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: M38VZ
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 | OptH |
| 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 | -175278.962448 |
|---|---|
| FMO2-HF: Nuclear repulsion | 156753.807739 |
| FMO2-HF: Total energy | -18525.154709 |
| FMO2-MP2: Total energy | -18579.503163 |
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. |
| -12.561 | -8.304 | 0.319 | -1.72 | -2.858 | 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 | 0.028 | 0.020 | 3.570 | -1.191 | 1.039 | 0.024 | -0.895 | -1.359 | 0.005 |
| 4 | C | 199 | CYS | 0 | -0.017 | -0.001 | 3.026 | -5.650 | -4.004 | 0.295 | -0.756 | -1.186 | 0.009 |
| 5 | C | 200 | ASP | -1 | -0.857 | -0.935 | 4.457 | -1.880 | -1.499 | 0.000 | -0.069 | -0.313 | 0.000 |
| 6 | C | 201 | GLU | -1 | -0.858 | -0.923 | 6.229 | 0.612 | 0.612 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 202 | LYS | 1 | 0.906 | 0.940 | 7.311 | -2.538 | -2.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 203 | THR | 0 | -0.006 | -0.008 | 8.483 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 204 | GLN | 0 | 0.062 | 0.041 | 10.814 | -0.327 | -0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 205 | SER | 0 | -0.059 | -0.007 | 12.056 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 206 | LEU | 0 | -0.049 | -0.040 | 11.842 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 207 | GLY | 0 | 0.016 | 0.005 | 14.695 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 208 | VAL | 0 | 0.008 | -0.002 | 16.536 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 209 | LYS | 1 | 0.974 | 1.012 | 17.323 | -0.697 | -0.697 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 210 | PHE | 0 | -0.059 | -0.024 | 18.965 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 211 | LEU | 0 | -0.027 | -0.021 | 20.718 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 212 | ASP | -1 | -0.824 | -0.916 | 22.166 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 213 | GLU | -1 | -0.921 | -0.978 | 23.646 | 0.306 | 0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 214 | TYR | 0 | -0.068 | -0.038 | 25.477 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 215 | GLN | 0 | 0.006 | 0.011 | 26.370 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 216 | SER | 0 | 0.001 | 0.014 | 28.526 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 217 | LYS | 1 | 0.939 | 0.959 | 28.328 | -0.262 | -0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 218 | VAL | 0 | -0.030 | -0.012 | 30.799 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 219 | LYS | 1 | 0.983 | 0.992 | 31.291 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 220 | ARG | 1 | 1.006 | 1.024 | 34.341 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 221 | GLN | 0 | 0.007 | -0.006 | 36.178 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 222 | ILE | 0 | -0.073 | -0.021 | 36.275 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 223 | PHE | 0 | -0.024 | -0.046 | 35.537 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 224 | SER | 0 | 0.005 | -0.007 | 39.634 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 225 | GLY | 0 | 0.030 | 0.021 | 41.557 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 226 | TYR | 0 | -0.034 | 0.005 | 41.155 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 227 | GLN | 0 | -0.003 | -0.082 | 41.652 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 228 | SER | 0 | 0.102 | 0.022 | 45.726 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 229 | ASP | -1 | -0.837 | -0.922 | 47.395 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 230 | ILE | 0 | -0.140 | 0.030 | 46.691 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 231 | ASP | -1 | -0.945 | -0.990 | 46.775 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | C | 232 | THR | 0 | -0.051 | -0.028 | 49.626 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | C | 233 | HIS | 0 | -0.106 | -0.048 | 52.711 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | C | 234 | ASN | 0 | -0.026 | 0.008 | 50.207 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | C | 235 | ARG | 1 | 0.984 | 0.987 | 52.597 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | C | 236 | ILE | 0 | -0.043 | -0.028 | 54.687 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | C | 237 | LYS | 1 | 0.890 | 0.931 | 58.254 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | C | 238 | ASP | -1 | -0.844 | -0.907 | 55.107 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | C | 239 | GLU | -1 | -0.926 | -0.956 | 56.579 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | C | 240 | LEU | 0 | -0.150 | -0.054 | 59.178 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |