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: 74NGK
Calculation Name: 7OTC-f-Other547
Preferred Name:
Target Type:
Ligand Name: argyrin b | adenosine-5'-triphosphate | guanosine-5'-diphosphate | n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 2n-methylguanosine-5'-monophosphate | 6n-dimethyladenosine-5'-monophoshate | 2-methyladenosine-5'-monophosphate | 4n,o2'-methylcytidine-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 | 3-methyluridine-5'-monophoshate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid | (3r)-3-(methylsulfanyl)-l-aspartic acid | spermidine | 1,4-diaminobutane | magnesium ion | zinc ion
Ligand 3-letter code: 1I7 | ATP | GDP | G7M | 1MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | H2U | OMC | OMU | 4D4 | D2T | SPD | PUT | MG | ZN
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7OTC
Chain ID: f
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 | 106 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -841454.06373 |
|---|---|
| FMO2-HF: Nuclear repulsion | 797431.183715 |
| FMO2-HF: Total energy | -44022.880016 |
| FMO2-MP2: Total energy | -44147.987244 |
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. |
| -159.357 | -151.716 | 16.36 | -10.963 | -13.038 | -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 | HIS | 0 | -0.030 | -0.014 | 3.851 | 3.656 | 5.309 | -0.020 | -0.732 | -0.900 | 0.000 |
| 4 | A | 4 | TYR | 0 | 0.016 | 0.003 | 4.243 | 2.708 | 2.806 | -0.001 | -0.005 | -0.092 | 0.000 |
| 33 | A | 33 | GLU | -1 | -0.904 | -0.965 | 3.532 | -60.043 | -58.985 | 0.016 | -0.455 | -0.620 | -0.003 |
| 35 | A | 35 | LYS | 1 | 0.786 | 0.892 | 3.739 | 44.466 | 44.616 | -0.001 | -0.015 | -0.133 | 0.000 |
| 65 | A | 65 | GLU | -1 | -0.862 | -0.909 | 2.566 | -55.625 | -54.657 | 2.586 | -1.202 | -2.353 | -0.016 |
| 66 | A | 66 | ALA | 0 | 0.053 | 0.013 | 3.881 | 1.768 | 2.424 | 0.005 | -0.240 | -0.421 | -0.001 |
| 67 | A | 67 | PRO | 0 | 0.022 | 0.008 | 2.125 | -28.321 | -26.772 | 11.805 | -7.776 | -5.578 | -0.051 |
| 68 | A | 68 | GLN | 0 | -0.119 | -0.064 | 2.334 | -19.622 | -18.229 | 1.971 | -0.514 | -2.850 | -0.040 |
| 69 | A | 69 | GLU | -1 | -0.776 | -0.899 | 4.428 | -46.982 | -46.866 | -0.001 | -0.024 | -0.091 | 0.000 |
| 5 | A | 5 | GLU | -1 | -0.953 | -0.967 | 8.959 | -18.736 | -18.736 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | ILE | 0 | 0.054 | 0.025 | 10.549 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | VAL | 0 | -0.002 | 0.001 | 14.324 | 0.808 | 0.808 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | PHE | 0 | 0.017 | 0.004 | 17.793 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | MET | 0 | -0.072 | -0.029 | 20.406 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | VAL | 0 | 0.009 | -0.006 | 24.195 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | HIS | 0 | 0.062 | 0.012 | 26.026 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.092 | -0.038 | 29.711 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ASP | -1 | -0.863 | -0.946 | 32.104 | -8.735 | -8.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | GLN | 0 | -0.026 | -0.005 | 30.496 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | SER | 0 | 0.038 | 0.012 | 29.614 | -0.419 | -0.419 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | GLU | -1 | -0.917 | -0.961 | 29.526 | -9.738 | -9.738 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLN | 0 | -0.022 | -0.027 | 26.564 | -0.417 | -0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | VAL | 0 | -0.018 | 0.011 | 24.323 | -0.434 | -0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | 0.010 | 0.003 | 23.788 | -0.610 | -0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | GLY | 0 | 0.084 | 0.048 | 22.926 | -0.514 | -0.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | MET | 0 | -0.068 | -0.030 | 20.809 | -0.471 | -0.471 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | ILE | 0 | -0.018 | -0.006 | 17.710 | -0.964 | -0.964 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | GLU | -1 | -0.864 | -0.943 | 17.732 | -14.701 | -14.701 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ARG | 1 | 0.925 | 0.962 | 18.221 | 13.149 | 13.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | TYR | 0 | 0.032 | 0.007 | 15.177 | -0.621 | -0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | THR | 0 | 0.004 | 0.002 | 13.499 | -2.151 | -2.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ALA | 0 | 0.008 | 0.025 | 13.346 | -1.242 | -1.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ALA | 0 | -0.022 | -0.001 | 13.540 | -0.640 | -0.640 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ILE | 0 | -0.005 | 0.010 | 7.069 | -1.534 | -1.534 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | THR | 0 | -0.062 | -0.050 | 8.890 | -1.811 | -1.811 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | GLY | 0 | -0.024 | -0.007 | 10.967 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | ALA | 0 | -0.027 | -0.011 | 7.674 | 0.368 | 0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | GLY | 0 | 0.047 | 0.026 | 5.548 | -2.021 | -2.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ILE | 0 | 0.050 | 0.017 | 8.157 | -1.366 | -1.366 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | HIS | 0 | 0.005 | 0.002 | 6.576 | 2.639 | 2.639 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | ARG | 1 | 0.870 | 0.929 | 11.219 | 18.323 | 18.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LEU | 0 | 0.014 | 0.014 | 14.661 | -0.777 | -0.777 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | GLU | -1 | -0.762 | -0.841 | 17.318 | -13.549 | -13.549 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | ASP | -1 | -0.801 | -0.877 | 20.556 | -12.361 | -12.361 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | TRP | 0 | -0.075 | -0.072 | 21.393 | 0.548 | 0.548 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | GLY | 0 | 0.046 | 0.031 | 25.814 | 0.530 | 0.530 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | ARG | 1 | 0.830 | 0.907 | 28.313 | 9.838 | 9.838 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | ARG | 1 | 0.919 | 0.959 | 27.454 | 11.328 | 11.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLN | 0 | 0.014 | 0.004 | 31.418 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | LEU | 0 | -0.038 | -0.014 | 29.697 | -0.293 | -0.293 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | ALA | 0 | 0.007 | 0.001 | 32.027 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | TYR | 0 | 0.009 | 0.013 | 28.579 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | PRO | 0 | -0.013 | -0.002 | 33.363 | -0.228 | -0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | ILE | 0 | 0.021 | 0.009 | 28.378 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | ASN | 0 | 0.012 | -0.003 | 29.404 | 0.259 | 0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | LYS | 1 | 0.932 | 0.964 | 33.605 | 8.561 | 8.561 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | LEU | 0 | 0.035 | 0.042 | 31.655 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | HIS | 0 | 0.069 | 0.013 | 34.507 | -0.282 | -0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | LYS | 1 | 0.864 | 0.941 | 33.334 | 9.231 | 9.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | ALA | 0 | 0.038 | 0.012 | 28.196 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | HIS | 0 | 0.007 | 0.003 | 25.583 | 0.710 | 0.710 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | TYR | 0 | -0.020 | -0.016 | 24.173 | -0.270 | -0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | VAL | 0 | 0.043 | 0.023 | 19.275 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | LEU | 0 | 0.010 | 0.014 | 16.475 | -0.393 | -0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | MET | 0 | -0.028 | -0.012 | 12.283 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ASN | 0 | -0.038 | -0.021 | 10.456 | -2.418 | -2.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | VAL | 0 | 0.037 | 0.002 | 7.580 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | VAL | 0 | 0.031 | 0.019 | 5.915 | 2.806 | 2.806 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | ILE | 0 | -0.021 | -0.014 | 7.170 | 2.519 | 2.519 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | ASP | -1 | -0.915 | -0.943 | 9.438 | -24.428 | -24.428 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | GLU | -1 | -0.910 | -0.968 | 11.414 | -24.089 | -24.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | LEU | 0 | -0.023 | -0.001 | 10.716 | 1.664 | 1.664 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | GLU | -1 | -0.830 | -0.923 | 13.486 | -16.706 | -16.706 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | THR | 0 | -0.039 | -0.020 | 15.418 | 1.886 | 1.886 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | THR | 0 | -0.099 | -0.064 | 16.836 | 1.151 | 1.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | PHE | 0 | -0.023 | -0.015 | 15.078 | 0.796 | 0.796 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ARG | 1 | 0.922 | 0.957 | 19.481 | 13.741 | 13.741 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | PHE | 0 | -0.076 | -0.039 | 21.249 | 0.876 | 0.876 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | ASN | 0 | -0.008 | 0.009 | 22.013 | 0.896 | 0.896 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | ASP | -1 | -0.865 | -0.923 | 24.578 | -10.807 | -10.807 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | ALA | 0 | -0.038 | -0.012 | 25.491 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | VAL | 0 | -0.015 | -0.016 | 21.215 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | ILE | 0 | -0.012 | -0.001 | 24.292 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | ARG | 1 | 0.881 | 0.925 | 22.394 | 12.263 | 12.263 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | SER | 0 | 0.049 | 0.030 | 17.790 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | MET | 0 | -0.048 | -0.013 | 16.695 | 0.777 | 0.777 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | VAL | 0 | 0.059 | 0.041 | 10.685 | -0.488 | -0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | MET | 0 | -0.018 | -0.003 | 12.894 | 0.633 | 0.633 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | ARG | 1 | 0.931 | 0.964 | 8.910 | 28.148 | 28.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | THR | 0 | 0.033 | 0.012 | 9.830 | 2.525 | 2.525 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | LYS | 1 | 0.890 | 0.949 | 9.961 | 21.775 | 21.775 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | HIS | 0 | -0.002 | -0.023 | 9.181 | -1.298 | -1.298 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | ALA | 0 | 0.076 | 0.041 | 7.974 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | VAL | 0 | -0.039 | -0.027 | 9.686 | 1.612 | 1.612 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | THR | 0 | 0.039 | 0.018 | 13.024 | -0.289 | -0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | GLU | -1 | -0.860 | -0.900 | 14.684 | -12.737 | -12.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | ALA | 0 | 0.039 | 0.024 | 17.915 | -0.577 | -0.577 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | SER | 0 | -0.061 | -0.076 | 20.289 | 0.542 | 0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | PRO | 0 | -0.001 | -0.015 | 22.031 | 0.358 | 0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | MET | 0 | -0.006 | -0.003 | 24.495 | 0.582 | 0.582 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | VAL | 0 | -0.022 | -0.004 | 22.935 | 0.370 | 0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | LYS | 1 | 0.825 | 0.906 | 22.553 | 12.707 | 12.707 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 105 | ALA | 0 | -0.044 | -0.009 | 27.540 | 0.292 | 0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 106 | LYS | 0 | -0.013 | 0.020 | 28.508 | 0.704 | 0.704 | 0.000 | 0.000 | 0.000 | 0.000 |