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: 2G47R
Calculation Name: 7OTC-5-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: 5
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 | 67 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -319641.325079 |
|---|---|
| FMO2-HF: Nuclear repulsion | 291895.102335 |
| FMO2-HF: Total energy | -27746.222745 |
| FMO2-MP2: Total energy | -27822.954894 |
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. |
| 22.09 | 26.264 | 0.708 | -1.923 | -2.957 | -0.015 |
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 | LYS | 1 | 0.978 | 0.970 | 2.707 | 26.908 | 29.406 | 0.642 | -1.364 | -1.775 | -0.010 |
| 4 | A | 4 | ASP | -1 | -0.860 | -0.909 | 5.280 | -30.516 | -30.400 | -0.001 | -0.006 | -0.108 | 0.000 |
| 6 | A | 6 | HIS | 0 | -0.052 | -0.014 | 3.740 | -2.616 | -1.173 | 0.068 | -0.552 | -0.959 | -0.005 |
| 9 | A | 9 | TYR | 0 | -0.026 | -0.025 | 4.622 | -0.091 | 0.026 | -0.001 | -0.001 | -0.115 | 0.000 |
| 5 | A | 5 | ILE | 0 | -0.017 | -0.021 | 6.578 | 1.456 | 1.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | PRO | 0 | 0.025 | 0.009 | 5.736 | 0.982 | 0.982 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.901 | 0.980 | 6.675 | 17.272 | 17.272 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLU | -1 | -0.856 | -0.945 | 7.812 | -26.756 | -26.756 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLU | -1 | -0.894 | -0.971 | 10.670 | -19.409 | -19.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ILE | 0 | -0.012 | 0.000 | 13.521 | 0.520 | 0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | THR | 0 | -0.082 | -0.070 | 16.563 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ALA | 0 | 0.050 | 0.024 | 19.771 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | SER | 0 | -0.017 | -0.012 | 21.726 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | CYS | 0 | -0.046 | -0.015 | 25.522 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | SER | 0 | 0.026 | -0.003 | 27.948 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | CYS | 0 | -0.043 | -0.017 | 30.396 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | GLY | 0 | 0.019 | 0.014 | 31.170 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ASN | 0 | -0.044 | -0.026 | 26.343 | -0.483 | -0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | VAL | 0 | 0.032 | 0.008 | 23.617 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | MET | 0 | 0.013 | 0.035 | 19.885 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | LYS | 1 | 0.889 | 0.955 | 17.721 | 15.134 | 15.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ILE | 0 | 0.008 | 0.000 | 14.854 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | ARG | 1 | 0.960 | 1.008 | 6.852 | 28.865 | 28.865 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | SER | 0 | -0.023 | -0.026 | 11.339 | -0.568 | -0.568 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | THR | 0 | 0.021 | -0.006 | 9.899 | -0.870 | -0.870 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | VAL | 0 | -0.033 | 0.004 | 11.813 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | GLY | 0 | -0.011 | 0.004 | 14.781 | 0.650 | 0.650 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | HIS | 0 | -0.045 | -0.037 | 16.084 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ASP | -1 | -0.787 | -0.872 | 18.782 | -14.315 | -14.315 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | LEU | 0 | -0.024 | -0.008 | 19.658 | 0.371 | 0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | ASN | 0 | 0.032 | 0.022 | 22.825 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | LEU | 0 | -0.029 | -0.009 | 22.403 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | ASP | -1 | -0.831 | -0.919 | 26.265 | -9.886 | -9.886 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | VAL | 0 | 0.013 | 0.017 | 27.315 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | CYS | 0 | -0.044 | -0.027 | 24.620 | -0.450 | -0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | SER | 0 | -0.010 | -0.024 | 23.513 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LYS | 1 | 0.876 | 0.896 | 23.470 | 11.842 | 11.842 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | CYS | 0 | -0.022 | 0.025 | 28.388 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | HIS | 0 | 0.165 | 0.064 | 29.021 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | PRO | 0 | -0.040 | -0.022 | 31.150 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | PHE | 0 | -0.023 | 0.008 | 29.046 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | PHE | 0 | 0.008 | 0.007 | 24.971 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | THR | 0 | -0.028 | -0.022 | 30.168 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLY | 0 | 0.049 | 0.032 | 33.216 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | LYS | 1 | 0.896 | 0.954 | 34.584 | 8.055 | 8.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | GLN | 0 | 0.055 | 0.021 | 37.113 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ARG | 1 | 0.906 | 0.954 | 36.170 | 7.455 | 7.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | ASP | -1 | -0.809 | -0.914 | 33.367 | -8.718 | -8.718 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | VAL | 0 | -0.037 | -0.001 | 36.131 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | ALA | 0 | -0.033 | -0.013 | 38.944 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | THR | 0 | -0.079 | -0.044 | 34.406 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | GLY | 0 | 0.082 | 0.038 | 37.693 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | GLY | 0 | -0.006 | -0.014 | 37.831 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | ARG | 1 | 0.917 | 0.941 | 38.798 | 7.615 | 7.615 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | VAL | 0 | 0.047 | 0.027 | 40.831 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | ASP | -1 | -0.800 | -0.888 | 42.089 | -6.997 | -6.997 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | ARG | 1 | 0.921 | 0.969 | 43.814 | 6.824 | 6.824 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | PHE | 0 | -0.055 | -0.041 | 44.297 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | ASN | 0 | 0.072 | 0.027 | 46.130 | 0.157 | 0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | LYS | 1 | 1.012 | 1.004 | 46.164 | 6.611 | 6.611 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | ARG | 1 | 0.851 | 0.961 | 48.853 | 6.185 | 6.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | PHE | 0 | -0.025 | -0.033 | 50.788 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | ASN | 0 | -0.066 | -0.038 | 53.079 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ILE | 0 | 0.010 | 0.010 | 54.688 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | PRO | -1 | -0.942 | -0.954 | 54.619 | -5.552 | -5.552 | 0.000 | 0.000 | 0.000 | 0.000 |