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: Z97NN
Calculation Name: 7OTC-3-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: 3
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 | 64 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -322537.36134 |
|---|---|
| FMO2-HF: Nuclear repulsion | 297927.059019 |
| FMO2-HF: Total energy | -24610.30232 |
| FMO2-MP2: Total energy | -24682.867261 |
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:PRO)
Summations of interaction energy for
fragment #1(A:2:PRO)
| 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. |
| 192.124 | 194.657 | 0.245 | -1.274 | -1.504 | -0.008 |
Interaction energy analysis for fragmet #1(A:2:PRO)
| 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 | ILE | 0 | 0.074 | 0.046 | 2.875 | -6.346 | -3.813 | 0.245 | -1.274 | -1.504 | -0.008 |
| 4 | A | 5 | LYS | 1 | 0.958 | 0.976 | 5.179 | 37.950 | 37.950 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | THR | 0 | 0.045 | 0.032 | 7.213 | 2.085 | 2.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | VAL | 0 | 0.083 | 0.038 | 10.950 | 0.441 | 0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | ARG | 1 | 0.938 | 0.957 | 11.882 | 21.518 | 21.518 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | GLY | 0 | 0.021 | 0.015 | 15.246 | 0.983 | 0.983 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | ALA | 0 | 0.065 | 0.032 | 16.863 | 1.002 | 1.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | ALA | 0 | 0.024 | 0.005 | 15.941 | 0.670 | 0.670 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | LYS | 1 | 0.884 | 0.953 | 18.077 | 15.733 | 15.733 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | ARG | 1 | 0.847 | 0.921 | 21.354 | 13.649 | 13.649 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | PHE | 0 | 0.024 | 0.016 | 20.135 | 0.608 | 0.608 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | LYS | 1 | 0.905 | 0.952 | 21.255 | 13.377 | 13.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | LYS | 1 | 0.955 | 0.999 | 18.900 | 16.461 | 16.461 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | THR | 0 | -0.037 | -0.041 | 23.112 | 0.572 | 0.572 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | GLY | 0 | 0.075 | 0.030 | 25.629 | -0.368 | -0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | LYS | 1 | 0.976 | 0.987 | 27.688 | 10.388 | 10.388 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | GLY | 0 | 0.030 | 0.028 | 23.596 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | GLY | 0 | 0.033 | 0.023 | 23.107 | -0.475 | -0.475 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | PHE | 0 | 0.033 | 0.013 | 18.599 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | LYS | 1 | 0.990 | 0.998 | 24.610 | 11.311 | 11.311 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | HIS | 0 | 0.028 | -0.001 | 25.538 | -0.456 | -0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | LYS | 1 | 0.867 | 0.922 | 27.329 | 9.770 | 9.770 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | HIS | 0 | 0.084 | 0.065 | 29.707 | -0.353 | -0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | ALA | 0 | 0.056 | 0.028 | 31.023 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | ASN | 0 | 0.004 | -0.020 | 32.710 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | LEU | 0 | -0.016 | 0.014 | 35.252 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | ARG | 1 | 0.930 | 0.951 | 29.653 | 9.489 | 9.489 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | HIS | 0 | 0.159 | 0.087 | 36.369 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ILE | 0 | 0.048 | 0.039 | 38.938 | 0.216 | 0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | LEU | 0 | 0.002 | -0.015 | 39.393 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | THR | 0 | 0.074 | 0.033 | 43.088 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | LYS | 1 | 1.019 | 1.015 | 44.528 | 6.913 | 6.913 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | LYS | 1 | 0.785 | 0.899 | 39.194 | 7.805 | 7.805 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | ALA | 0 | 0.129 | 0.055 | 45.541 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | THR | 0 | 0.048 | -0.001 | 45.764 | -0.211 | -0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | LYS | 1 | 1.019 | 1.020 | 45.578 | 6.401 | 6.401 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | ARG | 1 | 0.994 | 1.007 | 39.415 | 7.488 | 7.488 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | LYS | 1 | 0.913 | 0.946 | 41.134 | 6.703 | 6.703 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | ARG | 1 | 0.936 | 0.976 | 40.866 | 6.566 | 6.566 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | HIS | 0 | 0.028 | -0.002 | 40.356 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | LEU | 0 | -0.026 | -0.008 | 36.237 | -0.178 | -0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | ARG | 1 | 0.948 | 0.981 | 35.965 | 7.312 | 7.312 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | PRO | 0 | 0.000 | 0.006 | 35.719 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | LYS | 1 | 0.864 | 0.934 | 29.993 | 9.421 | 9.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | ALA | 0 | 0.045 | 0.037 | 31.228 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | MET | 0 | 0.016 | 0.006 | 27.915 | -0.368 | -0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | VAL | 0 | -0.021 | -0.015 | 24.218 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | SER | 0 | 0.065 | 0.039 | 27.437 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | LYS | 1 | 0.978 | 0.980 | 27.255 | 10.863 | 10.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | GLY | 0 | 0.004 | 0.008 | 27.084 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | ASP | -1 | -0.854 | -0.934 | 24.461 | -11.952 | -11.952 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | LEU | 0 | -0.043 | -0.032 | 22.646 | -0.703 | -0.703 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | GLY | 0 | 0.052 | 0.031 | 20.356 | -0.653 | -0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | LEU | 0 | 0.053 | 0.030 | 18.769 | -1.050 | -1.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | VAL | 0 | -0.039 | -0.022 | 17.936 | -0.890 | -0.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | ILE | 0 | 0.012 | -0.002 | 16.278 | -0.697 | -0.697 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | ALA | 0 | 0.015 | 0.021 | 14.379 | -1.300 | -1.300 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | CYS | 0 | -0.065 | -0.037 | 13.090 | -1.522 | -1.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | LEU | 0 | -0.134 | -0.069 | 13.537 | -0.797 | -0.797 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | PRO | 0 | 0.066 | 0.021 | 9.719 | 0.678 | 0.678 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 64 | TYR | 0 | -0.040 | -0.005 | 7.746 | -1.113 | -1.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 65 | ALA | -1 | -0.891 | -0.939 | 13.506 | -15.668 | -15.668 | 0.000 | 0.000 | 0.000 | 0.000 |