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: KVYK3
Calculation Name: 5B5E-t-Xray547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | pheophytin a | protoporphyrin ix containing fe | digalactosyl diacyl glycerol (dgdg) | 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone | heme c | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | (3r)-beta,beta-caroten-3-ol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | ca-mn4-o5 cluster | heptyl 1-thio-beta-d-glucopyranoside | n-formylmethionine | bicarbonate ion | dimethyl sulfoxide | calcium ion | fe (ii) ion | magnesium ion | chloride ion
Ligand 3-letter code: CLA | PHO | HEM | DGD | PL9 | HEC | SQD | RRX | BCR | LMG | LHG | LMT | OEX | HTG | FME | BCT | DMS | CA | FE2 | MG | CL
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5B5E
Chain ID: t
UniProt ID: P0A387
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 | 31 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -106744.775708 |
|---|---|
| FMO2-HF: Nuclear repulsion | 93682.216132 |
| FMO2-HF: Total energy | -13062.559577 |
| FMO2-MP2: Total energy | -13100.283007 |
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. |
| 59.238 | 62.614 | 0.227 | -1.167 | -2.438 | -0.003 |
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 | THR | 0 | 0.033 | 0.012 | 3.460 | 5.185 | 6.821 | 0.001 | -0.636 | -1.001 | -0.001 |
| 4 | A | 4 | ILE | 0 | 0.010 | 0.012 | 2.732 | 7.722 | 8.903 | 0.221 | -0.355 | -1.048 | -0.002 |
| 5 | A | 5 | THR | 0 | 0.001 | 0.007 | 3.415 | 10.172 | 10.731 | 0.005 | -0.176 | -0.389 | 0.000 |
| 6 | A | 6 | TYR | 0 | 0.012 | -0.006 | 6.034 | 5.284 | 5.284 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | VAL | 0 | 0.023 | 0.014 | 8.030 | 3.869 | 3.869 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | PHE | 0 | 0.015 | 0.012 | 8.664 | 3.074 | 3.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ILE | 0 | 0.033 | 0.016 | 9.385 | 2.637 | 2.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | PHE | 0 | 0.004 | 0.000 | 12.093 | 2.043 | 2.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ALA | 0 | 0.021 | 0.006 | 13.324 | 1.660 | 1.660 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | CYS | 0 | -0.035 | -0.020 | 13.614 | 1.628 | 1.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ILE | 0 | -0.019 | 0.002 | 15.887 | 1.246 | 1.246 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ILE | 0 | -0.011 | -0.001 | 18.030 | 1.103 | 1.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ALA | 0 | 0.010 | 0.003 | 18.943 | 0.917 | 0.917 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | LEU | 0 | -0.007 | 0.000 | 20.359 | 0.824 | 0.824 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PHE | 0 | -0.009 | -0.019 | 22.114 | 0.648 | 0.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PHE | 0 | 0.014 | 0.014 | 23.675 | 0.644 | 0.644 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PHE | 0 | 0.003 | -0.015 | 22.214 | 0.549 | 0.549 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ALA | 0 | 0.001 | 0.004 | 26.186 | 0.493 | 0.493 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ILE | 0 | -0.058 | -0.019 | 27.870 | 0.472 | 0.472 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | PHE | 0 | -0.059 | -0.043 | 28.462 | 0.435 | 0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | PHE | 0 | -0.051 | -0.021 | 28.735 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ARG | 1 | 0.941 | 0.991 | 31.062 | 8.918 | 8.918 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | GLU | -1 | -0.850 | -0.925 | 32.292 | -8.319 | -8.319 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | PRO | 0 | -0.061 | -0.035 | 35.152 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | PRO | 0 | -0.008 | -0.003 | 37.556 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ARG | 1 | 0.906 | 0.945 | 40.404 | 7.637 | 7.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ILE | 0 | 0.005 | 0.010 | 43.919 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | THR | 0 | -0.031 | -0.019 | 46.834 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | LYS | 0 | 0.064 | 0.047 | 48.965 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |