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: 2GJZR
Calculation Name: 5J4Z-A-Other547
Preferred Name: Cytochrome c oxidase subunit 1
Target Type: SINGLE PROTEIN
Ligand Name: heme-a | protoporphyrin ix containing fe | iron/sulfur cluster | fe2/s2 (inorganic) cluster | dinuclear copper ion | copper (ii) ion
Ligand 3-letter code: HEA | HEM | SF4 | FES | CUA | CU
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5J4Z
Chain ID: A
ChEMBL ID: CHEMBL6011
UniProt ID: O78749
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-06
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 | -181209.833579 |
|---|---|
| FMO2-HF: Nuclear repulsion | 162597.252857 |
| FMO2-HF: Total energy | -18612.580721 |
| FMO2-MP2: Total energy | -18666.860503 |
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. |
| -0.285 | 3.294 | 0.287 | -1.664 | -2.202 | 0.004 |
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 | 0 | -0.025 | -0.021 | 3.087 | -6.814 | -3.474 | 0.288 | -1.656 | -1.972 | 0.004 |
| 4 | A | 5 | GLU | -1 | -0.921 | -0.948 | 5.358 | 11.569 | 11.808 | -0.001 | -0.008 | -0.230 | 0.000 |
| 5 | A | 6 | GLY | 0 | 0.042 | 0.011 | 6.815 | -2.105 | -2.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | PRO | 0 | -0.021 | -0.015 | 10.631 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | GLY | 0 | -0.021 | -0.020 | 14.023 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | LYS | 0 | 0.013 | 0.010 | 8.325 | -0.844 | -0.844 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | ASN | 0 | -0.006 | 0.002 | 8.937 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | ILE | 0 | -0.004 | -0.006 | 10.387 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | PRO | 0 | -0.017 | -0.007 | 13.054 | -0.288 | -0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | PHE | 0 | -0.011 | -0.008 | 14.326 | -0.425 | -0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | SER | 0 | 0.015 | 0.014 | 16.772 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | VAL | 0 | 0.027 | 0.003 | 17.781 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | GLU | -1 | -0.979 | -0.974 | 19.966 | -0.300 | -0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ASN | 0 | 0.028 | 0.008 | 21.575 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | LYS | 1 | 1.039 | 1.010 | 25.312 | -0.467 | -0.467 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | TRP | 0 | 0.019 | 0.013 | 26.702 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ARG | 1 | 0.997 | 0.997 | 22.215 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | LEU | 0 | 0.049 | 0.022 | 21.820 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | LEU | 0 | 0.003 | 0.004 | 24.811 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | ALA | 0 | 0.027 | 0.020 | 28.176 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | MET | 0 | 0.007 | 0.017 | 20.654 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | MET | 0 | -0.018 | -0.004 | 25.866 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | THR | 0 | -0.047 | -0.054 | 26.769 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | LEU | 0 | 0.003 | 0.010 | 27.606 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | PHE | 0 | -0.021 | -0.011 | 21.608 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | PHE | 0 | 0.002 | -0.003 | 26.855 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | GLY | 0 | 0.039 | 0.016 | 28.417 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | SER | 0 | -0.024 | -0.003 | 29.482 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | GLY | 0 | 0.008 | 0.000 | 29.946 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | PHE | 0 | -0.028 | -0.011 | 31.012 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | ALA | 0 | 0.016 | 0.006 | 34.083 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | ALA | 0 | -0.003 | -0.001 | 33.819 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | PRO | 0 | 0.006 | -0.008 | 34.666 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | PHE | 0 | 0.008 | 0.010 | 37.787 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | PHE | 0 | -0.026 | -0.013 | 37.282 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | ILE | 0 | 0.027 | 0.012 | 37.778 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | VAL | 0 | 0.035 | 0.023 | 40.405 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | ARG | 1 | 0.962 | 0.981 | 43.336 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | HIS | 0 | -0.056 | -0.029 | 40.833 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | GLN | 0 | -0.010 | -0.007 | 44.229 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LEU | 0 | 0.018 | 0.011 | 46.086 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | LEU | 0 | -0.057 | -0.019 | 46.541 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | LYS | 1 | 0.888 | 0.951 | 45.467 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | LYS | 0 | 0.034 | 0.019 | 49.314 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |