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: N62RQ
Calculation Name: 7S1K-Z-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: Z
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 | 103 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -675908.733495 |
|---|---|
| FMO2-HF: Nuclear repulsion | 635900.639947 |
| FMO2-HF: Total energy | -40008.093548 |
| FMO2-MP2: Total energy | -40126.361162 |
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. |
| -90.569 | -78.285 | 17.225 | -11.011 | -18.5 | -0.111 |
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 | ALA | 0 | 0.077 | 0.044 | 2.653 | -0.876 | 1.194 | 1.779 | -1.246 | -2.603 | -0.009 |
| 4 | A | 4 | VAL | 0 | -0.032 | -0.026 | 4.508 | 1.686 | 1.730 | -0.001 | -0.016 | -0.028 | 0.000 |
| 15 | A | 15 | SER | 0 | 0.011 | -0.009 | 4.427 | -5.451 | -5.319 | -0.001 | -0.051 | -0.079 | 0.000 |
| 16 | A | 16 | GLU | -1 | -0.844 | -0.935 | 3.676 | -36.607 | -35.891 | 0.005 | -0.083 | -0.638 | 0.000 |
| 17 | A | 17 | GLY | 0 | 0.017 | 0.013 | 5.355 | 0.238 | 0.274 | -0.001 | -0.002 | -0.033 | 0.000 |
| 41 | A | 41 | ILE | 0 | -0.001 | 0.006 | 2.155 | -3.127 | -2.711 | 1.208 | -0.392 | -1.232 | 0.001 |
| 42 | A | 42 | ALA | 0 | 0.026 | 0.021 | 2.817 | 4.362 | 5.239 | 0.167 | -0.281 | -0.764 | -0.001 |
| 43 | A | 43 | ASN | 0 | 0.026 | -0.005 | 2.098 | -43.683 | -38.872 | 11.130 | -7.951 | -7.991 | -0.072 |
| 44 | A | 44 | GLY | 0 | -0.031 | -0.025 | 2.707 | -17.066 | -15.580 | 0.226 | -0.078 | -1.634 | -0.024 |
| 45 | A | 45 | GLU | -1 | -0.956 | -0.961 | 5.002 | -24.509 | -24.539 | -0.001 | -0.004 | 0.036 | 0.000 |
| 101 | A | 101 | ILE | 0 | -0.074 | -0.039 | 2.234 | -0.361 | 0.432 | 2.610 | -0.582 | -2.821 | -0.004 |
| 102 | A | 102 | SER | 0 | -0.013 | 0.008 | 4.146 | -2.458 | -1.525 | 0.104 | -0.325 | -0.713 | -0.002 |
| 5 | A | 5 | PHE | 0 | 0.030 | 0.023 | 8.331 | 0.701 | 0.701 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | GLN | 0 | 0.049 | 0.017 | 10.602 | 0.622 | 0.622 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | SER | 0 | 0.036 | 0.018 | 14.400 | 0.528 | 0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLY | 0 | 0.030 | 0.016 | 16.371 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | GLY | 0 | -0.024 | -0.009 | 19.518 | 0.553 | 0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.787 | 0.872 | 17.470 | 13.916 | 13.916 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLN | 0 | 0.023 | 0.012 | 13.723 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | HIS | 0 | -0.032 | -0.010 | 11.726 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ARG | 1 | 0.937 | 0.976 | 7.353 | 32.964 | 32.964 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | VAL | 0 | -0.032 | -0.011 | 6.307 | 1.606 | 1.606 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | GLN | 0 | -0.049 | -0.001 | 8.252 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | THR | 0 | -0.013 | -0.017 | 10.122 | 1.391 | 1.391 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | VAL | 0 | -0.017 | -0.011 | 12.141 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ARG | 1 | 0.789 | 0.866 | 14.540 | 15.002 | 15.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | LEU | 0 | -0.004 | 0.006 | 14.588 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | GLU | -1 | -0.796 | -0.885 | 18.687 | -11.783 | -11.783 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | LYS | 1 | 0.863 | 0.931 | 21.273 | 10.683 | 10.683 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LEU | 0 | 0.038 | 0.021 | 17.986 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ASP | -1 | -0.971 | -0.979 | 22.734 | -11.305 | -11.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ILE | 0 | 0.039 | 0.026 | 20.130 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ALA | 0 | 0.024 | 0.006 | 23.162 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | THR | 0 | -0.032 | -0.042 | 22.514 | -0.322 | -0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | GLY | 0 | -0.024 | -0.008 | 21.034 | 0.483 | 0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | GLU | -1 | -0.914 | -0.944 | 20.548 | -12.638 | -12.638 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | THR | 0 | -0.036 | -0.022 | 16.164 | -0.584 | -0.584 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | VAL | 0 | -0.063 | -0.040 | 14.721 | 0.796 | 0.796 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | GLU | -1 | -0.780 | -0.879 | 13.707 | -19.574 | -19.574 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | PHE | 0 | -0.042 | -0.039 | 10.874 | 1.007 | 1.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ALA | 0 | 0.108 | 0.045 | 10.743 | -1.483 | -1.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | GLU | -1 | -0.917 | -0.932 | 12.310 | -15.817 | -15.817 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | VAL | 0 | -0.038 | -0.037 | 6.304 | -0.742 | -0.742 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LEU | 0 | -0.003 | 0.003 | 9.596 | 0.602 | 0.602 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | MET | 0 | -0.008 | -0.008 | 6.966 | 0.710 | 0.710 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLU | -1 | -0.833 | -0.894 | 5.818 | -34.871 | -34.871 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | VAL | 0 | -0.005 | -0.031 | 6.443 | -5.670 | -5.670 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | LYS | 1 | 0.851 | 0.930 | 5.031 | 36.852 | 36.852 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ILE | 0 | -0.007 | -0.021 | 7.643 | -1.898 | -1.898 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | GLY | 0 | 0.050 | 0.024 | 10.498 | 0.949 | 0.949 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | VAL | 0 | -0.028 | -0.016 | 11.967 | 0.509 | 0.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | PRO | 0 | -0.081 | -0.021 | 15.800 | 0.380 | 0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | PHE | 0 | 0.032 | -0.005 | 12.373 | -0.322 | -0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | VAL | 0 | -0.066 | -0.037 | 6.932 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ASP | -1 | -0.916 | -0.954 | 10.150 | -19.568 | -19.568 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | GLY | 0 | 0.017 | 0.014 | 10.910 | 0.890 | 0.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | GLY | 0 | -0.033 | -0.005 | 7.398 | -0.462 | -0.462 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | VAL | 0 | -0.014 | -0.012 | 7.537 | 1.498 | 1.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | ILE | 0 | -0.051 | -0.022 | 6.052 | -2.460 | -2.460 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | LYS | 1 | 0.822 | 0.905 | 8.348 | 22.612 | 22.612 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | ALA | 0 | 0.037 | 0.007 | 9.736 | -1.999 | -1.999 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | GLU | -1 | -0.827 | -0.911 | 12.405 | -18.345 | -18.345 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | VAL | 0 | -0.025 | -0.003 | 15.848 | -0.531 | -0.531 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | VAL | 0 | -0.013 | -0.005 | 16.706 | 0.555 | 0.555 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | ALA | 0 | -0.005 | -0.008 | 19.473 | 0.690 | 0.690 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | HIS | 0 | 0.035 | 0.026 | 21.980 | -0.457 | -0.457 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | GLY | 0 | 0.004 | 0.003 | 24.794 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | ARG | 1 | 0.817 | 0.915 | 27.180 | 9.440 | 9.440 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | GLY | 0 | 0.059 | 0.025 | 27.493 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | GLU | -1 | -0.822 | -0.916 | 28.113 | -9.593 | -9.593 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | LYS | 1 | 0.847 | 0.934 | 30.747 | 8.424 | 8.424 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | VAL | 0 | 0.048 | 0.040 | 33.005 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | LYS | 1 | 0.893 | 0.926 | 34.938 | 7.759 | 7.759 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | ILE | 0 | 0.017 | 0.014 | 35.262 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | VAL | 0 | 0.003 | -0.011 | 39.179 | 0.237 | 0.237 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | LYS | 1 | 0.967 | 0.985 | 40.850 | 7.518 | 7.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | PHE | 0 | 0.039 | 0.003 | 44.767 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | ARG | 1 | 0.966 | 0.991 | 47.491 | 6.495 | 6.495 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ARG | 1 | 1.022 | 1.009 | 50.881 | 6.391 | 6.391 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | ARG | 1 | 0.963 | 0.966 | 53.223 | 5.718 | 5.718 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | LYS | 1 | 0.977 | 0.982 | 54.326 | 5.743 | 5.743 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | HIS | 0 | 0.047 | 0.047 | 55.847 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | TYR | 0 | 0.041 | 0.030 | 46.507 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | ARG | 1 | 0.959 | 0.963 | 49.166 | 6.047 | 6.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | LYS | 1 | 0.947 | 0.978 | 44.738 | 6.767 | 6.767 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | GLN | 0 | 0.019 | 0.015 | 43.893 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | GLN | 0 | 0.054 | 0.035 | 38.901 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | GLY | 0 | -0.027 | -0.013 | 38.494 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | HIS | 0 | -0.008 | -0.007 | 30.602 | 0.367 | 0.367 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | ARG | 1 | 0.922 | 0.951 | 31.353 | 9.750 | 9.750 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | GLN | 0 | 0.020 | 0.019 | 26.118 | 0.651 | 0.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | TRP | 0 | 0.008 | -0.008 | 27.443 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | PHE | 0 | -0.026 | -0.013 | 22.164 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | THR | 0 | 0.034 | 0.015 | 19.402 | 0.658 | 0.658 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | ASP | -1 | -0.782 | -0.839 | 18.308 | -15.431 | -15.431 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | VAL | 0 | 0.034 | 0.004 | 13.462 | 0.597 | 0.597 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | LYS | 1 | 0.913 | 0.973 | 11.601 | 19.283 | 19.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | ILE | 0 | -0.005 | 0.005 | 6.631 | 0.683 | 0.683 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | THR | 0 | -0.022 | -0.029 | 9.024 | -1.443 | -1.443 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | GLY | 0 | 0.037 | 0.026 | 6.281 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | ALA | -1 | -0.874 | -0.948 | 5.220 | -24.946 | -24.946 | 0.000 | 0.000 | 0.000 | 0.000 |