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: MZY9Z
Calculation Name: 1JB0-K-Xray549
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | phylloquinone | iron/sulfur cluster | calcium ion
Ligand 3-letter code: CLA | BCR | LMG | LHG | PQN | SF4 | CA
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1JB0
Chain ID: K
UniProt ID: P0A405
Base Structure: X-ray
Registration Date: 2025-10-11
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 47 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -175741.720308 |
|---|---|
| FMO2-HF: Nuclear repulsion | 159341.932509 |
| FMO2-HF: Total energy | -16399.7878 |
| FMO2-MP2: Total energy | -16448.239624 |
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(K:20:ILE)
Summations of interaction energy for
fragment #1(K:20:ILE)
| 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. |
| 64.744 | 68.28 | 0.117 | -1.064 | -2.587 | -0.002 |
Interaction energy analysis for fragmet #1(K:20:ILE)
| 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 | K | 22 | CYS | 0 | 0.027 | 0.016 | 3.198 | 4.857 | 6.794 | 0.034 | -0.690 | -1.281 | 0.001 |
| 4 | K | 23 | ASN | 0 | 0.051 | 0.029 | 3.493 | 11.314 | 12.040 | 0.004 | -0.189 | -0.541 | -0.001 |
| 5 | K | 24 | LEU | 0 | 0.026 | 0.024 | 5.015 | 6.423 | 6.599 | -0.001 | -0.017 | -0.158 | 0.000 |
| 44 | K | 74 | VAL | 0 | -0.082 | -0.043 | 3.003 | -3.283 | -2.648 | 0.081 | -0.168 | -0.547 | -0.002 |
| 45 | K | 75 | SER | 0 | -0.023 | -0.007 | 5.362 | 0.923 | 0.985 | -0.001 | 0.000 | -0.060 | 0.000 |
| 6 | K | 25 | PHE | 0 | 0.015 | 0.011 | 7.147 | 4.859 | 4.859 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | K | 26 | ALA | 0 | 0.032 | 0.023 | 8.201 | 3.562 | 3.562 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | K | 27 | ILE | 0 | 0.021 | 0.004 | 8.020 | 3.139 | 3.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | K | 28 | ALA | 0 | -0.025 | -0.010 | 10.960 | 2.083 | 2.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | K | 29 | LEU | 0 | -0.008 | -0.014 | 12.702 | 1.906 | 1.906 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | K | 30 | GLY | 0 | 0.016 | 0.004 | 13.962 | 1.461 | 1.461 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | K | 31 | ARG | 1 | 0.826 | 0.930 | 11.981 | 23.385 | 23.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | K | 32 | TYR | 0 | 0.070 | 0.020 | 17.047 | 0.968 | 0.968 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | K | 33 | ALA | 0 | -0.025 | -0.006 | 19.088 | 0.845 | 0.845 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | K | 34 | ILE | 0 | 0.025 | 0.021 | 20.090 | 0.749 | 0.749 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | K | 35 | GLN | 0 | -0.010 | -0.005 | 20.850 | 1.041 | 1.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | K | 36 | SER | 0 | 0.026 | 0.001 | 22.277 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | K | 37 | ARG | 1 | 0.976 | 0.996 | 24.713 | 9.829 | 9.829 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | K | 38 | GLY | 0 | 0.003 | 0.008 | 28.092 | 0.388 | 0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | K | 39 | LYS | 1 | 0.801 | 0.902 | 24.121 | 12.145 | 12.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | K | 40 | GLY | 0 | -0.015 | -0.007 | 27.386 | 0.388 | 0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | K | 41 | PRO | 0 | -0.036 | -0.024 | 28.935 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | K | 42 | GLY | 0 | 0.012 | 0.002 | 27.988 | -0.328 | -0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | K | 43 | LEU | -1 | -0.889 | -0.938 | 24.239 | -11.522 | -11.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | K | 55 | GLY | 1 | 0.840 | 0.884 | 22.622 | 13.128 | 13.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | K | 56 | LEU | 0 | 0.120 | 0.077 | 23.351 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | K | 57 | PRO | 0 | 0.037 | 0.027 | 20.937 | -0.806 | -0.806 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | K | 58 | GLU | -1 | -0.812 | -0.918 | 20.854 | -12.339 | -12.339 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | K | 59 | LEU | 0 | -0.043 | 0.005 | 19.094 | -0.328 | -0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | K | 60 | LEU | 0 | 0.036 | 0.026 | 15.486 | -1.054 | -1.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | K | 61 | ALA | 0 | 0.058 | 0.054 | 16.397 | -1.196 | -1.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | K | 62 | THR | 0 | -0.055 | -0.044 | 15.104 | -0.973 | -0.973 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | K | 63 | THR | 0 | -0.032 | -0.035 | 12.099 | -1.518 | -1.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | K | 64 | SER | 0 | -0.004 | 0.013 | 11.843 | -2.016 | -2.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | K | 65 | PHE | 0 | 0.070 | 0.021 | 13.038 | -0.953 | -0.953 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | K | 66 | GLY | 0 | 0.041 | 0.008 | 10.761 | -0.809 | -0.809 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | K | 67 | HIS | 1 | 0.878 | 0.927 | 8.408 | 23.096 | 23.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | K | 68 | LEU | 0 | 0.017 | 0.020 | 9.128 | -1.072 | -1.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | K | 69 | LEU | 0 | 0.015 | 0.004 | 10.335 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | K | 70 | ALA | 0 | -0.019 | -0.029 | 5.228 | -1.377 | -1.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | K | 71 | ALA | 0 | -0.018 | -0.007 | 6.332 | -2.221 | -2.221 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | K | 72 | GLY | 0 | 0.043 | 0.033 | 8.473 | 0.862 | 0.862 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | K | 73 | VAL | 0 | -0.028 | -0.029 | 4.883 | -0.609 | -0.609 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | K | 76 | GLY | 0 | -0.041 | -0.005 | 7.645 | 2.405 | 2.405 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | K | 77 | LEU | -1 | -0.957 | -0.968 | 9.220 | -22.244 | -22.244 | 0.000 | 0.000 | 0.000 | 0.000 |