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: 2G4MR
Calculation Name: 7OTC-4-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: 4
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 | 38 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -167121.903492 |
|---|---|
| FMO2-HF: Nuclear repulsion | 151196.933741 |
| FMO2-HF: Total energy | -15924.969751 |
| FMO2-MP2: Total energy | -15968.769335 |
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. |
| 165.962 | 174.681 | 9.732 | -5.675 | -12.778 | -0.044 |
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 | VAL | 0 | 0.045 | 0.023 | 3.014 | -2.364 | 0.610 | 0.189 | -1.302 | -1.861 | -0.009 |
| 4 | A | 4 | ARG | 1 | 0.961 | 0.990 | 4.778 | 33.590 | 33.646 | -0.001 | -0.008 | -0.047 | 0.000 |
| 24 | A | 24 | ARG | 1 | 0.939 | 0.965 | 3.072 | 26.746 | 27.440 | 0.063 | -0.134 | -0.623 | 0.000 |
| 26 | A | 26 | ILE | 0 | -0.030 | -0.017 | 4.416 | -6.727 | -6.571 | -0.001 | -0.008 | -0.147 | 0.000 |
| 32 | A | 32 | LYS | 1 | 0.950 | 0.982 | 4.585 | 19.020 | 19.196 | -0.001 | -0.008 | -0.167 | 0.000 |
| 34 | A | 34 | LYS | 1 | 0.923 | 0.985 | 2.330 | 51.688 | 53.378 | 2.064 | -0.730 | -3.024 | 0.003 |
| 35 | A | 35 | GLN | 0 | -0.079 | -0.067 | 2.437 | -20.505 | -16.863 | 2.859 | -3.027 | -3.475 | -0.034 |
| 36 | A | 36 | ARG | 1 | 0.940 | 0.964 | 2.833 | 32.950 | 32.318 | 4.544 | -0.559 | -3.353 | -0.005 |
| 37 | A | 37 | GLN | 0 | -0.019 | -0.019 | 4.411 | -1.850 | -1.887 | 0.016 | 0.101 | -0.081 | 0.001 |
| 5 | A | 5 | ALA | 0 | 0.153 | 0.084 | 8.185 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | SER | 0 | -0.019 | 0.000 | 11.126 | 0.882 | 0.882 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | VAL | 0 | -0.014 | -0.005 | 6.497 | -1.602 | -1.602 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.958 | 0.974 | 9.321 | 22.369 | 22.369 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | LYS | 1 | 0.954 | 0.979 | 9.913 | 16.040 | 16.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LEU | 0 | 0.004 | -0.034 | 8.597 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | CYS | 0 | -0.091 | -0.059 | 12.372 | 0.600 | 0.600 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ARG | 1 | 1.054 | 1.010 | 14.697 | 14.706 | 14.706 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ASN | 0 | 0.059 | 0.008 | 13.962 | 1.112 | 1.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | CYS | -1 | -0.828 | -0.804 | 10.677 | -27.363 | -27.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | LYS | 1 | 0.986 | 0.977 | 10.209 | 19.819 | 19.819 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ILE | 0 | 0.011 | 0.000 | 9.106 | -2.158 | -2.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | VAL | 0 | -0.019 | -0.018 | 7.666 | 1.330 | 1.330 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LYS | 1 | 0.988 | 1.001 | 8.858 | 14.703 | 14.703 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ARG | 1 | 0.929 | 0.962 | 6.182 | 24.967 | 24.967 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ASP | -1 | -0.830 | -0.920 | 9.436 | -20.028 | -20.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | GLY | 0 | 0.006 | 0.012 | 11.613 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | VAL | 0 | -0.025 | 0.000 | 7.449 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ILE | 0 | 0.024 | 0.011 | 9.226 | -0.472 | -0.472 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | VAL | 0 | -0.007 | 0.004 | 5.156 | 2.767 | 2.767 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | CYS | 0 | -0.028 | -0.016 | 6.481 | 3.110 | 3.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | SER | 0 | 0.030 | 0.014 | 9.387 | -1.561 | -1.561 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ALA | 0 | 0.004 | 0.015 | 12.084 | 0.624 | 0.624 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | GLU | -1 | -0.723 | -0.861 | 9.086 | -33.294 | -33.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | PRO | 0 | 0.038 | 0.004 | 6.080 | -2.641 | -2.641 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | HIS | 1 | 0.849 | 0.904 | 5.473 | 26.009 | 26.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | GLY | -1 | -0.867 | -0.934 | 7.721 | -26.630 | -26.630 | 0.000 | 0.000 | 0.000 | 0.000 |