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À La Mode Component ID: deoxyribose_C3endo_O3H_O5P_+sc

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

1'-amino-2'-deoxyribose

Component description:

Model constructed for 1'-amino-2'-deoxyribose 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 O3 ( 129.1 grams/mole)

Modeled component diagram:


Modeled component formula and formula weight:

C5 N1 O3 ( 122.1 grams/mole)

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

NC1CC(O)C(CO)O1

Component exchange SMILES string:

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

This model built from À La Mode sub-components:

Subcomponent ID Subcomponent Type Details
deoxyribose_C3endo sugar Ł'-amino-deoxyribose in the C3'-endo conformation.
deoxyribose_C3endo_O3H sugar C3*-O3* bond geometry.
deoxyribose_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 0.03
C3* C2* C4* O3* -2.5 0.10
C4* C3* O4* C5* 2.5 0.04


Chiral Center Neighbor U Neighbor V Neighbor W Out-of-plane Angle [2] Out-of-plane Angle E.S.D.
C1* O4* C2* N 54.2 0.78
C3* C2* C4* O3* -51.7 2.87
C4* C3* O4* C5* 51.0 1.10

[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* 1.5192 0.0069 sing
C2* C3* 1.5186 0.0110 sing
C3* C4* 1.5212 0.0081 sing
C4* O4* 1.4492 0.0060 sing
O4* C1* 1.4123 0.0065 sing
C3* O3* 1.4178 0.0067 sing
C4* C5* 1.5120 0.0117 sing
C5* O5* 1.4379 0.0099 sing
C1* N 1.4943 0.0113 sing
C1* HA1* n.a. n.a. sing
C2* HA2* n.a. n.a. sing
C2* HB2* n.a. n.a. sing
C3* HA3* n.a. n.a. sing
C4* HA4* n.a. n.a. sing
C5* HA5* n.a. n.a. sing
C5* HB5* n.a. n.a. sing


Bond Angle Table:


Atom 1 Atom 2 Atom 3 Angle E.S.D.
C1* C2* C3* 102.80 0.51
C2* C3* C4* 102.26 0.57
C3* C4* O4* 104.79 0.66
C4* O4* C1* 110.21 0.61
O4* C1* C2* 107.01 0.63
C2* C3* O3* 112.71 2.71
C4* C3* O3* 112.97 1.78
C5* C4* C3* 115.64 1.14
C5* C4* O4* 109.36 0.32
O5* C5* C4* 111.28 1.54
N C1* O4* 108.16 0.80
N C1* C2* 112.47 1.07


Torsion Angle Table:


Atom 1 Atom 2 Atom 3 Atom 4 Angle E.S.D.
C4* O4* C1* C2* 4.17 7.07
O4* C1* C2* C3* 335.52 5.35
C1* C2* C3* C4* 34.16 2.49
C2* C3* C4* O4* 327.62 3.09
C3* C4* O4* C1* 18.00 6.18
C2* C3* C4* C5* 207.16 3.23
C3* C4* C5* O5* 52.19 4.95
O3* C3* C4* C5* 85.70 4.91
O4* C4* C3* O3* 206.16 5.02
C4* O4* C1* N 242.77 7.52
O4* C4* C5* O5* 293.22 4.75
C5* C4* O4* C1* 142.55 6.60
C1* C2* C3* O3* 155.80 4.77
C3* C2* C1* N 94.17 5.14

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