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: 65ZMZ
Calculation Name: 7S1K-Q-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: Q
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 | 60 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -254712.059153 |
|---|---|
| FMO2-HF: Nuclear repulsion | 229387.080941 |
| FMO2-HF: Total energy | -25324.978212 |
| FMO2-MP2: Total energy | -25394.745833 |
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. |
| 31.052 | 36.043 | 1.325 | -2.283 | -4.034 | -0.018 |
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 | LYS | 1 | 0.972 | 0.976 | 3.261 | 38.902 | 41.039 | 0.143 | -1.076 | -1.205 | -0.004 |
| 6 | A | 6 | HIS | 0 | -0.071 | -0.038 | 2.564 | -0.418 | 2.301 | 1.183 | -1.203 | -2.699 | -0.014 |
| 9 | A | 9 | TYR | 0 | -0.036 | -0.032 | 4.667 | 0.699 | 0.834 | -0.001 | -0.004 | -0.130 | 0.000 |
| 4 | A | 4 | ASP | -1 | -0.861 | -0.928 | 5.897 | -28.588 | -28.588 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | ILE | 0 | -0.013 | 0.006 | 5.551 | 2.043 | 2.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | PRO | 0 | 0.032 | 0.011 | 5.533 | 0.937 | 0.937 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.858 | 0.917 | 5.237 | 16.366 | 16.366 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLU | -1 | -0.849 | -0.905 | 6.666 | -20.631 | -20.631 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLU | -1 | -0.885 | -0.969 | 9.566 | -17.514 | -17.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ILE | 0 | 0.044 | 0.048 | 12.695 | 0.658 | 0.658 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | THR | 0 | -0.025 | -0.028 | 15.568 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ALA | 0 | -0.004 | 0.010 | 18.727 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | SER | 0 | 0.027 | 0.002 | 20.410 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | CYS | 0 | -0.027 | -0.052 | 24.256 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | SER | 0 | 0.037 | 0.003 | 26.384 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | CYS | -1 | -0.940 | -0.836 | 29.107 | -9.558 | -9.558 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLY | 0 | 0.036 | 0.010 | 30.040 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ASN | 0 | -0.045 | -0.042 | 24.324 | -0.354 | -0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | VAL | 0 | 0.030 | 0.013 | 23.090 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | MET | 0 | -0.043 | -0.007 | 19.229 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | LYS | 1 | 0.816 | 0.922 | 17.036 | 14.996 | 14.996 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ILE | 0 | 0.028 | 0.016 | 13.316 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | ARG | 1 | 0.964 | 0.992 | 7.082 | 24.888 | 24.888 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | SER | 0 | 0.023 | 0.001 | 9.519 | -0.719 | -0.719 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | THR | 0 | 0.007 | -0.008 | 7.325 | -0.666 | -0.666 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | VAL | 0 | -0.041 | -0.009 | 9.681 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | GLY | 0 | 0.007 | 0.012 | 12.863 | 0.678 | 0.678 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | HIS | 0 | -0.057 | -0.025 | 14.116 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ASP | -1 | -0.813 | -0.920 | 17.209 | -13.686 | -13.686 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | LEU | 0 | -0.040 | -0.015 | 16.558 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | ASN | 0 | 0.020 | 0.016 | 20.519 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | LEU | 0 | -0.039 | -0.024 | 20.322 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | ASP | -1 | -0.870 | -0.938 | 24.313 | -9.066 | -9.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | VAL | 0 | 0.004 | 0.006 | 26.145 | 0.324 | 0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | CYS | 0 | -0.003 | -0.010 | 23.993 | -0.425 | -0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | SER | 0 | 0.024 | -0.003 | 23.677 | 0.386 | 0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LYS | 1 | 0.889 | 0.925 | 26.023 | 9.708 | 9.708 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | CYS | 0 | -0.033 | -0.047 | 28.418 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | HIS | 0 | 0.049 | 0.042 | 28.021 | 0.376 | 0.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | PRO | 0 | 0.032 | -0.001 | 30.258 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | PHE | 0 | -0.050 | -0.016 | 29.771 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | PHE | 0 | 0.016 | 0.003 | 25.366 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | THR | 0 | -0.043 | -0.005 | 31.081 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLY | 0 | 0.077 | 0.055 | 34.472 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | LYS | 1 | 1.070 | 1.087 | 37.129 | 7.903 | 7.903 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | GLN | 0 | 0.502 | 0.522 | 37.518 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 55 | GLY | 0 | -0.070 | -0.063 | 43.442 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 56 | ARG | 1 | 0.530 | 0.529 | 48.932 | 5.786 | 5.786 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 57 | VAL | 0 | -0.102 | -0.137 | 53.945 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 58 | ASP | -1 | -0.877 | -0.940 | 56.608 | -5.324 | -5.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 59 | ARG | 1 | 0.971 | 0.991 | 57.008 | 5.355 | 5.355 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 60 | PHE | 0 | -0.065 | -0.050 | 59.177 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 61 | ASN | 0 | 0.054 | 0.017 | 62.528 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 62 | LYS | 1 | 0.917 | 0.960 | 59.974 | 4.937 | 4.937 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 63 | ARG | 1 | 0.903 | 0.965 | 61.551 | 4.910 | 4.910 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 64 | PHE | 0 | -0.052 | -0.024 | 64.178 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 65 | ASN | 0 | -0.018 | -0.009 | 65.400 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 66 | ILE | -1 | -0.909 | -0.934 | 68.780 | -4.232 | -4.232 | 0.000 | 0.000 | 0.000 | 0.000 |