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: 3G9KL
Calculation Name: 7ELB-B-Other547
Preferred Name:
Target Type:
Ligand Name: manganese (ii) ion
Ligand 3-letter code: MN
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7ELB
Chain ID: B
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 | 49 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -265009.87434 |
|---|---|
| FMO2-HF: Nuclear repulsion | 242330.912284 |
| FMO2-HF: Total energy | -22678.962056 |
| FMO2-MP2: Total energy | -22737.708203 |
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:33:LEU)
Summations of interaction energy for
fragment #1(A:33:LEU)
| 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. |
| 11.101 | 13.918 | 1.064 | -1.618 | -2.261 | -0.016 |
Interaction energy analysis for fragmet #1(A:33:LEU)
| 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 | 35 | GLY | 0 | 0.058 | 0.023 | 2.535 | -4.440 | -1.922 | 1.066 | -1.604 | -1.979 | -0.016 |
| 4 | A | 36 | ARG | 1 | 0.922 | 0.955 | 4.531 | 20.764 | 20.913 | -0.001 | -0.011 | -0.136 | 0.000 |
| 24 | A | 56 | TYR | 0 | 0.029 | 0.011 | 4.851 | -1.936 | -1.786 | -0.001 | -0.003 | -0.146 | 0.000 |
| 5 | A | 37 | TYR | 0 | 0.008 | 0.008 | 6.430 | 3.247 | 3.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 38 | ASN | 0 | 0.047 | 0.013 | 8.412 | 2.376 | 2.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 39 | CYS | 0 | -0.026 | -0.013 | 11.204 | -1.091 | -1.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 40 | LYS | 1 | 0.909 | 0.971 | 10.829 | 26.952 | 26.952 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 41 | CYS | 0 | -0.029 | -0.018 | 13.750 | 0.726 | 0.726 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 42 | CYS | 0 | 0.038 | 0.015 | 17.485 | 0.425 | 0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 43 | TRP | 0 | -0.047 | -0.013 | 15.346 | 0.558 | 0.558 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 44 | PHE | 0 | 0.003 | 0.004 | 15.937 | -0.579 | -0.579 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 45 | ALA | 0 | 0.013 | 0.003 | 16.656 | 0.650 | 0.650 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 46 | ASP | -1 | -0.898 | -0.963 | 12.968 | -18.680 | -18.680 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 47 | THR | 0 | 0.017 | 0.017 | 14.294 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 48 | ASN | 0 | -0.056 | -0.044 | 14.326 | 0.478 | 0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 49 | LEU | 0 | -0.069 | -0.006 | 10.782 | 0.422 | 0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 50 | ILE | 0 | 0.039 | 0.020 | 12.373 | -0.625 | -0.625 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 51 | THR | 0 | -0.040 | -0.018 | 7.985 | -0.829 | -0.829 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 52 | CYS | 0 | 0.034 | 0.016 | 10.665 | 1.871 | 1.871 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 53 | ASN | 0 | -0.010 | -0.012 | 9.170 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 54 | ASP | -1 | -0.883 | -0.933 | 7.390 | -35.350 | -35.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 55 | HIS | 0 | -0.058 | -0.060 | 7.614 | -3.824 | -3.824 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 57 | LEU | 0 | 0.072 | 0.057 | 10.319 | 1.496 | 1.496 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 58 | CYS | 0 | 0.037 | 0.015 | 14.075 | 0.455 | 0.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 59 | LEU | 0 | 0.077 | 0.037 | 16.598 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 60 | ARG | 1 | 0.993 | 0.992 | 19.347 | 12.535 | 12.535 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 61 | CYS | 0 | -0.016 | -0.019 | 18.639 | 0.586 | 0.586 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 62 | HIS | 0 | 0.041 | 0.029 | 18.158 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 63 | GLN | 0 | 0.022 | 0.007 | 20.113 | 0.713 | 0.713 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 64 | THR | 0 | -0.096 | -0.054 | 23.445 | 0.710 | 0.710 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 65 | MET | 0 | -0.039 | -0.028 | 18.273 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 66 | LEU | 0 | 0.065 | 0.037 | 22.266 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 67 | ARG | 1 | 0.912 | 0.958 | 24.462 | 11.075 | 11.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 68 | ASN | 0 | -0.054 | -0.011 | 26.247 | 0.782 | 0.782 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 69 | SER | 0 | -0.026 | -0.021 | 25.144 | 0.338 | 0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 70 | GLU | -1 | -0.838 | -0.920 | 24.361 | -12.621 | -12.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 71 | LEU | 0 | -0.095 | -0.037 | 20.650 | -0.769 | -0.769 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 72 | CYS | 0 | -0.031 | -0.020 | 15.840 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 73 | HIS | 0 | 0.038 | 0.011 | 19.449 | -0.590 | -0.590 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 74 | ILE | 0 | -0.003 | -0.005 | 15.540 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 75 | CYS | 0 | -0.071 | -0.026 | 12.946 | -0.688 | -0.688 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 76 | TRP | 0 | 0.009 | 0.014 | 15.241 | -0.314 | -0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 77 | LYS | 1 | 0.946 | 0.973 | 13.204 | 20.689 | 20.689 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 78 | PRO | 0 | 0.047 | 0.022 | 17.008 | 0.447 | 0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 79 | LEU | 0 | -0.014 | -0.001 | 17.148 | -1.325 | -1.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 80 | PRO | 0 | -0.023 | -0.018 | 15.147 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 81 | THR | -1 | -0.896 | -0.940 | 17.885 | -14.563 | -14.563 | 0.000 | 0.000 | 0.000 | 0.000 |