The N¹-(2'-deoxy­ribofuran­oside) of 3-iodo-5-nitro­indole: a universal nucleoside forming nitro-iodo inter­actions

The title compound [systematic name: 1-(2-de­oxy-[beta]-D-erythro-pentofuranos­yl)-3-iodo-5-nitro-1H-indole], C₁₃H₁₃IN₂O₅, exhibits an anti glycosylic bond conformation with a [chi] torsion angle of -114.9 (3)°. The furanose moiety shows a twisted C2'-endo sugar pucker (S-type), with P = 141.3° and [tau]_m = 40.3°. The orientation of the exocyclic C4'-C5' bond is +ap (gauche, trans), with a [gamma] torsion angle of 177.4 (2)°. The extended crystal structure is stabilized by hydrogen bonding and I...O contacts, as well as by stacking inter­actions. The O atoms of the nitro group act as acceptors, forming bifurcated hydrogen bonds within the ac plane. Additionally, the iodo substituent forms an inter­planar contact with an O atom of the nitro group, and another contact with the O atom of the 5'-hydr­oxy group of the sugar moiety within the ac plane is observed. These contacts can be considered as the structure-determining factors for the mol­ecular packing in the crystal structure.

S1. Comment

Universal nucleosides pair equally well with the canonical nucleic acid constituents. They are utilized to overcome sequence ambiguities in primer and probe design (Loakes, 2001). The most commonly used universal nucleoside is 2'-deoxyinosine, which forms base pairs with the four common DNA constituents (Topal & Fresco, 1976). The base pairing properties of the closely related 7-deaza-2'-deoxyinosine are similar to those of 2'-deoxyinosine (purine numbering) (Seela & Mittelbach, 1999). Another universal nucleoside strategy makes use of base stacking as the dominant stabilizing effect of duplex DNA. In this context, a series of hydrophobic compounds were synthesized and incorporated into DNA, e.g. 5-nitroindole 2'-deoxyribonucleoside, the regioisomeric 4-nitroindazole N¹– and N²- (2'-deoxyribonucleosides) as well as 3-nitropyrrole and 4-nitrobenzimidazole 2'-deoxyribonucleosides (Loakes & Brown, 1994; Loakes et al., 1995; Seela & Jawalekar, 2002). The introduction of substituents such as halogens or alkyl, alkenyl and alkynyl groups at position C-7 of the pyrrole ring of modified nucleobases improves duplex stability relative to the unsubstituted analogue. This effect has been attributed to an increased hydrophobicity and a favourable increase in π-stacking energy (Balow et al., 1998). In this context, the title compound 3-iodo-5-nitroindole 2'-deoxyribonucleoside (I) was synthesized and incorporated into duplex DNA (Leonard et al., 2005, 2009). Hybridization studies showed that the iodinated 5-nitroindole 2'-deoxyribonucleoside (I) stabilizes duplex DNA compared to the unsubstituted nucleoside when placed opposite to the four canonical DNA constituents (Leonard et al., 2005, 2009). Furthermore, the iodinated 5-nitroindole 2'-deoxyribonucleoside (I) can be employed as a precursor for Sonogashira cross-coupling reactions, leading to a broad spectrum of alkylated, alkenylated and alkynylated indole nucleosides for various purposes (Leonard et al., 2005, 2009).

As the conformational properties of (I) are unknown, a single-crystal X-ray analysis was performed. The conformation and molecular dimensions of (I) are compared with those of the closely related structures of 5-nitroindole 2'-deoxyribonucleoside, (IIa) (Loakes et al., 1997), and 5-nitroindole ribonucleoside, (IIb) (Harki et al., 2007), as well as with those of the similar 4-nitroindazole 2'-deoxyribonucleoside, (III) (Seela et al., 2004) (see scheme).

The three-dimensional structure of (I) is shown in Fig. 1 and selected geometric parameters are listed in Table 1. For purine nucleosides the orientation of the nucleobase relative to the sugar moiety is defined by the torsion angle χ (O4'—C1'—N9—C4) (purine numbering; IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983). The preferred conformation at the N-glycosylic bond of the common purine nucleosides is usually anti (Saenger, 1984). The corresponding torsion angle in (I), namely χ (O4'—C1'—N1—C7A), is -115.1 (3)°, reflecting an anti conformation. For the parent 5-nitroindole 2'-deoxyribonucleoside (IIa) an almost identical torsion angle was observed [χ = -113.3 (2)°; Loakes et al., 1997], indicating that the introduction of the 3-iodo substituent in (I) has no significant influence on the orientation of the indole moiety relative to the sugar residue. In contrast, (IIb) adopts a syn conformation at the glycosylic bond [χ = -83.0 (2)°; Harki et al., 2007]. For (III), the torsion angle is shifted towards the high-anti range [χ = -105.3 (2)°; Seela et al., 2004]. The glycosylic bond length (C1'—N1) of (I) is 1.450 (3) Å, which is close to that of (IIa) [1.444 (2) Å; Loakes et al., 1997], (IIb) [1.446 (2) Å; Harki et al., 2007] and (III) [1.449 (2) Å; Seela et al., 2004].

The most frequently observed sugar ring conformations of purine nucleosides are C2'-endo (`south' or S) and C3'-endo (`north' or N) (Arnott & Hukins, 1972). The 2'-deoxyribose ring of (I) shows an S-type sugar pucker with the pseudorotation phase angle P = 141.3° and a maximum puckering amplitude τ_m = 40.3°, which corresponds to an unsymmetrical twist of C1'-exo—C2'-endo (₁T²). This sugar pucker is consistent with the predominant conformation of (I) observed in solution (73% S). The value of sugar conformation was obtained from the vicinal ³J(H,H) coupling constants of the ¹H NMR signals determined in a DMSO/D₂O mixture, applying the program PSEUROT 6.3 (Van Wijk et al., 1999).

The sugar moieties of (IIa) and (III) also adopt an S conformation with P =176.2 (2)° and τ_m = 39.2 (1)° (²T₃; Loakes et al., 1997) and P = 192.6° and τ_m =37.5° (₃T²; Seela et al., 2004), respectively, while the 5-nitroindole ribonucleoside (IIb) displays a C3'-endo (³T₂) sugar pucker with P = 4.8 (2)° and τ_m = 35.5 (1)°, which corresponds to an N sugar conformation (Harki et al., 2007). The γ torsion angle (O5'—C5'—C4'—C3') characterizes the orientation of the exocyclic 5'-hydroxy group relative to the 2'-deoxyribose ring. In the crystal structure of (I), the C4'—C5' bond is in an antiperiplanar (+ap, gauche, trans) orientation with γ = 177.4 (2)°. For compounds (IIa) and (III) the torsion angles are -69.8 (2) and -91.5 (2)°, respectively; both correspond to a –sc (trans, gauche) conformation (Loakes et al., 1997; Seela et al., 2004). Conversely, (IIb) adopts a +sc (gauche, gauche) conformation around the exocyclic C4'—C5' bond (Harki et al., 2007).

The indole ring of (I) is essentially planar. The deviations of the ring atoms from the N1/C2/C3/C3A/C4–C7/C7A least-squares plane range from -0.018 (2) (for atom N1) to 0.016 (2) Å (for atom C3), with an r.m.s. deviation of 0.0102 Å. The iodo substituent and atom N5 of the nitro group lie on different sides of the heterocyclic plane [at distances of 0.016 (3) and -0.026 (3) Å, respectively].

Within the crystal structure of (I), the individual molecules stack in columns and form several intermolecular hydrogen bonds (Table 2 and Fig. 2). Atoms O51 and O52 of the nitro group function as the main H-atom acceptor sites, forming bifurcated hydrogen bonds within the ac plane (O3'—H3'B···O52ⁱ, O5'—H5'A···O52ⁱⁱ, C5'—H5'C···O51ⁱⁱⁱ and C2—H2···O51ⁱⁱⁱ; see Table 2 for symmetry codes and geometry). One more hydrogen bond is formed between the sugar moiety and the heterocycle of neighboring molecules (C4—H4···O3'^iv). Moreover, a contact between atoms I3 and O5'(-x + 3/2, y - 1/2, -z + 1) of the hydroxy group of the sugar moiety within the ac plane is observed, with an intermolecular distance of 3.087 (0) Å.

Previously, the intermolecular iodo–nitro interactions of aromatic compounds containing an I atom together with a nitro group were reported to be a determining factor for crystal structures and have been employed in crystal engineering (Allen et al., 1994; Kelly et al., 2002; Ranganathan & Pedireddi, 1998; McWilliam et al., 2001; Garden et al., 2002). Owing to δ+ polarizability, I atoms can form bifurcated symmetrical as well as unsymmetrical contacts with oxygen as electron acceptor (Allen et al., 1994; Messina et al., 2001). A similar phenomenon is found for the crystal structure of compound (I). An interplanar interaction between atom I3 and atom O51(-x + 1, -y + 2, z) of the nitro group exists, with a distance of 3.536 (0) Å, which is within the range of iodo–nitro contacts described in the literature (Ranganathan & Pedireddi, 1998; Kelly et al., 2002). The iodo–nitro contact of (I) constrains the molecules within each column into an alternating arrangement with a reverse orientation of the molecules. This is controlled by the interaction of atoms I3 and O51. In the crystal structure of the parent compound (IIa), which lacks the iodo substituent, the nitro groups are stacked within a column (Loakes et al., 1997).

Related literature

For related literature, see: Allen et al. (1994); Arnott & Hukins (1972); Garden et al. (2002); Harki et al. (2007); Kelly et al. (2002); Leonard et al. (2005, 2009); Loakes (2001); Loakes & Brown (1994); Loakes et al. (1995, 1997); McWilliam et al. (2001); Ranganathan & Pedireddi (1998); Saenger (1984); Seela & Jawalekar (2002); Seela & Mittelbach (1999); Seela et al. (2004); Topal & Fresco (1976); Van Wijk, Haasnoot, de Leeuw, Huckriede, Westra Hoekzema & Altona (1999).

S2. Experimental

Compound (I) was synthesized as previously reported (Leonard et al., 2005, 2009). Slow crystallization from methanol afforded (I) as yellow needles [plates according to CIF] (decays above 413 K). For the diffraction experiment, a single crystal was mounted on a MiTeGen MicroMounts fibre in a thin smear of oil.

S3. Refinement

All H atoms were found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, H atoms bound to C atoms were placed in geometrically idealized positions (C—H = 0.93–0.98 Å; AFIX 43) and constrained to ride on their parent atoms with U_iso(H) values of 1.2U_eq(C). The OH groups were refined as rigid groups allowed to rotate but not tip (AFIX 147), with O—H distances of 0.82 Å and U_iso(H) values of 1.5U_eq(O).

Computing details

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXTL (Release 5.1; Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Release 5.1; Sheldrick, 2008); molecular graphics: SHELXTL (Release 5.1; Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Release 5.1; Sheldrick, 2008) and PLATON (Spek, 2009).

Figures

	Fig. 1. A perspective view of the nucleoside (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary size.
	Fig. 2. The crystal packing of (I), showing the intermolecular hydrogen-bonding network (projection parallel to the b axis). For the sake of clarity, H atoms not involved in the hydrogen-bonding network have been omitted

1-(2-deoxy-β-D-erythro-pentofuranosyl)-3-iodo-5-nitro-1H-indole

Crystal data

C13H13IN2O5	F(000) = 792
Mr = 404.15	Dx = 1.973 Mg m^−3
Orthorhombic, P21212	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2 2ab	Cell parameters from 9917 reflections
a = 17.549 (3) Å	θ = 2.2–26.3°
b = 7.0981 (10) Å	µ = 2.38 mm^−1
c = 10.9242 (19) Å	T = 100 K
V = 1360.8 (4) Å^3	Plate, yellow
Z = 4	0.10 × 0.10 × 0.03 mm

Data collection

Bruker APEXII CCD area-detector diffractometer	2791 independent reflections
Radiation source: fine-focus sealed tube	2678 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.044
ϕ and ω scans	θmax = 26.4°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −21→21
Tmin = 0.797, Tmax = 0.932	k = −8→8
37202 measured reflections	l = −13→13

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.017	H-atom parameters constrained
wR(F^2) = 0.034	w = 1/[σ^2(Fo^2) + (0.0147P)^2 + 0.4545P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max = 0.001
2791 reflections	Δρmax = 0.56 e Å^−3
192 parameters	Δρmin = −0.44 e Å^−3
0 restraints	Absolute structure: Flack (1983), 1163 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.013 (15)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
N1	0.56981 (10)	0.7680 (3)	0.62900 (17)	0.0125 (4)
C2	0.63823 (13)	0.7749 (3)	0.5649 (2)	0.0139 (5)
H2	0.6863	0.7834	0.6004	0.017*
C3	0.62439 (12)	0.7675 (4)	0.44308 (19)	0.0120 (5)
I3	0.704990 (8)	0.768390 (19)	0.304512 (13)	0.01372 (5)
C3A	0.54332 (12)	0.7542 (3)	0.42667 (19)	0.0110 (5)
C4	0.49620 (12)	0.7406 (3)	0.32481 (19)	0.0120 (5)
H4	0.5160	0.7374	0.2458	0.014*
C5	0.41833 (12)	0.7319 (3)	0.34631 (19)	0.0115 (5)
N5	0.36727 (11)	0.7166 (3)	0.24236 (18)	0.0131 (4)
O51	0.29870 (9)	0.7388 (2)	0.25733 (14)	0.0176 (3)
O52	0.39535 (10)	0.6816 (3)	0.13993 (16)	0.0180 (4)
C6	0.38607 (13)	0.7381 (4)	0.46373 (19)	0.0132 (5)
H6	0.3334	0.7335	0.4729	0.016*
C7	0.43190 (12)	0.7509 (4)	0.5649 (2)	0.0135 (5)
H7	0.4113	0.7549	0.6432	0.016*
C7A	0.51090 (13)	0.7578 (4)	0.54632 (19)	0.0120 (5)
C1'	0.56259 (13)	0.7764 (4)	0.7611 (2)	0.0125 (5)
H1'A	0.5089	0.7631	0.7843	0.015*
C2'	0.61044 (15)	0.6329 (3)	0.8303 (2)	0.0145 (6)
H2'A	0.5854	0.5111	0.8337	0.017*
H2'B	0.6604	0.6182	0.7936	0.017*
C3'	0.61555 (14)	0.7229 (4)	0.9563 (2)	0.0135 (5)
H3'A	0.6633	0.6890	0.9973	0.016*
O3'	0.55144 (11)	0.6781 (3)	1.03051 (17)	0.0228 (4)
H3'B	0.5572	0.5732	1.0606	0.034*
C4'	0.61242 (14)	0.9347 (3)	0.9285 (2)	0.0114 (5)
H4'A	0.5740	0.9946	0.9807	0.014*
C5'	0.68848 (13)	1.0310 (3)	0.9468 (2)	0.0134 (5)
H5'B	0.7037	1.0182	1.0318	0.016*
H5'C	0.7266	0.9689	0.8967	0.016*
O5'	0.68599 (9)	1.2270 (2)	0.91558 (14)	0.0173 (4)
H5'A	0.6638	1.2854	0.9696	0.026*
O4'	0.59064 (9)	0.9541 (2)	0.80168 (17)	0.0149 (4)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0098 (10)	0.0196 (12)	0.0082 (10)	−0.0019 (10)	−0.0020 (8)	−0.0018 (11)
C2	0.0088 (12)	0.0182 (13)	0.0147 (13)	0.0012 (10)	−0.0010 (9)	−0.0013 (11)
C3	0.0102 (11)	0.0134 (12)	0.0124 (12)	0.0001 (11)	−0.0004 (9)	0.0021 (11)
I3	0.01145 (8)	0.01801 (7)	0.01168 (8)	−0.00061 (6)	0.00220 (7)	−0.00049 (6)
C3A	0.0129 (12)	0.0093 (12)	0.0108 (12)	0.0002 (12)	−0.0002 (9)	0.0015 (11)
C4	0.0170 (12)	0.0102 (11)	0.0089 (12)	0.0014 (10)	0.0011 (9)	−0.0014 (11)
C5	0.0131 (11)	0.0130 (12)	0.0084 (11)	−0.0004 (10)	−0.0023 (9)	−0.0013 (10)
N5	0.0143 (11)	0.0090 (10)	0.0161 (10)	0.0009 (9)	−0.0031 (9)	−0.0008 (8)
O51	0.0089 (8)	0.0240 (8)	0.0198 (8)	0.0022 (10)	−0.0014 (7)	−0.0032 (7)
O52	0.0170 (10)	0.0278 (11)	0.0092 (9)	0.0028 (8)	−0.0001 (8)	−0.0037 (7)
C6	0.0088 (11)	0.0149 (13)	0.0160 (12)	0.0016 (12)	0.0017 (10)	−0.0017 (12)
C7	0.0138 (12)	0.0162 (12)	0.0104 (12)	0.0009 (11)	0.0023 (9)	−0.0011 (11)
C7A	0.0140 (12)	0.0104 (12)	0.0115 (12)	−0.0006 (12)	−0.0016 (9)	−0.0003 (11)
C1'	0.0114 (12)	0.0166 (13)	0.0096 (12)	0.0017 (12)	0.0016 (9)	−0.0026 (11)
C2'	0.0155 (14)	0.0135 (12)	0.0145 (16)	−0.0003 (10)	0.0022 (11)	0.0003 (9)
C3'	0.0120 (12)	0.0174 (14)	0.0111 (12)	−0.0041 (12)	−0.0007 (10)	0.0032 (11)
O3'	0.0312 (12)	0.0204 (10)	0.0168 (10)	−0.0054 (8)	0.0124 (9)	0.0021 (8)
C4'	0.0103 (13)	0.0149 (12)	0.0090 (13)	0.0022 (10)	0.0002 (11)	0.0000 (9)
C5'	0.0134 (15)	0.0137 (12)	0.0129 (13)	0.0008 (9)	0.0001 (11)	−0.0005 (9)
O5'	0.0208 (10)	0.0150 (8)	0.0160 (9)	−0.0027 (7)	0.0054 (7)	−0.0003 (7)
O4'	0.0196 (10)	0.0138 (8)	0.0113 (9)	−0.0008 (6)	−0.0067 (9)	0.0013 (8)

Geometric parameters (Å, º)

N1—C7A	1.375 (3)	C7—H7	0.9300
N1—C2	1.391 (3)	C1'—O4'	1.424 (3)
N1—C1'	1.450 (3)	C1'—C2'	1.522 (3)
C2—C3	1.354 (3)	C1'—H1'A	0.9800
C2—H2	0.9300	C2'—C3'	1.520 (3)
C3—C3A	1.437 (3)	C2'—H2'A	0.9700
C3—I3	2.072 (2)	C2'—H2'B	0.9700
C3A—C4	1.390 (3)	C3'—O3'	1.423 (3)
C3A—C7A	1.426 (3)	C3'—C4'	1.535 (3)
C4—C5	1.388 (3)	C3'—H3'A	0.9800
C4—H4	0.9300	O3'—H3'B	0.8200
C5—C6	1.403 (3)	C4'—O4'	1.444 (3)
C5—N5	1.451 (3)	C4'—C5'	1.513 (3)
N5—O51	1.225 (2)	C4'—H4'A	0.9800
N5—O52	1.248 (2)	C5'—O5'	1.433 (3)
C6—C7	1.370 (3)	C5'—H5'B	0.9700
C6—H6	0.9300	C5'—H5'C	0.9700
C7—C7A	1.402 (3)	O5'—H5'A	0.8200
C7A—N1—C2	108.69 (18)	N1—C1'—C2'	114.7 (2)
C7A—N1—C1'	126.18 (19)	O4'—C1'—H1'A	109.7
C2—N1—C1'	125.10 (19)	N1—C1'—H1'A	109.7
C3—C2—N1	109.78 (19)	C2'—C1'—H1'A	109.7
C3—C2—H2	125.1	C3'—C2'—C1'	101.58 (19)
N1—C2—H2	125.1	C3'—C2'—H2'A	111.5
C2—C3—C3A	107.63 (19)	C1'—C2'—H2'A	111.5
C2—C3—I3	126.56 (17)	C3'—C2'—H2'B	111.5
C3A—C3—I3	125.80 (15)	C1'—C2'—H2'B	111.5
C4—C3A—C7A	119.9 (2)	H2'A—C2'—H2'B	109.3
C4—C3A—C3	133.9 (2)	O3'—C3'—C2'	112.1 (2)
C7A—C3A—C3	106.24 (18)	O3'—C3'—C4'	107.7 (2)
C5—C4—C3A	116.97 (19)	C2'—C3'—C4'	103.32 (19)
C5—C4—H4	121.5	O3'—C3'—H3'A	111.2
C3A—C4—H4	121.5	C2'—C3'—H3'A	111.2
C4—C5—C6	123.4 (2)	C4'—C3'—H3'A	111.2
C4—C5—N5	118.62 (19)	C3'—O3'—H3'B	109.5
C6—C5—N5	117.96 (19)	O4'—C4'—C5'	108.52 (19)
O51—N5—O52	122.24 (19)	O4'—C4'—C3'	107.01 (18)
O51—N5—C5	119.52 (19)	C5'—C4'—C3'	112.6 (2)
O52—N5—C5	118.24 (18)	O4'—C4'—H4'A	109.5
C7—C6—C5	120.2 (2)	C5'—C4'—H4'A	109.5
C7—C6—H6	119.9	C3'—C4'—H4'A	109.5
C5—C6—H6	119.9	O5'—C5'—C4'	112.34 (19)
C6—C7—C7A	117.8 (2)	O5'—C5'—H5'B	109.1
C6—C7—H7	121.1	C4'—C5'—H5'B	109.1
C7A—C7—H7	121.1	O5'—C5'—H5'C	109.1
N1—C7A—C7	130.6 (2)	C4'—C5'—H5'C	109.1
N1—C7A—C3A	107.64 (19)	H5'B—C5'—H5'C	107.9
C7—C7A—C3A	121.8 (2)	C5'—O5'—H5'A	109.5
O4'—C1'—N1	108.4 (2)	C1'—O4'—C4'	107.81 (17)
O4'—C1'—C2'	104.34 (18)
C7A—N1—C2—C3	−0.6 (3)	C6—C7—C7A—C3A	0.8 (4)
C1'—N1—C2—C3	−178.8 (3)	C4—C3A—C7A—N1	178.8 (3)
N1—C2—C3—C3A	−0.3 (3)	C3—C3A—C7A—N1	−1.4 (3)
N1—C2—C3—I3	−178.92 (19)	C4—C3A—C7A—C7	−1.0 (4)
C2—C3—C3A—C4	−179.2 (3)	C3—C3A—C7A—C7	178.8 (3)
I3—C3—C3A—C4	−0.6 (4)	C7A—N1—C1'—O4'	−115.1 (3)
C2—C3—C3A—C7A	1.0 (3)	C2—N1—C1'—O4'	62.8 (3)
I3—C3—C3A—C7A	179.67 (18)	C7A—N1—C1'—C2'	128.8 (3)
C7A—C3A—C4—C5	0.3 (4)	C2—N1—C1'—C2'	−53.4 (4)
C3—C3A—C4—C5	−179.5 (3)	O4'—C1'—C2'—C3'	40.3 (2)
C3A—C4—C5—C6	0.7 (4)	N1—C1'—C2'—C3'	158.8 (2)
C3A—C4—C5—N5	−179.7 (2)	C1'—C2'—C3'—O3'	85.0 (2)
C4—C5—N5—O51	−168.4 (2)	C1'—C2'—C3'—C4'	−30.6 (2)
C6—C5—N5—O51	11.3 (3)	O3'—C3'—C4'—O4'	−107.2 (2)
C4—C5—N5—O52	11.3 (3)	C2'—C3'—C4'—O4'	11.5 (3)
C6—C5—N5—O52	−169.0 (2)	O3'—C3'—C4'—C5'	133.6 (2)
C4—C5—C6—C7	−0.9 (4)	C2'—C3'—C4'—C5'	−107.7 (2)
N5—C5—C6—C7	179.4 (2)	O4'—C4'—C5'—O5'	59.1 (2)
C5—C6—C7—C7A	0.1 (4)	C3'—C4'—C5'—O5'	177.43 (18)
C2—N1—C7A—C7	−178.9 (3)	N1—C1'—O4'—C4'	−156.98 (18)
C1'—N1—C7A—C7	−0.8 (5)	C2'—C1'—O4'—C4'	−34.3 (2)
C2—N1—C7A—C3A	1.2 (3)	C5'—C4'—O4'—C1'	135.96 (18)
C1'—N1—C7A—C3A	179.4 (3)	C3'—C4'—O4'—C1'	14.2 (2)
C6—C7—C7A—N1	−179.0 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3′—H3′B···O52^i	0.82	2.17	2.970 (3)	164
O5′—H5′A···O52^ii	0.82	2.14	2.909 (2)	156
C2—H2···O51^iii	0.93	2.52	3.422 (3)	165
C4—H4···O3′^iv	0.93	2.47	3.387 (3)	169
C5′—H5′C···O51^iii	0.97	2.57	3.519 (3)	166

Symmetry codes: (i) −x+1, −y+1, z+1; (ii) −x+1, −y+2, z+1; (iii) x+1/2, −y+3/2, −z+1; (iv) x, y, z−1.