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: 7K1RK
Calculation Name: 4XK8-j-Xray547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | chlorophyll b | digalactosyl diacyl glycerol (dgdg) | (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol | (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | phylloquinone | iron/sulfur cluster | heptyl 1-thio-beta-d-glucopyranoside
Ligand 3-letter code: CLA | CHL | DGD | XAT | LUT | BCR | LMG | LHG | LMT | PQN | SF4 | HTG
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4XK8
Chain ID: j
UniProt ID: Q01667
Base Structure: X-ray
Registration Date: 2025-10-05
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 | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 39 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -136263.962581 |
|---|---|
| FMO2-HF: Nuclear repulsion | 121179.702318 |
| FMO2-HF: Total energy | -15084.260263 |
| FMO2-MP2: Total energy | -15128.952522 |
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(A:1:MET)
Summations of interaction energy for
fragment #1(A: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. |
| -41.715 | -34.71 | 11.202 | -8.605 | -9.602 | -0.06 |
Interaction energy analysis for fragmet #1(A: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 | A | 3 | ASP | -1 | -0.781 | -0.880 | 2.000 | -100.580 | -94.374 | 5.750 | -6.553 | -5.403 | -0.080 |
| 4 | A | 4 | LEU | 0 | 0.017 | 0.025 | 2.976 | 8.295 | 9.706 | 0.167 | -0.375 | -1.202 | -0.002 |
| 5 | A | 5 | LYS | 1 | 0.962 | 0.968 | 2.572 | 40.099 | 39.416 | 5.286 | -1.673 | -2.931 | 0.022 |
| 6 | A | 6 | THR | 0 | -0.007 | 0.000 | 6.119 | 5.685 | 5.756 | -0.001 | -0.004 | -0.066 | 0.000 |
| 7 | A | 7 | TYR | 0 | 0.005 | 0.000 | 7.462 | 3.368 | 3.368 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LEU | 0 | -0.010 | -0.024 | 6.118 | 2.583 | 2.583 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | SER | 0 | -0.014 | -0.010 | 9.909 | 2.538 | 2.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | VAL | 0 | -0.021 | -0.002 | 12.181 | 1.637 | 1.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ALA | 0 | 0.060 | 0.022 | 14.166 | 0.453 | 0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | 0.030 | 0.027 | 16.761 | 0.522 | 0.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | VAL | 0 | 0.011 | 0.021 | 12.128 | 0.466 | 0.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | VAL | 0 | 0.040 | 0.024 | 14.151 | 0.521 | 0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | SER | 0 | -0.009 | -0.015 | 15.789 | 0.927 | 0.927 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | THR | 0 | -0.068 | -0.042 | 16.491 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LEU | 0 | -0.015 | -0.008 | 11.758 | 0.366 | 0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | TRP | 0 | -0.006 | 0.006 | 16.194 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PHE | 0 | 0.017 | -0.011 | 18.824 | 0.530 | 0.530 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | GLY | 0 | 0.017 | 0.023 | 19.726 | 0.527 | 0.527 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ALA | 0 | -0.012 | -0.008 | 18.082 | 0.428 | 0.428 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | LEU | 0 | 0.002 | 0.004 | 20.115 | 0.456 | 0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ALA | 0 | 0.008 | 0.004 | 23.521 | 0.471 | 0.471 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | GLY | 0 | 0.021 | 0.010 | 23.201 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LEU | 0 | -0.019 | -0.014 | 23.828 | 0.357 | 0.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LEU | 0 | 0.020 | 0.002 | 25.447 | 0.368 | 0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ILE | 0 | -0.009 | 0.012 | 26.527 | 0.375 | 0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLU | -1 | -0.835 | -0.908 | 25.736 | -9.607 | -9.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ILE | 0 | -0.026 | -0.012 | 28.918 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | ASN | 0 | -0.041 | -0.032 | 31.261 | 0.449 | 0.449 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ARG | 1 | 0.784 | 0.893 | 28.447 | 9.477 | 9.477 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | PHE | 0 | -0.044 | -0.031 | 29.562 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | PHE | 0 | -0.049 | -0.026 | 33.645 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | PRO | 0 | 0.035 | 0.028 | 36.781 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | ASP | -1 | -0.956 | -0.985 | 38.251 | -6.929 | -6.929 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ALA | 0 | -0.021 | 0.002 | 38.315 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | LEU | 0 | -0.020 | -0.012 | 40.398 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | ILE | 0 | -0.073 | -0.050 | 42.967 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | PHE | -1 | -0.939 | -0.947 | 39.333 | -7.384 | -7.384 | 0.000 | 0.000 | 0.000 | 0.000 |