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: RLRK8
Calculation Name: 5MDX-m-Other547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | chlorophyll b | pheophytin a | protoporphyrin ix containing fe | fe (ii) ion
Ligand 3-letter code: CLA | CHL | PHO | HEM | FE2
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5MDX
Chain ID: m
UniProt ID: P04778
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 | 29 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -87428.803864 |
|---|---|
| FMO2-HF: Nuclear repulsion | 76784.597067 |
| FMO2-HF: Total energy | -10644.206798 |
| FMO2-MP2: Total energy | -10676.667717 |
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. |
| 33.485 | 38.948 | 2.257 | -2.587 | -5.133 | 0.008 |
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 | LEU | 0 | 0.051 | 0.025 | 2.380 | -3.828 | -0.115 | 1.686 | -1.867 | -3.532 | 0.012 |
| 4 | A | 7 | ALA | 0 | 0.034 | 0.010 | 2.547 | 1.046 | 2.378 | 0.571 | -0.593 | -1.310 | -0.004 |
| 5 | A | 8 | PHE | 0 | -0.003 | 0.025 | 4.108 | 5.078 | 5.496 | 0.000 | -0.127 | -0.291 | 0.000 |
| 6 | A | 9 | ILE | 0 | 0.043 | 0.017 | 5.546 | 5.232 | 5.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 10 | ALA | 0 | 0.013 | 0.010 | 7.271 | 3.126 | 3.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 11 | THR | 0 | -0.012 | -0.021 | 6.964 | 3.205 | 3.205 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 12 | ALA | 0 | 0.002 | 0.000 | 9.445 | 2.794 | 2.794 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 13 | LEU | 0 | -0.004 | -0.009 | 11.626 | 2.233 | 2.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 14 | PHE | 0 | -0.026 | -0.013 | 12.332 | 1.641 | 1.641 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 15 | ILE | 0 | 0.016 | 0.012 | 12.378 | 1.279 | 1.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 16 | LEU | 0 | -0.003 | 0.003 | 15.521 | 1.343 | 1.343 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 17 | VAL | 0 | 0.015 | 0.013 | 17.463 | 1.072 | 1.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 18 | PRO | 0 | -0.002 | 0.000 | 18.048 | 1.018 | 1.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 19 | THR | 0 | 0.001 | -0.015 | 19.336 | 0.889 | 0.889 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 20 | ALA | 0 | 0.039 | 0.022 | 21.836 | 0.743 | 0.743 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 21 | PHE | 0 | -0.018 | -0.008 | 23.499 | 0.682 | 0.682 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 22 | LEU | 0 | 0.020 | 0.000 | 23.712 | 0.573 | 0.573 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 23 | LEU | 0 | 0.007 | 0.012 | 24.973 | 0.515 | 0.515 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 24 | ILE | 0 | -0.011 | -0.002 | 27.149 | 0.521 | 0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 25 | ILE | 0 | -0.022 | -0.009 | 28.260 | 0.444 | 0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 26 | TYR | 0 | 0.006 | 0.016 | 30.593 | 0.387 | 0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 27 | VAL | 0 | 0.012 | -0.007 | 32.011 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 28 | LYS | 1 | 0.941 | 0.965 | 33.179 | 9.713 | 9.713 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 29 | THR | 0 | -0.051 | -0.014 | 34.469 | 0.259 | 0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 30 | VAL | 0 | -0.040 | -0.020 | 36.253 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 31 | SER | 0 | -0.119 | -0.063 | 38.456 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 32 | GLN | -1 | -0.941 | -0.952 | 40.332 | -7.194 | -7.194 | 0.000 | 0.000 | 0.000 | 0.000 |