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: Q5NQY
Calculation Name: 7OTC-1-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: 1
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 | 50 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -248852.145358 |
|---|---|
| FMO2-HF: Nuclear repulsion | 229162.786134 |
| FMO2-HF: Total energy | -19689.359224 |
| FMO2-MP2: Total energy | -19748.758776 |
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:4:GLY)
Summations of interaction energy for
fragment #1(A:4:GLY)
| 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. |
| 160.77 | 162.225 | -0.011 | -0.62 | -0.823 | -0.002 |
Interaction energy analysis for fragmet #1(A:4:GLY)
| 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 | 6 | ARG | 1 | 0.871 | 0.927 | 3.774 | 40.369 | 41.735 | -0.010 | -0.607 | -0.748 | -0.002 |
| 4 | A | 7 | GLU | -1 | -0.803 | -0.880 | 4.551 | -36.290 | -36.201 | -0.001 | -0.013 | -0.075 | 0.000 |
| 5 | A | 8 | LYS | 1 | 0.960 | 0.965 | 7.045 | 36.260 | 36.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 9 | ILE | 0 | 0.033 | 0.031 | 9.637 | 0.784 | 0.784 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 10 | LYS | 1 | 0.870 | 0.947 | 13.102 | 15.392 | 15.392 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 11 | LEU | 0 | -0.004 | 0.011 | 16.631 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 12 | VAL | 0 | 0.034 | 0.004 | 19.275 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 13 | SER | 0 | -0.008 | -0.014 | 22.733 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 14 | SER | 0 | -0.069 | -0.068 | 25.990 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 15 | ALA | 0 | 0.005 | 0.004 | 28.672 | 0.304 | 0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 16 | GLY | 0 | 0.017 | 0.016 | 29.838 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 17 | THR | 0 | -0.009 | -0.009 | 29.259 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 18 | GLY | 0 | 0.009 | 0.012 | 27.209 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 19 | HIS | 0 | 0.023 | 0.018 | 23.553 | -0.267 | -0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 20 | PHE | 0 | 0.026 | -0.012 | 18.749 | -0.402 | -0.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 21 | TYR | 0 | -0.015 | -0.015 | 18.596 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 22 | THR | 0 | -0.012 | -0.017 | 13.878 | -0.617 | -0.617 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 23 | THR | 0 | 0.046 | 0.027 | 12.579 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 24 | THR | 0 | 0.012 | 0.013 | 7.016 | -1.748 | -1.748 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 25 | LYS | 1 | 0.868 | 0.958 | 9.433 | 21.989 | 21.989 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 26 | ASN | 0 | -0.012 | -0.014 | 8.026 | -2.335 | -2.335 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 27 | LYS | 1 | 0.922 | 0.947 | 9.407 | 26.146 | 26.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 28 | ARG | 1 | 0.993 | 1.004 | 7.951 | 36.699 | 36.699 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 29 | THR | 0 | 0.022 | 0.018 | 11.752 | 1.875 | 1.875 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 30 | LYS | 1 | 0.967 | 0.980 | 13.642 | 16.957 | 16.957 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 31 | PRO | 0 | 0.050 | 0.018 | 15.693 | -0.616 | -0.616 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 32 | GLU | -1 | -0.932 | -0.952 | 16.745 | -14.788 | -14.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 33 | LYS | 1 | 0.851 | 0.908 | 16.987 | 16.482 | 16.482 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 34 | LEU | 0 | -0.002 | 0.002 | 15.817 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 35 | GLU | -1 | -0.767 | -0.880 | 19.022 | -12.548 | -12.548 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 36 | LEU | 0 | -0.021 | -0.015 | 19.055 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 37 | LYS | 1 | 0.966 | 0.988 | 23.381 | 10.227 | 10.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 38 | LYS | 1 | 0.882 | 0.958 | 20.110 | 13.766 | 13.766 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 39 | PHE | 0 | 0.054 | 0.034 | 25.637 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 40 | ASP | -1 | -0.787 | -0.882 | 26.342 | -11.292 | -11.292 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 41 | PRO | 0 | -0.002 | -0.006 | 26.780 | 0.359 | 0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 42 | VAL | 0 | 0.001 | 0.009 | 29.315 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 43 | VAL | 0 | 0.002 | -0.012 | 31.644 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 44 | ARG | 1 | 0.900 | 0.964 | 32.459 | 8.786 | 8.786 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 45 | GLN | 0 | 0.079 | 0.050 | 32.094 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 46 | HIS | 0 | -0.028 | -0.022 | 27.935 | -0.555 | -0.555 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 47 | VAL | 0 | 0.005 | 0.008 | 27.992 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 48 | ILE | 0 | 0.011 | 0.004 | 26.280 | -0.375 | -0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 49 | TYR | 0 | -0.029 | -0.005 | 22.196 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 50 | LYS | 1 | 0.932 | 0.950 | 22.750 | 11.579 | 11.579 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 51 | GLU | -1 | -0.824 | -0.913 | 15.826 | -19.681 | -19.681 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 52 | ALA | 0 | -0.025 | -0.013 | 18.513 | 0.672 | 0.672 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 53 | LYS | 0 | -0.037 | -0.020 | 12.617 | 1.604 | 1.604 | 0.000 | 0.000 | 0.000 | 0.000 |