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: 2G4QR
Calculation Name: 7OTC-0-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: 0
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 | 56 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -226680.625571 |
|---|---|
| FMO2-HF: Nuclear repulsion | 204722.97832 |
| FMO2-HF: Total energy | -21957.647251 |
| FMO2-MP2: Total energy | -22022.227472 |
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:ALA)
Summations of interaction energy for
fragment #1(A:2:ALA)
| 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. |
| 113.358 | 114.877 | -0.016 | -0.756 | -0.746 | -0.001 |
Interaction energy analysis for fragmet #1(A:2:ALA)
| 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 | GLN | 0 | 0.005 | 0.008 | 3.864 | 2.227 | 3.746 | -0.016 | -0.756 | -0.746 | -0.001 |
| 4 | A | 5 | GLN | 0 | 0.070 | 0.026 | 6.616 | 2.385 | 2.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | ASN | 0 | 0.028 | 0.020 | 8.812 | 3.483 | 3.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | LYS | 1 | 0.987 | 0.996 | 10.993 | 15.784 | 15.784 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | PRO | 0 | 0.007 | 0.005 | 11.417 | 1.650 | 1.650 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | THR | 0 | 0.019 | 0.015 | 14.087 | 1.167 | 1.167 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | ARG | 1 | 0.968 | 0.961 | 17.834 | 13.090 | 13.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | SER | 0 | 0.082 | 0.044 | 20.578 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | LYS | 1 | 0.993 | 1.000 | 15.866 | 16.625 | 16.625 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | ARG | 1 | 0.915 | 0.955 | 17.127 | 14.687 | 14.687 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | GLY | 0 | 0.003 | 0.003 | 17.992 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | MET | 0 | 0.035 | 0.001 | 19.508 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | ARG | 1 | 0.946 | 0.976 | 14.310 | 20.400 | 20.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ARG | 1 | 0.949 | 0.971 | 18.392 | 15.324 | 15.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | SER | 0 | -0.041 | -0.007 | 21.300 | 0.636 | 0.636 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | HIS | 0 | -0.016 | -0.006 | 20.638 | 0.578 | 0.578 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ASP | -1 | -0.892 | -0.942 | 20.544 | -14.618 | -14.618 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | ALA | 0 | -0.015 | 0.000 | 23.262 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | LEU | 0 | 0.000 | -0.001 | 26.897 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | THR | 0 | -0.001 | 0.004 | 29.318 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | ALA | 0 | 0.004 | 0.006 | 32.121 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | VAL | 0 | -0.001 | -0.005 | 35.531 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | THR | 0 | 0.010 | 0.000 | 38.216 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | SER | 0 | -0.020 | -0.007 | 40.331 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | LEU | 0 | -0.022 | -0.003 | 42.420 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | SER | 0 | -0.030 | -0.004 | 45.251 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | VAL | 0 | 0.050 | 0.020 | 48.183 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | ASP | -1 | -0.746 | -0.855 | 51.600 | -5.892 | -5.892 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | LYS | 1 | 0.855 | 0.915 | 53.753 | 5.692 | 5.692 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | THR | 0 | -0.084 | -0.042 | 57.147 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | SER | 0 | 0.009 | -0.010 | 54.264 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | GLY | 0 | 0.014 | 0.016 | 55.925 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | GLU | -1 | -0.802 | -0.884 | 50.854 | -6.196 | -6.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | LYS | 1 | 0.911 | 0.940 | 47.620 | 6.637 | 6.637 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | HIS | 0 | -0.013 | -0.006 | 46.364 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | LEU | 0 | 0.046 | 0.023 | 39.177 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | ARG | 1 | 0.947 | 0.962 | 43.318 | 6.921 | 6.921 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | HIS | 0 | -0.013 | -0.019 | 43.098 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | HIS | 0 | -0.032 | -0.004 | 39.917 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | ILE | 0 | -0.019 | -0.013 | 44.895 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | THR | 0 | -0.063 | -0.046 | 46.735 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | ALA | 0 | -0.016 | -0.017 | 47.637 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | ASP | -1 | -0.800 | -0.883 | 48.576 | -6.084 | -6.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | GLY | 0 | 0.038 | 0.024 | 50.944 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | TYR | 0 | 0.013 | 0.001 | 51.917 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | TYR | 0 | 0.008 | -0.014 | 47.941 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | ARG | 1 | 0.905 | 0.963 | 50.694 | 6.289 | 6.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | GLY | 0 | -0.044 | -0.034 | 53.916 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | ARG | 1 | 0.947 | 0.983 | 55.790 | 5.788 | 5.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | LYS | 1 | 0.888 | 0.959 | 54.882 | 5.707 | 5.707 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | VAL | 0 | -0.058 | -0.033 | 51.213 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | ILE | 0 | -0.029 | -0.002 | 49.670 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | ALA | 0 | 0.008 | -0.006 | 53.381 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | LYS | 0 | 0.131 | 0.079 | 51.457 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |