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: Z97GN
Calculation Name: 7OTC-S-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: S
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 | 110 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -796776.431558 |
|---|---|
| FMO2-HF: Nuclear repulsion | 754186.570639 |
| FMO2-HF: Total energy | -42589.860919 |
| FMO2-MP2: Total energy | -42714.708397 |
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. |
| -20.224 | -13.908 | 14.775 | -9.487 | -11.605 | -0.089 |
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 | 0.033 | 0.008 | 3.343 | -3.843 | -1.229 | 0.058 | -1.042 | -1.630 | -0.003 |
| 4 | A | 4 | ILE | 0 | -0.056 | -0.036 | 4.684 | 5.279 | 5.335 | -0.001 | -0.009 | -0.046 | 0.000 |
| 62 | A | 62 | ASP | -1 | -0.849 | -0.896 | 2.801 | -55.031 | -53.465 | 2.965 | -1.701 | -2.830 | -0.015 |
| 63 | A | 63 | GLY | 0 | -0.016 | -0.018 | 3.599 | 3.157 | 3.620 | 0.139 | -0.099 | -0.502 | 0.001 |
| 64 | A | 64 | ALA | 0 | -0.012 | 0.004 | 5.393 | -2.862 | -2.882 | -0.001 | -0.009 | 0.030 | 0.000 |
| 108 | A | 108 | SER | 0 | -0.033 | -0.039 | 2.653 | -4.333 | -3.707 | 0.110 | -0.325 | -0.412 | -0.002 |
| 109 | A | 109 | ASP | -1 | -0.720 | -0.861 | 1.978 | -103.259 | -103.797 | 10.386 | -5.379 | -4.469 | -0.060 |
| 110 | A | 110 | ARG | 0 | -0.036 | 0.007 | 2.424 | 10.698 | 12.247 | 1.119 | -0.923 | -1.746 | -0.010 |
| 5 | A | 5 | ALA | 0 | 0.058 | 0.046 | 8.402 | 1.434 | 1.434 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | LYS | 1 | 0.918 | 0.935 | 11.690 | 21.028 | 21.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | HIS | 0 | 0.033 | 0.027 | 15.121 | 0.419 | 0.419 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ARG | 1 | 0.963 | 0.976 | 18.097 | 14.411 | 14.411 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | HIS | 0 | 0.051 | 0.014 | 21.082 | 0.470 | 0.470 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | ALA | 0 | 0.029 | 0.044 | 22.532 | 0.510 | 0.510 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ARG | 1 | 0.998 | 0.989 | 24.610 | 10.056 | 10.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | SER | 0 | -0.027 | -0.035 | 26.551 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | 0.004 | 0.016 | 27.538 | -0.299 | -0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ALA | 0 | 0.110 | 0.041 | 24.961 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLN | 0 | 0.013 | 0.012 | 25.637 | -0.282 | -0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | LYS | 1 | 0.931 | 0.950 | 27.548 | 9.734 | 9.734 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | VAL | 0 | -0.002 | 0.000 | 22.109 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ARG | 1 | 0.908 | 0.944 | 22.397 | 12.809 | 12.809 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | LEU | 0 | 0.029 | 0.019 | 22.793 | -0.307 | -0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | VAL | 0 | -0.003 | -0.003 | 22.311 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ALA | 0 | -0.005 | -0.003 | 18.726 | -0.477 | -0.477 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | ASP | -1 | -0.840 | -0.921 | 18.444 | -15.673 | -15.673 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | LEU | 0 | -0.038 | 0.000 | 20.099 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ILE | 0 | 0.023 | 0.008 | 15.567 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | ARG | 1 | 0.818 | 0.899 | 14.583 | 16.568 | 16.568 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | GLY | 0 | 0.017 | 0.011 | 12.424 | 1.266 | 1.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | LYS | 1 | 0.814 | 0.921 | 13.274 | 17.241 | 17.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | LYS | 1 | 0.898 | 0.930 | 11.160 | 24.459 | 24.459 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | VAL | 0 | 0.043 | 0.012 | 10.390 | 1.921 | 1.921 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | SER | 0 | 0.069 | 0.044 | 13.172 | 0.973 | 0.973 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | GLN | 0 | 0.082 | 0.031 | 16.330 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | ALA | 0 | -0.042 | -0.020 | 15.294 | 0.901 | 0.901 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | LEU | 0 | -0.002 | -0.012 | 16.026 | 1.036 | 1.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | ASP | -1 | -0.852 | -0.914 | 18.750 | -14.148 | -14.148 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | ILE | 0 | -0.034 | -0.021 | 19.518 | 0.798 | 0.798 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | LEU | 0 | -0.063 | -0.037 | 18.720 | 0.745 | 0.745 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | THR | 0 | -0.077 | -0.047 | 22.608 | 0.501 | 0.501 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | TYR | 0 | 0.045 | 0.036 | 25.058 | 0.771 | 0.771 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | THR | 0 | -0.062 | -0.015 | 24.724 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | ASN | 0 | 0.052 | 0.021 | 27.433 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | LYS | 1 | 0.931 | 0.953 | 27.421 | 10.759 | 10.759 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | LYS | 1 | 0.923 | 0.953 | 27.747 | 10.737 | 10.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | ALA | 0 | -0.017 | -0.011 | 24.861 | -0.195 | -0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | ALA | 0 | 0.052 | 0.040 | 23.317 | -0.574 | -0.574 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | VAL | 0 | 0.066 | 0.029 | 22.398 | -0.589 | -0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | LEU | 0 | -0.110 | -0.047 | 22.392 | -0.212 | -0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | VAL | 0 | 0.037 | 0.004 | 17.986 | -0.534 | -0.534 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | LYS | 1 | 0.967 | 1.008 | 17.651 | 14.821 | 14.821 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | LYS | 1 | 0.969 | 0.988 | 17.658 | 12.902 | 12.902 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | VAL | 0 | -0.046 | -0.024 | 14.219 | -0.289 | -0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | LEU | 0 | 0.018 | 0.004 | 12.486 | -1.217 | -1.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | GLU | -1 | -0.876 | -0.945 | 12.844 | -19.636 | -19.636 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | SER | 0 | -0.032 | -0.009 | 13.585 | -0.925 | -0.925 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | ALA | 0 | -0.018 | -0.021 | 9.245 | -0.776 | -0.776 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | ILE | 0 | 0.022 | 0.015 | 8.569 | -3.046 | -3.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | ALA | 0 | 0.060 | 0.028 | 9.975 | -1.106 | -1.106 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | ASN | 0 | -0.068 | -0.046 | 7.630 | 1.351 | 1.351 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | ALA | 0 | -0.020 | -0.011 | 5.896 | -1.123 | -1.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | GLU | -1 | -0.921 | -0.970 | 6.799 | -22.762 | -22.762 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | HIS | 0 | -0.078 | -0.036 | 9.738 | 2.272 | 2.272 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | ASN | 0 | -0.062 | -0.027 | 6.078 | 3.027 | 3.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | ASP | -1 | -0.873 | -0.937 | 7.750 | -23.636 | -23.636 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | ILE | 0 | -0.037 | -0.026 | 8.621 | -3.352 | -3.352 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | ASP | -1 | -0.906 | -0.935 | 11.109 | -20.955 | -20.955 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | ASP | -1 | -0.869 | -0.929 | 7.446 | -31.574 | -31.574 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | LEU | 0 | -0.084 | -0.026 | 5.426 | -1.960 | -1.960 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | LYS | 1 | 0.916 | 0.942 | 7.430 | 31.940 | 31.940 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | VAL | 0 | -0.008 | 0.006 | 7.972 | -3.575 | -3.575 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | THR | 0 | -0.013 | 0.005 | 6.520 | 5.065 | 5.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | LYS | 1 | 0.848 | 0.907 | 8.674 | 34.328 | 34.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | ILE | 0 | 0.032 | 0.019 | 11.547 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | PHE | 0 | -0.016 | -0.002 | 13.082 | 1.209 | 1.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | VAL | 0 | -0.016 | -0.009 | 17.648 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | ASP | -1 | -0.807 | -0.895 | 19.346 | -15.625 | -15.625 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | GLU | -1 | -0.889 | -0.958 | 22.351 | -10.474 | -10.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | GLY | 0 | -0.003 | 0.004 | 25.448 | -0.266 | -0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | PRO | 0 | 0.016 | 0.015 | 26.439 | 0.425 | 0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | SER | 0 | 0.009 | 0.003 | 29.379 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | MET | 0 | 0.012 | 0.003 | 32.501 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | LYS | 1 | 0.906 | 0.960 | 34.780 | 8.983 | 8.983 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | ARG | 1 | 0.911 | 0.944 | 36.419 | 8.325 | 8.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | ILE | 0 | 0.078 | 0.041 | 41.129 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | MET | 0 | -0.019 | -0.007 | 44.736 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | PRO | 0 | 0.061 | 0.028 | 46.584 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | ARG | 1 | 0.834 | 0.913 | 48.259 | 6.591 | 6.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | ALA | 0 | 0.065 | 0.026 | 52.175 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | LYS | 1 | 0.955 | 0.956 | 55.752 | 5.333 | 5.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | GLY | 0 | 0.069 | 0.053 | 56.311 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | ARG | 1 | 0.891 | 0.953 | 49.964 | 6.347 | 6.347 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | ALA | 0 | 0.011 | -0.003 | 49.015 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | ASP | -1 | -0.774 | -0.847 | 46.051 | -6.740 | -6.740 | 0.000 | 0.000 | 0.000 | 0.000 |
| 95 | A | 95 | ARG | 1 | 0.951 | 0.956 | 41.235 | 7.695 | 7.695 | 0.000 | 0.000 | 0.000 | 0.000 |
| 96 | A | 96 | ILE | 0 | 0.017 | 0.013 | 38.884 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 97 | A | 97 | LEU | 0 | 0.004 | -0.004 | 35.556 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 98 | A | 98 | LYS | 1 | 0.921 | 0.957 | 34.563 | 8.214 | 8.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 99 | A | 99 | ARG | 1 | 0.894 | 0.930 | 30.807 | 9.716 | 9.716 | 0.000 | 0.000 | 0.000 | 0.000 |
| 100 | A | 100 | THR | 0 | -0.037 | -0.012 | 26.969 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 101 | A | 101 | SER | 0 | -0.016 | -0.013 | 23.484 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 102 | A | 102 | HIS | 0 | -0.015 | 0.000 | 19.772 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 103 | A | 103 | ILE | 0 | -0.011 | 0.008 | 17.355 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 104 | A | 104 | THR | 0 | 0.016 | 0.006 | 13.010 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
| 105 | A | 105 | VAL | 0 | -0.006 | -0.012 | 11.733 | 0.749 | 0.749 | 0.000 | 0.000 | 0.000 | 0.000 |
| 106 | A | 106 | VAL | 0 | -0.016 | -0.006 | 7.026 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 107 | A | 107 | VAL | 0 | 0.019 | 0.007 | 6.351 | 3.125 | 3.125 | 0.000 | 0.000 | 0.000 | 0.000 |