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: N68LQ
Calculation Name: 6OSK-Y-Other547
Preferred Name:
Target Type:
Ligand Name: 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 | 4-thiouridine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (3s)-3-(methylsulfanyl)-l-aspartic acid | n-formylmethionine
Ligand 3-letter code: G7M | 1MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | 4SU | H2U | OMC | OMU | 0TD | FME
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 6OSK
Chain ID: Y
UniProt ID: P0ADY7
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 | -341372.728174 |
|---|---|
| FMO2-HF: Nuclear repulsion | 316627.727543 |
| FMO2-HF: Total energy | -24745.00063 |
| FMO2-MP2: Total energy | -24818.081074 |
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. |
| -104.526 | -94.247 | 27.552 | -18.206 | -19.624 | -0.187 |
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 | 0.951 | 0.984 | 3.632 | 66.626 | 68.605 | -0.012 | -0.889 | -1.079 | 0.000 |
| 4 | A | 5 | GLU | -1 | -0.772 | -0.898 | 1.740 | -222.977 | -221.602 | 24.266 | -14.098 | -11.543 | -0.159 |
| 5 | A | 6 | LEU | 0 | -0.005 | -0.007 | 2.263 | 1.135 | 2.966 | 2.783 | -1.086 | -3.528 | -0.011 |
| 6 | A | 7 | ARG | 1 | 0.836 | 0.905 | 4.970 | 64.772 | 64.892 | -0.001 | -0.010 | -0.109 | 0.000 |
| 8 | A | 9 | LYS | 1 | 0.821 | 0.909 | 4.330 | 79.627 | 79.730 | -0.001 | -0.004 | -0.097 | 0.000 |
| 16 | A | 17 | GLU | -1 | -0.889 | -0.950 | 3.430 | -102.223 | -101.063 | 0.020 | -0.543 | -0.637 | -0.004 |
| 20 | A | 21 | LEU | 0 | 0.033 | 0.005 | 3.572 | 2.862 | 3.117 | 0.002 | -0.036 | -0.221 | 0.000 |
| 48 | A | 49 | ASP | -1 | -0.811 | -0.897 | 3.155 | -113.411 | -110.682 | 0.421 | -1.405 | -1.744 | -0.013 |
| 49 | A | 50 | VAL | 0 | 0.030 | 0.019 | 5.018 | -0.643 | -0.624 | -0.001 | -0.001 | -0.016 | 0.000 |
| 51 | A | 52 | ARG | 1 | 0.846 | 0.919 | 3.175 | 89.898 | 90.606 | 0.075 | -0.134 | -0.650 | 0.000 |
| 7 | A | 8 | GLU | -1 | -0.862 | -0.925 | 7.619 | -53.151 | -53.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | SER | 0 | 0.054 | 0.020 | 9.622 | 2.354 | 2.354 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | VAL | 0 | 0.079 | 0.027 | 10.896 | -3.685 | -3.685 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | GLU | -1 | -0.802 | -0.905 | 12.116 | -37.957 | -37.957 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | GLU | -1 | -0.869 | -0.892 | 7.869 | -61.614 | -61.614 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | LEU | 0 | -0.004 | -0.014 | 6.235 | -6.320 | -6.320 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | ASN | 0 | -0.022 | -0.024 | 8.752 | -2.837 | -2.837 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | THR | 0 | -0.041 | -0.025 | 10.222 | 1.666 | 1.666 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | LEU | 0 | -0.061 | -0.024 | 7.291 | -1.032 | -1.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LEU | 0 | 0.001 | -0.010 | 9.340 | 1.705 | 1.705 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ASN | 0 | -0.019 | 0.004 | 7.224 | 8.132 | 8.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | LEU | 0 | -0.017 | -0.009 | 7.663 | 3.751 | 3.751 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | ARG | 1 | 0.934 | 0.972 | 11.177 | 41.765 | 41.765 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | GLU | -1 | -0.901 | -0.944 | 6.969 | -59.691 | -59.691 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | GLN | 0 | -0.021 | -0.025 | 10.748 | 2.086 | 2.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | PHE | 0 | -0.043 | -0.019 | 12.324 | 2.453 | 2.453 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | ASN | 0 | 0.041 | 0.010 | 13.370 | 3.293 | 3.293 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | LEU | 0 | -0.008 | -0.008 | 10.427 | 1.849 | 1.849 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | ARG | 1 | 0.941 | 0.969 | 14.887 | 33.519 | 33.519 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | MET | 0 | -0.005 | -0.006 | 17.369 | 1.712 | 1.712 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | GLN | 0 | -0.006 | -0.005 | 16.570 | 1.556 | 1.556 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ALA | 0 | -0.008 | -0.008 | 17.964 | 0.499 | 0.499 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | ALA | 0 | -0.016 | 0.009 | 19.945 | 0.821 | 0.821 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | SER | 0 | -0.013 | 0.007 | 22.700 | 1.402 | 1.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | GLY | 0 | 0.038 | 0.024 | 23.122 | -0.609 | -0.609 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | GLN | 0 | -0.037 | -0.025 | 21.445 | -0.368 | -0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | LEU | 0 | -0.016 | -0.005 | 14.609 | -0.809 | -0.809 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | GLN | 0 | 0.033 | 0.013 | 18.806 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | GLN | 0 | 0.005 | 0.008 | 14.521 | -2.191 | -2.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | SER | 0 | 0.040 | 0.003 | 14.665 | -1.794 | -1.794 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | HIS | 0 | -0.014 | -0.005 | 11.350 | 1.286 | 1.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | LEU | 0 | 0.045 | 0.030 | 9.572 | -3.367 | -3.367 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | LEU | 0 | 0.061 | 0.031 | 9.725 | -3.417 | -3.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LYS | 1 | 0.865 | 0.928 | 11.468 | 38.528 | 38.528 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | GLN | 0 | -0.018 | -0.006 | 6.283 | 1.239 | 1.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | VAL | 0 | 0.136 | 0.071 | 6.235 | -4.321 | -4.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | ARG | 1 | 0.907 | 0.954 | 7.252 | 37.663 | 37.663 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | ARG | 1 | 0.882 | 0.942 | 7.032 | 49.266 | 49.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | ALA | 0 | 0.000 | 0.003 | 7.974 | 2.467 | 2.467 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | VAL | 0 | 0.037 | 0.016 | 4.890 | 1.883 | 1.883 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | LYS | 1 | 0.960 | 0.975 | 7.425 | 45.037 | 45.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | THR | 0 | -0.016 | -0.011 | 9.437 | 3.889 | 3.889 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | LEU | 0 | -0.039 | -0.030 | 5.979 | 0.617 | 0.617 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | LEU | 0 | -0.021 | -0.008 | 10.011 | 1.509 | 1.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | ASN | 0 | -0.014 | -0.011 | 12.568 | 3.128 | 3.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | GLU | -1 | -0.842 | -0.900 | 11.758 | -47.538 | -47.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | LYS | 1 | 0.831 | 0.927 | 9.803 | 54.236 | 54.236 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | ALA | 0 | -0.019 | -0.009 | 15.203 | 1.505 | 1.505 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | GLY | 0 | -0.018 | -0.004 | 18.286 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | ALA | -1 | -0.959 | -0.954 | 17.484 | -29.919 | -29.919 | 0.000 | 0.000 | 0.000 | 0.000 |