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: JVGN9
Calculation Name: 4L6V-7-Xray547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | phylloquinone | iron/sulfur cluster
Ligand 3-letter code: CLA | BCR | LMG | LHG | PQN | SF4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4L6V
Chain ID: 7
UniProt ID: P29254
Base Structure: X-ray
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 | 31 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -92083.631119 |
|---|---|
| FMO2-HF: Nuclear repulsion | 80408.939809 |
| FMO2-HF: Total energy | -11674.69131 |
| FMO2-MP2: Total energy | -11708.891787 |
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:1:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
| 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. |
| -11.069 | -7.204 | 2.07 | -2.306 | -3.631 | -0.021 |
Interaction energy analysis for fragmet #1(A:1:MET)
| 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 | 3 | LEU | 0 | 0.014 | 0.005 | 2.516 | -5.845 | -2.942 | 1.992 | -1.956 | -2.939 | -0.019 |
| 4 | A | 4 | SER | 0 | 0.026 | 0.010 | 3.845 | 3.032 | 3.248 | 0.000 | -0.023 | -0.194 | 0.000 |
| 7 | A | 7 | GLN | 0 | -0.006 | -0.008 | 3.301 | -3.483 | -2.737 | 0.078 | -0.327 | -0.498 | -0.002 |
| 5 | A | 5 | ASP | -1 | -0.830 | -0.924 | 5.671 | -20.638 | -20.638 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | THR | 0 | 0.009 | -0.001 | 8.299 | 1.082 | 1.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ILE | 0 | 0.021 | 0.023 | 7.842 | 1.221 | 1.221 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | LEU | 0 | 0.033 | 0.007 | 10.355 | 1.500 | 1.500 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | ALA | 0 | -0.002 | 0.001 | 10.556 | 1.134 | 1.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ALA | 0 | -0.005 | -0.003 | 11.204 | 1.006 | 1.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | LEU | 0 | -0.002 | 0.000 | 12.988 | 1.060 | 1.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | VAL | 0 | -0.008 | -0.001 | 15.635 | 0.911 | 0.911 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | VAL | 0 | -0.021 | -0.014 | 14.412 | 0.749 | 0.749 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ALA | 0 | 0.011 | -0.002 | 17.106 | 0.665 | 0.665 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | LEU | 0 | 0.011 | 0.002 | 18.870 | 0.642 | 0.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LEU | 0 | -0.011 | 0.014 | 21.059 | 0.580 | 0.580 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | 0.008 | -0.006 | 20.404 | 0.483 | 0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ALA | 0 | 0.025 | 0.022 | 23.246 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | PHE | 0 | -0.008 | -0.005 | 25.121 | 0.514 | 0.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | LEU | 0 | -0.031 | -0.019 | 25.567 | 0.400 | 0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | ALA | 0 | 0.028 | 0.019 | 27.199 | 0.324 | 0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | PHE | 0 | 0.007 | 0.020 | 28.971 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ARG | 1 | 0.974 | 0.991 | 31.080 | 9.036 | 9.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LEU | 0 | -0.005 | 0.009 | 30.986 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | SER | 0 | -0.033 | -0.043 | 32.495 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | THR | 0 | -0.067 | -0.051 | 34.746 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLU | -1 | -0.944 | -0.979 | 36.591 | -7.330 | -7.330 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | LEU | 0 | -0.064 | -0.031 | 35.865 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | TYR | 0 | -0.105 | -0.035 | 39.068 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | LYS | 0 | 0.039 | 0.037 | 41.353 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |