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: VZ1L1
Calculation Name: 2AXT-T-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: T
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 | 30 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -102667.324094 |
|---|---|
| FMO2-HF: Nuclear repulsion | 90023.227465 |
| FMO2-HF: Total energy | -12644.096629 |
| FMO2-MP2: Total energy | -12680.538051 |
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(T:1:MET)
Summations of interaction energy for
fragment #1(T: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. |
| 50.393 | 52.776 | 0.843 | -1.038 | -2.185 | -0.002 |
Interaction energy analysis for fragmet #1(T: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 | T | 3 | THR | 0 | 0.042 | 0.008 | 3.353 | 5.715 | 7.213 | -0.008 | -0.583 | -0.906 | 0.000 |
| 4 | T | 4 | ILE | 0 | 0.024 | 0.024 | 2.475 | 6.451 | 6.885 | 0.848 | -0.325 | -0.956 | -0.002 |
| 5 | T | 5 | THR | 0 | 0.026 | 0.014 | 3.416 | 9.950 | 10.401 | 0.003 | -0.130 | -0.323 | 0.000 |
| 6 | T | 6 | TYR | 0 | 0.007 | -0.008 | 6.237 | 5.123 | 5.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | T | 7 | VAL | 0 | 0.012 | 0.006 | 8.390 | 3.684 | 3.684 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | T | 8 | PHE | 0 | 0.005 | 0.008 | 8.906 | 2.952 | 2.952 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | T | 9 | ILE | 0 | 0.041 | 0.022 | 9.678 | 2.487 | 2.487 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | T | 10 | PHE | 0 | 0.010 | 0.001 | 12.385 | 1.980 | 1.980 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | T | 11 | ALA | 0 | 0.021 | 0.004 | 13.528 | 1.616 | 1.616 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | T | 12 | CYS | 0 | -0.045 | -0.022 | 13.884 | 1.514 | 1.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | T | 13 | ILE | 0 | -0.024 | -0.002 | 16.604 | 1.197 | 1.197 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | T | 14 | ILE | 0 | -0.004 | 0.001 | 18.269 | 1.048 | 1.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | T | 15 | ALA | 0 | 0.008 | 0.002 | 19.185 | 0.875 | 0.875 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | T | 16 | LEU | 0 | -0.001 | 0.002 | 20.643 | 0.795 | 0.795 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | T | 17 | PHE | 0 | -0.003 | -0.016 | 22.453 | 0.624 | 0.624 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | T | 18 | PHE | 0 | 0.006 | 0.012 | 23.937 | 0.634 | 0.634 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | T | 19 | PHE | 0 | -0.001 | -0.018 | 22.531 | 0.525 | 0.525 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | T | 20 | ALA | 0 | -0.001 | 0.002 | 26.496 | 0.469 | 0.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | T | 21 | ILE | 0 | -0.055 | -0.016 | 28.227 | 0.451 | 0.451 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | T | 22 | PHE | 0 | -0.060 | -0.046 | 28.695 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | T | 23 | PHE | 0 | -0.044 | -0.019 | 28.979 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | T | 24 | ARG | 1 | 0.952 | 1.003 | 31.330 | 8.874 | 8.874 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | T | 25 | GLU | -1 | -0.894 | -0.944 | 32.634 | -8.554 | -8.554 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | T | 26 | PRO | 0 | -0.077 | -0.041 | 35.732 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | T | 27 | PRO | 0 | 0.009 | -0.001 | 37.979 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | T | 28 | ARG | 1 | 0.909 | 0.950 | 40.629 | 7.566 | 7.566 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | T | 29 | ILE | 0 | 0.000 | -0.003 | 44.154 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | T | 30 | THR | -1 | -0.932 | -0.949 | 46.443 | -6.359 | -6.359 | 0.000 | 0.000 | 0.000 | 0.000 |