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: Q5K7Y
Calculation Name: 7OTC-V-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: V
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 | 94 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -688938.012801 |
|---|---|
| FMO2-HF: Nuclear repulsion | 651661.068043 |
| FMO2-HF: Total energy | -37276.944758 |
| FMO2-MP2: Total energy | -37386.153639 |
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. |
| -109.625 | -110.69 | 32.401 | -17.188 | -14.149 | -0.196 |
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 | THR | 0 | 0.007 | 0.008 | 3.848 | -1.479 | -0.238 | -0.011 | -0.526 | -0.704 | 0.002 |
| 59 | A | 59 | GLU | -1 | -0.726 | -0.853 | 1.762 | -155.109 | -159.478 | 27.496 | -13.279 | -9.848 | -0.162 |
| 60 | A | 60 | VAL | 0 | -0.049 | -0.016 | 3.711 | 7.253 | 7.811 | 0.002 | -0.135 | -0.426 | 0.000 |
| 61 | A | 61 | LEU | 0 | -0.028 | -0.011 | 2.307 | -36.068 | -35.484 | 4.894 | -2.965 | -2.513 | -0.034 |
| 62 | A | 62 | THR | 0 | -0.012 | -0.008 | 2.748 | 2.528 | 3.344 | 0.022 | -0.276 | -0.562 | -0.002 |
| 63 | A | 63 | ILE | 0 | -0.007 | 0.002 | 5.149 | 1.948 | 1.946 | -0.001 | -0.003 | 0.006 | 0.000 |
| 71 | A | 71 | LYS | 1 | 0.867 | 0.934 | 4.164 | 49.861 | 49.968 | -0.001 | -0.004 | -0.102 | 0.000 |
| 4 | A | 4 | ILE | 0 | -0.019 | -0.011 | 6.340 | 4.884 | 4.884 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | ASN | 0 | -0.043 | -0.017 | 9.298 | 0.934 | 0.934 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | ALA | 0 | -0.007 | -0.001 | 12.430 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLU | -1 | -0.844 | -0.928 | 14.820 | -16.907 | -16.907 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | VAL | 0 | 0.003 | -0.005 | 18.303 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ARG | 1 | 0.834 | 0.933 | 20.214 | 14.056 | 14.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.965 | 0.996 | 22.950 | 11.596 | 11.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLU | -1 | -0.889 | -0.950 | 26.485 | -10.596 | -10.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | GLN | 0 | 0.036 | 0.007 | 26.148 | -0.864 | -0.864 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | GLY | 0 | 0.064 | 0.030 | 27.627 | 0.478 | 0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | LYS | 1 | 0.964 | 0.978 | 28.906 | 9.009 | 9.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | 0.020 | 0.001 | 30.368 | -0.150 | -0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ALA | 0 | 0.038 | 0.029 | 28.490 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | SER | 0 | 0.037 | 0.002 | 25.590 | -0.420 | -0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ARG | 1 | 0.892 | 0.953 | 26.540 | 9.661 | 9.661 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ARG | 1 | 0.978 | 0.987 | 28.925 | 9.925 | 9.925 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LEU | 0 | 0.012 | 0.020 | 21.993 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ARG | 1 | 0.856 | 0.913 | 23.073 | 13.064 | 13.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | ALA | 0 | -0.064 | -0.029 | 25.519 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ALA | 0 | -0.025 | -0.006 | 26.056 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ASN | 0 | -0.055 | -0.034 | 22.765 | -0.549 | -0.549 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | LYS | 1 | 0.918 | 0.972 | 20.206 | 14.639 | 14.639 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | PHE | 0 | -0.041 | -0.031 | 15.146 | 0.890 | 0.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | PRO | 0 | -0.048 | -0.023 | 19.020 | -0.471 | -0.471 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ALA | 0 | 0.024 | 0.006 | 15.576 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ILE | 0 | -0.047 | -0.014 | 17.067 | 0.876 | 0.876 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | ILE | 0 | 0.008 | 0.026 | 12.792 | -0.995 | -0.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | TYR | 0 | -0.016 | -0.050 | 15.559 | 1.126 | 1.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | GLY | 0 | 0.063 | 0.037 | 15.905 | -1.214 | -1.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | GLY | 0 | 0.018 | 0.021 | 17.936 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | LYS | 1 | 0.892 | 0.936 | 18.570 | 13.670 | 13.670 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | GLU | -1 | -0.839 | -0.919 | 18.492 | -16.017 | -16.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | ALA | 0 | 0.018 | 0.012 | 21.030 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | PRO | 0 | -0.015 | -0.004 | 19.332 | -0.752 | -0.752 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | LEU | 0 | 0.011 | 0.007 | 16.659 | 0.720 | 0.720 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | ALA | 0 | 0.012 | -0.001 | 18.066 | -0.792 | -0.792 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | ILE | 0 | -0.004 | -0.006 | 14.014 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | GLU | -1 | -0.905 | -0.976 | 18.321 | -13.486 | -13.486 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | LEU | 0 | 0.046 | 0.026 | 13.062 | -0.820 | -0.820 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | ASP | -1 | -0.833 | -0.913 | 16.655 | -16.425 | -16.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | HIS | 0 | -0.024 | -0.021 | 16.309 | -1.189 | -1.189 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | ASP | -1 | -0.806 | -0.890 | 16.831 | -16.115 | -16.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | LYS | 1 | 0.930 | 0.970 | 13.457 | 20.704 | 20.704 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | VAL | 0 | 0.074 | 0.032 | 11.657 | -1.516 | -1.516 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | MET | 0 | -0.048 | -0.008 | 12.922 | -1.056 | -1.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | ASN | 0 | 0.035 | 0.003 | 13.976 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | MET | 0 | -0.094 | -0.027 | 7.637 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | GLN | 0 | 0.003 | -0.005 | 9.953 | -0.805 | -0.805 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | ALA | 0 | -0.006 | 0.005 | 11.859 | 1.008 | 1.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | LYS | 1 | 0.912 | 0.964 | 7.925 | 29.299 | 29.299 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | ALA | 0 | 0.062 | 0.018 | 10.530 | -1.201 | -1.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | GLU | -1 | -0.824 | -0.898 | 5.754 | -37.051 | -37.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | PHE | 0 | -0.060 | -0.022 | 6.623 | -4.943 | -4.943 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | TYR | 0 | -0.009 | -0.026 | 7.659 | -0.646 | -0.646 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | SER | 0 | 0.002 | 0.006 | 8.655 | 2.116 | 2.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | VAL | 0 | 0.017 | 0.014 | 8.939 | 1.219 | 1.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | VAL | 0 | 0.007 | -0.001 | 11.271 | 1.096 | 1.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ASP | -1 | -0.868 | -0.938 | 14.815 | -17.162 | -17.162 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | GLY | 0 | 0.021 | 0.021 | 15.553 | 0.717 | 0.717 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | LYS | 1 | 0.812 | 0.910 | 14.180 | 18.350 | 18.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | GLU | -1 | -0.794 | -0.907 | 6.989 | -39.831 | -39.831 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | ILE | 0 | -0.042 | -0.028 | 9.770 | 2.144 | 2.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | VAL | 0 | -0.002 | -0.007 | 6.774 | 4.656 | 4.656 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | LYS | 1 | 0.855 | 0.919 | 6.717 | 34.016 | 34.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | ALA | 0 | -0.002 | -0.009 | 9.067 | 2.691 | 2.691 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | GLN | 0 | -0.055 | -0.025 | 10.929 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | ASP | -1 | -0.839 | -0.920 | 14.360 | -15.531 | -15.531 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | VAL | 0 | -0.072 | -0.040 | 15.273 | -0.741 | -0.741 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | GLN | 0 | 0.020 | 0.030 | 17.259 | 1.168 | 1.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ARG | 1 | 0.974 | 0.981 | 16.134 | 17.413 | 17.413 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | HIS | 0 | -0.030 | -0.026 | 21.638 | 0.596 | 0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | PRO | 0 | -0.008 | -0.015 | 24.990 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | TYR | 0 | 0.092 | 0.038 | 27.685 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | LYS | 1 | 0.849 | 0.950 | 26.214 | 10.890 | 10.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | PRO | 0 | 0.050 | 0.021 | 22.274 | -0.335 | -0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | LYS | 1 | 0.945 | 0.962 | 21.142 | 12.759 | 12.759 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | LEU | 0 | 0.028 | 0.024 | 15.263 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | GLN | 0 | -0.077 | -0.040 | 19.739 | 0.609 | 0.609 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | HIS | 0 | 0.000 | -0.020 | 19.526 | 0.729 | 0.729 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | ILE | 0 | 0.000 | 0.010 | 12.786 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | ASP | -1 | -0.769 | -0.843 | 16.398 | -16.042 | -16.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | PHE | 0 | -0.013 | -0.022 | 9.876 | -1.323 | -1.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | VAL | 0 | 0.020 | 0.019 | 12.663 | 1.800 | 1.800 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | ARG | 1 | 0.797 | 0.881 | 11.495 | 15.940 | 15.940 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | ALA | -1 | -0.899 | -0.943 | 9.839 | -28.670 | -28.670 | 0.000 | 0.000 | 0.000 | 0.000 |