FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-04-05
All entries: 36946
Number of unique PDB entries: 7781
FMODB ID: R5M98
Calculation Name: 1XCT-P-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1XCT
Chain ID: P
UniProt ID: P26661
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.
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 | 30 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -91201.386514 |
|---|---|
| FMO2-HF: Nuclear repulsion | 80131.49375 |
| FMO2-HF: Total energy | -11069.892764 |
| FMO2-MP2: Total energy | -11103.155701 |
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(P:16:ASN)
Summations of interaction energy for
fragment #1(P:16:ASN)
| 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. |
| -6.383 | -3.704 | -0.012 | -1.049 | -1.618 | 0.004 |
Interaction energy analysis for fragmet #1(P:16:ASN)
| 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 | P | 18 | ARG | 1 | 0.968 | 0.956 | 3.826 | -6.217 | -4.242 | -0.009 | -0.984 | -0.983 | 0.004 |
| 4 | P | 19 | PRO | 0 | -0.009 | 0.005 | 5.169 | -0.999 | -0.881 | -0.001 | -0.009 | -0.108 | 0.000 |
| 5 | P | 20 | GLN | 0 | 0.053 | 0.055 | 5.264 | -1.029 | -1.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | P | 21 | ASP | -1 | -0.922 | -0.963 | 6.098 | 5.620 | 5.620 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | P | 22 | VAL | 0 | 0.023 | 0.004 | 4.141 | 2.941 | 3.304 | 0.000 | -0.041 | -0.321 | 0.000 |
| 8 | P | 23 | LYS | 1 | 0.924 | 0.958 | 5.936 | -4.051 | -4.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | P | 24 | PHE | 0 | 0.010 | 0.006 | 7.258 | -0.468 | -0.468 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | P | 25 | PRO | 0 | 0.053 | 0.057 | 8.269 | -0.316 | -0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | P | 26 | GLY | 0 | -0.016 | -0.017 | 8.047 | 0.711 | 0.711 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | P | 27 | GLY | 0 | 0.007 | -0.018 | 8.201 | -0.356 | -0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | P | 28 | GLY | 0 | 0.006 | 0.002 | 8.551 | -0.208 | -0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | P | 29 | GLN | 0 | 0.024 | 0.027 | 7.892 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | P | 30 | ILE | 0 | -0.044 | -0.019 | 5.635 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | P | 31 | VAL | 0 | 0.046 | 0.020 | 4.369 | -0.662 | -0.594 | -0.001 | -0.007 | -0.060 | 0.000 |
| 17 | P | 32 | GLY | 0 | 0.061 | 0.023 | 5.229 | 0.234 | 0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | P | 33 | GLY | 0 | 0.005 | -0.008 | 7.785 | 0.396 | 0.396 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | P | 34 | VAL | 0 | 0.018 | 0.009 | 8.720 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | P | 35 | TYR | 0 | -0.015 | -0.006 | 4.945 | -0.082 | 0.073 | -0.001 | -0.008 | -0.146 | 0.000 |
| 21 | P | 36 | LEU | 0 | -0.063 | -0.014 | 9.056 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | P | 37 | LEU | 0 | 0.021 | 0.014 | 11.974 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | P | 38 | PRO | 0 | 0.005 | -0.006 | 15.208 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | P | 39 | ARG | 1 | 0.953 | 0.970 | 18.054 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | P | 40 | ARG | 1 | 0.997 | 0.989 | 19.018 | -0.447 | -0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | P | 41 | GLY | 0 | 0.000 | 0.007 | 18.541 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | P | 42 | PRO | 0 | 0.023 | 0.019 | 18.037 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | P | 43 | ARG | 1 | 0.876 | 0.936 | 11.660 | -1.303 | -1.303 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | P | 44 | LEU | 0 | 0.013 | 0.010 | 12.712 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | P | 45 | GLY | 0 | 0.027 | 0.023 | 12.583 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |