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: R4Q18
Calculation Name: 7OTC-n-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: n
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 | 100 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -641250.135248 |
|---|---|
| FMO2-HF: Nuclear repulsion | 601337.799999 |
| FMO2-HF: Total energy | -39912.335249 |
| FMO2-MP2: Total energy | -40029.113701 |
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:ALA)
Summations of interaction energy for
fragment #1(A:2:ALA)
| 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. |
| 247.054 | 251.168 | 9.691 | -6.316 | -7.49 | -0.073 |
Interaction energy analysis for fragmet #1(A:2:ALA)
| 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 | GLN | 0 | 0.148 | 0.065 | 3.894 | -5.518 | -4.294 | -0.013 | -0.545 | -0.666 | 0.000 |
| 5 | A | 6 | MET | 0 | -0.099 | -0.040 | 3.825 | 3.549 | 3.751 | 0.002 | -0.034 | -0.169 | 0.000 |
| 6 | A | 7 | LYS | 1 | 0.939 | 0.969 | 3.853 | 55.315 | 55.573 | 0.000 | -0.037 | -0.221 | 0.000 |
| 62 | A | 63 | ARG | 1 | 0.865 | 0.918 | 2.768 | 42.519 | 42.960 | 0.157 | -0.175 | -0.423 | -0.001 |
| 66 | A | 67 | THR | 0 | 0.054 | -0.038 | 2.970 | -3.800 | -3.220 | 0.035 | -0.258 | -0.357 | -0.002 |
| 67 | A | 68 | GLY | 0 | -0.010 | -0.020 | 2.003 | -43.770 | -43.140 | 7.575 | -4.561 | -3.646 | -0.055 |
| 68 | A | 69 | ARG | 1 | 0.914 | 0.956 | 2.661 | 31.883 | 32.520 | 1.928 | -0.678 | -1.887 | -0.015 |
| 69 | A | 70 | PRO | 0 | 0.011 | 0.001 | 3.525 | 5.229 | 5.371 | 0.007 | -0.028 | -0.121 | 0.000 |
| 4 | A | 5 | SER | 0 | 0.084 | 0.030 | 6.509 | 1.163 | 1.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | ALA | 0 | 0.063 | 0.030 | 6.415 | 2.801 | 2.801 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | ARG | 1 | 0.930 | 0.975 | 8.775 | 26.369 | 26.369 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | GLU | -1 | -0.827 | -0.940 | 7.845 | -24.054 | -24.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | VAL | 0 | 0.023 | 0.014 | 10.194 | 1.547 | 1.547 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | LYS | 1 | 0.999 | 1.009 | 12.165 | 18.016 | 18.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | ARG | 1 | 0.840 | 0.915 | 11.416 | 21.522 | 21.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | VAL | 0 | -0.023 | -0.011 | 13.222 | 0.927 | 0.927 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | ALA | 0 | 0.054 | 0.042 | 15.884 | 0.902 | 0.902 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | LEU | 0 | -0.038 | -0.026 | 17.944 | 0.961 | 0.961 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ALA | 0 | 0.005 | -0.006 | 18.771 | 0.769 | 0.769 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | ASP | -1 | -0.958 | -0.962 | 19.956 | -12.730 | -12.730 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LYS | 1 | 0.970 | 0.986 | 21.844 | 12.531 | 12.531 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | TYR | 0 | -0.069 | -0.073 | 23.439 | 0.550 | 0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | PHE | 0 | -0.028 | -0.011 | 23.641 | 0.408 | 0.408 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | ALA | 0 | 0.031 | 0.038 | 25.806 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | LYS | 1 | 0.958 | 0.990 | 28.337 | 10.267 | 10.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | ARG | 1 | 0.891 | 0.913 | 29.729 | 9.630 | 9.630 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | ALA | 0 | -0.019 | 0.016 | 26.786 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | GLU | -1 | -0.748 | -0.882 | 28.770 | -9.807 | -9.807 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | LEU | 0 | -0.007 | -0.005 | 30.678 | 0.214 | 0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | LYS | 1 | 0.884 | 0.925 | 30.527 | 9.869 | 9.869 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | ALA | 0 | -0.017 | 0.016 | 30.788 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | ILE | 0 | 0.043 | 0.020 | 32.887 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | ILE | 0 | -0.019 | -0.005 | 36.134 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | SER | 0 | -0.067 | -0.050 | 35.107 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | ASP | -1 | -0.977 | -0.984 | 35.978 | -8.143 | -8.143 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | VAL | 0 | -0.030 | -0.008 | 37.920 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | ASN | 0 | -0.010 | -0.021 | 41.294 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | ALA | 0 | -0.008 | 0.004 | 44.205 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | SER | 0 | -0.008 | 0.007 | 42.806 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | ASP | -1 | -0.945 | -0.972 | 44.203 | -6.598 | -6.598 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | GLU | -1 | -0.840 | -0.910 | 43.753 | -7.000 | -7.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | ASP | -1 | -0.813 | -0.910 | 42.087 | -7.213 | -7.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | ARG | 1 | 0.912 | 0.953 | 38.739 | 7.071 | 7.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | TRP | 0 | -0.024 | -0.010 | 37.651 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | ASN | 0 | 0.004 | -0.005 | 37.682 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | ALA | 0 | -0.059 | -0.032 | 35.972 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | VAL | 0 | 0.021 | 0.006 | 33.064 | -0.382 | -0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | LEU | 0 | 0.042 | 0.023 | 32.860 | -0.366 | -0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | LYS | 1 | 0.971 | 0.997 | 32.982 | 7.952 | 7.952 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | LEU | 0 | -0.082 | -0.037 | 28.293 | -0.355 | -0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | GLN | 0 | 0.000 | -0.001 | 28.226 | -0.270 | -0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | THR | 0 | -0.004 | -0.006 | 28.321 | -0.207 | -0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | LEU | 0 | -0.055 | -0.008 | 26.173 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | PRO | 0 | 0.040 | 0.011 | 22.649 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | ARG | 1 | 0.946 | 0.967 | 20.860 | 12.231 | 12.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | ASP | -1 | -0.894 | -0.950 | 16.465 | -18.010 | -18.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | SER | 0 | 0.012 | 0.023 | 18.683 | -0.536 | -0.536 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | SER | 0 | 0.013 | 0.024 | 19.795 | 0.263 | 0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | PRO | 0 | 0.115 | 0.043 | 18.587 | -0.773 | -0.773 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | SER | 0 | -0.004 | -0.005 | 17.394 | -0.767 | -0.767 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | ARG | 1 | 0.848 | 0.927 | 15.663 | 15.677 | 15.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | GLN | 0 | -0.008 | -0.009 | 13.209 | -0.514 | -0.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | ARG | 1 | 0.871 | 0.936 | 8.914 | 24.266 | 24.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | ASN | 0 | -0.021 | 0.000 | 10.083 | -1.753 | -1.753 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 64 | CYS | -1 | -0.913 | -0.786 | 5.896 | -38.436 | -38.436 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 65 | ARG | 1 | 1.004 | 1.003 | 6.299 | 16.477 | 16.477 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 66 | GLN | 0 | 0.072 | 0.045 | 7.628 | -1.627 | -1.627 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 71 | HIS | 0 | 0.108 | 0.053 | 6.538 | 3.552 | 3.552 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 72 | GLY | 0 | 0.035 | 0.009 | 8.723 | -2.001 | -2.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 73 | PHE | 0 | 0.005 | 0.019 | 9.572 | -0.279 | -0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 74 | LEU | 0 | 0.046 | 0.023 | 11.140 | 1.628 | 1.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 75 | ARG | 1 | 0.988 | 0.968 | 14.546 | 15.823 | 15.823 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 76 | LYS | 1 | 0.983 | 1.010 | 16.445 | 13.658 | 13.658 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 77 | PHE | 0 | 0.066 | 0.022 | 15.392 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 78 | GLY | 0 | 0.005 | 0.018 | 13.296 | -0.469 | -0.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 79 | LEU | 0 | 0.027 | -0.008 | 10.197 | -2.778 | -2.778 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 80 | SER | 0 | -0.018 | -0.102 | 7.350 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 81 | ARG | 1 | 0.989 | 0.989 | 9.723 | 23.985 | 23.985 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 82 | ILE | 0 | -0.018 | -0.018 | 7.993 | 1.085 | 1.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 83 | LYS | 1 | 0.868 | 0.934 | 7.876 | 33.153 | 33.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 84 | VAL | 0 | 0.047 | 0.016 | 11.251 | 1.180 | 1.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 85 | ARG | 1 | 0.975 | 0.996 | 14.527 | 18.446 | 18.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 86 | GLU | -1 | -0.840 | -0.919 | 11.435 | -26.244 | -26.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 87 | ALA | 0 | 0.032 | 0.018 | 14.970 | 0.713 | 0.713 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 88 | ALA | 0 | -0.019 | -0.010 | 16.632 | 0.986 | 0.986 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 89 | MET | 0 | -0.087 | -0.049 | 18.972 | 0.998 | 0.998 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 90 | ARG | 1 | 0.819 | 0.892 | 14.961 | 19.357 | 19.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 91 | GLY | 0 | 0.041 | 0.037 | 20.753 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 92 | GLU | -1 | -0.825 | -0.893 | 16.720 | -18.575 | -18.575 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 93 | ILE | 0 | -0.087 | -0.039 | 17.407 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 94 | PRO | 0 | 0.063 | 0.019 | 21.489 | 0.379 | 0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 95 | GLY | 0 | 0.016 | 0.011 | 25.282 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 96 | LEU | 0 | -0.074 | -0.019 | 20.235 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 97 | LYS | 1 | 0.993 | 0.991 | 24.622 | 10.439 | 10.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 98 | LYS | 1 | 0.918 | 0.951 | 24.254 | 12.232 | 12.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 99 | ALA | 0 | 0.006 | 0.003 | 26.003 | 0.392 | 0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 100 | SER | 0 | -0.038 | -0.035 | 28.311 | -0.187 | -0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 101 | TRP | -1 | -0.888 | -0.914 | 27.614 | -9.524 | -9.524 | 0.000 | 0.000 | 0.000 | 0.000 |