050 | -8.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 31 | THR | 0 | -0.100 | -0.042 | 37.081 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 32 | ASP | -1 | -0.965 | -0.977 | 39.082 | -7.208 | -7.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 33 | GLU | -2 | -1.954 | -1.970 | 42.097 | -13.690 | -13.690 | 0.000 | 0.000 | 0.000 | 0.000 |