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: Z9LNN
Calculation Name: 7OTC-o-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: o
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 | 88 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -603024.178462 |
|---|---|
| FMO2-HF: Nuclear repulsion | 568000.548767 |
| FMO2-HF: Total energy | -35023.629696 |
| FMO2-MP2: Total energy | -35127.717367 |
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:SER)
Summations of interaction energy for
fragment #1(A:2:SER)
| 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. |
| 82.443 | 85.634 | 3.608 | -2.729 | -4.07 | -0.042 |
Interaction energy analysis for fragmet #1(A:2:SER)
| 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 | SER | 0 | 0.052 | 0.032 | 3.829 | -1.851 | -0.572 | -0.013 | -0.465 | -0.800 | -0.002 |
| 34 | A | 35 | GLN | 0 | -0.015 | -0.010 | 2.349 | -25.965 | -24.391 | 3.622 | -2.182 | -3.013 | -0.040 |
| 37 | A | 38 | HIS | 0 | 0.023 | 0.020 | 4.303 | 0.310 | 0.491 | -0.001 | -0.060 | -0.121 | 0.000 |
| 38 | A | 39 | LEU | 0 | -0.027 | -0.023 | 3.797 | -0.389 | -0.232 | 0.000 | -0.022 | -0.136 | 0.000 |
| 4 | A | 5 | THR | 0 | 0.038 | 0.030 | 5.801 | 2.052 | 2.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | GLU | -1 | -0.809 | -0.915 | 8.737 | -30.407 | -30.407 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | ALA | 0 | -0.016 | -0.007 | 8.024 | 1.515 | 1.515 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | THR | 0 | -0.060 | -0.053 | 7.309 | 2.506 | 2.506 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | ALA | 0 | 0.037 | 0.016 | 10.126 | 2.003 | 2.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | LYS | 1 | 0.923 | 0.990 | 12.961 | 21.218 | 21.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | ILE | 0 | 0.017 | 0.009 | 10.305 | 0.843 | 0.843 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | VAL | 0 | -0.006 | -0.016 | 14.044 | 0.960 | 0.960 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | SER | 0 | -0.010 | -0.016 | 15.609 | 1.389 | 1.389 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | GLU | -1 | -0.889 | -0.938 | 16.993 | -17.844 | -17.844 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | PHE | 0 | -0.091 | -0.055 | 16.982 | 0.621 | 0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | GLY | 0 | 0.014 | 0.009 | 18.953 | 0.486 | 0.486 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | ARG | 1 | 0.834 | 0.908 | 20.245 | 12.499 | 12.499 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | ASP | -1 | -0.818 | -0.924 | 22.376 | -12.895 | -12.895 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | ALA | 0 | 0.009 | -0.001 | 19.325 | -0.582 | -0.582 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | ASN | 0 | -0.038 | -0.016 | 18.495 | -0.508 | -0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | ASP | -1 | -0.844 | -0.892 | 19.941 | -14.295 | -14.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | THR | 0 | -0.024 | -0.036 | 14.902 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | GLY | 0 | 0.009 | 0.010 | 15.543 | -1.017 | -1.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | SER | 0 | 0.005 | 0.011 | 18.120 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | THR | 0 | -0.024 | -0.030 | 17.731 | -0.872 | -0.872 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | GLU | -1 | -0.770 | -0.866 | 17.587 | -15.326 | -15.326 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | VAL | 0 | 0.048 | 0.047 | 15.088 | -1.126 | -1.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | GLN | 0 | -0.059 | -0.026 | 13.161 | -2.330 | -2.330 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | VAL | 0 | -0.010 | -0.015 | 12.709 | -1.828 | -1.828 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | ALA | 0 | 0.050 | 0.051 | 13.768 | -1.091 | -1.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | LEU | 0 | 0.019 | 0.006 | 9.300 | -2.447 | -2.447 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | LEU | 0 | -0.055 | -0.038 | 8.552 | -4.030 | -4.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | THR | 0 | -0.014 | -0.015 | 9.318 | -1.396 | -1.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | ALA | 0 | 0.040 | 0.039 | 8.871 | -0.848 | -0.848 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | ILE | 0 | -0.006 | -0.015 | 5.644 | -2.737 | -2.737 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | ASN | 0 | -0.026 | -0.028 | 8.326 | 0.705 | 0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | GLN | 0 | 0.003 | 0.007 | 6.629 | 3.054 | 3.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | GLY | 0 | 0.017 | 0.015 | 9.589 | 2.137 | 2.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | HIS | 0 | -0.001 | 0.009 | 7.236 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | PHE | 0 | -0.040 | -0.037 | 8.313 | 2.220 | 2.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | ALA | 0 | 0.007 | 0.020 | 11.819 | 1.925 | 1.925 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | GLU | -1 | -0.881 | -0.931 | 12.732 | -21.045 | -21.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | HIS | 1 | 0.879 | 0.925 | 10.138 | 27.086 | 27.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | LYS | 1 | 0.962 | 0.971 | 13.583 | 16.338 | 16.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | LYS | 1 | 0.947 | 0.961 | 16.068 | 14.523 | 14.523 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | ASP | -1 | -0.761 | -0.834 | 10.041 | -27.343 | -27.343 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | HIS | 0 | 0.040 | -0.008 | 12.783 | -1.717 | -1.717 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | HIS | 0 | 0.025 | 0.018 | 12.693 | -0.724 | -0.724 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | SER | 0 | 0.033 | -0.008 | 7.640 | -1.455 | -1.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | ARG | 1 | 0.845 | 0.942 | 9.221 | 19.160 | 19.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | ARG | 1 | 0.976 | 0.988 | 11.477 | 18.288 | 18.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | GLY | 0 | 0.019 | 0.013 | 8.983 | 0.746 | 0.746 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | LEU | 0 | 0.034 | 0.016 | 8.532 | -0.363 | -0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | LEU | 0 | 0.010 | -0.009 | 9.512 | 1.214 | 1.214 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | ARG | 1 | 0.884 | 0.944 | 9.460 | 27.332 | 27.332 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | MET | 0 | -0.013 | -0.001 | 5.334 | 0.702 | 0.702 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | VAL | 0 | 0.016 | 0.007 | 11.233 | 1.346 | 1.346 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | SER | 0 | -0.018 | -0.007 | 13.846 | 1.396 | 1.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | GLN | 0 | 0.029 | 0.020 | 12.505 | -0.312 | -0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | ARG | 1 | 0.968 | 0.973 | 13.448 | 22.084 | 22.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 64 | ARG | 1 | 0.782 | 0.866 | 15.762 | 14.885 | 14.885 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 65 | LYS | 1 | 0.968 | 0.980 | 18.783 | 16.329 | 16.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 66 | LEU | 0 | -0.008 | 0.006 | 15.360 | 0.724 | 0.724 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 67 | LEU | 0 | 0.030 | 0.015 | 18.558 | 0.620 | 0.620 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 68 | ASP | -1 | -0.832 | -0.905 | 21.330 | -12.420 | -12.420 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 69 | TYR | 0 | -0.069 | -0.034 | 22.279 | 0.884 | 0.884 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 70 | LEU | 0 | 0.034 | 0.009 | 21.050 | 0.478 | 0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 71 | LYS | 1 | 0.951 | 0.978 | 24.759 | 11.215 | 11.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 72 | ARG | 1 | 0.898 | 0.954 | 26.279 | 11.717 | 11.717 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 73 | LYS | 1 | 0.868 | 0.958 | 26.974 | 11.630 | 11.630 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 74 | ASP | -1 | -0.802 | -0.925 | 28.345 | -10.765 | -10.765 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 75 | VAL | 0 | 0.024 | 0.000 | 28.480 | -0.400 | -0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 76 | ALA | 0 | 0.039 | 0.047 | 29.115 | -0.207 | -0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 77 | ARG | 1 | 0.895 | 0.936 | 23.189 | 12.354 | 12.354 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 78 | TYR | 0 | -0.056 | -0.056 | 23.372 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 79 | THR | 0 | -0.015 | -0.028 | 24.352 | -0.420 | -0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 80 | GLN | 0 | 0.099 | 0.061 | 23.910 | -0.466 | -0.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 81 | LEU | 0 | -0.037 | -0.016 | 18.526 | -0.424 | -0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 82 | ILE | 0 | -0.059 | -0.045 | 20.799 | -0.740 | -0.740 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 83 | GLU | -1 | -0.914 | -0.952 | 21.578 | -12.011 | -12.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 84 | ARG | 1 | 0.843 | 0.924 | 20.300 | 14.442 | 14.442 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 85 | LEU | 0 | -0.058 | -0.020 | 14.802 | -0.865 | -0.865 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 86 | GLY | 0 | 0.014 | 0.020 | 17.434 | -0.905 | -0.905 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 87 | LEU | 0 | -0.096 | -0.039 | 15.867 | -0.350 | -0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 88 | ARG | 1 | 0.954 | 0.958 | 19.831 | 15.050 | 15.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 89 | ARG | 0 | 0.178 | 0.140 | 21.866 | -1.342 | -1.342 | 0.000 | 0.000 | 0.000 | 0.000 |