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: M268Z
Calculation Name: 2J0S-T-Xray549
Preferred Name:
Target Type:
Ligand Name: phosphoaminophosphonic acid-adenylate ester | magnesium ion
Ligand 3-letter code: ANP | MG
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2J0S
Chain ID: T
UniProt ID: O15234
Base Structure: X-ray
Registration Date: 2025-10-12
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 44 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -162201.52433 |
|---|---|
| FMO2-HF: Nuclear repulsion | 143454.223992 |
| FMO2-HF: Total energy | -18747.300338 |
| FMO2-MP2: Total energy | -18803.022642 |
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(T:169:HIS)
Summations of interaction energy for
fragment #1(T:169:HIS)
| 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. |
| -129.847 | -125.459 | 2.011 | -2.084 | -4.314 | -0.014 |
Interaction energy analysis for fragmet #1(T:169:HIS)
| 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 | T | 171 | ASP | -1 | -0.828 | -0.900 | 2.708 | -55.037 | -50.914 | 2.005 | -2.102 | -4.026 | -0.014 |
| 4 | T | 172 | ASP | -1 | -0.877 | -0.945 | 3.643 | -29.053 | -28.788 | 0.006 | 0.018 | -0.288 | 0.000 |
| 5 | T | 173 | ASP | -1 | -0.924 | -0.964 | 6.202 | -27.629 | -27.629 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | T | 174 | GLU | -1 | -0.911 | -0.960 | 6.417 | -40.990 | -40.990 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | T | 175 | ASP | -1 | -0.850 | -0.910 | 6.134 | -31.651 | -31.651 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | T | 176 | ARG | 1 | 0.924 | 0.950 | 8.119 | 22.900 | 22.900 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | T | 177 | LYS | 1 | 0.785 | 0.875 | 7.669 | 32.971 | 32.971 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | T | 178 | ASN | 0 | -0.018 | 0.006 | 6.268 | 3.951 | 3.951 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | T | 179 | PRO | 0 | -0.016 | -0.016 | 9.916 | 0.745 | 0.745 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | T | 180 | ALA | 0 | 0.005 | 0.004 | 9.545 | 1.273 | 1.273 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | T | 181 | TYR | 0 | -0.052 | -0.006 | 10.685 | 1.256 | 1.256 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | T | 182 | ILE | 0 | 0.031 | 0.009 | 11.822 | 2.213 | 2.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | T | 183 | PRO | 0 | -0.065 | -0.037 | 13.994 | -0.705 | -0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | T | 184 | ARG | 1 | 1.006 | 0.998 | 13.192 | 21.899 | 21.899 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | T | 185 | LYS | 1 | 0.901 | 0.960 | 12.660 | 23.123 | 23.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | T | 186 | GLY | 0 | 0.041 | 0.001 | 18.161 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | T | 187 | LEU | 0 | -0.002 | -0.009 | 21.916 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | T | 188 | PHE | 0 | 0.017 | 0.026 | 19.790 | 0.332 | 0.332 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | T | 189 | PHE | 0 | -0.025 | -0.011 | 17.978 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | T | 190 | GLU | -1 | -0.944 | -0.969 | 22.365 | -11.434 | -11.434 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | T | 191 | HIS | 0 | -0.043 | -0.014 | 21.107 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | T | 192 | ASP | -1 | -0.826 | -0.904 | 22.509 | -13.496 | -13.496 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | T | 193 | LEU | 0 | -0.072 | -0.040 | 17.235 | -0.619 | -0.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | T | 194 | ARG | 1 | 0.865 | 0.901 | 20.521 | 13.289 | 13.289 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | T | 195 | GLY | 0 | -0.045 | -0.018 | 17.956 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | T | 196 | GLN | -1 | -0.937 | -0.942 | 14.554 | -21.842 | -21.842 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | T | 215 | GLU | -1 | -0.966 | -0.999 | 49.575 | -6.568 | -6.568 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | T | 216 | GLY | 0 | -0.001 | -0.009 | 48.363 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | T | 217 | ARG | 1 | 0.952 | 0.986 | 48.425 | 6.044 | 6.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | T | 218 | TRP | 0 | -0.030 | -0.007 | 43.493 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | T | 219 | GLU | -1 | -0.875 | -0.933 | 50.321 | -5.887 | -5.887 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | T | 220 | HIS | 0 | -0.022 | -0.018 | 52.687 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | T | 221 | ASP | -1 | -0.840 | -0.905 | 52.901 | -6.188 | -6.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | T | 222 | LYS | 1 | 0.782 | 0.865 | 50.878 | 6.421 | 6.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | T | 223 | PHE | 0 | -0.040 | -0.007 | 55.393 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | T | 224 | ARG | 1 | 0.913 | 0.954 | 57.624 | 5.358 | 5.358 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | T | 225 | GLU | -1 | -0.921 | -0.964 | 61.131 | -5.116 | -5.116 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | T | 226 | ASP | -1 | -0.949 | -0.971 | 63.176 | -5.077 | -5.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | T | 227 | GLU | -1 | -0.939 | -0.980 | 58.702 | -5.471 | -5.471 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | T | 228 | GLN | 0 | -0.077 | -0.034 | 56.206 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | T | 229 | ALA | 0 | -0.009 | 0.004 | 60.086 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | T | 230 | PRO | -1 | -0.977 | -0.981 | 61.556 | -5.088 | -5.088 | 0.000 | 0.000 | 0.000 | 0.000 |