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

À La Mode Component ID: ribose_C3endo_O3H_O5P_+sc

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

1'-amino-ribose

Component description:

Model constructed for 1'-amino-ribose in the C3'-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_C3endo sugar Ł'-amino-ribose in the C3'-endo conformation.
ribose_C3endo_O3H sugar C3*-O3* bond geometry.
ribose_O5P 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 2.5 0.06
C2* C1* C3* O2* -2.8 0.05
C3* C2* C4* O3* -2.5 0.08
C4* C3* O4* C5* 2.5 0.06


Chiral Center Neighbor U Neighbor V Neighbor W Out-of-plane Angle [2] Out-of-plane Angle E.S.D.
C1* O4* C2* N 54.0 1.12
C2* C1* C3* O2* -58.7 1.70
C3* C2* C4* O3* -51.2 2.20
C4* C3* O4* C5* 50.8 1.30

[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* 1.5301 0.0131 sing
C1* HA1* 1.5160 0.0080 sing
C2* C3* 1.5271 0.0074 sing
C2* HA2* 1.5160 0.0080 sing
C3* C4* 1.5196 0.0121 sing
C3* HA3* 1.5160 0.0080 sing
C4* O4* 1.4489 0.0094 sing
C4* HA4* 1.5160 0.0080 sing
O4* C1* 1.4076 0.0078 sing
C2* O2* 1.4201 0.0094 sing
O2* HAO2* 1.4350 0.0130 sing
C3* O3* 1.4132 0.0049 sing
C5* C4* 1.5065 0.0081 sing
C5* O5* 1.4439 0.0100 sing
C5* HA5* 1.5160 0.0080 sing
C5* HB5* 1.5160 0.0080 sing
C1* N 1.4826 0.0120 sing


Bond Angle Table:


Atom 1 Atom 2 Atom 3 Angle E.S.D.
C1* C2* C3* 101.03 0.80
C2* C3* C4* 102.21 1.01
C3* C4* O4* 104.10 0.66
C4* O4* C1* 109.97 0.70
O4* C1* C2* 107.59 0.65
C1* C2* O2* 108.24 1.82
C3* C2* O2* 110.24 1.94
C2* C3* O3* 113.59 1.53
C4* C3* O3* 112.68 1.76
C5* C4* C3* 115.79 1.39
C5* C4* O4* 109.78 1.07
O5* C5* C4* 110.66 2.05
N C1* O4* 108.59 0.74
N C1* C2* 111.99 1.13


Torsion Angle Table:


Atom 1 Atom 2 Atom 3 Atom 4 Angle E.S.D.
C4* O4* C1* C2* 3.53 4.87
O4* C1* C2* C3* 334.37 3.95
C1* C2* C3* C4* 36.70 2.48
C2* C3* C4* O4* 324.20 2.68
C3* C4* O4* C1* 20.45 4.27
C2* C3* C4* C5* 203.61 2.82
C3* C4* C5* O5* 52.19 4.95
O3* C3* C4* C5* 81.27 3.80
O4* C4* C3* O3* 201.87 3.83
C4* O4* C1* N 242.12 5.64
O4* C4* C5* O5* 293.22 4.75
C5* C4* O4* C1* 145.01 4.68
C1* C2* C3* O3* 158.39 3.34
C3* C2* C1* N 93.63 4.24
O3* C3* C2* O2* 44.06 3.47

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

ndbadmin@ndbserver.rutgers.edu
The Nucleic Acid Database Project
Rutgers, The State University of New Jersey