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: Z9LLN
Calculation Name: 7OTC-W-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: W
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 | 84 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -448913.114141 |
|---|---|
| FMO2-HF: Nuclear repulsion | 417846.110648 |
| FMO2-HF: Total energy | -31067.003492 |
| FMO2-MP2: Total energy | -31159.088147 |
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. |
| 136.986 | 140.065 | 0.507 | -1.617 | -1.97 | -0.013 |
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 | LYS | 1 | 1.005 | 1.020 | 3.202 | 41.539 | 43.304 | 0.021 | -0.791 | -0.996 | -0.003 |
| 4 | A | 5 | LYS | 1 | 0.956 | 0.972 | 2.708 | 30.032 | 31.287 | 0.487 | -0.823 | -0.920 | -0.010 |
| 5 | A | 6 | ALA | 0 | 0.012 | 0.010 | 5.141 | 4.376 | 4.435 | -0.001 | -0.003 | -0.054 | 0.000 |
| 6 | A | 7 | GLY | 0 | 0.024 | 0.013 | 7.155 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | GLY | 0 | 0.025 | 0.016 | 10.858 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | SER | 0 | 0.005 | -0.002 | 13.935 | 0.342 | 0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | THR | 0 | 0.019 | 0.009 | 17.107 | 0.442 | 0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | ARG | 1 | 1.017 | 1.004 | 20.555 | 12.974 | 12.974 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | ASN | 0 | 0.006 | -0.016 | 23.610 | 0.651 | 0.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | GLY | 0 | 0.002 | 0.023 | 25.209 | 0.310 | 0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | ARG | 1 | 0.859 | 0.921 | 26.418 | 11.005 | 11.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | ASP | -1 | -0.804 | -0.887 | 30.097 | -8.914 | -8.914 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | SER | 0 | -0.118 | -0.063 | 33.490 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | GLU | -1 | -0.819 | -0.912 | 36.904 | -8.078 | -8.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | ALA | 0 | 0.066 | 0.037 | 39.135 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LYS | 1 | 0.898 | 0.939 | 41.256 | 7.696 | 7.696 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ARG | 1 | 0.955 | 0.979 | 41.459 | 7.562 | 7.562 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | LEU | 0 | -0.032 | 0.002 | 46.587 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | GLY | 0 | 0.023 | 0.009 | 48.920 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | VAL | 0 | -0.015 | -0.018 | 51.291 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | LYS | 1 | 0.786 | 0.895 | 50.259 | 6.133 | 6.133 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | ARG | 1 | 0.924 | 0.961 | 55.940 | 5.347 | 5.347 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | PHE | 0 | 0.076 | 0.022 | 54.117 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | GLY | 0 | -0.004 | -0.011 | 60.078 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | GLY | 0 | -0.051 | -0.030 | 63.403 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | GLU | -1 | -0.843 | -0.904 | 60.698 | -5.204 | -5.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | SER | 0 | 0.002 | 0.011 | 64.676 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | VAL | 0 | -0.077 | -0.047 | 63.614 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | LEU | 0 | 0.089 | 0.059 | 65.924 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | ALA | 0 | 0.036 | 0.014 | 66.080 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | GLY | 0 | -0.020 | -0.011 | 64.244 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | SER | 0 | -0.061 | -0.037 | 61.880 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | ILE | 0 | -0.039 | -0.031 | 55.958 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | ILE | 0 | 0.036 | 0.031 | 59.222 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | VAL | 0 | 0.006 | -0.006 | 54.483 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | ARG | 1 | 0.912 | 0.971 | 48.795 | 6.333 | 6.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | GLN | 0 | 0.000 | -0.012 | 51.841 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | ARG | 1 | 0.900 | 0.947 | 47.104 | 6.414 | 6.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | GLY | 0 | 0.088 | 0.046 | 50.604 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | THR | 0 | -0.011 | -0.010 | 53.538 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LYS | 1 | 0.911 | 0.955 | 49.314 | 6.426 | 6.426 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | PHE | 0 | 0.011 | 0.002 | 54.979 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | HIS | 0 | -0.007 | -0.010 | 58.703 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | ALA | 0 | 0.022 | 0.010 | 61.813 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | GLY | 0 | 0.026 | 0.018 | 64.333 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | ALA | 0 | 0.039 | 0.011 | 67.667 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | ASN | 0 | 0.025 | 0.010 | 69.441 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | VAL | 0 | 0.005 | 0.024 | 63.610 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | GLY | 0 | -0.015 | -0.005 | 64.653 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | CYS | 0 | -0.059 | -0.032 | 59.951 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | GLY | 0 | 0.057 | 0.035 | 58.670 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | ARG | 1 | 0.995 | 0.983 | 52.736 | 5.814 | 5.814 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | ASP | -1 | -0.927 | -0.947 | 52.344 | -5.967 | -5.967 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | HIS | 0 | 0.024 | -0.006 | 53.626 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | THR | 0 | -0.048 | -0.029 | 54.433 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | LEU | 0 | 0.001 | 0.000 | 56.534 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | PHE | 0 | -0.015 | -0.013 | 59.480 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | ALA | 0 | 0.085 | 0.047 | 62.027 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | LYS | 1 | 0.866 | 0.926 | 65.501 | 4.638 | 4.638 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | ALA | 0 | 0.015 | 0.011 | 68.454 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 64 | ASP | -1 | -0.807 | -0.897 | 69.359 | -4.627 | -4.627 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 65 | GLY | 0 | 0.050 | 0.031 | 70.006 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 66 | LYS | 1 | 0.933 | 0.983 | 68.611 | 4.573 | 4.573 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 67 | VAL | 0 | -0.026 | -0.013 | 62.864 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 68 | LYS | 1 | 0.887 | 0.950 | 66.317 | 4.612 | 4.612 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 69 | PHE | 0 | -0.018 | -0.014 | 58.763 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 70 | GLU | -1 | -0.824 | -0.888 | 64.072 | -4.621 | -4.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 71 | VAL | 0 | 0.001 | -0.001 | 63.092 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 72 | LYS | 1 | 0.871 | 0.923 | 65.633 | 4.735 | 4.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 73 | GLY | 0 | 0.053 | 0.025 | 66.335 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 74 | PRO | 0 | 0.042 | 0.010 | 67.520 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 75 | LYS | 1 | 0.914 | 0.954 | 62.670 | 5.044 | 5.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 76 | ASN | 0 | 0.027 | 0.024 | 62.539 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 77 | ARG | 1 | 0.949 | 0.985 | 60.095 | 5.177 | 5.177 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 78 | LYS | 1 | 0.934 | 0.976 | 55.644 | 5.770 | 5.770 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 79 | PHE | 0 | -0.031 | -0.029 | 61.553 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 80 | ILE | 0 | -0.009 | -0.001 | 59.435 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 81 | SER | 0 | -0.039 | -0.033 | 64.038 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 82 | ILE | 0 | -0.019 | -0.014 | 65.823 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 83 | GLU | -1 | -0.837 | -0.909 | 69.343 | -4.526 | -4.526 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 84 | ALA | 0 | -0.032 | -0.024 | 72.165 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 85 | GLU | -2 | -1.862 | -1.921 | 73.042 | -8.543 | -8.543 | 0.000 | 0.000 | 0.000 | 0.000 |