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À La Mode Component ID: ribose_C2endo_O3H_O5H_+sc

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

1'-amino-ribose

Component description:

Model constructed for 1'-amino-ribose in the C2'-endo conformation. the gamma torsion (synclinal), the corresponding O4*-C4*-C5*-O5* torsion, and the C3*-O3* and C5*-O5* bond geometries are inserted from other models.

Component formula and formula weight:

H7 C5 N1 O4 ( 145.1 grams/mole)

Modeled component diagram:


Modeled component formula and formula weight:

C5 N1 O4 ( 138.1 grams/mole)

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

NC1OC(CO)C(O)C1O

Component exchange SMILES string:

C1(C(C(C(C(O[H])([H])[H])(O1)[H])(O[H])[H])(O[H])[H])([H])N([H])[H]

This model built from À La Mode sub-components:

Subcomponent ID Subcomponent Type Details
ribose_C2endo sugar Ł'-amino-ribose in the C2'-endo conformation.
ribose_C2endo_O3H sugar C3*-O3* bond geometry.
ribose_C2endo_O5H sugar C5*-O5* bond geometry.
all_ribose_gamma_+sc sugar gamma torsion geometry.
all_ribose_gamma_+sc sugar O4*-C4*-C5*-O5* torsion geometry.


Stereochemical Features Table:


Chiral Center Neighbor U Neighbor V Neighbor W Volume [1] Volume E.S.D.
C1* O4* C2* N 2.4 0.08
C2* C1* C3* O2* -2.5 0.09
C3* C2* C4* O3* -2.7 0.05
C4* C3* O4* C5* 2.5 0.07


Chiral Center Neighbor U Neighbor V Neighbor W Out-of-plane Angle [2] Out-of-plane Angle E.S.D.
C1* O4* C2* N 52.8 1.92
C2* C1* C3* O2* -51.1 2.20
C3* C2* C4* O3* -57.8 1.38
C4* C3* O4* C5* 50.9 1.82

[1] Neighboring atoms U, V and W form vectors with the chiral center. The chiral volume is computed as (UxV)*W
[2] The out-of-plane angle is computed as 90.0 - ACOS(((UxV)*W)/(|UxV||W|))

Bond Distance Table:


Atom 1 Atom 2 Distance E.S.D. Type
C1* C2* 1.5260 0.0113 sing
C1* HA1* 1.5160 0.0080 sing
C2* C3* 1.5255 0.0110 sing
C2* HA2* 1.5160 0.0080 sing
C3* C4* 1.5246 0.0129 sing
C3* HA3* 1.5160 0.0080 sing
C4* O4* 1.4539 0.0076 sing
C4* HA4* 1.5160 0.0080 sing
O4* C1* 1.4135 0.0091 sing
C2* O2* 1.4113 0.0124 sing
O2* HAO2* 1.4350 0.0130 sing
C3* O3* 1.4216 0.0072 sing
C5* C4* 1.5106 0.0103 sing
C5* O5* 1.4228 0.0149 sing
C5* HA5* 1.5160 0.0080 sing
C5* HB5* 1.5160 0.0080 sing
C1* N 1.4610 0.0129 sing


Bond Angle Table:


Atom 1 Atom 2 Atom 3 Angle E.S.D.
C1* C2* C3* 101.27 0.95
C2* C3* C4* 102.50 0.75
C3* C4* O4* 106.07 0.61
C4* O4* C1* 109.60 0.69
O4* C1* C2* 105.67 0.83
C1* C2* O2* 112.23 2.08
C3* C2* O2* 114.61 1.81
C2* C3* O3* 109.34 2.28
C4* C3* O3* 109.56 1.96
C5* C4* C3* 115.27 1.39
C5* C4* O4* 109.16 1.17
O5* C5* C4* 111.20 1.95
N C1* O4* 108.10 0.87
N C1* C2* 114.51 1.73


Torsion Angle Table:


Atom 1 Atom 2 Atom 3 Atom 4 Angle E.S.D.
C4* O4* C1* C2* 338.59 5.62
O4* C1* C2* C3* 35.91 3.42
C1* C2* C3* C4* 324.07 2.42
C2* C3* C4* O4* 24.52 4.40
C3* C4* O4* C1* 357.83 6.08
C2* C3* C4* C5* 263.59 4.21
C3* C4* C5* O5* 52.19 4.95
O3* C3* C4* C5* 147.56 4.89
O4* C4* C3* O3* 268.49 5.15
C4* O4* C1* N 215.55 6.31
O4* C4* C5* O5* 293.22 4.75
C5* C4* O4* C1* 122.63 6.13
C1* C2* C3* O3* 80.26 3.14
C3* C2* C1* N 154.79 3.69
O3* C3* C2* O2* 319.19 3.93

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