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: 2GLVR
Calculation Name: 7OTC-R-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: R
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 | -676429.858364 |
|---|---|
| FMO2-HF: Nuclear repulsion | 636421.586875 |
| FMO2-HF: Total energy | -40008.271489 |
| FMO2-MP2: Total energy | -40126.509849 |
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. |
| -80.125 | -69.888 | 10.969 | -8.79 | -12.415 | -0.077 |
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 | 0.061 | 0.039 | 3.830 | 0.003 | 1.751 | -0.023 | -0.767 | -0.958 | 0.001 |
| 15 | A | 15 | SER | 0 | -0.003 | -0.013 | 4.643 | -8.857 | -8.788 | -0.001 | -0.032 | -0.036 | 0.000 |
| 16 | A | 16 | GLU | -1 | -0.812 | -0.924 | 3.986 | -26.483 | -26.019 | 0.002 | -0.069 | -0.396 | 0.000 |
| 41 | A | 41 | ILE | 0 | 0.004 | 0.002 | 3.748 | -2.257 | -1.965 | 0.005 | -0.045 | -0.252 | 0.000 |
| 42 | A | 42 | ALA | 0 | -0.007 | 0.008 | 4.584 | 4.039 | 4.273 | -0.001 | -0.068 | -0.165 | 0.000 |
| 43 | A | 43 | ASN | 0 | -0.076 | -0.075 | 2.042 | -50.672 | -45.155 | 7.999 | -6.964 | -6.552 | -0.062 |
| 44 | A | 44 | GLY | 0 | 0.006 | 0.024 | 3.032 | 5.260 | 5.139 | 0.055 | 0.508 | -0.442 | -0.003 |
| 45 | A | 45 | GLU | -1 | -0.904 | -0.950 | 4.997 | -32.268 | -32.246 | -0.001 | -0.003 | -0.018 | 0.000 |
| 101 | A | 101 | ILE | 0 | -0.068 | -0.029 | 2.363 | -0.935 | 0.357 | 0.966 | -0.424 | -1.834 | 0.000 |
| 102 | A | 102 | SER | 0 | -0.001 | 0.006 | 2.594 | -6.240 | -5.680 | 1.967 | -0.907 | -1.620 | -0.013 |
| 103 | A | 103 | ALA | -1 | -0.812 | -0.900 | 4.033 | -26.647 | -26.487 | 0.001 | -0.019 | -0.142 | 0.000 |
| 4 | A | 4 | VAL | 0 | -0.017 | -0.019 | 6.132 | 1.431 | 1.431 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | PHE | 0 | 0.020 | 0.017 | 9.967 | 0.589 | 0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | GLN | 0 | -0.021 | -0.011 | 12.207 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | SER | 0 | 0.035 | 0.019 | 15.955 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLY | 0 | 0.045 | 0.032 | 18.082 | 0.754 | 0.754 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | GLY | 0 | -0.024 | -0.024 | 21.166 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.786 | 0.874 | 19.213 | 13.607 | 13.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLN | 0 | 0.021 | -0.001 | 15.233 | -0.735 | -0.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | HIS | 0 | -0.037 | -0.015 | 12.951 | 1.267 | 1.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ARG | 1 | 0.905 | 0.970 | 7.348 | 33.583 | 33.583 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | VAL | 0 | 0.002 | 0.007 | 7.272 | 1.300 | 1.300 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLY | 0 | -0.015 | 0.001 | 5.641 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | GLN | 0 | -0.015 | -0.004 | 8.318 | 2.757 | 2.757 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | THR | 0 | 0.008 | 0.005 | 10.555 | 1.087 | 1.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | VAL | 0 | -0.026 | -0.012 | 12.661 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ARG | 1 | 0.803 | 0.879 | 15.436 | 14.654 | 14.654 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | LEU | 0 | -0.010 | 0.003 | 15.915 | -0.374 | -0.374 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | GLU | -1 | -0.818 | -0.894 | 19.710 | -11.874 | -11.874 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | LYS | 1 | 0.874 | 0.926 | 22.211 | 10.752 | 10.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LEU | 0 | 0.062 | 0.045 | 18.571 | 0.433 | 0.433 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ASP | -1 | -0.982 | -0.991 | 23.191 | -11.123 | -11.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ILE | 0 | 0.048 | 0.033 | 19.812 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ALA | 0 | 0.034 | 0.015 | 23.491 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | THR | 0 | -0.070 | -0.062 | 22.737 | -0.338 | -0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | GLY | 0 | 0.026 | 0.008 | 21.599 | 0.472 | 0.472 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | GLU | -1 | -0.921 | -0.934 | 20.645 | -12.101 | -12.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | THR | 0 | -0.029 | -0.028 | 14.497 | -0.799 | -0.799 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | VAL | 0 | -0.049 | -0.030 | 15.162 | 0.789 | 0.789 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | GLU | -1 | -0.783 | -0.871 | 12.550 | -19.576 | -19.576 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | PHE | 0 | 0.002 | -0.017 | 11.407 | 1.104 | 1.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ALA | 0 | 0.078 | 0.027 | 10.929 | -1.609 | -1.609 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | GLU | -1 | -0.885 | -0.912 | 12.773 | -15.393 | -15.393 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | VAL | 0 | -0.022 | -0.024 | 8.385 | -0.567 | -0.567 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | LEU | 0 | -0.012 | 0.008 | 11.170 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | MET | 0 | -0.025 | -0.015 | 8.479 | 0.949 | 0.949 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | GLU | -1 | -0.866 | -0.913 | 6.021 | -37.475 | -37.475 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | VAL | 0 | -0.037 | -0.041 | 6.372 | -5.889 | -5.889 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | LYS | 1 | 0.866 | 0.932 | 6.894 | 30.428 | 30.428 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ILE | 0 | 0.023 | -0.004 | 9.902 | -1.307 | -1.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | GLY | 0 | 0.035 | 0.024 | 12.614 | 0.836 | 0.836 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | VAL | 0 | -0.001 | -0.017 | 14.317 | 0.788 | 0.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | PRO | 0 | -0.032 | -0.014 | 16.582 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | PHE | 0 | -0.036 | -0.024 | 13.922 | -0.363 | -0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | VAL | 0 | -0.041 | -0.018 | 8.709 | 0.481 | 0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ASP | -1 | -0.892 | -0.941 | 11.742 | -19.256 | -19.256 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | GLY | 0 | -0.008 | 0.002 | 10.797 | 0.954 | 0.954 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | GLY | 0 | -0.046 | -0.019 | 7.790 | -1.100 | -1.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | VAL | 0 | -0.020 | -0.023 | 7.371 | 1.923 | 1.923 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | ILE | 0 | -0.051 | -0.019 | 6.415 | -2.699 | -2.699 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | LYS | 1 | 0.868 | 0.927 | 8.067 | 21.635 | 21.635 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | ALA | 0 | -0.021 | -0.017 | 9.925 | -1.639 | -1.639 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | GLU | -1 | -0.879 | -0.929 | 12.591 | -15.518 | -15.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | VAL | 0 | -0.020 | -0.015 | 15.939 | -0.474 | -0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | VAL | 0 | 0.013 | 0.021 | 17.527 | 0.635 | 0.635 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | ALA | 0 | 0.001 | -0.002 | 20.267 | 0.800 | 0.800 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | HIS | 0 | 0.007 | 0.021 | 22.658 | -0.314 | -0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | GLY | 0 | 0.004 | 0.000 | 25.443 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | ARG | 1 | 0.829 | 0.918 | 27.513 | 9.482 | 9.482 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | GLY | 0 | 0.051 | 0.032 | 28.182 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | GLU | -1 | -0.853 | -0.926 | 28.858 | -9.842 | -9.842 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | LYS | 1 | 0.896 | 0.944 | 31.566 | 8.401 | 8.401 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | VAL | 0 | 0.056 | 0.045 | 32.270 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | LYS | 1 | 0.939 | 0.972 | 35.211 | 7.604 | 7.604 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | ILE | 0 | 0.012 | 0.009 | 36.606 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | VAL | 0 | 0.003 | -0.012 | 40.167 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | LYS | 1 | 0.959 | 0.986 | 41.784 | 7.528 | 7.528 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | PHE | 0 | 0.044 | 0.011 | 45.764 | 0.152 | 0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | ARG | 1 | 0.963 | 0.984 | 47.792 | 6.552 | 6.552 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ARG | 1 | 1.008 | 1.001 | 48.446 | 6.621 | 6.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | ARG | 1 | 0.998 | 0.983 | 53.810 | 5.766 | 5.766 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | LYS | 1 | 0.954 | 0.975 | 55.155 | 5.657 | 5.657 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | HIS | 0 | 0.055 | 0.044 | 56.667 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | TYR | 0 | 0.041 | 0.031 | 47.482 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | ARG | 1 | 0.957 | 0.958 | 50.230 | 6.084 | 6.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | LYS | 1 | 0.940 | 0.977 | 46.849 | 6.557 | 6.557 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | GLN | 0 | 0.014 | 0.003 | 44.723 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | GLN | 0 | 0.030 | 0.020 | 39.108 | 0.201 | 0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | GLY | 0 | -0.019 | -0.012 | 39.007 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | HIS | 0 | 0.009 | 0.009 | 31.389 | 0.365 | 0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | ARG | 1 | 0.867 | 0.912 | 31.466 | 9.766 | 9.766 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | GLN | 0 | 0.008 | 0.011 | 26.990 | 0.604 | 0.604 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | TRP | 0 | 0.018 | 0.001 | 28.253 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | PHE | 0 | -0.027 | -0.016 | 22.920 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | THR | 0 | 0.045 | 0.009 | 20.147 | 0.552 | 0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | ASP | -1 | -0.806 | -0.859 | 19.091 | -15.129 | -15.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | VAL | 0 | 0.018 | -0.002 | 14.400 | 0.465 | 0.465 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | LYS | 1 | 0.921 | 0.973 | 11.717 | 21.130 | 21.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | ILE | 0 | -0.024 | -0.014 | 7.121 | 0.638 | 0.638 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | THR | 0 | -0.098 | -0.062 | 9.867 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | GLY | 0 | 0.115 | 0.057 | 6.339 | 0.572 | 0.572 | 0.000 | 0.000 | 0.000 | 0.000 |