Biological Structure Resource | NDB | Structure Finder | à la mode | mmCIF

À La Mode Component ID: thy

Component name: (view abbreviated component mmCIF) (view full component mmCIF)

thymine

Component description:

Model constructed for thymine with an N1-glycosidic linkage.

Component formula and formula weight:

H5 C6 N2 O2 ( 137.1 grams/mole)

Modeled component diagram:


Modeled component formula and formula weight:

C6 N2 O2 ( 132.1 grams/mole)

Component canonical SMILES string [Created by the Daylight Toolkit]:

Cc1cn(C)c(=O)[nH]c1=O

Component exchange SMILES string:

N1(C(N(C(C(=C1[H])C([H])([H])[H])=O)[H])=O)C([H])([H])[H]

Component constructed from 83 CSD V. 512 structures (CSD ID[Molecule No.])

bicrua[1]bicrua[2]bicrua01[1]bicrua01[2]bolved[1]cezfoc[1]
clqunb10[1]dayvoo[1]dejsam[1]doxziz[1]duksor[1]duxxez[1]
firpol[1]fixgau[1]fixgau[2]fixgau01[1]fixgau01[2]fixgau03[1]
fixgau03[2]fixgau04[1]fixgau04[2]fixgau05[1]fixgau05[2]gebtem[1]
gexxiq[1]gexxiq01[1]heknoa[1]kagzex[1]kasvef[1]katyin[1]
katyin[2]kexkih[1]kexkih[2]kezruc[1]kezruc[2]kicjel[1]
kinhiy[1]kitsov[1]kogbir[1]kotcol[1]kunnem[1]kuthow[1]
kuzxei[1]ledran[1]ledrer[1]lepvor[1]letjez[1]methym01[1]
naglem[1]palwuz[1]palwuz[2]pizniv[1]soddeu[1]sosbil[1]
sulria[1]tektos[1]thydin01[1]tpataa[1]trfutm[1]tymcxa[1]
tymcxa[2]vabvid[1]vevbut[1]vevbut[2]vevbut01[1]vevbut01[2]
vevbut01[3]vevbut01[4]viggex[1]vikfea[1]welmef[1]welmef[2]
yavkub[1]yogyey[1]yogyic[1]yuyyia[1]zabsaw[1]zasquf[1]
zasram[1]zexwii[1]zexwii[2]zugric[1]zugric[2]

Bond Distance Table:


Atom 1 Atom 2 Distance E.S.D. Type
N1 C2 1.3773 0.0086 sing
C2 N3 1.3734 0.0079 sing
N3 C4 1.3821 0.0084 sing
C4 C5 1.4446 0.0088 sing
C5 C6 1.3390 0.0064 doub
C6 N1 1.3796 0.0072 sing
C2 O2 1.2190 0.0079 doub
C4 O4 1.2282 0.0090 doub
C5 C5M 1.4977 0.0071 sing
N3 H3 n.a. n.a. sing
C6 H6 n.a. n.a. sing
N1 C1* 1.4721 0.0133 sing
C5M HC5MA n.a. n.a. sing
C5M HC5MB n.a. n.a. sing
C5M HC5MC n.a. n.a. sing

View histograms of bond distance distributions.

Bond Angle Table:


Atom 1 Atom 2 Atom 3 Angle E.S.D.
C6 N1 C2 121.22 0.51
N1 C2 N3 114.54 0.59
C2 N3 C4 127.22 0.53
N3 C4 C5 115.18 0.61
C4 C5 C6 118.08 0.51
C5 C6 N1 123.63 0.56
N1 C2 O2 123.17 0.83
N3 C2 O2 122.28 0.63
N3 C4 O4 119.75 0.65
C5 C4 O4 125.07 0.74
C4 C5 C5M 118.99 0.57
C6 C5 C5M 122.91 0.60
C6 N1 C1* 120.52 1.53
C2 N1 C1* 118.11 1.57

View histograms of bond angle distributions.

Torsion Angle Table:


Atom 1 Atom 2 Atom 3 Atom 4 Angle E.S.D.
N1 C2 N3 C4 359.98 2.89
C2 N3 C4 C5 359.70 3.25
N3 C4 C5 C6 0.30 2.52
C4 C5 C6 N1 359.99 1.37
C5 C6 N1 C2 359.67 2.27
C6 N1 C2 N3 0.33 2.74
C6 N1 C2 O2 180.25 2.64
C4 N3 C2 O2 180.07 2.74
C2 N3 C4 O4 179.80 2.86
C6 C5 C4 O4 180.19 2.21
O4 C4 C5 C5M 0.26 2.16
N3 C4 C5 C5M 180.37 2.35
N1 C6 C5 C5M 179.92 1.53
C5 C6 N1 C1* 180.14 4.18
O2 C2 N1 C1* 359.79 3.90
N3 C2 N1 C1* 179.88 3.85

View histograms of torsion angle distributions.
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