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: 4G92N
Calculation Name: 7SA3-K-Other547
Preferred Name:
Target Type:
Ligand Name: chlorophyll f | chlorophyll a | chlorophyll d | 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 | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | calcium ion | fe (ii) ion | chloride ion
Ligand 3-letter code: F6C | CLA | CL7 | PHO | HEM | DGD | PL9 | BCR | LMG | LHG | LMT | CA | FE2 | CL
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7SA3
Chain ID: K
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 | 37 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -128161.026864 |
|---|---|
| FMO2-HF: Nuclear repulsion | 114057.512163 |
| FMO2-HF: Total energy | -14103.514701 |
| FMO2-MP2: Total energy | -14146.540773 |
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:9:GLU)
Summations of interaction energy for
fragment #1(A:9:GLU)
| 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. |
| -1.425 | 0.766 | -0.023 | -0.818 | -1.35 | 0.001 |
Interaction energy analysis for fragmet #1(A:9:GLU)
| 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 | 11 | PRO | 0 | 0.083 | 0.039 | 3.856 | 1.846 | 3.730 | -0.021 | -0.796 | -1.066 | 0.001 |
| 4 | A | 12 | GLU | -1 | -0.812 | -0.912 | 4.605 | 2.163 | 2.333 | -0.001 | -0.007 | -0.162 | 0.000 |
| 7 | A | 15 | ARG | 1 | 0.851 | 0.921 | 4.128 | 0.532 | 0.669 | -0.001 | -0.015 | -0.122 | 0.000 |
| 5 | A | 13 | ALA | 0 | -0.024 | -0.006 | 7.736 | -0.696 | -0.696 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 14 | TYR | 0 | -0.010 | -0.016 | 9.041 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 16 | ALA | 0 | 0.005 | 0.008 | 7.921 | -0.562 | -0.562 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 17 | PHE | 0 | 0.009 | 0.006 | 10.961 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 18 | GLY | 0 | 0.018 | 0.018 | 8.294 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 19 | PRO | 0 | 0.058 | 0.012 | 8.970 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 20 | LEU | 0 | -0.021 | 0.005 | 11.822 | 0.547 | 0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 21 | ILE | 0 | -0.035 | -0.027 | 8.790 | 0.536 | 0.536 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 22 | ASP | -1 | -0.888 | -0.951 | 8.670 | -9.990 | -9.990 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 23 | VAL | 0 | -0.033 | -0.014 | 11.364 | 0.678 | 0.678 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 24 | LEU | 0 | -0.027 | -0.010 | 13.889 | 0.516 | 0.516 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 25 | PRO | 0 | -0.014 | -0.014 | 13.036 | 0.532 | 0.532 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 26 | ILE | 0 | -0.005 | 0.001 | 16.200 | 0.370 | 0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 27 | LEU | 0 | 0.027 | 0.025 | 18.647 | 0.289 | 0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 28 | PRO | 0 | -0.002 | -0.016 | 20.003 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 29 | ILE | 0 | 0.012 | 0.008 | 21.600 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 30 | PHE | 0 | 0.016 | 0.008 | 20.716 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 31 | PHE | 0 | 0.018 | 0.007 | 23.773 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 32 | LEU | 0 | -0.011 | 0.008 | 26.935 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 33 | LEU | 0 | 0.005 | -0.003 | 26.700 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 34 | LEU | 0 | -0.001 | -0.010 | 28.321 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 35 | ALA | 0 | 0.005 | 0.018 | 30.976 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 36 | PHE | 0 | 0.008 | -0.006 | 32.460 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 37 | VAL | 0 | -0.010 | 0.002 | 31.989 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 38 | TRP | 0 | -0.005 | -0.001 | 34.823 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 39 | GLN | 0 | 0.008 | -0.009 | 36.699 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 40 | ALA | 0 | 0.009 | 0.007 | 38.059 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 41 | SER | 0 | -0.065 | -0.034 | 38.490 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 42 | VAL | 0 | -0.078 | -0.030 | 40.375 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 43 | GLY | 0 | -0.026 | -0.012 | 42.813 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 44 | PHE | 0 | -0.074 | -0.041 | 39.178 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 45 | ARG | 0 | 0.036 | 0.042 | 43.855 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |