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: LG2J9
Calculation Name: 7EW6-C-Other547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | chlorophyll b | chlorophyll a isomer | digalactosyl diacyl glycerol (dgdg) | (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol | (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 | XAT | LUT | BCR | LMG | LHG | PQN | SF4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7EW6
Chain ID: C
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 | 81 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -496801.287471 |
|---|---|
| FMO2-HF: Nuclear repulsion | 462775.30525 |
| FMO2-HF: Total energy | -34025.982221 |
| FMO2-MP2: Total energy | -34115.005286 |
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. |
| -133.642 | -130.932 | 22.181 | -12.079 | -12.81 | -0.129 |
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 | HIS | 0 | 0.063 | 0.050 | 3.212 | 5.428 | 7.134 | 0.019 | -0.679 | -1.045 | 0.000 |
| 4 | A | 4 | SER | 0 | -0.015 | -0.015 | 1.801 | -41.416 | -42.493 | 8.721 | -4.395 | -3.249 | -0.059 |
| 5 | A | 5 | VAL | 0 | 0.008 | 0.003 | 4.152 | 10.261 | 10.421 | -0.001 | -0.024 | -0.135 | 0.000 |
| 6 | A | 6 | LYS | 1 | 0.902 | 0.945 | 3.628 | 37.348 | 37.549 | 0.000 | -0.023 | -0.178 | 0.000 |
| 45 | A | 45 | THR | 0 | -0.014 | -0.010 | 1.856 | -25.617 | -27.319 | 11.375 | -4.637 | -5.036 | -0.042 |
| 46 | A | 46 | GLU | -1 | -0.931 | -0.973 | 2.432 | -84.523 | -81.340 | 2.064 | -2.309 | -2.938 | -0.028 |
| 47 | A | 47 | ASP | -1 | -0.786 | -0.882 | 3.526 | -30.773 | -30.616 | 0.004 | -0.011 | -0.150 | 0.000 |
| 48 | A | 48 | CYS | 0 | -0.090 | -0.026 | 4.767 | 8.867 | 8.949 | -0.001 | -0.001 | -0.079 | 0.000 |
| 7 | A | 7 | ILE | 0 | 0.029 | 0.009 | 8.288 | 0.990 | 0.990 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | TYR | 0 | -0.014 | 0.003 | 11.389 | -0.805 | -0.805 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.846 | -0.932 | 14.144 | -15.403 | -15.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | THR | 0 | -0.026 | -0.012 | 17.201 | 0.715 | 0.715 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | CYS | -1 | -0.868 | -0.890 | 16.585 | -16.684 | -16.684 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ILE | 0 | 0.050 | 0.001 | 18.662 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | GLY | 0 | 0.019 | -0.008 | 19.694 | 0.572 | 0.572 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | CYS | 0 | -0.042 | -0.012 | 20.204 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | THR | 0 | -0.007 | -0.009 | 19.423 | 0.542 | 0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | GLN | 0 | 0.009 | -0.008 | 20.293 | -0.302 | -0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | CYS | 0 | 0.017 | 0.021 | 14.720 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | VAL | 0 | 0.039 | 0.011 | 14.932 | -0.737 | -0.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ARG | 1 | 0.886 | 0.946 | 15.966 | 14.002 | 14.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ALA | 0 | 0.016 | 0.018 | 17.035 | 0.508 | 0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | CYS | 0 | -0.070 | -0.017 | 11.470 | -1.118 | -1.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | PRO | 0 | -0.043 | -0.028 | 12.876 | 0.734 | 0.734 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | THR | 0 | -0.016 | -0.032 | 9.649 | 1.413 | 1.413 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ASP | -1 | -0.861 | -0.901 | 11.050 | -24.671 | -24.671 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | VAL | 0 | 0.033 | 0.013 | 6.702 | -1.571 | -1.571 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LEU | 0 | -0.042 | -0.039 | 9.256 | -1.271 | -1.271 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | GLU | -1 | -0.824 | -0.909 | 11.439 | -21.903 | -21.903 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | MET | 0 | -0.064 | -0.025 | 14.021 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ILE | 0 | 0.018 | 0.020 | 13.007 | 0.234 | 0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | PRO | 0 | 0.023 | -0.001 | 16.774 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | TRP | 0 | -0.004 | 0.003 | 18.489 | -0.662 | -0.662 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | ASP | -1 | -0.889 | -0.964 | 20.402 | -12.316 | -12.316 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | GLY | 0 | 0.030 | 0.027 | 21.604 | 0.601 | 0.601 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | CYS | 0 | 0.003 | 0.018 | 21.219 | 0.314 | 0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | LYS | 1 | 0.939 | 0.960 | 24.007 | 10.659 | 10.659 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ALA | 0 | -0.027 | -0.016 | 23.514 | 0.341 | 0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | LYS | 1 | 0.825 | 0.913 | 23.716 | 11.231 | 11.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | GLN | 0 | -0.016 | 0.005 | 20.025 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | ILE | 0 | 0.009 | 0.007 | 15.094 | 0.348 | 0.348 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | ALA | 0 | 0.016 | -0.004 | 13.702 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | SER | 0 | 0.000 | -0.001 | 10.557 | -1.188 | -1.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | ALA | 0 | 0.023 | -0.009 | 6.936 | 0.503 | 0.503 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | PRO | 0 | -0.021 | -0.001 | 5.979 | -6.278 | -6.278 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | ARG | 1 | 0.819 | 0.902 | 6.550 | 24.160 | 24.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | VAL | 0 | 0.032 | 0.012 | 6.472 | -2.747 | -2.747 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | GLY | 0 | 0.062 | 0.037 | 8.009 | 2.069 | 2.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | CYS | 0 | -0.057 | -0.030 | 9.269 | 2.430 | 2.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | LYS | 1 | 0.926 | 0.956 | 11.622 | 22.737 | 22.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | ARG | 1 | 0.971 | 0.993 | 13.781 | 18.657 | 18.657 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | CYS | 0 | 0.001 | 0.004 | 11.751 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | GLU | -1 | -0.829 | -0.919 | 12.698 | -20.469 | -20.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | SER | 0 | -0.023 | -0.010 | 15.231 | 1.185 | 1.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | ALA | 0 | -0.006 | 0.008 | 17.715 | 0.991 | 0.991 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | CYS | 0 | -0.050 | 0.003 | 17.094 | -0.220 | -0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | PRO | 0 | -0.006 | 0.001 | 19.238 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | THR | 0 | -0.021 | -0.008 | 20.434 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | ASP | -1 | -0.877 | -0.940 | 22.871 | -12.285 | -12.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | PHE | 0 | -0.041 | -0.023 | 18.050 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | LEU | 0 | -0.036 | -0.013 | 15.755 | -0.448 | -0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | SER | 0 | 0.052 | 0.005 | 16.441 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | VAL | 0 | -0.014 | -0.013 | 11.232 | -0.972 | -0.972 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ARG | 1 | 0.883 | 0.938 | 11.440 | 21.734 | 21.734 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | VAL | 0 | -0.001 | -0.012 | 7.093 | -2.752 | -2.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | TYR | 0 | -0.038 | -0.025 | 7.647 | 3.977 | 3.977 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | LEU | 0 | -0.008 | -0.007 | 6.754 | -5.518 | -5.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | GLY | 0 | 0.013 | 0.007 | 6.552 | 1.867 | 1.867 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | PRO | 0 | -0.041 | -0.013 | 5.926 | 3.518 | 3.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | GLU | -1 | -0.774 | -0.890 | 7.070 | -37.073 | -37.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | THR | 0 | -0.016 | -0.004 | 5.981 | 3.326 | 3.326 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | THR | 0 | 0.047 | 0.004 | 8.930 | 0.879 | 0.879 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | ARG | 1 | 0.863 | 0.929 | 7.090 | 35.725 | 35.725 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | SER | 0 | -0.048 | -0.030 | 6.361 | -2.364 | -2.364 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | MET | 0 | 0.011 | 0.002 | 8.523 | 0.911 | 0.911 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | ALA | 0 | -0.036 | -0.018 | 11.673 | 1.905 | 1.905 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | LEU | 0 | -0.035 | 0.001 | 13.625 | 1.537 | 1.537 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | SER | 0 | -0.049 | -0.044 | 15.827 | -0.549 | -0.549 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | TYR | -1 | -0.936 | -0.945 | 18.689 | -15.101 | -15.101 | 0.000 | 0.000 | 0.000 | 0.000 |