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: N6MQQ
Calculation Name: 2AXT-K-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):
PDB ID: 2AXT
Chain ID: K
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 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 37 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -121059.692093 |
|---|---|
| FMO2-HF: Nuclear repulsion | 107369.776538 |
| FMO2-HF: Total energy | -13689.915555 |
| FMO2-MP2: Total energy | -13731.667723 |
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(K:10:LYS)
Summations of interaction energy for
fragment #1(K:10:LYS)
| 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. |
| -132.012 | -130.594 | -0.011 | -0.439 | -0.967 | 0 |
Interaction energy analysis for fragmet #1(K:10:LYS)
| 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 | K | 12 | PRO | 0 | -0.011 | -0.012 | 3.837 | 0.547 | 1.965 | -0.011 | -0.439 | -0.967 | 0.000 |
| 4 | K | 13 | GLU | -1 | -0.858 | -0.934 | 5.681 | -57.058 | -57.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | K | 14 | ALA | 0 | -0.007 | 0.006 | 7.955 | 2.434 | 2.434 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | K | 15 | TYR | 0 | 0.000 | -0.018 | 8.047 | 2.638 | 2.638 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | K | 16 | ALA | 0 | -0.009 | 0.008 | 6.478 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | K | 17 | ILE | 0 | -0.003 | 0.002 | 7.681 | 2.569 | 2.569 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | K | 18 | PHE | 0 | -0.036 | -0.030 | 10.026 | 3.405 | 3.405 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | K | 19 | ASP | -1 | -0.916 | -0.946 | 6.315 | -62.437 | -62.437 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | K | 20 | PRO | 0 | 0.062 | 0.033 | 8.318 | 0.939 | 0.939 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | K | 21 | LEU | 0 | -0.053 | -0.024 | 11.586 | 2.892 | 2.892 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | K | 22 | VAL | 0 | -0.046 | -0.036 | 7.567 | 1.224 | 1.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | K | 23 | ASP | -1 | -0.869 | -0.933 | 8.670 | -52.442 | -52.442 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | K | 24 | VAL | 0 | -0.044 | -0.025 | 10.884 | 2.507 | 2.507 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | K | 25 | LEU | 0 | -0.029 | -0.011 | 12.595 | 2.282 | 2.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | K | 26 | PRO | 0 | -0.021 | -0.017 | 12.072 | 2.185 | 2.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | K | 27 | VAL | 0 | 0.011 | 0.008 | 15.080 | 1.741 | 1.741 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | K | 28 | ILE | 0 | 0.013 | 0.010 | 18.009 | 1.961 | 1.961 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | K | 29 | PRO | 0 | -0.004 | -0.014 | 19.042 | 1.561 | 1.561 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | K | 30 | VAL | 0 | 0.006 | 0.008 | 21.242 | 1.236 | 1.236 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | K | 31 | LEU | 0 | 0.007 | 0.004 | 21.814 | 1.238 | 1.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | K | 32 | PHE | 0 | 0.010 | 0.007 | 23.366 | 1.060 | 1.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | K | 33 | LEU | 0 | -0.007 | 0.012 | 26.938 | 0.887 | 0.887 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | K | 34 | ALA | 0 | 0.030 | 0.005 | 28.029 | 0.784 | 0.784 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | K | 35 | LEU | 0 | -0.001 | -0.003 | 28.940 | 0.735 | 0.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | K | 36 | ALA | 0 | 0.004 | 0.005 | 30.791 | 0.673 | 0.673 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | K | 37 | PHE | 0 | 0.013 | 0.002 | 32.854 | 0.663 | 0.663 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | K | 38 | VAL | 0 | -0.015 | -0.001 | 32.341 | 0.532 | 0.532 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | K | 39 | TRP | 0 | -0.020 | -0.001 | 34.780 | 0.461 | 0.461 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | K | 40 | GLN | 0 | -0.008 | -0.020 | 36.611 | 0.747 | 0.747 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | K | 41 | ALA | 0 | 0.010 | 0.013 | 38.237 | 0.437 | 0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | K | 42 | ALA | 0 | -0.048 | -0.024 | 38.886 | 0.396 | 0.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | K | 43 | VAL | 0 | -0.092 | -0.049 | 40.558 | 0.366 | 0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | K | 44 | GLY | 0 | -0.011 | -0.003 | 42.698 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | K | 45 | PHE | 0 | -0.096 | -0.054 | 39.163 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | K | 46 | ARG | 0 | 0.065 | 0.057 | 43.880 | 0.702 | 0.702 | 0.000 | 0.000 | 0.000 | 0.000 |