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: ZL43N
Calculation Name: 6JO6-C-Other547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | chlorophyll b | chlorophyll a isomer | digalactosyl diacyl glycerol (dgdg) | (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | phylloquinone | iron/sulfur cluster
Ligand 3-letter code: CLA | CHL | CL0 | DGD | LUT | BCR | LMG | LHG | PQN | SF4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 6JO6
Chain ID: C
UniProt ID: P12154
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-04
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 | 80 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -483045.338618 |
|---|---|
| FMO2-HF: Nuclear repulsion | 449589.507861 |
| FMO2-HF: Total energy | -33455.830757 |
| FMO2-MP2: Total energy | -33543.157345 |
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:2:ALA)
Summations of interaction energy for
fragment #1(A:2:ALA)
| 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. |
| -120.611 | -118.977 | 12.6 | -7.353 | -6.878 | -0.07 |
Interaction energy analysis for fragmet #1(A:2:ALA)
| 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 | 4 | ILE | 0 | 0.004 | 0.008 | 3.678 | 2.558 | 3.893 | -0.005 | -0.591 | -0.739 | 0.000 |
| 44 | A | 45 | THR | 0 | -0.037 | -0.022 | 3.832 | -1.119 | -1.002 | 0.000 | -0.025 | -0.093 | 0.000 |
| 45 | A | 46 | GLU | -1 | -0.940 | -0.985 | 2.418 | -49.394 | -48.261 | 1.697 | -1.656 | -1.174 | -0.010 |
| 46 | A | 47 | ASP | -1 | -0.835 | -0.899 | 3.418 | -37.888 | -38.046 | -0.004 | 0.424 | -0.261 | -0.001 |
| 47 | A | 48 | CYS | 0 | -0.101 | -0.030 | 4.744 | 5.371 | 5.416 | -0.001 | -0.010 | -0.034 | 0.000 |
| 48 | A | 49 | VAL | 0 | 0.053 | 0.017 | 4.232 | -7.972 | -7.837 | -0.001 | -0.026 | -0.108 | 0.000 |
| 70 | A | 71 | SER | 0 | -0.021 | -0.014 | 3.181 | 4.220 | 4.807 | 0.012 | -0.217 | -0.381 | -0.001 |
| 71 | A | 72 | GLU | -1 | -0.774 | -0.877 | 1.828 | -92.700 | -95.801 | 10.768 | -4.623 | -3.043 | -0.054 |
| 72 | A | 73 | SER | 0 | -0.073 | -0.044 | 2.894 | -2.355 | -1.539 | 0.044 | -0.272 | -0.588 | -0.002 |
| 73 | A | 74 | THR | 0 | 0.040 | 0.022 | 4.754 | 2.242 | 2.261 | -0.001 | -0.004 | -0.013 | 0.000 |
| 75 | A | 76 | SER | 0 | -0.037 | -0.034 | 2.855 | -3.883 | -3.159 | 0.092 | -0.348 | -0.468 | -0.002 |
| 76 | A | 77 | MET | 0 | 0.000 | -0.012 | 4.985 | 4.143 | 4.125 | -0.001 | -0.005 | 0.024 | 0.000 |
| 4 | A | 5 | VAL | 0 | 0.013 | -0.002 | 6.244 | 3.003 | 3.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | LYS | 1 | 0.894 | 0.949 | 8.591 | 26.787 | 26.787 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | ILE | 0 | 0.012 | 0.006 | 12.029 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | TYR | 0 | -0.021 | -0.016 | 15.074 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | ASP | -1 | -0.905 | -0.956 | 18.650 | -12.955 | -12.955 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | THR | 0 | 0.016 | -0.016 | 21.744 | 0.429 | 0.429 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | CYS | -1 | -0.882 | -0.876 | 20.229 | -13.759 | -13.759 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | ILE | 0 | 0.019 | -0.009 | 22.270 | 0.552 | 0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | GLY | 0 | 0.030 | -0.028 | 22.916 | 0.397 | 0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | CYS | 0 | -0.059 | -0.026 | 22.564 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | THR | 0 | -0.006 | -0.022 | 20.743 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | GLN | 0 | 0.000 | -0.009 | 20.576 | -0.648 | -0.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | CYS | 0 | 0.016 | 0.008 | 16.225 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | VAL | 0 | 0.009 | 0.010 | 16.038 | -0.928 | -0.928 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | ARG | 1 | 0.960 | 0.975 | 17.109 | 12.102 | 12.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ALA | 0 | 0.007 | 0.020 | 17.766 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | CYS | 0 | -0.058 | -0.008 | 12.036 | -1.108 | -1.108 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | PRO | 0 | -0.062 | -0.042 | 12.998 | 0.610 | 0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | LEU | 0 | -0.003 | -0.024 | 8.736 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | ASP | -1 | -0.847 | -0.892 | 11.563 | -20.141 | -20.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | VAL | 0 | 0.045 | 0.007 | 7.766 | -0.520 | -0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | LEU | 0 | -0.072 | -0.040 | 10.036 | -0.464 | -0.464 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | GLU | -1 | -0.815 | -0.895 | 12.717 | -16.989 | -16.989 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | MET | 0 | -0.060 | -0.003 | 15.994 | -0.561 | -0.561 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | VAL | 0 | 0.013 | 0.014 | 17.646 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | PRO | 0 | 0.012 | -0.009 | 20.396 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | TRP | 0 | -0.043 | -0.015 | 22.792 | -0.321 | -0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ASP | -1 | -0.867 | -0.939 | 24.847 | -10.112 | -10.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | GLY | 0 | -0.043 | -0.008 | 26.262 | 0.315 | 0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | CYS | 0 | -0.023 | 0.010 | 24.853 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | LYS | 1 | 0.947 | 0.966 | 27.910 | 8.850 | 8.850 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | ALA | 0 | 0.000 | -0.008 | 26.912 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | SER | 0 | -0.042 | -0.013 | 27.735 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | GLN | 0 | -0.040 | -0.016 | 22.918 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | MET | 0 | 0.032 | 0.013 | 18.466 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | ALA | 0 | 0.030 | -0.001 | 16.146 | -0.223 | -0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | SER | 0 | -0.015 | -0.017 | 14.283 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | ALA | 0 | 0.007 | -0.024 | 9.017 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | PRO | 0 | -0.020 | 0.002 | 9.043 | -2.148 | -2.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | ARG | 1 | 0.842 | 0.905 | 7.819 | 20.407 | 20.407 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | GLY | 0 | -0.003 | -0.005 | 6.834 | 0.737 | 0.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | CYS | 0 | -0.049 | -0.023 | 8.204 | 2.407 | 2.407 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | LYS | 1 | 0.861 | 0.925 | 11.580 | 25.599 | 25.599 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | ARG | 1 | 0.992 | 1.006 | 13.618 | 18.677 | 18.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | CYS | 0 | -0.016 | 0.001 | 12.167 | 0.752 | 0.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | GLU | -1 | -0.741 | -0.872 | 14.257 | -20.813 | -20.813 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | THR | 0 | -0.030 | -0.022 | 16.969 | 1.005 | 1.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | ALA | 0 | -0.011 | 0.002 | 19.032 | 0.789 | 0.789 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | CYS | 0 | -0.062 | -0.007 | 18.891 | 0.351 | 0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | PRO | 0 | -0.006 | -0.016 | 20.940 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | THR | 0 | -0.044 | -0.012 | 22.624 | 0.248 | 0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | ASP | -1 | -0.919 | -0.936 | 23.800 | -12.094 | -12.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | PHE | 0 | 0.025 | 0.002 | 19.478 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | LEU | 0 | -0.004 | -0.002 | 18.043 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 64 | SER | 0 | 0.055 | 0.017 | 19.254 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 65 | VAL | 0 | -0.027 | -0.007 | 13.192 | -0.546 | -0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 66 | ARG | 1 | 0.862 | 0.933 | 13.704 | 19.377 | 19.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 67 | VAL | 0 | -0.004 | -0.005 | 8.364 | -1.452 | -1.452 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 68 | TYR | 0 | -0.016 | -0.015 | 9.107 | 2.632 | 2.632 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 69 | LEU | 0 | -0.015 | -0.001 | 7.003 | -4.614 | -4.614 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 70 | GLY | 0 | 0.033 | 0.012 | 4.862 | 4.752 | 4.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 75 | ARG | 1 | 0.945 | 0.960 | 5.313 | 39.737 | 39.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 78 | GLY | 0 | -0.016 | -0.003 | 8.131 | 3.626 | 3.626 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 79 | LEU | 0 | -0.080 | -0.022 | 10.160 | 2.444 | 2.444 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 80 | SER | 0 | -0.051 | -0.034 | 12.337 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 81 | TYR | -1 | -0.912 | -0.951 | 13.495 | -20.868 | -20.868 | 0.000 | 0.000 | 0.000 | 0.000 |