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

À La Mode Component ID: cyt_pro

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

protonated cytosine

Component description:

Model constructed for protonated cytosine with an N1-glycosidic linkage.

Component formula and formula weight:

H4 C5 N3 O1 ( 122.1 grams/mole)

Modeled component diagram:


Modeled component formula and formula weight:

C5 N3 O1 ( 118.1 grams/mole)

Component formal charge: 1


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

Cn1ccc(N)[nH+]c1=O

Component exchange SMILES string:

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

Component constructed from 21 CSD V. 512 structures (CSD ID[Molecule No.])

aracyp[1]arfcyt10[1]bzcytn[1]cyticl[1]cytidn[1]dinyii10[1]
dinyii10[2]docytc[1]jibdih[1]kogbox[1]kogbox01[1]mectsi[1]
mectsi[2]poggat[1]poggat[2]poggat[3]poggat[4]vuymad[1]
xfurcc10[1]yidkif[1]yidkif[2]

Bond Distance Table:


Atom 1 Atom 2 Distance E.S.D. Type
N1 C2 1.3798 0.0117 sing
C2 N3 1.3755 0.0161 sing
N3 C4 1.3515 0.0082 doub
C4 C5 1.4131 0.0072 sing
C5 C6 1.3401 0.0101 doub
C6 N1 1.3673 0.0094 sing
C2 O2 1.2171 0.0128 doub
C4 N4 1.3140 0.0127 sing
N1 C1* 1.4771 0.0215 sing
N4 H4A n.a. n.a. sing
N4 H4B n.a. n.a. sing
C5 H5 n.a. n.a. sing
C6 H6 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 121.38 0.82
N1 C2 N3 115.77 1.99
C2 N3 C4 124.27 2.11
N3 C4 C5 118.03 1.57
C4 C5 C6 118.65 0.86
C5 C6 N1 121.81 0.84
N1 C2 O2 122.57 1.72
N3 C2 O2 121.64 0.79
N3 C4 N4 119.01 0.99
C5 C4 N4 122.95 1.23
C6 N1 C1* 120.88 1.03
C2 N1 C1* 117.57 1.45

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 1.42 2.24
C2 N3 C4 C5 358.63 2.10
N3 C4 C5 C6 0.80 2.11
C4 C5 C6 N1 359.60 1.10
C5 C6 N1 C2 0.48 1.66
C6 N1 C2 N3 359.07 2.58
C6 N1 C2 O2 178.69 2.43
C4 N3 C2 O2 181.78 2.33
C2 N3 C4 N4 178.99 2.06
C6 C5 C4 N4 180.44 2.01
C5 C6 N1 C1* 178.48 4.54
O2 C2 N1 C1* 0.67 4.19
N3 C2 N1 C1* 181.04 4.67

View histograms of torsion angle distributions.
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