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À La Mode Component ID: Cpro_deoxyriboseC3endo_O3H_O5P_anti_+sc

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

protonated 2'-deoxycytidine-5'-phosphate

Component description:

Model constructed for protonated 2'-deoxycytidine-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 C9 N3 O7 P1 ( 304.2 grams/mole)

Modeled component diagram:


Modeled component formula and formula weight:

C9 N3 O7 P1 ( 293.1 grams/mole)

Component formal charge: -1


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

Nc1ccn(C2CC(O)C(COP(=O)([O-])[O-])O2)c(=O)[nH+]1

Component exchange SMILES string:

N1(C([N+](=C(C(=C1[H])[H])N([H])[H])[H])=O)C2(C(C(C(C(OP(=O)([O-])[O-])([H])[H])(O2)[H])(O[H])[H])([H])[H])[H]

This model built from À La Mode sub-components:

Subcomponent ID Subcomponent Type Details
cyt_pro base Model constructed for protonated cytosine with an N1-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 1.3798 0.0117 sing
C2 N3 1.3755 0.0161 sing
N3 C4 1.3515 0.0082 doub
C4 C5 1.4131 0.0072 sing
C5 C6 1.3401 0.0101 doub
C6 N1 1.3673 0.0094 sing
C2 O2 1.2171 0.0128 doub
C4 N4 1.3140 0.0127 sing
N4 H4A n.a. n.a. sing
N4 H4B n.a. n.a. sing
C5 H5 n.a. n.a. sing
C6 H6 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* N1 1.4947 0.0031 sing
P O5* 1.5930 0.0100 sing


Bond Angle Table:


Atom 1 Atom 2 Atom 3 Angle E.S.D.
C6 N1 C2 121.38 0.82
N1 C2 N3 115.77 1.99
C2 N3 C4 124.27 2.11
N3 C4 C5 118.03 1.57
C4 C5 C6 118.65 0.86
C5 C6 N1 121.81 0.84
N1 C2 O2 122.57 1.72
N3 C2 O2 121.64 0.79
N3 C4 N4 119.01 0.99
C5 C4 N4 122.95 1.23
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 1.42 2.24
C2 N3 C4 C5 358.63 2.10
N3 C4 C5 C6 0.80 2.11
C4 C5 C6 N1 359.60 1.10
C5 C6 N1 C2 0.48 1.66
C6 N1 C2 N3 359.07 2.58
C6 N1 C2 O2 178.69 2.43
C4 N3 C2 O2 181.78 2.33
C2 N3 C4 N4 178.99 2.06
C6 C5 C4 N4 180.44 2.01
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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