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: G7V31
Calculation Name: 6V3A-Q-Other547
Preferred Name:
Target Type:
Ligand Name: 7n-methyl-8-hydroguanosine-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'-methyluridine 5'-monophosphate
Ligand 3-letter code: 7MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | 4SU | H2U | OMU
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 6V3A
Chain ID: Q
UniProt ID: B7I9B0
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 | 103 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -662070.592403 |
|---|---|
| FMO2-HF: Nuclear repulsion | 622082.533046 |
| FMO2-HF: Total energy | -39988.059357 |
| FMO2-MP2: Total energy | -40105.109975 |
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. |
| -103.46 | -96.177 | 26.782 | -13.543 | -20.519 | -0.131 |
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 | ALA | 0 | 0.068 | 0.036 | 3.825 | 2.000 | 4.350 | 0.153 | -0.885 | -1.619 | 0.000 |
| 15 | A | 15 | VAL | 0 | 0.012 | -0.011 | 4.633 | -6.633 | -6.496 | -0.001 | -0.037 | -0.098 | 0.000 |
| 16 | A | 16 | GLU | -1 | -0.846 | -0.934 | 4.348 | -35.433 | -35.112 | -0.001 | -0.018 | -0.303 | 0.000 |
| 41 | A | 41 | VAL | 0 | 0.030 | 0.023 | 2.335 | -1.823 | -2.003 | 2.404 | -0.510 | -1.713 | 0.000 |
| 42 | A | 42 | VAL | 0 | -0.013 | -0.001 | 4.104 | 2.532 | 3.363 | 0.026 | -0.379 | -0.479 | 0.000 |
| 43 | A | 43 | ASN | 0 | 0.045 | 0.004 | 2.111 | -27.205 | -26.274 | 16.405 | -9.226 | -8.110 | -0.050 |
| 44 | A | 44 | GLY | 0 | -0.040 | -0.027 | 2.065 | -30.930 | -31.648 | 3.626 | 0.209 | -3.116 | -0.048 |
| 45 | A | 45 | ASP | -1 | -0.865 | -0.910 | 4.516 | -31.500 | -31.451 | -0.001 | -0.024 | -0.023 | 0.000 |
| 48 | A | 48 | GLN | 0 | -0.011 | -0.012 | 4.770 | 5.438 | 5.458 | -0.001 | -0.001 | -0.018 | 0.000 |
| 101 | A | 101 | ILE | 0 | -0.066 | -0.025 | 2.309 | 0.799 | 1.832 | 1.442 | -0.447 | -2.028 | 0.000 |
| 102 | A | 102 | SER | 0 | -0.015 | -0.009 | 2.451 | -8.397 | -7.736 | 1.984 | -1.087 | -1.557 | -0.017 |
| 103 | A | 103 | GLY | -1 | -0.805 | -0.893 | 2.613 | -39.504 | -37.656 | 0.746 | -1.138 | -1.455 | -0.016 |
| 4 | A | 4 | VAL | 0 | -0.050 | -0.022 | 5.981 | 1.180 | 1.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | ILE | 0 | 0.062 | 0.042 | 8.635 | 0.611 | 0.611 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | GLN | 0 | 0.003 | -0.005 | 11.288 | 0.452 | 0.452 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | SER | 0 | 0.057 | 0.026 | 15.073 | 0.516 | 0.516 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLY | 0 | 0.019 | 0.006 | 17.471 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | GLY | 0 | -0.038 | -0.023 | 21.069 | 0.339 | 0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.799 | 0.886 | 19.635 | 13.698 | 13.698 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLN | 0 | 0.035 | 0.013 | 15.243 | -0.651 | -0.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | HIS | 0 | -0.004 | -0.001 | 13.039 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ARG | 1 | 0.912 | 0.965 | 7.863 | 31.289 | 31.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | VAL | 0 | 0.006 | 0.009 | 7.185 | 0.642 | 0.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLY | 0 | -0.007 | 0.000 | 6.109 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | GLU | -1 | -0.910 | -0.940 | 9.325 | -26.852 | -26.852 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | THR | 0 | -0.025 | -0.029 | 11.055 | 1.256 | 1.256 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LEU | 0 | -0.019 | -0.004 | 12.582 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | LYS | 1 | 0.909 | 0.976 | 15.865 | 14.520 | 14.520 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | VAL | 0 | -0.001 | 0.007 | 17.042 | -0.363 | -0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | GLU | -1 | -0.832 | -0.917 | 19.916 | -11.680 | -11.680 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | LEU | 0 | -0.043 | -0.020 | 22.595 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LEU | 0 | 0.031 | 0.018 | 19.026 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LYS | 1 | 0.895 | 0.933 | 23.698 | 10.176 | 10.176 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ALA | 0 | 0.035 | 0.037 | 21.778 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | GLU | -1 | -0.875 | -0.950 | 23.782 | -10.634 | -10.634 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | SER | 0 | -0.036 | -0.024 | 23.263 | -0.411 | -0.411 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | GLY | 0 | 0.004 | -0.001 | 21.642 | 0.441 | 0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ALA | 0 | -0.041 | -0.004 | 21.248 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | THR | 0 | 0.007 | -0.004 | 16.673 | -0.496 | -0.496 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | ILE | 0 | -0.041 | -0.028 | 14.482 | 0.805 | 0.805 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | THR | 0 | -0.019 | -0.010 | 12.411 | -1.500 | -1.500 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | PHE | 0 | -0.026 | -0.007 | 10.468 | 1.264 | 1.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ASP | -1 | -0.784 | -0.895 | 10.208 | -19.399 | -19.399 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | ASP | -1 | -0.908 | -0.957 | 12.265 | -17.710 | -17.710 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | VAL | 0 | -0.004 | 0.001 | 6.320 | -0.440 | -0.440 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LEU | 0 | 0.005 | 0.008 | 9.757 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | MET | 0 | -0.056 | -0.031 | 8.547 | 0.418 | 0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | ASN | 0 | -0.017 | -0.018 | 5.972 | 4.605 | 4.605 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | ILE | 0 | -0.024 | -0.017 | 6.299 | -5.085 | -5.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ILE | 0 | 0.010 | -0.013 | 8.403 | -0.813 | -0.813 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | GLY | 0 | 0.029 | 0.010 | 10.534 | 1.525 | 1.525 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | ALA | 0 | -0.022 | -0.018 | 12.052 | 0.324 | 0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | PRO | 0 | -0.070 | -0.021 | 15.386 | 0.352 | 0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | VAL | 0 | 0.054 | 0.010 | 12.180 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | VAL | 0 | -0.059 | -0.014 | 6.824 | 0.675 | 0.675 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ALA | 0 | -0.011 | -0.005 | 9.886 | -0.415 | -0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | GLY | 0 | -0.006 | -0.005 | 10.365 | -0.291 | -0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | ALA | 0 | -0.010 | 0.006 | 6.005 | -0.986 | -0.986 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | LYS | 1 | 0.823 | 0.894 | 6.592 | 20.693 | 20.693 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | VAL | 0 | -0.027 | -0.006 | 5.486 | -2.972 | -2.972 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | THR | 0 | -0.009 | -0.008 | 7.673 | 2.245 | 2.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | ALA | 0 | -0.005 | -0.012 | 10.192 | -1.610 | -1.610 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | GLU | -1 | -0.877 | -0.935 | 12.976 | -16.625 | -16.625 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | VAL | 0 | -0.037 | -0.021 | 16.300 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | ILE | 0 | -0.001 | 0.005 | 17.489 | 0.592 | 0.592 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | GLY | 0 | 0.024 | -0.004 | 20.463 | 0.695 | 0.695 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | HIS | 0 | 0.024 | 0.041 | 22.981 | -0.513 | -0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | GLY | 0 | 0.020 | 0.012 | 25.739 | 0.309 | 0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | ARG | 1 | 0.834 | 0.916 | 27.433 | 9.399 | 9.399 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | HIS | 0 | 0.069 | 0.049 | 24.378 | 0.428 | 0.428 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | ASP | -1 | -0.859 | -0.913 | 29.274 | -10.012 | -10.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | LYS | 1 | 0.851 | 0.928 | 32.298 | 8.255 | 8.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | ILE | 0 | 0.094 | 0.055 | 31.815 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | ARG | 1 | 0.947 | 0.961 | 36.152 | 7.941 | 7.941 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | ILE | 0 | 0.012 | 0.011 | 37.350 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | ILE | 0 | 0.022 | 0.005 | 41.010 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | LYS | 1 | 0.957 | 0.982 | 42.285 | 7.395 | 7.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | MET | 0 | 0.018 | 0.003 | 46.656 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | ARG | 1 | 0.964 | 0.990 | 49.470 | 6.349 | 6.349 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ARG | 1 | 1.050 | 1.011 | 52.410 | 6.254 | 6.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | ARG | 1 | 0.965 | 0.975 | 54.819 | 5.596 | 5.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | LYS | 1 | 0.947 | 0.966 | 56.031 | 5.533 | 5.533 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | HIS | 0 | 0.048 | 0.042 | 57.712 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | TYR | 0 | 0.054 | 0.036 | 48.489 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | ARG | 1 | 0.976 | 0.966 | 50.764 | 5.956 | 5.956 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | LYS | 1 | 0.941 | 0.981 | 47.104 | 6.660 | 6.660 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | GLN | 0 | -0.004 | -0.006 | 45.600 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | GLN | 0 | 0.020 | 0.019 | 40.412 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | GLY | 0 | -0.013 | -0.012 | 39.664 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | HIS | 0 | -0.008 | -0.002 | 31.871 | 0.355 | 0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | ARG | 1 | 0.854 | 0.891 | 31.703 | 9.608 | 9.608 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | GLN | 0 | 0.032 | 0.043 | 27.471 | 0.611 | 0.611 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | TRP | 0 | 0.027 | -0.001 | 28.369 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | PHE | 0 | -0.016 | -0.012 | 23.101 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | THR | 0 | 0.027 | 0.001 | 20.301 | 0.550 | 0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | GLU | -1 | -0.894 | -0.955 | 19.518 | -15.200 | -15.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | LEU | 0 | 0.000 | -0.003 | 15.052 | 0.383 | 0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | LYS | 1 | 0.912 | 0.971 | 12.551 | 19.888 | 19.888 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | ILE | 0 | 0.003 | 0.008 | 7.178 | 0.831 | 0.831 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | THR | 0 | -0.037 | -0.031 | 10.078 | -0.937 | -0.937 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | GLY | 0 | 0.058 | 0.035 | 7.200 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |