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: 87ZKY
Calculation Name: 7O3C-l-Other547
Preferred Name:
Target Type:
Ligand Name: cardiolipin | heme-a | protoporphyrin ix containing fe | heme c | 1,2-diacyl-sn-glycero-3-phosphocholine | tristearoylglycerol | 1,2-distearoyl-sn-glycerophosphoethanolamine | fe2/s2 (inorganic) cluster | dinuclear copper ion | copper (ii) ion | magnesium ion | zinc ion
Ligand 3-letter code: CDL | HEA | HEM | HEC | PC1 | TGL | 3PE | FES | CUA | CU | MG | ZN
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7O3C
Chain ID: l
Base Structure: ElectronMicroscopy
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 | 46 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -182496.244589 |
|---|---|
| FMO2-HF: Nuclear repulsion | 163847.25732 |
| FMO2-HF: Total energy | -18648.987269 |
| FMO2-MP2: Total energy | -18703.356994 |
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:2:HIS)
Summations of interaction energy for
fragment #1(A:2:HIS)
| 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. |
| -71.703 | -69.993 | 13.775 | -7.693 | -7.792 | -0.089 |
Interaction energy analysis for fragmet #1(A:2:HIS)
| 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 | 4 | GLU | -1 | -0.887 | -0.935 | 2.697 | -53.540 | -50.751 | 2.158 | -1.775 | -3.172 | -0.008 |
| 4 | A | 5 | GLU | -1 | -0.872 | -0.932 | 1.764 | -76.836 | -77.915 | 11.617 | -5.918 | -4.620 | -0.081 |
| 5 | A | 6 | GLY | 0 | 0.031 | 0.014 | 5.869 | 2.226 | 2.226 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | PRO | 0 | -0.019 | -0.033 | 9.138 | 0.592 | 0.592 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | GLY | 0 | -0.020 | -0.020 | 12.874 | -0.165 | -0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | LYS | 1 | 0.916 | 0.977 | 8.404 | 26.301 | 26.301 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | ASN | 0 | -0.009 | 0.006 | 9.236 | -0.619 | -0.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | LEU | 0 | -0.002 | 0.002 | 10.554 | 1.763 | 1.763 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | PRO | 0 | 0.006 | 0.008 | 13.755 | -0.927 | -0.927 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | PHE | 0 | -0.035 | -0.015 | 15.881 | 0.413 | 0.413 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | SER | 0 | -0.055 | -0.050 | 16.929 | -0.249 | -0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | VAL | 0 | 0.030 | -0.003 | 16.427 | 0.975 | 0.975 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | GLU | -1 | -0.837 | -0.892 | 16.678 | -17.669 | -17.669 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ASN | 0 | -0.008 | -0.004 | 19.008 | 1.073 | 1.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | LYS | 1 | 1.036 | 1.008 | 22.643 | 11.261 | 11.261 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | TRP | 0 | 0.038 | 0.016 | 24.730 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ARG | 1 | 0.973 | 0.983 | 21.021 | 14.943 | 14.943 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | LEU | 0 | 0.032 | 0.035 | 20.894 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | LEU | 0 | 0.010 | -0.001 | 24.339 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | ALA | 0 | -0.005 | -0.001 | 27.896 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | MET | 0 | -0.008 | -0.008 | 22.045 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | MET | 0 | 0.012 | 0.003 | 24.744 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | THR | 0 | -0.018 | -0.004 | 27.178 | 0.324 | 0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | VAL | 0 | 0.013 | 0.011 | 29.507 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | TYR | 0 | -0.011 | 0.014 | 25.751 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | PHE | 0 | 0.035 | 0.003 | 25.807 | 0.207 | 0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | GLY | 0 | 0.018 | 0.019 | 30.898 | 0.314 | 0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | SER | 0 | -0.073 | -0.045 | 31.513 | 0.248 | 0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | GLY | 0 | 0.011 | -0.001 | 32.434 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | PHE | 0 | -0.017 | -0.010 | 33.323 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | ALA | 0 | 0.034 | 0.009 | 36.233 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | ALA | 0 | 0.007 | 0.011 | 36.065 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | PRO | 0 | 0.020 | 0.001 | 37.368 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | PHE | 0 | 0.004 | 0.013 | 40.557 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | PHE | 0 | -0.033 | -0.036 | 38.768 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | ILE | 0 | -0.015 | 0.003 | 38.965 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | VAL | 0 | 0.045 | 0.029 | 43.212 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | ARG | 1 | 0.971 | 0.984 | 45.174 | 7.233 | 7.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | HIS | 0 | 0.027 | 0.018 | 44.707 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | GLN | 0 | -0.001 | -0.021 | 45.147 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LEU | 0 | -0.018 | -0.013 | 49.423 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | LEU | 0 | -0.032 | -0.009 | 49.261 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | LYS | 1 | 0.791 | 0.900 | 46.652 | 6.935 | 6.935 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | LYS | 0 | 0.043 | 0.052 | 52.773 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |