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À La Mode Component ID: deoxyribose_C2endo_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 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 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_C2endo sugar Ł'-amino-deoxyribose in the C2'-endo conformation.
deoxyribose_C2endo_O3H sugar C3*-O3* bond geometry.
deoxyribose_C2endo_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 2.4 0.07
C3* C2* C4* O3* -2.7 0.07
C4* C3* O4* C5* 2.5 0.11


Chiral Center Neighbor U Neighbor V Neighbor W Out-of-plane Angle [2] Out-of-plane Angle E.S.D.
C1* O4* C2* N 53.0 1.49
C3* C2* C4* O3* -56.8 1.92
C4* C3* O4* C5* 51.9 2.29

[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* 1.5177 0.0085 sing
C2* C3* 1.5139 0.0086 sing
C3* C4* 1.5250 0.0126 sing
C4* O4* 1.4458 0.0107 sing
O4* C1* 1.4177 0.0122 sing
C3* O3* 1.4276 0.0101 sing
C4* C5* 1.5158 0.0282 sing
C5* O5* 1.4377 0.0104 sing
C1* N 1.4684 0.0182 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* 102.17 1.20
C2* C3* C4* 103.13 0.98
C3* C4* O4* 105.99 0.69
C4* O4* C1* 109.90 0.81
O4* C1* C2* 105.99 0.96
C2* C3* O3* 109.67 2.25
C4* C3* O3* 110.06 2.19
C5* C4* C3* 114.33 1.87
C5* C4* O4* 109.15 1.77
O5* C5* C4* 109.98 2.10
N C1* O4* 108.07 0.65
N C1* C2* 114.19 1.25


Torsion Angle Table:


Atom 1 Atom 2 Atom 3 Atom 4 Angle E.S.D.
C4* O4* C1* C2* 341.21 6.45
O4* C1* C2* C3* 32.80 4.56
C1* C2* C3* C4* 326.41 3.22
C2* C3* C4* O4* 23.45 4.79
C3* C4* O4* C1* 356.93 6.58
C2* C3* C4* C5* 263.15 5.23
C3* C4* C5* O5* 52.19 4.95
O3* C3* C4* C5* 146.20 5.54
O4* C4* C3* O3* 266.50 5.07
C4* O4* C1* N 218.39 6.55
O4* C4* C5* O5* 293.22 4.75
C5* C4* O4* C1* 120.54 7.03
C1* C2* C3* O3* 83.64 3.71
C3* C2* C1* N 151.66 4.67

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