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: 5GK1Z
Calculation Name: 2AXT-Z-Xray549
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | pheophytin a | protoporphyrin ix containing fe | digalactosyl diacyl glycerol (dgdg) | 5-[(2e,6e,10e,14e,18e,22e)-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18,22,26-heptaenyl]-2,3-dimethylbenzo-1,4-quinone | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta-carotene | (1s)-2-(alpha-l-allopyranosyloxy)-1-[(tridecanoyloxy)methyl]ethyl palmitate | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | oxygen evolving system | bicarbonate ion | calcium ion | fe (ii) ion
Ligand 3-letter code: CLA | PHO | HEM | DGD | PQ9 | SQD | BCR | MGE | LHG | LMT | OEC | BCT | CA | FE2
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2AXT
Chain ID: Z
UniProt ID: P0A386
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 | 62 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -299448.259946 |
|---|---|
| FMO2-HF: Nuclear repulsion | 276245.929311 |
| FMO2-HF: Total energy | -23202.330636 |
| FMO2-MP2: Total energy | -23270.932925 |
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(Z:1:MET)
Summations of interaction energy for
fragment #1(Z: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. |
| -35.47 | -25.965 | 7.817 | -5.921 | -11.402 | -0.044 |
Interaction energy analysis for fragmet #1(Z: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 | Z | 3 | ILE | 0 | 0.043 | 0.033 | 3.796 | 4.796 | 7.167 | -0.009 | -1.040 | -1.323 | -0.002 |
| 4 | Z | 4 | LEU | 0 | 0.021 | 0.015 | 3.136 | 5.794 | 6.962 | 0.814 | -0.409 | -1.574 | 0.000 |
| 5 | Z | 5 | PHE | 0 | 0.038 | 0.022 | 3.347 | 5.601 | 6.171 | 0.011 | -0.113 | -0.467 | 0.000 |
| 6 | Z | 6 | GLN | 0 | 0.048 | 0.022 | 5.063 | 1.548 | 1.620 | -0.001 | -0.008 | -0.063 | 0.000 |
| 57 | Z | 57 | LEU | 0 | -0.028 | -0.033 | 3.044 | -2.900 | -2.998 | 2.067 | -0.322 | -1.647 | -0.002 |
| 58 | Z | 58 | ASN | 0 | -0.018 | 0.001 | 4.170 | -5.487 | -5.316 | 0.000 | -0.041 | -0.130 | 0.000 |
| 60 | Z | 60 | PHE | 0 | -0.074 | -0.027 | 2.302 | -3.990 | -2.441 | 4.077 | -1.942 | -3.683 | -0.016 |
| 61 | Z | 61 | VAL | 0 | -0.130 | -0.074 | 2.733 | -18.489 | -14.895 | 0.859 | -2.031 | -2.422 | -0.024 |
| 62 | Z | 62 | VAL | -1 | -0.925 | -0.941 | 4.802 | -26.637 | -26.529 | -0.001 | -0.015 | -0.093 | 0.000 |
| 7 | Z | 7 | LEU | 0 | 0.003 | 0.002 | 8.136 | 3.689 | 3.689 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | Z | 8 | ALA | 0 | 0.019 | 0.018 | 7.901 | 2.779 | 2.779 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | Z | 9 | LEU | 0 | 0.027 | 0.008 | 9.121 | 2.348 | 2.348 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | Z | 10 | ALA | 0 | -0.002 | -0.008 | 10.923 | 1.977 | 1.977 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | Z | 11 | ALA | 0 | 0.001 | -0.001 | 12.797 | 1.626 | 1.626 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | Z | 12 | LEU | 0 | 0.027 | 0.020 | 13.483 | 1.300 | 1.300 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | Z | 13 | VAL | 0 | -0.010 | 0.016 | 15.172 | 1.317 | 1.317 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | Z | 14 | ILE | 0 | 0.003 | -0.004 | 17.130 | 1.062 | 1.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | Z | 15 | LEU | 0 | -0.003 | 0.009 | 18.167 | 0.876 | 0.876 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | Z | 16 | SER | 0 | 0.002 | -0.019 | 18.551 | 0.847 | 0.847 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | Z | 17 | PHE | 0 | -0.012 | 0.000 | 21.039 | 0.702 | 0.702 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | Z | 18 | VAL | 0 | -0.002 | -0.011 | 22.821 | 0.601 | 0.601 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | Z | 19 | MET | 0 | -0.031 | 0.005 | 22.784 | 0.583 | 0.583 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | Z | 20 | VAL | 0 | -0.013 | -0.004 | 24.965 | 0.500 | 0.500 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | Z | 21 | ILE | 0 | -0.021 | -0.008 | 27.093 | 0.441 | 0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | Z | 22 | GLY | 0 | 0.019 | 0.010 | 28.189 | 0.359 | 0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | Z | 23 | VAL | 0 | -0.006 | -0.010 | 27.823 | 0.355 | 0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | Z | 24 | PRO | 0 | -0.018 | -0.010 | 30.215 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | Z | 25 | VAL | 0 | 0.030 | 0.018 | 33.091 | 0.306 | 0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | Z | 26 | ALA | 0 | -0.010 | 0.017 | 32.801 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | Z | 27 | TYR | 0 | -0.031 | -0.019 | 31.792 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | Z | 28 | ALA | 0 | -0.022 | 0.003 | 36.587 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | Z | 29 | SER | 0 | -0.055 | -0.049 | 37.214 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | Z | 30 | PRO | 0 | 0.016 | -0.005 | 39.121 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | Z | 31 | GLN | 0 | -0.043 | -0.017 | 40.998 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | Z | 32 | ASP | -1 | -0.810 | -0.912 | 37.358 | -8.501 | -8.501 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | Z | 33 | TRP | 0 | 0.037 | 0.017 | 33.550 | -0.338 | -0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | Z | 34 | ASP | -1 | -0.865 | -0.912 | 36.269 | -8.244 | -8.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | Z | 35 | ARG | 1 | 0.936 | 0.967 | 32.989 | 8.753 | 8.753 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | Z | 36 | SER | 0 | 0.002 | -0.009 | 32.465 | -0.442 | -0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | Z | 37 | LYS | 1 | 0.906 | 0.940 | 31.584 | 7.971 | 7.971 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | Z | 38 | GLN | 0 | -0.017 | -0.002 | 28.991 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | Z | 39 | LEU | 0 | -0.038 | -0.013 | 27.946 | -0.437 | -0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | Z | 40 | ILE | 0 | 0.054 | 0.025 | 26.773 | -0.500 | -0.500 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | Z | 41 | PHE | 0 | -0.027 | 0.012 | 26.284 | -0.402 | -0.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | Z | 42 | LEU | 0 | -0.009 | -0.005 | 21.843 | -0.413 | -0.413 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | Z | 43 | GLY | 0 | 0.033 | -0.001 | 22.395 | -0.599 | -0.599 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | Z | 44 | SER | 0 | -0.008 | -0.035 | 21.752 | -0.498 | -0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | Z | 45 | GLY | 0 | 0.001 | 0.005 | 21.687 | -0.371 | -0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | Z | 46 | LEU | 0 | -0.018 | -0.011 | 16.593 | -0.667 | -0.667 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | Z | 47 | TRP | 0 | 0.018 | 0.001 | 17.073 | -0.995 | -0.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | Z | 48 | ILE | 0 | 0.011 | 0.004 | 17.018 | -0.732 | -0.732 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | Z | 49 | ALA | 0 | -0.014 | -0.003 | 15.253 | -0.687 | -0.687 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | Z | 50 | LEU | 0 | -0.016 | -0.013 | 12.387 | -1.336 | -1.336 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | Z | 51 | VAL | 0 | 0.017 | 0.010 | 12.161 | -1.507 | -1.507 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | Z | 52 | LEU | 0 | -0.022 | -0.005 | 12.764 | -0.942 | -0.942 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | Z | 53 | VAL | 0 | -0.030 | -0.012 | 8.162 | -1.382 | -1.382 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | Z | 54 | VAL | 0 | -0.007 | -0.010 | 8.039 | -2.716 | -2.716 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | Z | 55 | GLY | 0 | 0.007 | 0.004 | 8.281 | -1.640 | -1.640 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | Z | 56 | VAL | 0 | -0.017 | -0.013 | 6.008 | -0.536 | -0.536 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | Z | 59 | PHE | 0 | 0.058 | 0.030 | 6.330 | -1.371 | -1.371 | 0.000 | 0.000 | 0.000 | 0.000 |