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: 7425K
Calculation Name: 7O3C-V-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: V
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 | 53 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -229272.416811 |
|---|---|
| FMO2-HF: Nuclear repulsion | 207878.958934 |
| FMO2-HF: Total energy | -21393.457876 |
| FMO2-MP2: Total energy | -21456.26515 |
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. |
| 100.494 | 108.778 | 10.102 | -6.175 | -12.211 | -0.047 |
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 | SER | 0 | 0.084 | 0.041 | 3.843 | 4.220 | 6.192 | -0.019 | -0.879 | -1.074 | -0.004 |
| 5 | A | 5 | PHE | 0 | 0.003 | -0.011 | 2.108 | -1.491 | -0.671 | 3.428 | -1.762 | -2.486 | -0.008 |
| 6 | A | 6 | LEU | 0 | 0.044 | 0.026 | 2.475 | -12.803 | -9.363 | 3.451 | -2.470 | -4.421 | -0.031 |
| 7 | A | 7 | GLY | 0 | 0.056 | 0.019 | 3.929 | 3.892 | 3.798 | 0.015 | 0.305 | -0.226 | 0.000 |
| 8 | A | 8 | PRO | 0 | 0.040 | 0.017 | 4.604 | -3.362 | -3.261 | -0.001 | -0.004 | -0.096 | 0.000 |
| 10 | A | 10 | TYR | 0 | 0.013 | 0.007 | 2.246 | -0.451 | -0.176 | 1.578 | -0.560 | -1.293 | -0.001 |
| 11 | A | 11 | ARG | 1 | 0.931 | 0.974 | 2.799 | 30.191 | 31.732 | 1.643 | -0.765 | -2.419 | -0.003 |
| 12 | A | 12 | GLU | -1 | -0.869 | -0.939 | 3.982 | -20.213 | -20.152 | 0.002 | -0.009 | -0.054 | 0.000 |
| 14 | A | 14 | ALA | 0 | -0.033 | -0.012 | 3.542 | 0.955 | 1.123 | 0.005 | -0.031 | -0.142 | 0.000 |
| 4 | A | 4 | ARG | 1 | 0.960 | 0.987 | 5.620 | 37.966 | 37.966 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ARG | 1 | 1.053 | 1.028 | 6.343 | 24.443 | 24.443 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | LEU | 0 | 0.006 | -0.008 | 6.008 | 0.762 | 0.762 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ARG | 1 | 0.899 | 0.940 | 5.670 | 21.738 | 21.738 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ASN | 0 | 0.035 | 0.018 | 8.812 | 2.135 | 2.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | TRP | 0 | 0.020 | 0.010 | 8.607 | 1.219 | 1.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ILE | 0 | -0.010 | 0.002 | 7.486 | 0.400 | 0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | 0.004 | 0.003 | 10.301 | 0.872 | 0.872 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | THR | 0 | 0.026 | 0.016 | 13.551 | 0.982 | 0.982 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ALA | 0 | -0.005 | -0.001 | 11.689 | 0.645 | 0.645 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | GLY | 0 | 0.021 | 0.015 | 13.624 | 0.484 | 0.484 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | MET | 0 | 0.014 | 0.023 | 15.554 | 1.011 | 1.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | TRP | 0 | 0.021 | 0.000 | 16.254 | 0.819 | 0.819 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | GLY | 0 | 0.001 | 0.006 | 17.108 | 0.442 | 0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | THR | 0 | -0.025 | -0.021 | 18.355 | 0.744 | 0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | VAL | 0 | -0.010 | -0.009 | 21.273 | 0.617 | 0.617 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLY | 0 | 0.000 | 0.003 | 21.230 | 0.522 | 0.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ALA | 0 | -0.012 | -0.005 | 22.198 | 0.443 | 0.443 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | VAL | 0 | 0.009 | -0.003 | 23.723 | 0.527 | 0.527 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | GLY | 0 | 0.013 | 0.004 | 25.803 | 0.479 | 0.479 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | LEU | 0 | -0.009 | -0.005 | 23.982 | 0.361 | 0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | VAL | 0 | -0.011 | 0.001 | 26.864 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | TRP | 0 | -0.026 | -0.008 | 29.566 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | ALA | 0 | -0.009 | -0.003 | 29.670 | 0.306 | 0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | THR | 0 | -0.076 | -0.060 | 29.196 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | ASP | -1 | -0.795 | -0.868 | 32.172 | -8.475 | -8.475 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | TRP | 0 | -0.027 | -0.005 | 26.376 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | ARG | 1 | 1.007 | 0.986 | 33.234 | 9.045 | 9.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | LEU | 0 | -0.015 | -0.002 | 31.465 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | ILE | 0 | -0.050 | -0.026 | 28.076 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | LEU | 0 | -0.022 | -0.011 | 32.403 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | ASP | -1 | -0.845 | -0.919 | 35.121 | -8.094 | -8.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | TRP | 0 | -0.090 | -0.023 | 33.338 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | VAL | 0 | -0.041 | -0.013 | 34.018 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | PRO | 0 | 0.000 | -0.014 | 36.928 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | TYR | 0 | -0.009 | -0.015 | 38.148 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | ILE | 0 | -0.017 | -0.002 | 36.255 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ASN | 0 | 0.050 | 0.011 | 39.576 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | GLY | 0 | -0.014 | 0.013 | 41.817 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | LYS | 1 | 0.853 | 0.913 | 41.213 | 7.722 | 7.722 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | PHE | 0 | -0.043 | -0.017 | 42.103 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | LYS | 0 | 0.002 | -0.008 | 37.287 | -0.392 | -0.392 | 0.000 | 0.000 | 0.000 | 0.000 |