FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: 7GN2K
Calculation Name: 1XTC-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1XTC
Chain ID: C
UniProt ID: P01555
Base Structure: X-ray
Registration Date: 2023-03-13
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptHSide |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 45 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -175145.471266 |
|---|---|
| FMO2-HF: Nuclear repulsion | 156618.909954 |
| FMO2-HF: Total energy | -18526.561312 |
| FMO2-MP2: Total energy | -18580.70036 |
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(C:196:SER)
Summations of interaction energy for
fragment #1(C:196: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. |
| -12.115 | -7.367 | 0.41 | -2.066 | -3.092 | 0.014 |
Interaction energy analysis for fragmet #1(C:196: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 | C | 198 | THR | 0 | 0.011 | 0.009 | 3.137 | -2.872 | -0.178 | 0.055 | -1.199 | -1.549 | 0.006 |
| 4 | C | 199 | CYS | 0 | 0.037 | 0.013 | 2.921 | -4.995 | -3.318 | 0.355 | -0.796 | -1.236 | 0.008 |
| 5 | C | 200 | ASP | -1 | -0.886 | -0.933 | 4.460 | -1.396 | -1.019 | 0.000 | -0.071 | -0.307 | 0.000 |
| 6 | C | 201 | GLU | -1 | -0.790 | -0.882 | 6.229 | 1.550 | 1.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 202 | LYS | 1 | 0.839 | 0.899 | 7.110 | -2.482 | -2.482 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 203 | THR | 0 | -0.006 | 0.001 | 8.496 | -0.404 | -0.404 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 204 | GLN | 0 | 0.045 | 0.029 | 10.330 | -0.325 | -0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 205 | SER | 0 | -0.103 | -0.025 | 12.004 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 206 | LEU | 0 | 0.002 | -0.021 | 11.903 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 207 | GLY | 0 | 0.020 | 0.007 | 14.692 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 208 | VAL | 0 | 0.001 | -0.005 | 16.534 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 209 | LYS | 1 | 0.983 | 1.009 | 17.691 | -0.624 | -0.624 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 210 | PHE | 0 | -0.056 | -0.024 | 18.965 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 211 | LEU | 0 | 0.005 | -0.005 | 20.715 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 212 | ASP | -1 | -0.858 | -0.930 | 22.284 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 213 | GLU | -1 | -0.913 | -0.972 | 23.124 | 0.315 | 0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 214 | TYR | 0 | -0.055 | -0.034 | 25.473 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 215 | GLN | 0 | 0.012 | 0.013 | 25.072 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 216 | SER | 0 | -0.028 | -0.003 | 28.224 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 217 | LYS | 1 | 0.897 | 0.945 | 27.636 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 218 | VAL | 0 | -0.006 | -0.001 | 31.177 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 219 | LYS | 1 | 0.971 | 0.996 | 30.925 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 220 | ARG | 1 | 1.012 | 1.027 | 34.338 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 221 | GLN | 0 | 0.019 | 0.020 | 36.178 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 222 | ILE | 0 | -0.050 | -0.026 | 36.738 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 223 | PHE | 0 | -0.032 | -0.049 | 35.466 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 224 | SER | 0 | 0.003 | -0.015 | 39.359 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 225 | GLY | 0 | 0.018 | 0.011 | 41.520 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 226 | TYR | 0 | -0.036 | 0.000 | 40.909 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 227 | GLN | 0 | -0.054 | -0.049 | 41.793 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 228 | SER | 0 | 0.059 | 0.020 | 45.719 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 229 | ASP | -1 | -0.855 | -0.899 | 47.365 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 230 | ILE | 0 | -0.050 | -0.018 | 47.718 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 231 | ASP | -1 | -0.877 | -0.930 | 45.949 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | C | 232 | THR | 0 | -0.061 | -0.055 | 49.512 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | C | 233 | HIS | 0 | -0.107 | -0.045 | 52.598 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | C | 234 | ASN | 0 | -0.024 | -0.013 | 50.591 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | C | 235 | ARG | 1 | 0.951 | 0.966 | 51.926 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | C | 236 | ILE | 0 | -0.033 | -0.019 | 54.486 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | C | 237 | LYS | 1 | 0.892 | 0.933 | 58.106 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | C | 238 | ASP | -1 | -0.866 | -0.923 | 55.287 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | C | 239 | GLU | -1 | -0.960 | -0.963 | 56.224 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | C | 240 | LEU | 0 | -0.113 | -0.040 | 58.912 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |