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: KQK13
Calculation Name: 7S1K-l-Other547
Preferred Name:
Target Type:
Ligand Name: radezolid | n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 5'-o-(dihydroxyphosphanyl)-2,8-dimethyladenosine | 2n-methylguanosine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | (1s)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-ribitol | 5-methylcytidine-5'-monophosphate | 5-methyluridine 5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid
Ligand 3-letter code: RD8 | G7M | 1MG | 8AH | 2MG | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | H2U | OMC | OMU | 4D4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7S1K
Chain ID: l
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 | 64 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -322469.248222 |
|---|---|
| FMO2-HF: Nuclear repulsion | 297858.966981 |
| FMO2-HF: Total energy | -24610.281241 |
| FMO2-MP2: Total energy | -24682.853546 |
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:PRO)
Summations of interaction energy for
fragment #1(A:2:PRO)
| 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. |
| 190.694 | 192.837 | 0.15 | -1.06 | -1.233 | -0.006 |
Interaction energy analysis for fragmet #1(A:2:PRO)
| 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 | ILE | 0 | 0.072 | 0.045 | 2.987 | -5.062 | -2.919 | 0.150 | -1.060 | -1.233 | -0.006 |
| 4 | A | 5 | LYS | 1 | 0.956 | 0.967 | 4.974 | 40.185 | 40.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | THR | 0 | 0.030 | 0.025 | 7.250 | 2.338 | 2.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | VAL | 0 | 0.065 | 0.035 | 10.745 | 0.693 | 0.693 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | ARG | 1 | 1.001 | 0.990 | 12.486 | 20.732 | 20.732 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | GLY | 0 | -0.003 | -0.002 | 15.342 | 1.007 | 1.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | ALA | 0 | 0.045 | 0.035 | 17.078 | 1.026 | 1.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | ALA | 0 | 0.091 | 0.047 | 15.905 | 0.744 | 0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | LYS | 1 | 0.932 | 0.965 | 18.014 | 14.849 | 14.849 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | ARG | 1 | 0.848 | 0.917 | 20.926 | 13.675 | 13.675 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | PHE | 0 | 0.030 | 0.023 | 20.430 | 0.623 | 0.623 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | LYS | 1 | 0.819 | 0.902 | 21.503 | 13.096 | 13.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | LYS | 1 | 0.938 | 1.004 | 19.878 | 15.783 | 15.783 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | THR | 0 | -0.087 | -0.063 | 23.358 | 0.592 | 0.592 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | GLY | 0 | 0.073 | 0.027 | 26.106 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LYS | 1 | 0.995 | 1.001 | 28.027 | 9.885 | 9.885 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | GLY | 0 | 0.035 | 0.027 | 23.938 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | GLY | 0 | 0.046 | 0.032 | 23.606 | -0.498 | -0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | PHE | 0 | 0.032 | 0.015 | 19.164 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | LYS | 1 | 0.958 | 0.986 | 24.964 | 11.826 | 11.826 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | HIS | 0 | 0.030 | 0.003 | 25.888 | -0.470 | -0.470 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | LYS | 1 | 0.926 | 0.960 | 27.785 | 9.823 | 9.823 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | HIS | 0 | 0.061 | 0.050 | 30.155 | -0.375 | -0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | ALA | 0 | 0.051 | 0.023 | 31.262 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | ASN | 0 | 0.006 | -0.014 | 32.848 | 0.314 | 0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | LEU | 0 | -0.016 | 0.011 | 35.538 | 0.272 | 0.272 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | ARG | 1 | 0.925 | 0.956 | 29.482 | 9.575 | 9.575 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | HIS | 0 | 0.165 | 0.078 | 36.208 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ILE | 0 | 0.050 | 0.017 | 39.144 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | LEU | 0 | 0.003 | -0.006 | 39.507 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | THR | 0 | 0.055 | 0.024 | 43.360 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | LYS | 1 | 1.034 | 1.025 | 44.857 | 6.884 | 6.884 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | LYS | 1 | 0.779 | 0.907 | 39.292 | 7.803 | 7.803 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | ALA | 0 | 0.126 | 0.051 | 45.578 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | THR | 0 | 0.035 | -0.007 | 45.928 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | LYS | 1 | 0.989 | 1.007 | 45.893 | 6.471 | 6.471 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | ARG | 1 | 1.000 | 1.002 | 39.977 | 7.427 | 7.427 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | LYS | 1 | 0.904 | 0.949 | 41.360 | 6.679 | 6.679 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | ARG | 1 | 0.957 | 0.988 | 40.998 | 6.583 | 6.583 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | HIS | 0 | 0.029 | -0.004 | 41.169 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LEU | 0 | -0.012 | 0.005 | 36.683 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | ARG | 1 | 0.954 | 0.978 | 36.198 | 7.279 | 7.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | PRO | 0 | -0.008 | -0.001 | 36.055 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | LYS | 1 | 0.901 | 0.947 | 30.613 | 9.391 | 9.391 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | ALA | 0 | 0.021 | 0.024 | 31.583 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | MET | 0 | 0.012 | -0.007 | 29.434 | -0.442 | -0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | VAL | 0 | -0.014 | -0.007 | 24.486 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | SER | 0 | -0.007 | -0.007 | 27.746 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | LYS | 1 | 1.006 | 0.978 | 27.455 | 9.813 | 9.813 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | GLY | 0 | 0.026 | 0.022 | 26.615 | -0.335 | -0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | ASP | -1 | -0.828 | -0.894 | 24.698 | -11.921 | -11.921 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | LEU | 0 | -0.043 | -0.030 | 22.914 | -0.693 | -0.693 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | GLY | 0 | 0.048 | 0.028 | 20.446 | -0.651 | -0.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | LEU | 0 | 0.047 | 0.028 | 18.915 | -1.019 | -1.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | VAL | 0 | -0.030 | -0.023 | 18.232 | -0.903 | -0.903 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | ILE | 0 | 0.013 | -0.006 | 16.492 | -0.711 | -0.711 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | ALA | 0 | 0.021 | 0.026 | 14.499 | -1.210 | -1.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | CYS | 0 | -0.077 | -0.041 | 13.333 | -1.506 | -1.506 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | LEU | 0 | -0.109 | -0.061 | 13.611 | -0.822 | -0.822 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | PRO | 0 | 0.050 | 0.026 | 9.987 | 0.744 | 0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 64 | TYR | 0 | -0.044 | -0.025 | 7.321 | -2.506 | -2.506 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 65 | ALA | -1 | -0.879 | -0.937 | 13.287 | -16.072 | -16.072 | 0.000 | 0.000 | 0.000 | 0.000 |