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: 4GQ9N
Calculation Name: 7OTC-Y-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: Y
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 | 62 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -337523.212892 |
|---|---|
| FMO2-HF: Nuclear repulsion | 312778.428622 |
| FMO2-HF: Total energy | -24744.78427 |
| FMO2-MP2: Total energy | -24817.861145 |
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:LYS)
Summations of interaction energy for
fragment #1(A:2:LYS)
| 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. |
| -15.394 | -0.86800000000005 | 18.737 | -15.016 | -18.245 | -0.172 |
Interaction energy analysis for fragmet #1(A:2:LYS)
| 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 | LYS | 1 | 0.953 | 1.003 | 3.068 | 84.167 | 87.476 | 0.000 | -1.467 | -1.842 | -0.006 |
| 4 | A | 5 | GLU | -1 | -0.723 | -0.874 | 2.513 | -146.993 | -139.054 | 1.942 | -4.897 | -4.983 | -0.059 |
| 5 | A | 6 | LEU | 0 | -0.062 | -0.040 | 2.013 | 0.770 | 1.509 | 2.651 | -1.019 | -2.372 | -0.015 |
| 16 | A | 17 | GLU | -1 | -0.901 | -0.949 | 4.908 | -83.630 | -83.490 | -0.001 | -0.004 | -0.135 | 0.000 |
| 20 | A | 21 | LEU | 0 | 0.044 | 0.023 | 3.353 | 0.016 | 0.268 | 0.003 | -0.069 | -0.186 | -0.001 |
| 44 | A | 45 | GLN | 0 | -0.032 | -0.027 | 3.550 | 7.970 | 8.173 | 0.000 | -0.039 | -0.164 | 0.000 |
| 48 | A | 49 | ASP | -1 | -0.796 | -0.894 | 1.924 | -164.420 | -163.017 | 10.582 | -6.408 | -5.576 | -0.084 |
| 49 | A | 50 | VAL | 0 | 0.051 | 0.030 | 4.268 | 1.446 | 1.561 | -0.001 | -0.045 | -0.069 | 0.000 |
| 51 | A | 52 | ARG | 1 | 0.883 | 0.950 | 2.244 | 105.163 | 105.589 | 3.561 | -1.068 | -2.918 | -0.007 |
| 6 | A | 7 | ARG | 1 | 0.769 | 0.869 | 6.149 | 58.111 | 58.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | GLU | -1 | -0.887 | -0.953 | 7.862 | -61.835 | -61.835 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | LYS | 1 | 0.846 | 0.952 | 5.224 | 83.209 | 83.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | SER | 0 | -0.031 | -0.020 | 11.155 | 0.779 | 0.779 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | VAL | 0 | -0.001 | -0.010 | 12.261 | -3.281 | -3.281 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | GLU | -1 | -0.847 | -0.924 | 13.803 | -35.914 | -35.914 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | GLU | -1 | -0.767 | -0.891 | 10.809 | -44.072 | -44.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | LEU | 0 | -0.004 | 0.024 | 7.621 | -4.258 | -4.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | ASN | 0 | 0.018 | -0.007 | 9.976 | -3.887 | -3.887 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | THR | 0 | -0.077 | -0.051 | 11.695 | 0.779 | 0.779 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | LEU | 0 | -0.076 | -0.037 | 7.987 | -1.707 | -1.707 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LEU | 0 | -0.011 | -0.020 | 9.199 | 0.846 | 0.846 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ASN | 0 | -0.014 | -0.006 | 8.189 | 7.186 | 7.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | LEU | 0 | -0.053 | -0.029 | 7.767 | 2.575 | 2.575 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | ARG | 1 | 0.946 | 0.981 | 11.321 | 41.953 | 41.953 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | GLU | -1 | -0.840 | -0.915 | 7.993 | -53.971 | -53.971 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | GLN | 0 | -0.052 | -0.028 | 10.278 | 5.169 | 5.169 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | PHE | 0 | 0.000 | -0.004 | 11.716 | 2.153 | 2.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | ASN | 0 | 0.048 | 0.018 | 14.400 | 2.926 | 2.926 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | LEU | 0 | 0.001 | -0.009 | 11.704 | 1.348 | 1.348 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | ARG | 1 | 0.921 | 0.956 | 14.834 | 33.853 | 33.853 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | MET | 0 | -0.026 | -0.004 | 17.109 | 2.022 | 2.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | GLN | 0 | 0.032 | 0.015 | 17.715 | 1.707 | 1.707 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ALA | 0 | -0.053 | -0.032 | 18.035 | 0.761 | 0.761 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | ALA | 0 | -0.043 | -0.013 | 19.941 | 0.995 | 0.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | SER | 0 | -0.015 | -0.026 | 22.789 | 0.662 | 0.662 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | GLY | 0 | 0.013 | 0.020 | 23.221 | 0.865 | 0.865 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | GLN | 0 | 0.013 | 0.018 | 22.048 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | LEU | 0 | -0.079 | -0.023 | 15.210 | -0.976 | -0.976 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | GLN | 0 | 0.067 | 0.038 | 19.154 | 0.558 | 0.558 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | GLN | 0 | 0.011 | 0.001 | 14.270 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | SER | 0 | 0.055 | 0.008 | 14.309 | -1.949 | -1.949 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | HIS | 0 | -0.017 | -0.007 | 10.590 | 0.801 | 0.801 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | LEU | 0 | 0.039 | 0.016 | 9.399 | -3.998 | -3.998 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | LEU | 0 | 0.047 | 0.032 | 9.411 | -4.325 | -4.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LYS | 1 | 0.888 | 0.941 | 10.705 | 39.283 | 39.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | VAL | 0 | 0.070 | 0.035 | 5.641 | -7.895 | -7.895 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | ARG | 1 | 0.966 | 0.987 | 6.695 | 38.323 | 38.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | ARG | 1 | 0.922 | 0.958 | 6.840 | 50.569 | 50.569 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | ALA | 0 | -0.005 | 0.003 | 7.431 | 2.953 | 2.953 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | VAL | 0 | 0.051 | 0.027 | 5.211 | 2.232 | 2.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | LYS | 1 | 0.964 | 0.969 | 7.769 | 43.313 | 43.313 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | THR | 0 | -0.037 | -0.021 | 10.082 | 3.962 | 3.962 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | LEU | 0 | -0.016 | -0.019 | 6.302 | 1.237 | 1.237 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | LEU | 0 | -0.017 | 0.002 | 10.479 | 2.174 | 2.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | ASN | 0 | -0.007 | -0.001 | 12.976 | 2.420 | 2.420 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | GLU | -1 | -0.766 | -0.857 | 12.684 | -43.377 | -43.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | LYS | 1 | 0.899 | 0.955 | 13.320 | 42.476 | 42.476 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | ALA | 0 | -0.032 | -0.020 | 15.285 | 1.343 | 1.343 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | GLY | 0 | -0.039 | -0.015 | 18.072 | 1.651 | 1.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | ALA | -1 | -0.978 | -0.970 | 19.387 | -29.381 | -29.381 | 0.000 | 0.000 | 0.000 | 0.000 |