FMODB ID: N6ZKQ
Calculation Name: 7S1K-u-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: u
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
| 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 method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 115 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
| FMO2-HF: Electronic energy | -775736.655261 |
|---|---|
| FMO2-HF: Nuclear repulsion | 731512.690855 |
| FMO2-HF: Total energy | -44223.964407 |
| FMO2-MP2: Total energy | -44353.709525 |
| 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)
| 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. |
| 40.57 | 49.104 | 4.486 | -5.221 | -7.797 | -0.042 |
| 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 | 0.041 | 2.759 | 0.299 | 1.986 | 0.177 | -0.711 | -1.154 | 0.000 |
| 7 | A | 8 | ASN | 0 | -0.031 | -0.028 | 2.525 | 1.514 | 2.377 | 0.205 | -0.330 | -0.737 | -0.001 |
| 8 | A | 9 | ILE | 0 | 0.014 | 0.035 | 1.877 | 4.136 | 5.067 | 2.244 | -1.276 | -1.898 | -0.008 |
| 9 | A | 10 | PRO | 0 | -0.061 | -0.043 | 2.626 | -22.678 | -20.276 | 0.447 | -1.613 | -1.235 | -0.020 |
| 10 | A | 11 | ASP | -1 | -0.803 | -0.897 | 3.635 | -47.619 | -47.367 | 0.000 | -0.036 | -0.216 | 0.000 |
| 11 | A | 12 | HIS | 0 | 0.041 | 0.014 | 5.008 | 5.908 | 5.944 | -0.001 | -0.001 | -0.033 | 0.000 |
| 44 | A | 45 | ILE | 0 | -0.018 | -0.015 | 3.281 | -3.342 | -2.784 | 0.052 | -0.185 | -0.425 | -0.001 |
| 49 | A | 50 | GLU | -1 | -0.805 | -0.909 | 4.183 | -51.891 | -51.564 | 0.000 | -0.059 | -0.268 | 0.000 |
| 52 | A | 53 | ILE | 0 | -0.023 | -0.011 | 2.415 | -3.007 | -2.426 | 1.195 | -0.577 | -1.199 | -0.007 |
| 56 | A | 57 | ARG | 1 | 0.680 | 0.799 | 2.641 | 44.280 | 45.177 | 0.167 | -0.433 | -0.632 | -0.005 |
| 4 | A | 5 | ALA | 0 | 0.046 | 0.039 | 6.076 | 4.593 | 4.593 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | GLY | 0 | 0.005 | 0.011 | 9.106 | 2.289 | 2.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | ILE | 0 | 0.022 | 0.011 | 6.774 | -1.028 | -1.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | LYS | 1 | 0.891 | 0.940 | 8.248 | 31.834 | 31.834 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | HIS | 0 | 0.093 | 0.055 | 8.810 | -4.108 | -4.108 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | ALA | 0 | 0.090 | 0.058 | 8.207 | -1.218 | -1.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | VAL | 0 | -0.010 | -0.001 | 9.174 | -0.695 | -0.695 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ILE | 0 | -0.064 | -0.027 | 11.394 | 1.392 | 1.392 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | ALA | 0 | 0.019 | 0.021 | 5.933 | 0.586 | 0.586 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LEU | 0 | 0.066 | 0.018 | 6.465 | -1.730 | -1.730 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | THR | 0 | -0.116 | -0.066 | 8.930 | 2.022 | 2.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | SER | 0 | -0.039 | -0.012 | 7.997 | 1.439 | 1.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | ILE | 0 | -0.013 | 0.011 | 7.389 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | TYR | 0 | -0.020 | -0.017 | 10.835 | 2.220 | 2.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | GLY | 0 | 0.056 | 0.009 | 14.570 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | VAL | 0 | -0.018 | 0.008 | 11.564 | 1.214 | 1.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | GLY | 0 | 0.044 | 0.029 | 14.547 | -0.459 | -0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | LYS | 1 | 0.996 | 0.978 | 16.136 | 16.918 | 16.918 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | THR | 0 | 0.026 | 0.005 | 16.972 | -0.531 | -0.531 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | ARG | 1 | 0.914 | 0.965 | 15.650 | 16.743 | 16.743 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | SER | 0 | -0.008 | -0.009 | 12.455 | -0.755 | -0.755 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | LYS | 1 | 0.965 | 0.974 | 13.539 | 15.163 | 15.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ALA | 0 | 0.000 | 0.007 | 16.159 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | ILE | 0 | -0.007 | -0.003 | 10.548 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | LEU | 0 | -0.009 | -0.008 | 10.059 | -0.541 | -0.541 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | ALA | 0 | 0.036 | 0.014 | 13.130 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | ALA | 0 | -0.063 | -0.031 | 15.686 | 0.572 | 0.572 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | ALA | 0 | -0.009 | 0.003 | 11.766 | 0.268 | 0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | GLY | 0 | -0.004 | 0.019 | 13.734 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | ILE | 0 | -0.075 | -0.036 | 9.855 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | ALA | 0 | 0.049 | 0.021 | 13.947 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | GLU | -1 | -0.924 | -0.990 | 13.166 | -19.357 | -19.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | ASP | -1 | -0.992 | -1.012 | 13.414 | -19.329 | -19.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | VAL | 0 | 0.047 | 0.053 | 10.118 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LYS | 1 | 0.871 | 0.940 | 9.117 | 23.534 | 23.534 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | SER | 0 | 0.004 | -0.027 | 5.323 | -2.070 | -2.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | GLU | -1 | -0.896 | -0.958 | 7.324 | -24.946 | -24.946 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | LEU | 0 | -0.040 | 0.009 | 5.923 | 1.965 | 1.965 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | SER | 0 | 0.014 | 0.010 | 6.885 | -1.917 | -1.917 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | GLY | 0 | 0.042 | 0.025 | 6.794 | -0.804 | -0.804 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | GLN | 0 | 0.024 | 0.015 | 8.735 | 0.910 | 0.910 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | ASP | -1 | -0.832 | -0.916 | 5.899 | -30.641 | -30.641 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | THR | 0 | -0.028 | -0.013 | 7.927 | 1.567 | 1.567 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | LEU | 0 | 0.017 | 0.008 | 6.332 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | ASP | -1 | -0.785 | -0.889 | 8.327 | -18.588 | -18.588 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | GLU | 0 | -0.031 | -0.022 | 11.816 | 0.916 | 0.916 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | VAL | 0 | -0.031 | -0.017 | 8.971 | 1.173 | 1.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | ALA | 0 | -0.014 | -0.001 | 12.013 | 1.134 | 1.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | LYS | 1 | 0.826 | 0.924 | 14.204 | 19.517 | 19.517 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | PHE | 0 | -0.052 | -0.026 | 14.920 | 1.291 | 1.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 64 | VAL | 0 | 0.041 | 0.036 | 16.483 | -0.863 | -0.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 65 | VAL | 0 | 0.006 | -0.016 | 12.986 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 66 | GLU | -1 | -0.733 | -0.866 | 11.995 | -22.796 | -22.796 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 67 | GLY | 0 | -0.024 | -0.014 | 15.414 | 1.312 | 1.312 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 68 | ASP | -1 | -0.832 | -0.896 | 17.914 | -14.074 | -14.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 69 | LEU | 0 | 0.030 | 0.029 | 18.722 | 0.868 | 0.868 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 70 | ARG | 1 | 0.831 | 0.888 | 14.703 | 20.346 | 20.346 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 71 | ARG | 1 | 0.882 | 0.950 | 19.858 | 15.772 | 15.772 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 72 | GLU | -1 | -0.901 | -0.943 | 23.424 | -12.407 | -12.407 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 73 | ILE | 0 | 0.007 | -0.005 | 23.357 | 0.704 | 0.704 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 74 | SER | 0 | 0.002 | -0.005 | 24.684 | 0.651 | 0.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 75 | MET | 0 | -0.005 | 0.014 | 27.160 | 0.726 | 0.726 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 76 | SER | 0 | -0.052 | -0.043 | 28.529 | 0.544 | 0.544 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 77 | ILE | 0 | -0.055 | -0.040 | 29.013 | 0.495 | 0.495 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 78 | LYS | 1 | 0.856 | 0.914 | 31.323 | 9.463 | 9.463 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 79 | ARG | 1 | 1.021 | 1.008 | 33.214 | 9.315 | 9.315 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 80 | LEU | 0 | -0.052 | -0.031 | 33.338 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 81 | MET | 0 | -0.024 | -0.018 | 35.976 | 0.320 | 0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 82 | ASP | -1 | -0.770 | -0.874 | 37.319 | -8.485 | -8.485 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 83 | LEU | 0 | -0.046 | -0.015 | 38.786 | 0.200 | 0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 84 | GLY | 0 | 0.026 | 0.028 | 41.466 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 85 | CYS | 0 | -0.019 | 0.018 | 39.911 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 86 | TYR | 0 | 0.093 | 0.039 | 41.616 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 87 | ARG | 1 | 0.971 | 0.975 | 33.708 | 9.032 | 9.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 88 | GLY | 0 | 0.062 | 0.021 | 37.364 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 89 | LEU | 0 | -0.016 | -0.009 | 38.431 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 90 | ARG | 1 | 0.882 | 0.933 | 38.040 | 7.614 | 7.614 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 91 | HIS | 0 | 0.021 | 0.013 | 31.957 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 92 | ARG | 1 | 0.980 | 0.998 | 36.084 | 7.663 | 7.663 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 93 | ARG | 1 | 0.920 | 0.959 | 38.402 | 7.433 | 7.433 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 94 | GLY | 0 | 0.058 | 0.051 | 35.984 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 95 | LEU | 0 | -0.034 | -0.026 | 37.022 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 96 | PRO | 0 | -0.014 | -0.009 | 36.374 | -0.285 | -0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 97 | VAL | 0 | 0.016 | 0.001 | 34.580 | 0.189 | 0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 98 | ARG | 1 | 0.918 | 0.961 | 30.540 | 10.105 | 10.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 99 | GLY | 0 | 0.088 | 0.050 | 37.250 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 100 | GLN | 0 | -0.013 | 0.004 | 36.715 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 101 | ARG | 1 | 0.968 | 0.986 | 39.943 | 7.226 | 7.226 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 102 | THR | 0 | 0.059 | -0.011 | 41.232 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 103 | LYS | 1 | 0.944 | 0.996 | 43.066 | 6.297 | 6.297 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 104 | THR | 0 | 0.041 | 0.016 | 43.857 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 105 | ASN | 0 | 0.010 | -0.008 | 39.288 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 106 | ALA | 0 | 0.068 | 0.039 | 37.948 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 107 | ARG | 1 | 0.860 | 0.921 | 36.041 | 8.112 | 8.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 108 | THR | 0 | 0.052 | 0.026 | 30.458 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 108 | A | 109 | ARG | 1 | 0.799 | 0.902 | 31.927 | 9.370 | 9.370 | 0.000 | 0.000 | 0.000 | 0.000 |
| 109 | A | 110 | LYS | 1 | 0.962 | 0.980 | 34.567 | 7.673 | 7.673 | 0.000 | 0.000 | 0.000 | 0.000 |
| 110 | A | 111 | GLY | 0 | 0.077 | 0.065 | 34.152 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 111 | A | 112 | PRO | 0 | 0.068 | 0.025 | 34.116 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 112 | A | 113 | ARG | 1 | 0.871 | 0.934 | 36.909 | 7.870 | 7.870 | 0.000 | 0.000 | 0.000 | 0.000 |
| 113 | A | 114 | LYS | 1 | 0.990 | 0.993 | 40.656 | 7.602 | 7.602 | 0.000 | 0.000 | 0.000 | 0.000 |
| 114 | A | 115 | PRO | 0 | 0.015 | 0.008 | 42.832 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 115 | A | 116 | ILE | -1 | -0.906 | -0.937 | 46.628 | -6.549 | -6.549 | 0.000 | 0.000 | 0.000 | 0.000 |