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: Y7K82
Calculation Name: 2AXT-U-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: U
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 | 98 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -705667.828204 |
|---|---|
| FMO2-HF: Nuclear repulsion | 667596.192022 |
| FMO2-HF: Total energy | -38071.636183 |
| FMO2-MP2: Total energy | -38185.626274 |
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(U:37:GLU)
Summations of interaction energy for
fragment #1(U:37:GLU)
| 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. |
| -2.085 | -0.816 | -0.027 | -0.302 | -0.94 | -0.001 |
Interaction energy analysis for fragmet #1(U:37:GLU)
| 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 | U | 39 | LEU | 0 | -0.014 | -0.001 | 3.726 | 5.271 | 6.540 | -0.027 | -0.302 | -0.940 | -0.001 |
| 4 | U | 40 | VAL | 0 | 0.015 | 0.013 | 6.709 | 0.457 | 0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | U | 41 | ASN | 0 | -0.038 | -0.014 | 9.445 | 0.952 | 0.952 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | U | 42 | VAL | 0 | 0.072 | 0.028 | 13.144 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | U | 43 | VAL | 0 | -0.015 | -0.005 | 14.943 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | U | 44 | ASP | -1 | -0.888 | -0.950 | 14.851 | -2.601 | -2.601 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | U | 45 | GLU | -1 | -0.947 | -0.974 | 11.693 | -4.261 | -4.261 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | U | 46 | LYS | 1 | 0.855 | 0.941 | 15.302 | 1.890 | 1.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | U | 47 | LEU | 0 | -0.039 | -0.016 | 18.543 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | U | 48 | GLY | 0 | -0.015 | 0.013 | 18.218 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | U | 49 | THR | 0 | -0.079 | -0.053 | 18.909 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | U | 50 | ALA | 0 | 0.082 | 0.032 | 21.317 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | U | 51 | TYR | 0 | -0.042 | -0.021 | 22.536 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | U | 52 | GLY | 0 | 0.059 | 0.023 | 23.223 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | U | 53 | GLU | -1 | -1.018 | -0.997 | 25.067 | -1.150 | -1.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | U | 54 | LYS | 1 | 0.842 | 0.926 | 28.119 | 0.960 | 0.960 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | U | 55 | ILE | 0 | -0.046 | -0.017 | 28.803 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | U | 56 | ASP | -1 | -0.736 | -0.850 | 24.855 | -1.099 | -1.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | U | 57 | LEU | 0 | -0.017 | -0.016 | 28.336 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | U | 58 | ASN | 0 | 0.028 | 0.022 | 26.062 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | U | 59 | ASN | 0 | -0.029 | -0.031 | 23.444 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | U | 60 | THR | 0 | -0.005 | 0.010 | 26.357 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | U | 61 | ASN | 0 | 0.005 | 0.004 | 28.598 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | U | 62 | ILE | 0 | 0.013 | -0.001 | 31.065 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | U | 63 | ALA | 0 | 0.018 | -0.001 | 34.600 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | U | 64 | ALA | 0 | 0.019 | 0.020 | 32.198 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | U | 65 | PHE | 0 | 0.028 | 0.002 | 33.800 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | U | 66 | ILE | 0 | -0.079 | -0.039 | 37.190 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | U | 67 | GLN | 0 | -0.060 | -0.022 | 33.603 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | U | 68 | TYR | 0 | 0.030 | 0.019 | 35.475 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | U | 69 | ARG | 1 | 0.954 | 0.965 | 41.004 | 0.402 | 0.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | U | 70 | GLY | 0 | -0.032 | -0.019 | 44.080 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | U | 71 | LEU | 0 | 0.037 | 0.028 | 38.350 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | U | 72 | TYR | 0 | 0.056 | 0.022 | 38.889 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | U | 73 | PRO | 0 | -0.013 | -0.005 | 41.353 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | U | 74 | THR | 0 | -0.037 | -0.026 | 43.086 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | U | 75 | LEU | 0 | 0.031 | 0.017 | 41.096 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | U | 76 | ALA | 0 | 0.055 | 0.049 | 37.400 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | U | 77 | LYS | 1 | 0.955 | 0.981 | 37.330 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | U | 78 | LEU | 0 | -0.033 | -0.023 | 38.455 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | U | 79 | ILE | 0 | 0.032 | 0.029 | 34.200 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | U | 80 | VAL | 0 | 0.020 | 0.021 | 32.301 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | U | 81 | LYS | 1 | 0.871 | 0.945 | 33.653 | 0.430 | 0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | U | 82 | ASN | 0 | -0.102 | -0.064 | 36.046 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | U | 83 | ALA | 0 | 0.019 | 0.020 | 31.884 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | U | 84 | PRO | 0 | 0.002 | -0.001 | 27.700 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | U | 85 | TYR | 0 | -0.020 | -0.040 | 29.921 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | U | 86 | GLU | -1 | -0.906 | -0.951 | 28.974 | -0.614 | -0.614 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | U | 87 | SER | 0 | -0.036 | -0.040 | 29.177 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | U | 88 | VAL | 0 | -0.014 | -0.009 | 31.130 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | U | 89 | GLU | -1 | -0.888 | -0.963 | 33.299 | -0.566 | -0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | U | 90 | ASP | -1 | -0.848 | -0.894 | 34.211 | -0.511 | -0.511 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | U | 91 | VAL | 0 | 0.002 | 0.000 | 35.203 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | U | 92 | LEU | 0 | -0.088 | -0.055 | 37.579 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | U | 93 | ASN | 0 | -0.031 | -0.014 | 38.641 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | U | 94 | ILE | 0 | -0.012 | 0.015 | 37.640 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | U | 95 | PRO | 0 | 0.004 | -0.012 | 40.942 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | U | 96 | GLY | 0 | -0.022 | -0.012 | 43.970 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | U | 97 | LEU | 0 | -0.023 | 0.016 | 41.802 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | U | 98 | THR | 0 | 0.002 | -0.023 | 46.315 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | U | 99 | GLU | -1 | -0.788 | -0.903 | 48.102 | -0.325 | -0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | U | 100 | ARG | 1 | 0.896 | 0.943 | 49.126 | 0.327 | 0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | U | 101 | GLN | 0 | 0.067 | 0.039 | 45.132 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | U | 102 | LYS | 1 | 0.963 | 0.987 | 44.197 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | U | 103 | GLN | 0 | -0.053 | -0.005 | 44.596 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | U | 104 | ILE | 0 | 0.018 | 0.013 | 43.305 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | U | 105 | LEU | 0 | 0.007 | 0.005 | 39.217 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | U | 106 | ARG | 1 | 0.881 | 0.925 | 40.485 | 0.339 | 0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | U | 107 | GLU | -1 | -0.949 | -0.969 | 41.863 | -0.391 | -0.391 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | U | 108 | ASN | 0 | -0.039 | -0.042 | 38.833 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | U | 109 | LEU | 0 | 0.039 | 0.030 | 36.569 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | U | 110 | GLU | -1 | -0.878 | -0.935 | 35.111 | -0.575 | -0.575 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | U | 111 | HIS | 1 | 0.779 | 0.887 | 34.416 | 0.574 | 0.574 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | U | 112 | PHE | 0 | 0.016 | 0.015 | 32.437 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | U | 113 | THR | 0 | -0.005 | -0.021 | 26.686 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | U | 114 | VAL | 0 | -0.009 | 0.010 | 26.637 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | U | 115 | THR | 0 | -0.009 | -0.016 | 20.892 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | U | 116 | GLU | -1 | -0.855 | -0.929 | 19.212 | -1.111 | -1.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | U | 117 | VAL | 0 | -0.030 | -0.016 | 21.901 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | U | 118 | GLU | -1 | -0.830 | -0.912 | 17.386 | -1.987 | -1.987 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | U | 119 | THR | 0 | 0.041 | 0.003 | 19.129 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | U | 120 | ALA | 0 | -0.012 | -0.017 | 18.425 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | U | 121 | LEU | 0 | -0.045 | -0.013 | 20.513 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | U | 122 | VAL | 0 | -0.080 | -0.042 | 23.540 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | U | 123 | GLU | -1 | -0.899 | -0.938 | 23.391 | -0.631 | -0.631 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | U | 124 | GLY | 0 | -0.020 | -0.013 | 25.358 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | U | 125 | GLY | 0 | -0.039 | -0.017 | 27.882 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | U | 126 | ASP | -1 | -0.835 | -0.911 | 26.461 | -0.863 | -0.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | U | 127 | ARG | 1 | 0.831 | 0.905 | 28.172 | 0.816 | 0.816 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | U | 128 | TYR | 0 | -0.078 | -0.057 | 30.478 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | U | 129 | ASN | 0 | -0.061 | -0.049 | 32.450 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | U | 130 | ASN | 0 | 0.077 | 0.048 | 28.278 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | U | 131 | GLY | 0 | 0.013 | 0.016 | 29.381 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | U | 132 | LEU | 0 | -0.059 | -0.013 | 28.846 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | U | 133 | TYR | 0 | -0.006 | -0.013 | 32.693 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | U | 134 | LYS | 0 | 0.011 | 0.023 | 35.800 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |