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À La Mode Component ID: Apro_deoxyriboseC3endo_O3H_O5P_anti_+sc

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

protonated 2'-deoxyadenosine-5'-phosphate

Component description:

Model constructed for protonated 2'-deoxyadenosine-5'-phosphate from subcomponents for protonated base, sugar and phosphate. The sugar is deoxyribose in the C3'-endo conformation, and geometries for the gamma torsion angle (synclinal), the chi torsion angle (antiperiplanar), and the C3*-O3* and C5*-O5* bonds are inserted from other models.

Component formula and formula weight:

H11 C10 N5 O6 P1 ( 328.2 grams/mole)

Modeled component diagram:


Modeled component formula and formula weight:

C10 N5 O6 P1 ( 317.1 grams/mole)

Component formal charge: -1


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

Nc1[nH+]cnc2[N](=[CH]3CC(O)C(COP(=O)([O-])[O-])O3)C=Nc21

Component exchange SMILES string:

[N+]=1(C(=NC2=C(C1N([H])[H])N=C(N2(=C3(C(C(C(C(OP(=O)([O-])[O-])([H])[H])(O3)[H])(O[H])[H])([H])[H])[H])[H])[H])[H])[H]

This model built from À La Mode sub-components:

Subcomponent ID Subcomponent Type Details
ade_pro base Model constructed for protonated adenine with an N9-glycosidic linkage.
deoxyribose_C3endo_O3H_O5P_+sc sugar 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.
PO4 phosphate n.a.


Stereochemical Features Table:


Chiral Center Neighbor U Neighbor V Neighbor W Volume [1] Volume E.S.D.
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.
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
N1 C2 1.3577 0.0088 sing
C2 N3 1.3015 0.0058 doub
N3 C4 1.3554 0.0047 sing
C4 C5 1.3764 0.0076 doub
C5 C6 1.4018 0.0079 sing
C6 N1 1.3616 0.0089 doub
C5 N7 1.3786 0.0044 sing
N7 C8 1.3103 0.0055 doub
C8 N9 1.3715 0.0088 sing
N9 C4 1.3596 0.0066 sing
C6 N6 1.3150 0.0084 sing
C2 H2 n.a. n.a. sing
C8 H8 n.a. n.a. sing
N6 HA6 n.a. n.a. sing
N6 HB6 n.a. n.a. sing
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* 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
P O1P 1.4850 0.0170 doub
P O2P 1.4850 0.0170 sing
P O 1.4850 0.0170 sing
C1* N9 1.4722 0.0124 2
P O5* 1.5930 0.0100 sing


Bond Angle Table:


Atom 1 Atom 2 Atom 3 Angle E.S.D.
C6 N1 C2 122.88 0.94
N1 C2 N3 126.02 0.50
C2 N3 C4 111.70 0.42
N3 C4 C5 127.15 0.64
C4 C5 C6 118.31 0.76
C5 C6 N1 113.88 0.43
C4 C5 N7 110.96 0.34
C5 N7 C8 103.59 0.31
N7 C8 N9 113.61 0.40
C8 N9 C4 105.83 0.42
N9 C4 C5 106.00 0.50
N3 C4 N9 126.84 0.45
C6 C5 N7 130.71 0.57
N1 C6 N6 120.39 0.71
C5 C6 N6 125.72 0.52
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
O1P P O2P 119.60 1.50
O1P P O 108.30 3.20
O2P P O 107.30 3.20


Torsion Angle Table:


Atom 1 Atom 2 Atom 3 Atom 4 Angle E.S.D.
N1 C2 N3 C4 359.80 0.80
C2 N3 C4 C5 359.87 1.33
N3 C4 C5 C6 0.53 1.74
C4 C5 C6 N1 359.43 1.76
C5 C6 N1 C2 0.30 2.25
C6 N1 C2 N3 0.11 2.01
N9 C4 C5 N7 0.25 0.78
C4 C5 N7 C8 359.81 0.58
C5 N7 C8 N9 0.06 0.74
N7 C8 N9 C4 0.09 0.99
C8 N9 C4 C5 359.80 0.93
C2 N1 C6 N6 180.46 2.17
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
O4* C4* C5* O5* 293.22 4.75
C5* C4* O4* C1* 142.55 6.60
C1* C2* C3* O3* 155.80 4.77

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