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: 8KG8Y
Calculation Name: 7F9O-P-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 | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | 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 | SQD | BCR | LMG | LHG | PQN | SF4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7F9O
Chain ID: P
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 | 100 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -641855.869115 |
|---|---|
| FMO2-HF: Nuclear repulsion | 602766.373222 |
| FMO2-HF: Total energy | -39089.495893 |
| FMO2-MP2: Total energy | -39203.108339 |
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. |
| -91.57 | -83.977 | 22.099 | -13.632 | -16.062 | -0.113 |
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 | PHE | 0 | 0.024 | 0.011 | 3.847 | 4.230 | 5.831 | -0.010 | -0.647 | -0.943 | 0.001 |
| 4 | A | 4 | GLU | -1 | -0.856 | -0.919 | 1.970 | -118.854 | -116.594 | 17.577 | -11.038 | -8.800 | -0.102 |
| 5 | A | 5 | HIS | 0 | 0.031 | -0.011 | 2.210 | 2.039 | 5.002 | 4.432 | -2.015 | -5.380 | -0.011 |
| 6 | A | 6 | VAL | 0 | 0.040 | 0.021 | 3.355 | 6.900 | 7.130 | 0.047 | 0.140 | -0.418 | -0.001 |
| 8 | A | 8 | PHE | 0 | -0.006 | -0.011 | 2.972 | 2.793 | 3.332 | 0.053 | -0.072 | -0.521 | 0.000 |
| 7 | A | 7 | LEU | 0 | 0.019 | 0.016 | 6.831 | 4.459 | 4.459 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | LEU | 0 | -0.022 | -0.005 | 6.625 | 3.153 | 3.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | SER | 0 | -0.019 | -0.023 | 8.271 | 2.994 | 2.994 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | VAL | 0 | 0.036 | 0.012 | 10.680 | 1.985 | 1.985 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | TYR | 0 | -0.028 | -0.022 | 7.614 | 1.372 | 1.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | LEU | 0 | -0.009 | 0.016 | 12.071 | 1.190 | 1.190 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | PHE | 0 | 0.042 | 0.008 | 14.261 | 1.316 | 1.316 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | SER | 0 | -0.021 | -0.010 | 15.643 | 1.321 | 1.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ILE | 0 | 0.005 | 0.002 | 15.379 | 0.964 | 0.964 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLY | 0 | 0.031 | 0.020 | 18.441 | 0.758 | 0.758 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ILE | 0 | 0.008 | -0.003 | 20.350 | 0.777 | 0.777 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | TYR | 0 | 0.003 | 0.004 | 21.241 | 0.628 | 0.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | GLY | 0 | 0.000 | -0.014 | 22.445 | 0.550 | 0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | LEU | 0 | -0.019 | -0.018 | 24.249 | 0.530 | 0.530 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | ILE | 0 | 0.013 | 0.011 | 25.781 | 0.470 | 0.470 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | THR | 0 | -0.049 | -0.011 | 26.040 | 0.442 | 0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | SER | 0 | -0.033 | -0.017 | 28.647 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | ARG | 1 | 0.915 | 0.940 | 30.316 | 9.108 | 9.108 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ASN | 0 | -0.022 | -0.014 | 33.080 | 0.428 | 0.428 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | MET | 0 | 0.089 | 0.043 | 32.781 | -0.252 | -0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | VAL | 0 | 0.047 | 0.021 | 32.353 | -0.221 | -0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ARG | 1 | 0.958 | 0.989 | 27.663 | 9.618 | 9.618 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | ALA | 0 | 0.043 | 0.027 | 27.831 | -0.350 | -0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | LEU | 0 | 0.010 | 0.012 | 28.082 | -0.267 | -0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | ILE | 0 | 0.022 | 0.009 | 24.947 | -0.265 | -0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | CYS | 0 | -0.073 | -0.024 | 23.668 | -0.510 | -0.510 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | LEU | 0 | 0.025 | 0.018 | 23.364 | -0.483 | -0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | GLU | -1 | -0.832 | -0.928 | 24.056 | -11.783 | -11.783 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | LEU | 0 | -0.037 | -0.006 | 18.666 | -0.572 | -0.572 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | ILE | 0 | -0.029 | -0.006 | 19.278 | -0.840 | -0.840 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | LEU | 0 | 0.037 | 0.017 | 19.764 | -0.764 | -0.764 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | ASN | 0 | -0.031 | -0.033 | 18.942 | -0.748 | -0.748 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | SER | 0 | 0.011 | 0.008 | 14.825 | -1.057 | -1.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | ILE | 0 | -0.037 | -0.020 | 15.662 | -1.121 | -1.121 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | ASN | 0 | 0.023 | 0.004 | 17.705 | -0.765 | -0.765 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | LEU | 0 | -0.009 | -0.004 | 11.327 | -0.622 | -0.622 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | ASN | 0 | -0.047 | -0.008 | 13.108 | -2.220 | -2.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | LEU | 0 | -0.038 | 0.006 | 14.191 | -0.351 | -0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | VAL | 0 | 0.032 | 0.006 | 14.822 | -0.464 | -0.464 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | THR | 0 | 0.006 | 0.000 | 9.663 | 0.379 | 0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | PHE | 0 | -0.008 | -0.014 | 11.572 | -1.417 | -1.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | SER | 0 | -0.050 | -0.018 | 13.269 | 0.905 | 0.905 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | ASP | -1 | -0.900 | -0.932 | 11.701 | -24.071 | -24.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | LEU | 0 | -0.039 | -0.025 | 7.610 | -0.340 | -0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | PHE | 0 | -0.007 | -0.008 | 11.612 | 0.630 | 0.630 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | ASP | -1 | -0.869 | -0.956 | 15.023 | -15.144 | -15.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | SER | 0 | 0.042 | 0.025 | 15.881 | 0.816 | 0.816 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ARG | 1 | 0.866 | 0.937 | 18.679 | 12.926 | 12.926 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | GLN | 0 | -0.056 | -0.042 | 21.871 | 1.257 | 1.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | LEU | 0 | 0.053 | 0.044 | 18.789 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | LYS | 1 | 0.910 | 0.965 | 20.767 | 14.093 | 14.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | GLY | 0 | 0.017 | 0.011 | 18.816 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | ASP | -1 | -0.833 | -0.930 | 19.080 | -16.212 | -16.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | ILE | 0 | -0.017 | -0.008 | 21.389 | 0.520 | 0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | PHE | 0 | 0.003 | 0.003 | 21.707 | 0.498 | 0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ALA | 0 | 0.052 | 0.021 | 20.212 | 0.276 | 0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | ILE | 0 | -0.029 | -0.011 | 22.227 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | PHE | 0 | -0.021 | -0.019 | 25.473 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | VAL | 0 | 0.022 | 0.013 | 22.637 | 0.382 | 0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | ILE | 0 | -0.020 | -0.009 | 22.152 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | ALA | 0 | -0.023 | -0.013 | 26.094 | 0.379 | 0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | LEU | 0 | -0.036 | -0.012 | 28.885 | 0.438 | 0.438 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | ALA | 0 | 0.071 | 0.045 | 26.266 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | ALA | 0 | -0.006 | -0.002 | 28.362 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | ALA | 0 | -0.014 | -0.004 | 30.664 | 0.378 | 0.378 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | GLU | -1 | -0.929 | -0.971 | 29.607 | -10.072 | -10.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | ALA | 0 | -0.007 | -0.002 | 29.975 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | ALA | 0 | -0.011 | -0.007 | 32.021 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | ILE | 0 | 0.002 | -0.004 | 35.477 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | GLY | 0 | 0.023 | 0.008 | 34.595 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | LEU | 0 | -0.024 | -0.023 | 33.581 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | SER | 0 | -0.004 | 0.011 | 37.024 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | ILE | 0 | 0.029 | 0.006 | 38.786 | 0.253 | 0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | LEU | 0 | -0.032 | -0.015 | 36.234 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | SER | 0 | -0.019 | -0.013 | 39.714 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | SER | 0 | -0.002 | 0.000 | 42.711 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | ILE | 0 | -0.022 | -0.014 | 40.643 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | HIS | 0 | 0.034 | 0.012 | 42.681 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | ARG | 1 | 0.933 | 0.978 | 44.611 | 6.601 | 6.601 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | ASN | 0 | 0.020 | 0.022 | 47.315 | 0.227 | 0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | ARG | 1 | 0.920 | 0.963 | 44.347 | 6.814 | 6.814 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | LYS | 1 | 0.856 | 0.927 | 45.758 | 6.103 | 6.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | SER | 0 | -0.020 | -0.038 | 43.275 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | THR | 0 | -0.002 | 0.013 | 38.361 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | ARG | 1 | 0.902 | 0.961 | 37.917 | 7.291 | 7.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | ILE | 0 | 0.045 | 0.017 | 34.965 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | ASN | 0 | 0.057 | 0.007 | 34.093 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | GLN | 0 | -0.033 | -0.004 | 38.417 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | SER | 0 | -0.011 | -0.005 | 41.382 | 0.278 | 0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | ASN | 0 | 0.034 | 0.021 | 42.389 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | LEU | 0 | -0.036 | -0.014 | 43.561 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | LEU | 0 | -0.013 | -0.011 | 43.793 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | ASN | -1 | -0.942 | -0.946 | 44.021 | -6.686 | -6.686 | 0.000 | 0.000 | 0.000 | 0.000 |