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: G78J1
Calculation Name: 7S1K-v-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: 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 | 96 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -606470.151931 |
|---|---|
| FMO2-HF: Nuclear repulsion | 568217.318219 |
| FMO2-HF: Total energy | -38252.833712 |
| FMO2-MP2: Total energy | -38364.927347 |
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:ALA)
Summations of interaction energy for
fragment #1(A:2:ALA)
| 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. |
| 259.76 | 265.106 | 5.719 | -5.181 | -5.884 | -0.056 |
Interaction energy analysis for fragmet #1(A:2:ALA)
| 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 | GLN | 0 | 0.080 | 0.025 | 3.893 | -10.051 | -8.828 | -0.015 | -0.637 | -0.571 | -0.001 |
| 5 | A | 6 | MET | 0 | -0.032 | -0.029 | 4.308 | 2.196 | 2.312 | -0.001 | -0.011 | -0.104 | 0.000 |
| 6 | A | 7 | LYS | 1 | 0.968 | 0.980 | 4.323 | 53.255 | 53.413 | -0.001 | -0.011 | -0.145 | 0.000 |
| 58 | A | 63 | ARG | 1 | 0.837 | 0.905 | 4.229 | 36.621 | 36.738 | -0.001 | -0.012 | -0.103 | 0.000 |
| 62 | A | 67 | THR | 0 | -0.004 | -0.026 | 2.886 | -16.755 | -15.109 | 0.094 | -0.862 | -0.879 | -0.009 |
| 63 | A | 68 | GLY | 0 | 0.006 | -0.014 | 2.179 | -37.553 | -36.345 | 5.493 | -3.369 | -3.333 | -0.043 |
| 64 | A | 69 | ARG | 1 | 0.889 | 0.936 | 3.415 | 32.905 | 33.735 | 0.150 | -0.261 | -0.719 | -0.003 |
| 65 | A | 70 | PRO | 0 | 0.016 | 0.018 | 4.162 | 4.130 | 4.178 | 0.000 | -0.018 | -0.030 | 0.000 |
| 4 | A | 5 | SER | 0 | 0.095 | 0.068 | 6.607 | 2.670 | 2.670 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | ALA | 0 | 0.073 | 0.046 | 6.129 | 2.669 | 2.669 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | ARG | 1 | 0.948 | 0.966 | 9.143 | 27.482 | 27.482 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | GLU | -1 | -0.818 | -0.919 | 8.017 | -23.985 | -23.985 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | VAL | 0 | 0.041 | 0.019 | 9.995 | 1.616 | 1.616 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | LYS | 1 | 0.984 | 1.001 | 12.007 | 18.554 | 18.554 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | ARG | 1 | 0.820 | 0.903 | 11.141 | 22.154 | 22.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | VAL | 0 | 0.001 | 0.009 | 13.374 | 0.948 | 0.948 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | ALA | 0 | 0.067 | 0.037 | 15.952 | 0.931 | 0.931 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | LEU | 0 | -0.044 | -0.021 | 17.839 | 0.908 | 0.908 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ALA | 0 | -0.011 | -0.026 | 18.877 | 0.827 | 0.827 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | ASP | -1 | -0.935 | -0.952 | 20.206 | -12.669 | -12.669 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LYS | 1 | 0.954 | 0.986 | 22.129 | 12.007 | 12.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | TYR | 0 | -0.048 | -0.034 | 23.472 | 0.503 | 0.503 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | PHE | 0 | 0.022 | -0.027 | 23.304 | 0.455 | 0.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | ALA | 0 | 0.029 | 0.033 | 24.635 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | LYS | 1 | 1.062 | 1.042 | 26.198 | 9.848 | 9.848 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | ARG | 1 | 0.825 | 0.899 | 28.391 | 9.556 | 9.556 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | ALA | 0 | -0.005 | -0.001 | 27.309 | 0.256 | 0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | GLU | -1 | -0.871 | -0.918 | 29.277 | -9.268 | -9.268 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | LEU | 0 | 0.020 | 0.001 | 31.380 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | LYS | 1 | 0.787 | 0.894 | 29.855 | 10.028 | 10.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | ALA | 0 | 0.011 | 0.011 | 31.128 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | ILE | 0 | 0.096 | 0.056 | 33.234 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | ILE | 0 | -0.030 | 0.000 | 36.228 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | SER | 0 | -0.087 | -0.084 | 35.463 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | ASP | -1 | -0.927 | -0.958 | 34.491 | -8.868 | -8.868 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | VAL | 0 | -0.022 | -0.011 | 37.373 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | ASN | 0 | -0.046 | -0.013 | 41.038 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | ALA | 0 | 0.144 | 0.093 | 43.521 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 41 | ARG | 1 | 0.965 | 0.960 | 43.804 | 6.839 | 6.839 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 42 | TRP | 0 | 0.046 | 0.026 | 39.070 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 43 | ASN | 0 | -0.060 | -0.043 | 39.154 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 44 | ALA | 0 | 0.022 | 0.026 | 39.556 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 45 | VAL | 0 | 0.057 | 0.021 | 35.307 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 46 | LEU | 0 | -0.010 | 0.013 | 33.948 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 47 | LYS | 1 | 0.963 | 0.961 | 33.524 | 7.432 | 7.432 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 48 | LEU | 0 | 0.012 | 0.034 | 32.363 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 49 | GLN | 0 | -0.051 | -0.046 | 29.017 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 50 | THR | 0 | 0.023 | 0.015 | 27.913 | -0.356 | -0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 51 | LEU | 0 | -0.013 | 0.010 | 26.277 | -0.220 | -0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 52 | PRO | 0 | 0.043 | 0.027 | 21.732 | -0.232 | -0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 53 | ARG | 1 | 1.028 | 1.017 | 20.294 | 12.372 | 12.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 54 | ASP | -1 | -0.877 | -0.921 | 15.904 | -17.942 | -17.942 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 55 | SER | 0 | -0.018 | -0.017 | 17.943 | -0.297 | -0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 56 | SER | 0 | 0.023 | 0.018 | 20.457 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 57 | PRO | 0 | 0.090 | 0.033 | 18.906 | -0.764 | -0.764 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 58 | SER | 0 | -0.038 | -0.022 | 18.130 | -0.508 | -0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 59 | ARG | 1 | 0.858 | 0.927 | 15.805 | 15.958 | 15.958 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 60 | GLN | 0 | 0.006 | 0.008 | 13.469 | -0.542 | -0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 61 | ARG | 1 | 0.818 | 0.908 | 9.352 | 23.488 | 23.488 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 62 | ASN | 0 | 0.008 | 0.000 | 9.973 | -1.558 | -1.558 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 64 | CYS | -1 | -0.919 | -0.870 | 5.980 | -36.025 | -36.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 65 | ARG | 1 | 1.014 | 0.996 | 6.651 | 16.279 | 16.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 66 | GLN | 0 | 0.062 | 0.039 | 7.573 | -1.500 | -1.500 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 71 | HIS | 0 | 0.102 | 0.040 | 7.109 | 3.362 | 3.362 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 72 | GLY | 0 | 0.031 | 0.015 | 9.044 | -2.045 | -2.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 73 | PHE | 0 | -0.014 | 0.009 | 9.987 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 74 | LEU | 0 | 0.066 | 0.034 | 11.639 | 1.473 | 1.473 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 75 | ARG | 1 | 0.996 | 0.976 | 15.003 | 15.257 | 15.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 76 | LYS | 1 | 0.976 | 1.007 | 16.748 | 13.325 | 13.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 77 | PHE | 0 | 0.062 | 0.020 | 15.430 | 0.281 | 0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 78 | GLY | 0 | -0.013 | 0.010 | 13.525 | -0.452 | -0.452 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 79 | LEU | 0 | 0.041 | -0.001 | 10.420 | -2.914 | -2.914 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 80 | SER | 0 | -0.009 | -0.042 | 7.849 | 2.460 | 2.460 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 81 | ARG | 1 | 1.042 | 1.002 | 9.929 | 21.954 | 21.954 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 82 | ILE | 0 | -0.033 | -0.008 | 8.942 | 0.756 | 0.756 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 83 | LYS | 1 | 0.979 | 0.980 | 7.571 | 33.907 | 33.907 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 84 | VAL | 0 | 0.007 | 0.010 | 11.470 | 1.082 | 1.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 85 | ARG | 1 | 0.931 | 0.959 | 14.834 | 18.877 | 18.877 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 86 | GLU | -1 | -0.889 | -0.945 | 12.927 | -19.533 | -19.533 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 87 | ALA | 0 | 0.013 | 0.020 | 15.164 | 0.645 | 0.645 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 88 | ALA | 0 | -0.034 | -0.018 | 16.707 | 0.993 | 0.993 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 89 | MET | 0 | -0.065 | -0.041 | 18.982 | 0.882 | 0.882 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 90 | ARG | 1 | 0.866 | 0.929 | 14.909 | 19.298 | 19.298 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 91 | GLY | 0 | 0.041 | 0.034 | 21.273 | 0.341 | 0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 92 | GLU | -1 | -0.839 | -0.914 | 17.182 | -18.204 | -18.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 93 | ILE | 0 | -0.097 | -0.045 | 16.935 | -0.409 | -0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 94 | PRO | 0 | 0.053 | 0.015 | 21.080 | 0.430 | 0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 95 | GLY | 0 | 0.005 | 0.007 | 24.850 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 96 | LEU | 0 | -0.087 | -0.027 | 20.429 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 97 | LYS | 1 | 1.006 | 0.997 | 24.617 | 10.259 | 10.259 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 98 | LYS | 1 | 0.935 | 0.958 | 24.523 | 12.137 | 12.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 99 | ALA | 0 | 0.000 | 0.004 | 26.476 | 0.316 | 0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 100 | SER | 0 | -0.027 | -0.025 | 28.884 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 101 | TRP | -1 | -0.896 | -0.923 | 28.601 | -9.167 | -9.167 | 0.000 | 0.000 | 0.000 | 0.000 |