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: N6ZJQ
Calculation Name: 7OTC-j-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: j
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 | 99 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -659699.07019 |
|---|---|
| FMO2-HF: Nuclear repulsion | 620822.665879 |
| FMO2-HF: Total energy | -38876.40431 |
| FMO2-MP2: Total energy | -38992.084489 |
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:4:GLN)
Summations of interaction energy for
fragment #1(A:4:GLN)
| 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. |
| -64.496 | -58.509 | 1.998 | -2.747 | -5.238 | -0.023 |
Interaction energy analysis for fragmet #1(A:4:GLN)
| 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 | 6 | ILE | 0 | 0.075 | 0.060 | 3.193 | 4.158 | 6.113 | 0.019 | -0.707 | -1.267 | 0.000 |
| 76 | A | 79 | PRO | 0 | -0.029 | 0.006 | 2.563 | 3.073 | 4.464 | 0.344 | -0.479 | -1.256 | -0.001 |
| 77 | A | 80 | THR | 0 | 0.087 | 0.049 | 2.580 | -13.792 | -11.903 | 0.601 | -1.123 | -1.368 | -0.015 |
| 78 | A | 81 | GLU | -1 | -0.838 | -0.912 | 4.974 | -35.807 | -35.740 | -0.001 | 0.000 | -0.065 | 0.000 |
| 99 | A | 102 | LEU | -1 | -0.886 | -0.946 | 2.422 | -50.475 | -49.790 | 1.035 | -0.438 | -1.282 | -0.007 |
| 4 | A | 7 | ARG | 1 | 0.917 | 0.959 | 5.472 | 32.907 | 32.907 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 8 | ILE | 0 | 0.027 | 0.015 | 9.127 | 0.794 | 0.794 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 9 | ARG | 1 | 0.945 | 0.975 | 12.000 | 18.085 | 18.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 10 | LEU | 0 | 0.039 | 0.029 | 15.133 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 11 | LYS | 1 | 0.922 | 0.954 | 18.396 | 14.443 | 14.443 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 12 | ALA | 0 | 0.093 | 0.061 | 21.944 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 13 | PHE | 0 | 0.027 | -0.001 | 25.389 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 14 | ASP | -1 | -0.841 | -0.924 | 28.561 | -9.904 | -9.904 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 15 | HIS | 0 | -0.024 | -0.017 | 27.397 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 16 | ARG | 1 | 0.973 | 0.972 | 27.268 | 9.193 | 9.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 17 | LEU | 0 | 0.012 | 0.021 | 25.442 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 18 | ILE | 0 | -0.019 | 0.000 | 22.527 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 19 | ASP | -1 | -0.841 | -0.898 | 22.171 | -13.168 | -13.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 20 | GLN | 0 | -0.017 | -0.011 | 23.419 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 21 | ALA | 0 | 0.032 | 0.022 | 20.357 | -0.292 | -0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 22 | THR | 0 | -0.097 | -0.086 | 18.024 | -0.700 | -0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 23 | ALA | 0 | -0.031 | -0.019 | 19.173 | -0.532 | -0.532 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 24 | GLU | -1 | -0.877 | -0.925 | 19.377 | -15.628 | -15.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 25 | ILE | 0 | 0.053 | 0.033 | 14.593 | -0.774 | -0.774 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 26 | VAL | 0 | -0.056 | -0.022 | 15.066 | -1.376 | -1.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 27 | GLU | -1 | -0.858 | -0.940 | 16.456 | -15.923 | -15.923 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 28 | THR | 0 | -0.030 | -0.019 | 14.766 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 29 | ALA | 0 | 0.004 | -0.013 | 12.334 | -0.642 | -0.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 30 | LYS | 1 | 0.909 | 0.963 | 13.169 | 18.064 | 18.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 31 | ARG | 1 | 0.924 | 0.969 | 15.920 | 14.901 | 14.901 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 32 | THR | 0 | -0.052 | -0.027 | 11.000 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 33 | GLY | 0 | -0.008 | 0.016 | 11.934 | -1.127 | -1.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 34 | ALA | 0 | 0.035 | 0.034 | 9.083 | -0.591 | -0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 35 | GLN | 0 | -0.016 | -0.016 | 9.764 | -0.479 | -0.479 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 36 | VAL | 0 | -0.013 | -0.021 | 10.391 | -2.646 | -2.646 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 37 | ARG | 1 | 0.920 | 0.966 | 11.797 | 25.939 | 25.939 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 38 | GLY | 0 | 0.018 | 0.011 | 14.025 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 39 | PRO | 0 | 0.014 | -0.001 | 16.857 | -0.473 | -0.473 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 40 | ILE | 0 | 0.003 | 0.015 | 16.962 | 1.032 | 1.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 41 | PRO | 0 | -0.015 | -0.024 | 19.693 | -0.179 | -0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 42 | LEU | 0 | -0.010 | 0.001 | 18.048 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 43 | PRO | 0 | -0.016 | -0.011 | 22.198 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 44 | THR | 0 | -0.030 | -0.021 | 25.776 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 45 | ARG | 1 | 0.872 | 0.944 | 27.183 | 11.200 | 11.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 46 | LYS | 1 | 0.917 | 0.946 | 28.948 | 9.842 | 9.842 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 47 | GLU | -1 | -0.853 | -0.910 | 31.550 | -9.479 | -9.479 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 48 | ARG | 1 | 0.852 | 0.901 | 34.250 | 8.454 | 8.454 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 49 | PHE | 0 | 0.034 | 0.022 | 34.744 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 50 | THR | 0 | -0.020 | -0.007 | 40.183 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 51 | VAL | 0 | -0.017 | -0.007 | 43.857 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 52 | LEU | 0 | -0.053 | -0.030 | 46.159 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 53 | ILE | 0 | 0.016 | 0.015 | 48.884 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 54 | SER | 0 | -0.020 | -0.008 | 51.237 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 55 | PRO | 0 | 0.002 | -0.006 | 54.043 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 56 | HIS | 0 | -0.001 | 0.004 | 55.099 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 57 | VAL | 0 | 0.001 | -0.001 | 57.085 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 58 | ASN | 0 | 0.027 | 0.012 | 56.132 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 59 | LYS | 1 | 0.943 | 0.970 | 52.090 | 5.936 | 5.936 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 60 | ASP | -1 | -0.854 | -0.922 | 53.542 | -5.793 | -5.793 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 61 | ALA | 0 | -0.002 | 0.006 | 53.462 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 62 | ARG | 1 | 0.841 | 0.899 | 48.724 | 6.278 | 6.278 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 63 | ASP | -1 | -0.751 | -0.845 | 46.208 | -6.597 | -6.597 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 64 | GLN | 0 | -0.045 | -0.038 | 42.676 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 65 | TYR | 0 | -0.017 | -0.005 | 40.185 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 66 | GLU | -1 | -0.781 | -0.868 | 36.543 | -8.699 | -8.699 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 67 | ILE | 0 | 0.024 | 0.022 | 31.389 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 68 | ARG | 1 | 0.817 | 0.885 | 31.325 | 8.867 | 8.867 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 69 | THR | 0 | -0.018 | -0.007 | 26.160 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 70 | HIS | 0 | 0.010 | 0.005 | 25.644 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 71 | LEU | 0 | -0.007 | -0.007 | 20.018 | -0.372 | -0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 72 | ARG | 1 | 0.858 | 0.931 | 19.037 | 13.805 | 13.805 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 73 | LEU | 0 | -0.009 | 0.004 | 13.235 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 74 | VAL | 0 | 0.030 | 0.010 | 11.987 | 0.879 | 0.879 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 75 | ASP | -1 | -0.849 | -0.921 | 9.656 | -28.074 | -28.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 76 | ILE | 0 | -0.008 | -0.016 | 6.598 | 2.465 | 2.465 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 77 | VAL | 0 | -0.046 | -0.019 | 6.360 | -5.759 | -5.759 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 78 | GLU | -1 | -0.906 | -0.955 | 5.251 | -49.633 | -49.633 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 82 | LYS | 1 | 0.933 | 0.972 | 6.508 | 23.368 | 23.368 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 83 | THR | 0 | -0.060 | -0.053 | 5.961 | 1.596 | 1.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 84 | VAL | 0 | 0.022 | 0.011 | 5.590 | 1.777 | 1.777 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 85 | ASP | -1 | -0.847 | -0.934 | 8.407 | -20.651 | -20.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 86 | ALA | 0 | -0.132 | -0.067 | 11.048 | 2.111 | 2.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 87 | LEU | 0 | -0.005 | -0.022 | 10.125 | 1.273 | 1.273 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 88 | MET | 0 | -0.038 | -0.012 | 11.686 | 1.146 | 1.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 89 | ARG | 1 | 0.916 | 0.962 | 14.323 | 17.648 | 17.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 90 | LEU | 0 | -0.082 | -0.016 | 15.246 | 0.783 | 0.783 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 91 | ASP | -1 | -0.910 | -0.948 | 18.342 | -12.839 | -12.839 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 92 | LEU | 0 | -0.001 | 0.000 | 17.994 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 93 | ALA | 0 | 0.014 | 0.004 | 22.136 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 94 | ALA | 0 | 0.037 | 0.001 | 24.230 | -0.301 | -0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 95 | GLY | 0 | -0.014 | -0.001 | 26.074 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 96 | VAL | 0 | -0.067 | -0.051 | 21.158 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 97 | ASP | -1 | -0.871 | -0.909 | 20.277 | -13.691 | -13.691 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 98 | VAL | 0 | 0.011 | -0.011 | 15.424 | -0.634 | -0.634 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 99 | GLN | 0 | -0.086 | -0.067 | 14.709 | 1.145 | 1.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 100 | ILE | 0 | 0.014 | 0.011 | 9.789 | -0.685 | -0.685 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 101 | SER | 0 | -0.036 | -0.017 | 7.943 | 2.024 | 2.024 | 0.000 | 0.000 | 0.000 | 0.000 |