FMODB ID: XR8Y8
Calculation Name: 3CS4-A-Xray14
Preferred Name: Vitamin D receptor
Target Type: SINGLE PROTEIN
Ligand Name: (1s,3r,5z,7e,14beta,17alpha)-17-[(2s,4s)-4-(2-hydroxy-2-methylpropyl)-2-methyltetrahydrofuran-2-yl]-9,10-secoandrosta-5,7,10-triene-1,3-diol
ligand 3-letter code: COV
PDB ID: 3CS4
Chain ID: A
ChEMBL ID: CHEMBL1977
UniProt ID: P11473
Base Structure: X-ray
Registration Date: 2018-03-13
Reference:
Modeling method
Optimization | Other |
---|---|
Restraint | OptH |
Protonation | Based on pKa values evaluated by PROPKA |
Complement | |
Water | Other |
Procedure | Manual calculation |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 414 |
LigandCharge | COV=0 |
Software | MIZUHO/ABINIT-MP 4.0(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -4231937.687255 |
---|---|
FMO2-HF: Nuclear repulsion | 4116053.265059 |
FMO2-HF: Total energy | -115884.422195 |
FMO2-MP2: Total energy | -116213.871386 |
3D Structure
Ligand structure
COV
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. |
-135.282 | -106.055 | 109.583 | -40.496 | -98.320 | -0.018 |
Interactive mode: IFIE and PIEDA for fragment #424(::)
Summations of interaction energy for
fragment #424(::)
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. |
Interaction energy analysis for fragmet #424(::)
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]. |
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