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: G7KG1
Calculation Name: 2AXT-M-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: M
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 | 36 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -117615.928106 |
|---|---|
| FMO2-HF: Nuclear repulsion | 103821.24671 |
| FMO2-HF: Total energy | -13794.681396 |
| FMO2-MP2: Total energy | -13835.101457 |
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(M:1:MET)
Summations of interaction energy for
fragment #1(M: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. |
| 21.081 | 22.982 | 0.658 | -0.785 | -1.774 | -0.005 |
Interaction energy analysis for fragmet #1(M: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 | M | 3 | VAL | 0 | 0.000 | 0.004 | 2.548 | 6.650 | 8.495 | 0.659 | -0.779 | -1.726 | -0.005 |
| 4 | M | 4 | ASN | 0 | 0.036 | 0.009 | 4.996 | 3.142 | 3.198 | -0.001 | -0.006 | -0.048 | 0.000 |
| 5 | M | 5 | GLN | 0 | 0.049 | 0.021 | 8.666 | 3.072 | 3.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | M | 6 | LEU | 0 | 0.046 | 0.021 | 10.084 | 1.298 | 1.298 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | M | 7 | GLY | 0 | 0.000 | 0.005 | 10.682 | 1.521 | 1.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | M | 8 | LEU | 0 | 0.017 | 0.022 | 10.485 | 1.030 | 1.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | M | 9 | ILE | 0 | 0.026 | 0.010 | 12.129 | 1.357 | 1.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | M | 10 | ALA | 0 | -0.001 | -0.002 | 14.695 | 1.104 | 1.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | M | 11 | THR | 0 | -0.013 | -0.022 | 13.061 | 0.958 | 0.958 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | M | 12 | ALA | 0 | 0.004 | 0.005 | 15.714 | 0.949 | 0.949 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | M | 13 | LEU | 0 | -0.002 | -0.009 | 17.653 | 0.954 | 0.954 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | M | 14 | PHE | 0 | -0.018 | -0.004 | 18.690 | 0.766 | 0.766 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | M | 15 | VAL | 0 | 0.001 | 0.004 | 18.644 | 0.563 | 0.563 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | M | 16 | LEU | 0 | -0.008 | -0.015 | 21.063 | 0.704 | 0.704 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | M | 17 | VAL | 0 | 0.000 | 0.006 | 23.401 | 0.575 | 0.575 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | M | 18 | PRO | 0 | 0.008 | 0.005 | 24.293 | 0.550 | 0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | M | 19 | SER | 0 | 0.008 | 0.005 | 25.399 | 0.589 | 0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | M | 20 | VAL | 0 | 0.025 | -0.001 | 26.919 | 0.390 | 0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | M | 21 | PHE | 0 | -0.011 | 0.001 | 29.198 | 0.399 | 0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | M | 22 | LEU | 0 | 0.017 | 0.003 | 29.566 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | M | 23 | ILE | 0 | -0.002 | 0.006 | 28.856 | 0.306 | 0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | M | 24 | ILE | 0 | -0.022 | -0.009 | 32.899 | 0.292 | 0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | M | 25 | LEU | 0 | -0.021 | -0.011 | 35.284 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | M | 26 | TYR | 0 | 0.005 | 0.017 | 35.708 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | M | 27 | VAL | 0 | 0.056 | 0.022 | 36.167 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | M | 28 | GLN | 0 | -0.044 | -0.023 | 38.736 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | M | 29 | THR | 0 | -0.021 | -0.001 | 40.717 | 0.227 | 0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | M | 30 | GLU | -1 | -0.887 | -0.943 | 40.483 | -7.235 | -7.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | M | 31 | SER | 0 | 0.029 | 0.026 | 42.580 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | M | 32 | GLN | 0 | -0.071 | -0.040 | 44.898 | 0.263 | 0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | M | 33 | GLN | 0 | -0.027 | -0.029 | 46.982 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | M | 34 | LYS | 1 | 0.755 | 0.881 | 47.543 | 6.509 | 6.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | M | 35 | SER | 0 | -0.065 | -0.008 | 43.338 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | M | 36 | SER | -1 | -0.884 | -0.955 | 40.657 | -7.528 | -7.528 | 0.000 | 0.000 | 0.000 | 0.000 |