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: KQ213
Calculation Name: 7M4X-Y-Other547
Preferred Name:
Target Type:
Ligand Name: eravacycline | n7-methyl-guanosine-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 | 4-thiouridine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | zinc ion
Ligand 3-letter code: YQM | G7M | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | 4SU | H2U | OMU | ZN
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7M4X
Chain ID: Y
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 | 58 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -323019.266828 |
|---|---|
| FMO2-HF: Nuclear repulsion | 299160.786397 |
| FMO2-HF: Total energy | -23858.480431 |
| FMO2-MP2: Total energy | -23925.87453 |
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. |
| -31.196 | -21.339 | 9.601 | -7.124 | -12.335 | -0.063 |
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 | 0.014 | 0.003 | 3.014 | 8.001 | 11.573 | 0.008 | -1.796 | -1.784 | -0.002 |
| 4 | A | 4 | ILE | 0 | 0.047 | 0.031 | 2.381 | -11.798 | -10.373 | 4.338 | -1.861 | -3.902 | -0.020 |
| 5 | A | 5 | LYS | 1 | 0.896 | 0.935 | 4.575 | 29.878 | 29.939 | -0.001 | -0.031 | -0.030 | 0.000 |
| 39 | A | 39 | ASP | -1 | -0.865 | -0.908 | 2.813 | -48.038 | -46.396 | 0.274 | -0.510 | -1.406 | -0.002 |
| 40 | A | 40 | THR | 0 | 0.045 | 0.011 | 4.712 | -1.198 | -1.244 | -0.001 | -0.011 | 0.059 | 0.000 |
| 58 | A | 58 | GLU | -2 | -1.835 | -1.931 | 2.278 | -88.227 | -85.024 | 4.983 | -2.915 | -5.272 | -0.039 |
| 6 | A | 6 | VAL | 0 | 0.001 | 0.000 | 8.174 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | THR | 0 | 0.023 | 0.001 | 11.124 | 0.622 | 0.622 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLN | 0 | -0.047 | -0.031 | 14.551 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | THR | 0 | 0.027 | 0.000 | 16.585 | 0.712 | 0.712 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LYS | 1 | 0.895 | 0.944 | 19.346 | 13.459 | 13.459 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | SER | 0 | 0.055 | 0.035 | 22.495 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | SER | 0 | 0.101 | 0.040 | 22.681 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.024 | -0.008 | 24.636 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | HIS | 0 | 0.044 | 0.021 | 28.445 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ARG | 1 | 0.875 | 0.952 | 24.044 | 11.349 | 11.349 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | LEU | 0 | 0.082 | 0.038 | 25.668 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LYS | 1 | 1.006 | 0.998 | 25.689 | 9.448 | 9.448 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | ASN | 0 | 0.048 | 0.005 | 23.362 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | HIS | 0 | 0.068 | 0.056 | 21.278 | -0.509 | -0.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LYS | 1 | 0.894 | 0.945 | 21.030 | 9.960 | 9.960 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | LEU | 0 | 0.015 | 0.005 | 22.225 | -0.264 | -0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | CYS | 0 | -0.028 | 0.006 | 17.589 | -0.474 | -0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | LEU | 0 | 0.012 | 0.009 | 17.308 | -0.705 | -0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | GLN | 0 | -0.004 | -0.003 | 18.044 | -0.294 | -0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | GLY | 0 | -0.015 | -0.010 | 18.048 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LEU | 0 | -0.022 | -0.008 | 12.016 | -0.846 | -0.846 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | GLY | 0 | 0.019 | 0.019 | 14.692 | -0.564 | -0.564 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | LEU | 0 | -0.050 | -0.031 | 14.582 | 0.629 | 0.629 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ARG | 1 | 0.913 | 0.948 | 18.132 | 13.908 | 13.908 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | ARG | 1 | 0.936 | 0.974 | 21.087 | 12.863 | 12.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ILE | 0 | 0.014 | 0.002 | 20.997 | -0.553 | -0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | GLY | 0 | 0.050 | 0.028 | 19.786 | 0.384 | 0.384 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | HIS | 0 | -0.063 | -0.018 | 17.558 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | THR | 0 | 0.036 | 0.019 | 12.889 | -0.326 | -0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | VAL | 0 | -0.060 | -0.017 | 11.746 | 0.754 | 0.754 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | GLU | -1 | -0.845 | -0.911 | 7.441 | -29.684 | -29.684 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | VAL | 0 | -0.026 | -0.005 | 8.001 | 1.791 | 1.791 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | GLN | 0 | 0.028 | 0.010 | 6.617 | -4.184 | -4.184 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | PRO | 0 | 0.068 | 0.019 | 7.837 | 1.405 | 1.405 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | SER | 0 | 0.014 | 0.013 | 10.583 | 1.074 | 1.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | ASN | 0 | -0.014 | -0.017 | 9.020 | 3.363 | 3.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | ARG | 1 | 0.921 | 0.952 | 5.323 | 35.732 | 35.732 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | GLY | 0 | 0.025 | 0.019 | 10.112 | 1.328 | 1.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | MET | 0 | -0.072 | -0.039 | 13.680 | 1.751 | 1.751 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | ILE | 0 | 0.039 | 0.015 | 9.007 | 1.153 | 1.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | ASN | 0 | 0.004 | -0.006 | 12.146 | 0.494 | 0.494 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | LYS | 1 | 0.897 | 0.958 | 14.367 | 15.365 | 15.365 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | VAL | 0 | -0.036 | -0.029 | 15.530 | 1.028 | 1.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | TYR | 0 | 0.076 | 0.036 | 14.771 | 0.486 | 0.486 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | TYR | 0 | -0.012 | -0.015 | 15.743 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | MET | 0 | -0.096 | -0.041 | 18.311 | 0.938 | 0.938 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | VAL | 0 | -0.004 | 0.001 | 13.487 | 0.246 | 0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | SER | 0 | 0.018 | 0.019 | 12.057 | 0.638 | 0.638 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | VAL | 0 | -0.051 | -0.038 | 6.364 | 0.425 | 0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | GLU | -1 | -0.924 | -0.947 | 7.459 | -23.042 | -23.042 | 0.000 | 0.000 | 0.000 | 0.000 |