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: 8KQNY
Calculation Name: 6KMX-A-Other547
Preferred Name:
Target Type:
Ligand Name: chlorophyll f | chlorophyll a | chlorophyll a isomer | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | phylloquinone | iron/sulfur cluster | calcium ion
Ligand 3-letter code: F6C | CLA | CL0 | BCR | LMG | LHG | LMT | PQN | SF4 | CA
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 6KMX
Chain ID: A
UniProt ID: A0A1Z3
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 | 46 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -161655.851194 |
|---|---|
| FMO2-HF: Nuclear repulsion | 145749.419835 |
| FMO2-HF: Total energy | -15906.431359 |
| FMO2-MP2: Total energy | -15952.317151 |
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:35:CYS)
Summations of interaction energy for
fragment #1(A:35:CYS)
| 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. |
| 26.944 | 30.687 | 0.117 | -1.357 | -2.504 | -0.003 |
Interaction energy analysis for fragmet #1(A:35:CYS)
| 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 | 37 | LEU | 0 | 0.067 | 0.041 | 3.546 | 4.591 | 6.874 | -0.007 | -0.944 | -1.332 | -0.002 |
| 4 | A | 38 | PHE | 0 | 0.014 | 0.013 | 3.253 | 7.445 | 8.349 | 0.028 | -0.282 | -0.651 | -0.001 |
| 5 | A | 39 | VAL | 0 | 0.014 | 0.009 | 3.859 | 6.448 | 6.983 | 0.097 | -0.129 | -0.503 | 0.000 |
| 33 | A | 80 | HIS | 0 | -0.083 | -0.049 | 5.048 | -11.103 | -11.082 | -0.001 | -0.002 | -0.018 | 0.000 |
| 6 | A | 40 | LEU | 0 | 0.020 | 0.008 | 6.463 | 5.195 | 5.195 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 41 | ALA | 0 | -0.008 | 0.001 | 7.957 | 3.928 | 3.928 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 42 | ILE | 0 | -0.008 | -0.028 | 8.253 | 3.309 | 3.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 43 | GLY | 0 | 0.005 | 0.018 | 10.326 | 2.154 | 2.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 44 | LYS | 1 | 0.917 | 0.953 | 12.268 | 21.187 | 21.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 45 | TYR | 0 | -0.013 | -0.019 | 12.436 | 1.792 | 1.792 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 46 | ALA | 0 | -0.005 | 0.003 | 15.124 | 0.678 | 0.678 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 47 | ILE | 0 | -0.025 | 0.002 | 16.875 | 0.816 | 0.816 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 48 | GLN | 0 | -0.022 | -0.016 | 17.712 | 0.866 | 0.866 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 49 | ARG | 1 | 0.895 | 0.959 | 14.598 | 18.978 | 18.978 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 50 | PRO | 0 | 0.038 | 0.027 | 20.843 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 51 | GLY | 0 | 0.014 | 0.009 | 23.614 | 0.356 | 0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 52 | ALA | 0 | -0.047 | -0.038 | 20.552 | -0.767 | -0.767 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 53 | GLY | 0 | 0.024 | 0.008 | 21.377 | 0.546 | 0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 54 | PRO | 0 | -0.046 | -0.018 | 22.326 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 68 | GLY | 0 | 0.016 | -0.001 | 20.871 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 69 | LEU | 0 | 0.008 | 0.023 | 18.282 | -0.713 | -0.713 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 70 | PRO | 0 | 0.013 | -0.001 | 17.015 | -1.078 | -1.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 71 | GLU | -1 | -0.747 | -0.888 | 16.708 | -16.708 | -16.708 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 72 | LEU | 0 | 0.004 | 0.041 | 11.644 | -1.637 | -1.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 73 | LEU | 0 | 0.059 | 0.020 | 11.950 | -2.210 | -2.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 74 | ALA | 0 | 0.015 | 0.026 | 12.831 | -1.360 | -1.360 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 75 | THR | 0 | -0.020 | -0.034 | 10.101 | -0.563 | -0.563 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 76 | ALA | 0 | 0.004 | -0.004 | 8.139 | -3.070 | -3.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 77 | SER | 0 | -0.017 | -0.009 | 8.036 | -3.397 | -3.397 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 78 | LEU | 0 | 0.009 | 0.010 | 9.680 | -1.318 | -1.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 79 | GLY | 0 | 0.004 | -0.006 | 6.269 | -0.637 | -0.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 81 | ILE | 0 | -0.002 | 0.013 | 6.718 | 0.541 | 0.541 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 82 | LEU | 0 | 0.033 | 0.000 | 8.269 | 0.651 | 0.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 83 | GLY | 0 | -0.033 | -0.010 | 4.884 | -1.347 | -1.347 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 84 | ALA | 0 | 0.008 | -0.001 | 5.541 | 0.598 | 0.598 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 85 | GLY | 0 | 0.029 | 0.016 | 8.615 | 1.743 | 1.743 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 86 | MET | 0 | -0.014 | -0.006 | 7.513 | 0.646 | 0.646 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 87 | ILE | 0 | -0.045 | -0.026 | 4.809 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 88 | LEU | 0 | -0.017 | -0.009 | 8.344 | 2.237 | 2.237 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 89 | GLY | 0 | 0.027 | 0.025 | 11.968 | 1.398 | 1.398 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 90 | LEU | 0 | -0.043 | -0.041 | 8.763 | 0.862 | 0.862 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 91 | GLY | 0 | -0.032 | -0.001 | 12.224 | 0.388 | 0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 92 | ASN | 0 | -0.120 | -0.066 | 13.470 | 0.458 | 0.458 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 93 | ALA | -1 | -0.924 | -0.938 | 15.748 | -15.571 | -15.571 | 0.000 | 0.000 | 0.000 | 0.000 |