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: 9Q692
Calculation Name: 2AXT-E-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: E
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 | 82 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -416614.275269 |
|---|---|
| FMO2-HF: Nuclear repulsion | 384634.044138 |
| FMO2-HF: Total energy | -31980.231132 |
| FMO2-MP2: Total energy | -32076.347452 |
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(E:3:GLY)
Summations of interaction energy for
fragment #1(E:3:GLY)
| 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. |
| -17.732 | -16.63 | 0.005 | -0.465 | -0.642 | -0.001 |
Interaction energy analysis for fragmet #1(E:3:GLY)
| 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 | E | 5 | THR | 0 | -0.021 | -0.007 | 3.250 | -5.896 | -4.863 | 0.006 | -0.459 | -0.580 | -0.001 |
| 4 | E | 6 | GLY | 0 | 0.008 | -0.001 | 5.391 | 4.074 | 4.143 | -0.001 | -0.006 | -0.062 | 0.000 |
| 5 | E | 7 | GLU | -1 | -0.926 | -0.959 | 9.112 | -23.515 | -23.515 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | E | 8 | ARG | 1 | 0.867 | 0.929 | 12.061 | 17.627 | 17.627 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | E | 9 | PRO | 0 | 0.039 | 0.026 | 11.321 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | E | 10 | PHE | 0 | 0.066 | 0.012 | 12.641 | 1.982 | 1.982 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | E | 11 | SER | 0 | 0.039 | 0.023 | 13.399 | 1.378 | 1.378 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | E | 12 | ASP | -1 | -0.793 | -0.903 | 14.731 | -19.452 | -19.452 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | E | 13 | ILE | 0 | -0.112 | -0.026 | 17.458 | 0.973 | 0.973 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | E | 14 | ILE | 0 | 0.055 | 0.033 | 17.777 | 0.966 | 0.966 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | E | 15 | THR | 0 | 0.005 | -0.002 | 19.339 | 0.882 | 0.882 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | E | 16 | SER | 0 | -0.089 | -0.039 | 21.760 | 0.729 | 0.729 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | E | 17 | VAL | 0 | 0.080 | 0.020 | 23.412 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | E | 18 | ARG | 1 | 0.958 | 0.978 | 25.203 | 12.623 | 12.623 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | E | 19 | TYR | 0 | 0.032 | 0.025 | 22.672 | 0.312 | 0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | E | 20 | TRP | 0 | 0.040 | 0.007 | 24.126 | 0.533 | 0.533 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | E | 21 | VAL | 0 | -0.021 | -0.008 | 28.137 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | E | 22 | ILE | 0 | -0.027 | -0.003 | 26.551 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | E | 23 | HIS | 0 | -0.014 | -0.028 | 24.893 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | E | 24 | SER | 0 | -0.046 | -0.018 | 29.048 | 0.152 | 0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | E | 25 | ILE | 0 | -0.012 | 0.010 | 32.070 | 0.374 | 0.374 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | E | 26 | THR | 0 | 0.012 | -0.011 | 28.943 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | E | 27 | ILE | 0 | 0.031 | 0.024 | 26.751 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | E | 28 | PRO | 0 | 0.008 | -0.005 | 31.204 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | E | 29 | ALA | 0 | 0.020 | 0.021 | 34.828 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | E | 30 | LEU | 0 | 0.001 | -0.003 | 30.268 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | E | 31 | PHE | 0 | -0.012 | 0.005 | 34.137 | 0.152 | 0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | E | 32 | ILE | 0 | 0.022 | 0.004 | 35.540 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | E | 33 | ALA | 0 | 0.005 | 0.007 | 37.134 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | E | 34 | GLY | 0 | 0.009 | 0.002 | 37.193 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | E | 35 | TRP | 0 | -0.005 | -0.003 | 38.136 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | E | 36 | LEU | 0 | 0.007 | -0.008 | 40.757 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | E | 37 | PHE | 0 | -0.004 | 0.028 | 40.363 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | E | 38 | VAL | 0 | 0.027 | 0.008 | 40.993 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | E | 39 | SER | 0 | -0.044 | -0.024 | 43.757 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | E | 40 | THR | 0 | -0.067 | -0.045 | 46.142 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | E | 41 | GLY | 0 | -0.022 | -0.009 | 47.398 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | E | 42 | LEU | 0 | 0.029 | 0.008 | 44.305 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | E | 43 | ALA | 0 | -0.014 | -0.010 | 42.961 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | E | 44 | TYR | 0 | -0.016 | -0.005 | 44.345 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | E | 45 | ASP | -1 | -0.800 | -0.867 | 47.335 | -6.357 | -6.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | E | 46 | VAL | 0 | -0.060 | -0.029 | 42.402 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | E | 47 | PHE | 0 | -0.041 | -0.027 | 39.264 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | E | 48 | GLY | 0 | 0.018 | 0.028 | 44.982 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | E | 49 | THR | 0 | -0.065 | -0.034 | 45.758 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | E | 50 | PRO | 0 | -0.002 | -0.009 | 48.204 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | E | 51 | ARG | 1 | 0.877 | 0.917 | 50.187 | 6.147 | 6.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | E | 52 | PRO | 0 | -0.026 | -0.034 | 50.963 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | E | 53 | ASP | -1 | -0.899 | -0.928 | 53.558 | -5.745 | -5.745 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | E | 54 | SER | 0 | -0.035 | -0.027 | 54.247 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | E | 55 | TYR | 0 | -0.053 | -0.025 | 49.686 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | E | 56 | TYR | 0 | -0.017 | -0.015 | 55.756 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | E | 57 | ALA | 0 | 0.053 | 0.041 | 59.514 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | E | 58 | GLN | 0 | -0.051 | -0.041 | 62.754 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | E | 59 | GLU | -1 | -0.884 | -0.931 | 64.755 | -4.790 | -4.790 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | E | 60 | GLN | 0 | 0.025 | 0.013 | 61.225 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | E | 61 | ARG | 1 | 0.858 | 0.936 | 59.525 | 5.209 | 5.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | E | 62 | SER | 0 | -0.037 | -0.019 | 61.032 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | E | 63 | ILE | 0 | 0.030 | 0.006 | 54.492 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | E | 64 | PRO | 0 | 0.039 | 0.037 | 55.160 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | E | 65 | LEU | 0 | -0.038 | -0.020 | 53.102 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | E | 66 | VAL | 0 | -0.018 | -0.010 | 52.744 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | E | 67 | THR | 0 | -0.062 | -0.043 | 54.966 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | E | 68 | ASP | -1 | -0.859 | -0.922 | 56.890 | -5.535 | -5.535 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | E | 69 | ARG | 1 | 0.911 | 0.951 | 50.368 | 6.162 | 6.162 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | E | 70 | PHE | 0 | -0.029 | -0.033 | 53.515 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | E | 71 | GLU | -1 | -0.821 | -0.914 | 55.688 | -5.473 | -5.473 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | E | 72 | ALA | 0 | -0.018 | -0.004 | 53.200 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | E | 73 | LYS | 1 | 0.848 | 0.909 | 52.286 | 5.984 | 5.984 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | E | 74 | GLN | 0 | 0.067 | 0.044 | 54.912 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | E | 75 | GLN | 0 | 0.021 | 0.030 | 57.254 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | E | 76 | VAL | 0 | 0.021 | 0.008 | 52.544 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | E | 77 | GLU | -1 | -0.857 | -0.916 | 55.860 | -5.734 | -5.734 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | E | 78 | THR | 0 | 0.002 | -0.018 | 57.682 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | E | 79 | PHE | 0 | -0.062 | -0.041 | 56.267 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | E | 80 | LEU | 0 | -0.021 | -0.011 | 53.976 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | E | 81 | GLU | -1 | -0.934 | -0.957 | 58.287 | -5.160 | -5.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | E | 82 | GLN | 0 | -0.104 | -0.067 | 61.873 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | E | 83 | LEU | 0 | -0.066 | -0.022 | 57.024 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | E | 84 | LYS | 0 | -0.009 | 0.017 | 61.437 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |