A non-natural dinucleotide containing an isomeric L-related deoxy­nucleoside: dinucleotide inhibitors of anti-HIV integrase activity

The first X-ray crystal structure of a non-natural dinucleotide, 5′-O-phosphoryl-1′-deoxy-2′-isoadenylyl-(3′ → 5′)-cytidine 6.5-hydrate (pIsodApC), C₁₉H₂₆N₈O₁₃P₂·6.5H₂O, belonging to a family of dinucleotides that contain an isomeric nucleoside component, is described. A complex system of hydrogen bonds between water mol­ecules and various sites on the dinucleotide was found. All H atoms were located from electron-density difference maps, which allowed identification of protonation sites. Compounds of this family have been found to bind at the active site of HIV integrase and to be inhibitors of this key viral enzyme. These dinucleotides are completely resistant to cleavage by exonucleases; an abnormal dihedral angle twist in an inter­nucleotide phosphate bond revealed in the X-ray crystal structure may be contributing to this unusual stability towards nucleases.

S1. Comment

The retroviral enzyme HIV-1 integrase incorporates HIV double-helical DNA into host chromosomal DNA (Dyda et al., 1994; Mazumder et al., 1996; Frankel & Young, 1998; Esposito & Craigie, 1999; Haren et al., 1999; Nair, 2002, 2003). This viral enzyme initially catalyzes the excision of two terminal nucleotides at the 3'-end of each strand of viral DNA (3'-processing), leaving recessed ends that terminate with xxCA—OH. In the next steps (strand transfer and integration), attack of the terminal 3'-OH of the tailored HIV DNA on a specific internucleotide phosphodiester bond results in cleavage of host DNA, which is followed by integration of the HIV DNA into host DNA (Dyda et al., 1994; Mazumder et al., 1996; Frankel & Young, 1998; Esposito & Craigie, 1999; Haren et al., 1999; Nair, 2002, 2003). The integration process is essential for the replication of HIV.

In designing inhibitors of this viral enzyme, it was suggested that residues immediately upstream of the dinucleotide cleavage site in the 3'-processing step may provide critical recognition/binding sites for HIV integrase. With this design concept in mind, natural dinucleotides were investigated by Pommier and co-workers, and non-natural dinucleotides were synthesized and investigated by Nair and co-workers, as potential anti-HIV integrase inhibitors (Mazumder et al., 1997; Taktakishvili, Neamati, Pommier & Nair, 2000; Taktakishvili, Neamati, Pommier, Pal & Nair, 2000; Taktakishvili et al., 2001). The non-natural dinucleotides contain one natural D-nucleoside component and one isomeric L-related nucleoside moiety (Nair & Jahnke, 1995), which are joined together by an internucleotide phosphodiester bond and are 5'-phosphorylated. While both the natural and non-natural dinucleotides with the AC base components were found to be strong inhibitors of HIV-1 integrase (IC₅₀ low µM range for both the processing and strand-transfer steps), one remarkable aspect of the non-natural dinucleotides was that the internucleotide bond exhibited resistance to cleavage by mammalian 3'- and 5'-exonucleases (Taktakishvili, Neamati, Pommier & Nair, 2000; Taktakishvili, Neamati, Pommier, Pal & Nair, 2000; Taktakishvili et al., 2001; Nair & Pal, 2004). This was not the case for the natural dinucleotides, which were substrates for 5'-exonucleases (Nair & Pal, 2004). The observed hypochromicity from the quantitative UV spectra of non-natural dinucleotides suggested the presence of base stacking in preferred conformations, which implied the presence of conformationally unusual internucleotide phosphate bonds, because of the spatial arrangement of the two sugar rings required to accommodate base stacking (Taktakishvili, Neamati, Pommier & Nair, 2000; Taktakishvili, Neamati, Pommier, Pal & Nair, 2000; Taktakishvili et al., 2001). In order to obtain further structural information (conformation, internucleotide phosphate bond, base-stacking property) on this family of non-natural dinucleotides, we crystallized one of these compounds, the title compound, pIsodApC or (I), and examined its detailed X-ray crystallographic structure, which we report here.

The numbering scheme for (I) is shown in Fig. 1. Atoms included in the adenosine portion have an A as the last letter of their label and those atoms included in the cytosine portion have a C as the last letter of their label. This coding allows easy recognition of the nucleotide components. All atom labels follow the usual chemical numbering for ribose, adenosine and cytosine. The O atoms of the seven (formally 6.5) water molecules are labeled O1W–O7W. Atom O7W occupies a diagonal twofold axis of the space group, is likely to be disordered and has an occupancy factor of 0.5. The H atoms attached to atom O7W are also assigned an occupancy factor of 0.5.

H atoms were located from electron-density difference maps, providing information about protonation sites: adenosine atom N1A and cytosine atom N3C are protonated. Both phosphate groups are monoanions, giving a neutral structure overall. All bond lengths and angles involving non-H atoms are within expected limits. Overall, the structure is formally dimeric, with two dinucleotide molecules being connected by hydrogen bonds from the water molecule at the O7W site to the O6W water molecule, which is also hydrogen-bonded to the terminal phosphate group.

The seven water molecules form a very complex association with the dinucleotide structure. Table 1 lists all the water contacts of less than 3.25 Å between the dinucleotide and the water molecules and between water molecules. A summary of significant contacts of less than 3.0 Å (inter- and intra-molecular) is as follows. For O1W contacts, N3C—O1W 2.636 (5) Å and O1W—O3W 2.686 (6) Å. For O2W contacts, O2W—O21P 2.776 (4) Å, O2W—O11P 2.854 (4) Å and N6A—O2W 2.769 (4) Å. For additional O3W contacts, O3W—O3'C 2.821 (5) Å and O3W—O21P 2.978 (5) Å. For O4W contacts, O4W—O22P 2.672 (5) Å and O4W—O12P 2.782 (5) Å. For O5W contacts, O5W—O12P 2.756 (4) Å, O5W—N4C 2.948 (5) Å and O6W—O5W 2.897 (5) Å. For additional O6W contacts, O6W—O23P 2.833 (5) Å and O7W—O6W 2.924 (6) Å. Finally, O7W (disordered) sits on a diagonal twofold axis and bridges between two symmetry-related molecules through an O6W water molecule.

Fig. 2 shows a plot of a single molecule of (I) with the seven associated water molecules. From this diagram, the overlap of the cytosine and adenosine rings can be readily observed. Best-plane calculations of the adenosine and cytosine rings were performed and the angle between these planes was found to be 12.6°. The mean deviation of atoms in the adenosine plane is 0.006 Å, and 0.016 Å for the cytosine ring. The atom contacts from the adenosine plane to the cytosine best plane range from 3.223 (atom C8A) to 4.122 Å (atom C2A), while the atom contacts from the cytosine ring to the adenosine best plane range from 3.096 (atom N4C) to 4.015 Å (atom O2C).

The dihedral angles along the connecting phosphate backbone were compared with equivalent dihedral angles in structures of two previously reported normal dinucleotides, namely ApU (Seeman et al., 1976) and GpC (Rosenberg et al., 1976); both ApU and GpC are hydrated sodium salts. ApU had two independent molecules in the asymmetric unit and both units, labeled ApU1 and ApU2, were used in this comparison. The seven dihedral angles along the ribose–phosphate backbone around the C3'A—O3'A, O3'A—P1, P1—O5'C and O5'C—C4'C bonds were compared. All dihedral angles for these four structures, except for those around the C3'A—O3'A bond, were found to have approximately the same value (deviations range from 1–14° between (I) and the normal dinucleotides). However, around the C3'—O3' bond there is a 49° difference, on average, between the dihedral angles of (I) and ApU1, ApU2 and GpC. With the adenosine ring moved to C2', some change in the twisting of the flexible phosphate backbone is clearly necessary to accommodate the adenosine–cytosine overlap. This abnormal twist may contribute to the unusual stability of (I) towards nucleases. Fig. 3 compares Newman projections of the C3'—O3' bonds in ApU1, ApU2, GpC (Fig. 3a–c) with (I) (Fig. 3 d).

Another notable difference between (I) and the ApU and GpC dinucleotides is the conformations of the ribose rings. On the pyrimidine base side (the 5'-side), ApU and GpC have envelope conformations, with atom C3' in the flap position; in (I), the conformation is twisted around C2'—C3'. On the purine base side (the 3'-side), ApU and GpC have twisted conformations around C2'—C3'; in (I), the conformation is twisted around C1'—O4'.

S2. Experimental

The dinucleotide 5'-monophosphate, (I), was synthesized through the coupling of 4-N-2',3'-O-tribenzoylcytidine and 6-N-benzoyl-5'-O-DMTr-isodeoxyadenosine (Wenzel & Nair, 1998), followed by 5'-phosphorylation (Chi et al., 2004). Its structure was characterized by multinuclear NMR, high-resolution MS and quantitative UV spectroscopy (see below). Crystals were obtained by very slow evaporation of an aqueous solution of (I) in a refrigerator. Experimental spectroscopic data for (I): ¹H NMR (D₂O, δ, p.p.m.): 8.28 (s, 1H), 8.23 (s, 1H), 7.50 (d, 1H, J = 8.0 Hz), 5.96 (d, 1H, J = 8.0 Hz), 5.49 (d, 1H, J = 4.5 Hz), 5.24 (m, 1H), 4.52 (m, 1H), 4.26 (dd, 1H, J = 11.0 and 6.0 Hz), 3.87–4.20 (m, 9H); ¹³CNMR (D₂O, δ, p.p.m): 159.3, 150.7, 148.6, 148.5, 146.3, 142.5, 117.7, 95.4, 89.1, 84.8, 82.8, 80.4, 74.1, 71.1, 69.0, 64.2, 63.7, 61.7, one C atom not observable; ³¹P NMR (D₂O, δ, p.p.m.): 0.86, −0.44. FAB–HRMS: [M+H]⁺ calculated for C₁₉H₂₇N₈O₁₃P₂: 637.1173, found: 637.1170; UV (H₂O): λ_max 264 cm⁻¹ (ε 19800)

S3. Refinement

All H atoms were initially located in a difference Fourier synthesis. H atoms bonded to C, O and N atoms were constrained to ride on their parent atoms, with U_iso(H) = 1.2U_eq(C,O,N). Water molecules were restrained geometrically to an O—H distance of 0.82 Å and to an H—H distance of 1.3 Å. The H atoms on atom O7W were fixed with occupancy factors of 0.5. A l l pertinent crystallographic data (experimental detail, xyz coordinates, displacement parameters, bond lengths and angles) have been deposited with the Cambridge Crystallographic Data Centre, deposition number CCDC 254123.

Computing details

Data collection: PROTEUM (Bruker, 2003); loop mounted and flash frozen (Hope, 1988); cell refinement: PROTEUM; data reduction: PROTEUM and SADABS (Sheldrick, 1996); program(s) used to solve structure: SHELXTL (Sheldrick, 1997); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL and PLATON (Spek, 2003); software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. A plot of dinucleotide (I), showing the atom-numbering scheme; atom labels ending in A are associated with the adenosine portion and those ending in C are associated with the cytosine portion. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. A comparison of the dihedral angles between (a) ApU1, (b) ApU2, (c) GpC and (d) (I), showing dihedral angle values in degrees.

4-amino-1-(6-O-{[2-(6-aminopurin-9-yl)-6-O-hydroxy(oxido)phosphoryl-1,2,5- trideoxy-3-furanosyl]oxidophosphoryl}-1,5-dideoxy-1-furanosyl)pyrimidin- 2(1H)-one 6.5 hydrate

Crystal data

C19H26N8O13P2·6.5H2O	Dx = 1.638 Mg m^−3
Mr = 753.52	Cu Kα radiation, λ = 1.54178 Å
Tetragonal, P41212	Cell parameters from 1009 reflections
a = 12.566 (5) Å	θ = 2–50°
c = 38.708 (5) Å	µ = 2.20 mm^−1
V = 6112 (4) Å^3	T = 100 K
Z = 8	Needle, colorless
F(000) = 3160	0.35 × 0.15 × 0.15 mm

Data collection

Bruker SMART 6000 CCD area-detector diffractometer	5272 independent reflections
Radiation source: Rigaku FR-D rotating anode generator	5266 reflections with I > 2σ(I)
Rigaku/MSC HiRes2 confocal optics monochromator	Rint = 0.025
ω scans	θmax = 67.0°, θmin = 3.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −11→14
Tmin = 0.513, Tmax = 0.734	k = −14→12
23451 measured reflections	l = −42→42

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)] = 0.047	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.124	w = 1/[σ^2(Fo^2) + (0.0609P)^2 + 10.5537P] where P = (Fo^2 + 2Fc^2)/3
S = 1.10	(Δ/σ)max = 0.002
5272 reflections	Δρmax = 0.69 e Å^−3
474 parameters	Δρmin = −0.49 e Å^−3
22 restraints	Absolute structure: Flack (1983), with how many Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.04 (3)

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	Occ. (<1)
P1	0.48271 (7)	0.48721 (6)	0.68406 (2)	0.01756 (19)
P2	0.83819 (7)	0.37702 (8)	0.58340 (3)	0.0272 (2)
O2'C	0.41287 (19)	0.0256 (2)	0.70951 (6)	0.0238 (5)
H2'O	0.4689	−0.0016	0.7032	0.080*
O3'C	0.21760 (19)	0.12178 (19)	0.71591 (6)	0.0225 (5)
H3'O	0.2353	0.0794	0.7309	0.080*
O2C	0.3899 (2)	−0.0555 (2)	0.60528 (7)	0.0292 (6)
O4'C	0.29711 (19)	0.19956 (19)	0.64610 (6)	0.0198 (5)
O5'C	0.42734 (18)	0.37265 (18)	0.68109 (6)	0.0202 (5)
O3'A	0.46199 (19)	0.54196 (18)	0.64719 (6)	0.0203 (5)
O5'A	0.72489 (19)	0.4268 (2)	0.59338 (7)	0.0239 (5)
O4'A	0.6082 (2)	0.6112 (2)	0.57538 (7)	0.0271 (6)
O11P	0.42431 (19)	0.55657 (19)	0.70886 (6)	0.0211 (5)
O12P	0.59773 (19)	0.46431 (19)	0.68946 (6)	0.0223 (5)
O21P	0.8128 (2)	0.2829 (2)	0.56132 (7)	0.0343 (7)
O22P	0.8877 (2)	0.3455 (3)	0.61966 (8)	0.0397 (7)
O23P	0.9073 (3)	0.4611 (3)	0.56827 (11)	0.0541 (9)
H23P	0.9009	0.4610	0.5472	0.080*
N1A	0.2373 (2)	0.1937 (2)	0.55125 (7)	0.0210 (6)
H1NA	0.2000	0.1487	0.5486	0.080*
N1C	0.4458 (2)	0.1040 (2)	0.62829 (7)	0.0191 (6)
N3A	0.2732 (2)	0.3564 (2)	0.58083 (8)	0.0200 (6)
N3C	0.5264 (2)	0.0315 (2)	0.57907 (8)	0.0233 (6)
H2NC	0.5306	−0.0183	0.5639	0.080*
N4C	0.6683 (2)	0.1135 (3)	0.55172 (8)	0.0276 (7)
H4AC	0.6721	0.0613	0.5374	0.080*
H4BC	0.7119	0.1660	0.5500	0.080*
N6A	0.3494 (2)	0.1157 (3)	0.50967 (8)	0.0246 (7)
H6NA	0.3052	0.0640	0.5072	0.080*
H6NB	0.4071	0.1169	0.4977	0.080*
N7A	0.4928 (2)	0.3093 (3)	0.52318 (7)	0.0228 (6)
N9A	0.4429 (2)	0.4318 (2)	0.56227 (7)	0.0209 (6)
C1'C	0.3594 (3)	0.1079 (3)	0.65397 (9)	0.0189 (7)
H1'C	0.3155	0.0437	0.6521	0.080*
C2'C	0.3972 (3)	0.1224 (3)	0.69174 (9)	0.0187 (7)
H2'C	0.4630	0.1642	0.6921	0.080*
C2A	0.2141 (3)	0.2738 (3)	0.57430 (9)	0.0201 (7)
H2A	0.1503	0.2682	0.5864	0.080*
C2C	0.4493 (3)	0.0212 (3)	0.60468 (9)	0.0215 (7)
C3'C	0.3061 (3)	0.1879 (3)	0.70735 (9)	0.0189 (7)
H3'C	0.3298	0.2304	0.7271	0.080*
C4'C	0.2697 (3)	0.2577 (3)	0.67719 (8)	0.0184 (7)
H4'C	0.1919	0.2620	0.6782	0.080*
C4A	0.3642 (3)	0.3565 (3)	0.56165 (8)	0.0182 (7)
C4C	0.5952 (3)	0.1135 (3)	0.57640 (9)	0.0220 (7)
C5'C	0.3119 (3)	0.3709 (3)	0.67603 (9)	0.0202 (7)
H5AC	0.2947	0.4025	0.6538	0.080*
H5BC	0.2778	0.4129	0.6939	0.080*
C5A	0.3951 (3)	0.2813 (3)	0.53764 (9)	0.0198 (7)
C5C	0.5872 (3)	0.1983 (3)	0.60042 (9)	0.0223 (7)
H5C	0.6316	0.2573	0.5990	0.080*
C3'A	0.5181 (3)	0.5054 (3)	0.61694 (8)	0.0192 (7)
H3'A	0.5374	0.4301	0.6189	0.080*
C6A	0.3289 (3)	0.1928 (3)	0.53158 (9)	0.0212 (7)
C6C	0.5126 (3)	0.1901 (3)	0.62562 (9)	0.0208 (7)
H6C	0.5063	0.2448	0.6417	0.080*
C4'A	0.6172 (3)	0.5755 (3)	0.61027 (9)	0.0207 (7)
H4'A	0.6147	0.6374	0.6256	0.080*
C5'A	0.7231 (3)	0.5216 (3)	0.61415 (10)	0.0252 (8)
H5AA	0.7795	0.5693	0.6069	0.080*
H5BA	0.7349	0.5035	0.6382	0.080*
C8A	0.5172 (3)	0.3995 (3)	0.53873 (9)	0.0223 (7)
H8A	0.5810	0.4394	0.5338	0.080*
C1'A	0.4964 (3)	0.6227 (3)	0.56883 (10)	0.0266 (8)
H1'A	0.4822	0.6245	0.5442	0.080*
H1'B	0.4693	0.6876	0.5792	0.080*
C2'A	0.4461 (3)	0.5252 (3)	0.58535 (9)	0.0190 (7)
H2'A	0.3739	0.5424	0.5931	0.080*
O1W	0.5664 (4)	0.8772 (3)	0.53483 (11)	0.0613 (11)
H1WA	0.508 (4)	0.871 (5)	0.5217 (16)	0.080*
H1WB	0.566 (5)	0.8102 (17)	0.5370 (17)	0.080*
O2W	0.2172 (2)	0.9491 (2)	0.49094 (7)	0.0277 (6)
H2WA	0.157 (3)	0.972 (5)	0.4863 (16)	0.080*
H2WB	0.231 (5)	0.916 (5)	0.4732 (10)	0.080*
O3W	0.4182 (3)	0.7666 (3)	0.50005 (10)	0.0583 (10)
H3WA	0.385 (5)	0.716 (4)	0.5102 (14)	0.080*
H3WB	0.380 (5)	0.773 (5)	0.4819 (10)	0.080*
O4W	0.7512 (3)	0.8130 (3)	0.57915 (9)	0.0498 (9)
H4WA	0.799 (4)	0.852 (4)	0.5744 (16)	0.080*
H4WB	0.709 (4)	0.819 (5)	0.5945 (13)	0.080*
O5W	0.7784 (2)	0.9744 (3)	0.50187 (8)	0.0379 (7)
H5WA	0.723 (3)	0.972 (6)	0.5118 (14)	0.080*
H5WB	0.823 (4)	0.957 (5)	0.5159 (13)	0.080*
O6W	0.8290 (3)	0.6533 (3)	0.53969 (9)	0.0466 (8)
H6WA	0.860 (5)	0.688 (4)	0.5243 (13)	0.080*
H6WB	0.852 (5)	0.594 (3)	0.5463 (16)	0.080*
O7W	0.6322 (4)	0.6322 (4)	0.5000	0.099 (3)
H7WA	0.6894	0.6369	0.5091	0.080*	0.50
H7WB	0.6283	0.6885	0.4865	0.080*	0.50

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
P1	0.0181 (4)	0.0162 (4)	0.0184 (4)	−0.0018 (3)	−0.0012 (3)	0.0010 (3)
P2	0.0160 (4)	0.0265 (5)	0.0393 (6)	−0.0013 (4)	0.0039 (4)	0.0030 (4)
O2'C	0.0192 (12)	0.0254 (13)	0.0268 (13)	0.0058 (10)	0.0055 (10)	0.0098 (10)
O3'C	0.0184 (12)	0.0220 (12)	0.0271 (13)	0.0007 (10)	0.0031 (10)	0.0069 (10)
O2C	0.0228 (13)	0.0290 (14)	0.0359 (15)	−0.0065 (11)	0.0052 (11)	−0.0059 (11)
O4'C	0.0208 (12)	0.0184 (12)	0.0203 (12)	0.0026 (10)	−0.0016 (9)	0.0001 (9)
O5'C	0.0167 (11)	0.0163 (12)	0.0278 (13)	0.0006 (9)	0.0005 (10)	0.0017 (10)
O3'A	0.0228 (13)	0.0166 (12)	0.0215 (12)	0.0021 (9)	0.0010 (9)	0.0000 (9)
O5'A	0.0167 (12)	0.0248 (13)	0.0301 (14)	−0.0030 (10)	0.0010 (10)	−0.0001 (10)
O4'A	0.0205 (13)	0.0280 (13)	0.0329 (14)	−0.0014 (10)	0.0004 (10)	0.0098 (11)
O11P	0.0225 (12)	0.0208 (12)	0.0200 (12)	−0.0039 (10)	0.0021 (10)	0.0004 (10)
O12P	0.0199 (12)	0.0234 (13)	0.0236 (13)	−0.0019 (10)	−0.0025 (10)	0.0001 (10)
O21P	0.0210 (13)	0.0453 (17)	0.0366 (16)	0.0013 (12)	0.0063 (11)	−0.0098 (13)
O22P	0.0293 (15)	0.0461 (18)	0.0438 (17)	0.0099 (13)	−0.0125 (13)	−0.0092 (14)
O23P	0.0313 (17)	0.0443 (19)	0.087 (3)	0.0027 (14)	0.0194 (17)	0.0176 (18)
N1A	0.0194 (14)	0.0220 (15)	0.0216 (15)	−0.0003 (12)	0.0002 (11)	0.0021 (12)
N1C	0.0212 (14)	0.0190 (14)	0.0171 (14)	−0.0027 (12)	0.0019 (11)	0.0016 (11)
N3A	0.0165 (14)	0.0218 (15)	0.0217 (15)	0.0021 (12)	0.0040 (11)	0.0036 (12)
N3C	0.0224 (15)	0.0264 (16)	0.0212 (15)	−0.0001 (13)	0.0015 (12)	−0.0027 (12)
N4C	0.0240 (16)	0.0362 (18)	0.0226 (16)	0.0010 (14)	0.0070 (12)	0.0062 (14)
N6A	0.0208 (15)	0.0309 (17)	0.0221 (16)	0.0048 (13)	0.0000 (12)	−0.0068 (13)
N7A	0.0145 (14)	0.0366 (17)	0.0173 (14)	0.0016 (12)	0.0000 (11)	−0.0025 (12)
N9A	0.0202 (14)	0.0270 (16)	0.0156 (14)	−0.0001 (12)	0.0017 (11)	0.0009 (12)
C1'C	0.0138 (15)	0.0195 (16)	0.0234 (18)	−0.0004 (13)	0.0028 (13)	0.0040 (13)
C2'C	0.0175 (16)	0.0191 (16)	0.0196 (18)	0.0013 (13)	0.0016 (13)	0.0025 (13)
C2A	0.0216 (17)	0.0193 (17)	0.0194 (17)	0.0023 (14)	0.0060 (13)	0.0047 (13)
C2C	0.0162 (16)	0.0254 (18)	0.0228 (17)	0.0005 (14)	−0.0009 (13)	0.0018 (14)
C3'C	0.0169 (16)	0.0210 (17)	0.0188 (17)	0.0014 (14)	0.0027 (13)	0.0012 (14)
C4'C	0.0182 (16)	0.0183 (17)	0.0188 (17)	−0.0006 (13)	0.0001 (13)	0.0022 (13)
C4A	0.0177 (16)	0.0234 (17)	0.0135 (16)	0.0047 (13)	0.0002 (12)	0.0045 (13)
C4C	0.0146 (16)	0.0309 (19)	0.0205 (18)	0.0035 (14)	0.0001 (13)	0.0099 (15)
C5'C	0.0163 (16)	0.0173 (17)	0.0269 (19)	0.0004 (13)	−0.0042 (13)	0.0020 (13)
C5A	0.0177 (16)	0.0250 (17)	0.0167 (17)	0.0042 (14)	−0.0012 (13)	0.0040 (14)
C5C	0.0214 (17)	0.0213 (17)	0.0241 (18)	−0.0019 (14)	−0.0020 (14)	0.0032 (14)
C3'A	0.0185 (16)	0.0166 (16)	0.0226 (17)	−0.0020 (13)	−0.0011 (13)	0.0006 (12)
C6A	0.0167 (16)	0.0269 (18)	0.0200 (18)	0.0067 (14)	−0.0029 (13)	0.0027 (14)
C6C	0.0188 (17)	0.0233 (17)	0.0202 (16)	−0.0017 (14)	0.0024 (13)	0.0038 (13)
C4'A	0.0191 (17)	0.0193 (17)	0.0238 (18)	−0.0033 (14)	0.0011 (14)	0.0024 (13)
C5'A	0.0254 (18)	0.0231 (18)	0.0269 (19)	−0.0065 (15)	−0.0056 (15)	−0.0021 (15)
C8A	0.0139 (15)	0.0351 (19)	0.0178 (17)	−0.0024 (15)	0.0034 (13)	−0.0001 (14)
C1'A	0.0203 (18)	0.0289 (19)	0.031 (2)	0.0003 (15)	−0.0010 (15)	0.0068 (16)
C2'A	0.0188 (16)	0.0196 (16)	0.0187 (17)	0.0035 (13)	0.0012 (13)	0.0013 (13)
O1W	0.081 (3)	0.0348 (18)	0.068 (3)	−0.0053 (18)	0.036 (2)	−0.0154 (18)
O2W	0.0286 (14)	0.0281 (14)	0.0265 (14)	0.0073 (11)	−0.0027 (11)	−0.0089 (11)
O3W	0.063 (2)	0.060 (2)	0.052 (2)	−0.0147 (18)	−0.0090 (19)	0.0216 (19)
O4W	0.063 (2)	0.0411 (19)	0.045 (2)	−0.0199 (17)	0.0126 (16)	−0.0045 (15)
O5W	0.0404 (17)	0.0433 (17)	0.0301 (15)	−0.0010 (14)	−0.0093 (13)	−0.0043 (14)
O6W	0.0409 (19)	0.0468 (19)	0.052 (2)	−0.0048 (15)	0.0127 (15)	0.0044 (16)
O7W	0.124 (4)	0.124 (4)	0.048 (3)	−0.061 (5)	−0.024 (3)	0.024 (3)

Geometric parameters (Å, º)

P1—O12P	1.489 (3)	C1'C—C2'C	1.548 (5)
P1—O11P	1.490 (2)	C1'C—H1'C	0.9800
P1—O5'C	1.603 (3)	C2'C—C3'C	1.533 (5)
P1—O3'A	1.606 (2)	C2'C—H2'C	0.9797
P2—O23P	1.488 (3)	C2A—H2A	0.9306
P2—O21P	1.494 (3)	C3'C—C4'C	1.531 (5)
P2—O22P	1.586 (3)	C3'C—H3'C	0.9793
P2—O5'A	1.602 (3)	C4'C—C5'C	1.519 (5)
O2'C—C2'C	1.410 (4)	C4'C—H4'C	0.9799
O2'C—H2'O	0.8200	C4A—C5A	1.381 (5)
O3'C—C3'C	1.427 (4)	C4C—C5C	1.418 (5)
O3'C—H3'O	0.8196	C5'C—H5AC	0.9703
O2C—C2C	1.220 (5)	C5'C—H5BC	0.9712
O4'C—C1'C	1.426 (4)	C5A—C6A	1.408 (5)
O4'C—C4'C	1.449 (4)	C5C—C6C	1.357 (5)
O5'C—C5'C	1.464 (4)	C5C—H5C	0.9295
O3'A—C3'A	1.442 (4)	C3'A—C2'A	1.542 (5)
O5'A—C5'A	1.438 (4)	C3'A—C4'A	1.547 (5)
O4'A—C4'A	1.428 (4)	C3'A—H3'A	0.9797
O4'A—C1'A	1.434 (4)	C6C—H6C	0.9301
O23P—H23P	0.8210	C4'A—C5'A	1.501 (5)
N1A—C2A	1.376 (5)	C4'A—H4'A	0.9793
N1A—C6A	1.380 (4)	C5'A—H5AA	0.9697
N1A—H1NA	0.7417	C5'A—H5BA	0.9697
N1C—C6C	1.373 (5)	C8A—H8A	0.9646
N1C—C2C	1.385 (5)	C1'A—C2'A	1.520 (5)
N1C—C1'C	1.473 (4)	C1'A—H1'A	0.9699
N3A—C2A	1.301 (5)	C1'A—H1'B	0.9708
N3A—C4A	1.363 (4)	C2'A—H2'A	0.9795
N3C—C4C	1.349 (5)	O1W—H1WA	0.90 (2)
N3C—C2C	1.391 (5)	O1W—H1WB	0.85 (2)
N3C—H2NC	0.8611	O2W—H2WA	0.82 (2)
N4C—C4C	1.326 (4)	O2W—H2WB	0.82 (2)
N4C—H4AC	0.8602	O3W—H3WA	0.85 (2)
N4C—H4BC	0.8601	O3W—H3WB	0.85 (2)
N6A—C6A	1.313 (5)	O4W—H4WA	0.80 (2)
N6A—H6NA	0.8598	O4W—H4WB	0.799 (19)
N6A—H6NB	0.8596	O5W—H5WA	0.80 (2)
N7A—C8A	1.320 (5)	O5W—H5WB	0.82 (2)
N7A—C5A	1.395 (5)	O6W—H6WA	0.83 (2)
N9A—C8A	1.366 (4)	O6W—H6WB	0.84 (2)
N9A—C4A	1.369 (5)	O7W—H7WA	0.8029
N9A—C2'A	1.476 (4)	O7W—H7WB	0.8809
O12P—P1—O11P	120.05 (14)	O4'C—C4'C—H4'C	107.4
O12P—P1—O5'C	104.95 (14)	C5'C—C4'C—H4'C	107.3
O11P—P1—O5'C	110.96 (13)	C3'C—C4'C—H4'C	107.4
O12P—P1—O3'A	111.43 (14)	N3A—C4A—N9A	126.7 (3)
O11P—P1—O3'A	104.01 (13)	N3A—C4A—C5A	127.0 (3)
O5'C—P1—O3'A	104.52 (13)	N9A—C4A—C5A	106.4 (3)
O23P—P2—O21P	117.5 (2)	N4C—C4C—N3C	120.0 (3)
O23P—P2—O22P	107.2 (2)	N4C—C4C—C5C	121.4 (4)
O21P—P2—O22P	113.12 (17)	N3C—C4C—C5C	118.6 (3)
O23P—P2—O5'A	109.66 (16)	O5'C—C5'C—C4'C	110.9 (3)
O21P—P2—O5'A	104.91 (15)	O5'C—C5'C—H5AC	109.5
O22P—P2—O5'A	103.46 (16)	C4'C—C5'C—H5AC	109.4
C2'C—O2'C—H2'O	109.5	O5'C—C5'C—H5BC	109.5
C3'C—O3'C—H3'O	109.4	C4'C—C5'C—H5BC	109.5
C1'C—O4'C—C4'C	111.1 (2)	H5AC—C5'C—H5BC	108.1
C5'C—O5'C—P1	117.0 (2)	C4A—C5A—N7A	110.2 (3)
C3'A—O3'A—P1	120.4 (2)	C4A—C5A—C6A	119.1 (3)
C5'A—O5'A—P2	118.2 (2)	N7A—C5A—C6A	130.7 (3)
C4'A—O4'A—C1'A	106.1 (3)	C6C—C5C—C4C	117.6 (3)
P2—O23P—H23P	109.5	C6C—C5C—H5C	121.2
C2A—N1A—C6A	122.7 (3)	C4C—C5C—H5C	121.2
C2A—N1A—H1NA	120.9	O3'A—C3'A—C2'A	107.8 (3)
C6A—N1A—H1NA	116.3	O3'A—C3'A—C4'A	110.3 (3)
C6C—N1C—C2C	121.5 (3)	C2'A—C3'A—C4'A	104.4 (3)
C6C—N1C—C1'C	118.4 (3)	O3'A—C3'A—H3'A	111.4
C2C—N1C—C1'C	119.5 (3)	C2'A—C3'A—H3'A	111.3
C2A—N3A—C4A	112.0 (3)	C4'A—C3'A—H3'A	111.3
C4C—N3C—C2C	124.9 (3)	N6A—C6A—N1A	121.8 (3)
C4C—N3C—H2NC	117.6	N6A—C6A—C5A	125.0 (3)
C2C—N3C—H2NC	117.6	N1A—C6A—C5A	113.2 (3)
C4C—N4C—H4AC	120.2	C5C—C6C—N1C	122.5 (3)
C4C—N4C—H4BC	119.8	C5C—C6C—H6C	118.9
H4AC—N4C—H4BC	120.0	N1C—C6C—H6C	118.7
C6A—N6A—H6NA	120.1	O4'A—C4'A—C5'A	107.9 (3)
C6A—N6A—H6NB	120.0	O4'A—C4'A—C3'A	105.8 (3)
H6NA—N6A—H6NB	120.0	C5'A—C4'A—C3'A	116.1 (3)
C8A—N7A—C5A	103.8 (3)	O4'A—C4'A—H4'A	108.8
C8A—N9A—C4A	106.1 (3)	C5'A—C4'A—H4'A	109.0
C8A—N9A—C2'A	128.4 (3)	C3'A—C4'A—H4'A	109.0
C4A—N9A—C2'A	125.5 (3)	O5'A—C5'A—C4'A	109.4 (3)
O4'C—C1'C—N1C	106.7 (3)	O5'A—C5'A—H5AA	109.8
O4'C—C1'C—C2'C	106.0 (3)	C4'A—C5'A—H5AA	109.9
N1C—C1'C—C2'C	114.5 (3)	O5'A—C5'A—H5BA	109.9
O4'C—C1'C—H1'C	109.9	C4'A—C5'A—H5BA	109.7
N1C—C1'C—H1'C	109.8	H5AA—C5'A—H5BA	108.1
C2'C—C1'C—H1'C	109.8	N7A—C8A—N9A	113.6 (3)
O2'C—C2'C—C3'C	112.0 (3)	N7A—C8A—H8A	123.3
O2'C—C2'C—C1'C	113.7 (3)	N9A—C8A—H8A	123.1
C3'C—C2'C—C1'C	101.9 (3)	O4'A—C1'A—C2'A	104.6 (3)
O2'C—C2'C—H2'C	109.7	O4'A—C1'A—H1'A	110.9
C3'C—C2'C—H2'C	109.6	C2'A—C1'A—H1'A	110.8
C1'C—C2'C—H2'C	109.7	O4'A—C1'A—H1'B	110.8
N3A—C2A—N1A	126.0 (3)	C2'A—C1'A—H1'B	110.9
N3A—C2A—H2A	117.1	H1'A—C1'A—H1'B	108.8
N1A—C2A—H2A	116.9	N9A—C2'A—C1'A	113.5 (3)
O2C—C2C—N1C	124.2 (3)	N9A—C2'A—C3'A	111.5 (3)
O2C—C2C—N3C	120.8 (3)	C1'A—C2'A—C3'A	102.7 (3)
N1C—C2C—N3C	115.0 (3)	N9A—C2'A—H2'A	109.6
O3'C—C3'C—C4'C	106.1 (3)	C1'A—C2'A—H2'A	109.6
O3'C—C3'C—C2'C	111.1 (3)	C3'A—C2'A—H2'A	109.7
C4'C—C3'C—C2'C	103.3 (3)	H1WA—O1W—H1WB	88 (4)
O3'C—C3'C—H3'C	111.9	H2WA—O2W—H2WB	100 (4)
C4'C—C3'C—H3'C	112.0	H3WA—O3W—H3WB	100 (4)
C2'C—C3'C—H3'C	111.9	H4WA—O4W—H4WB	128 (5)
O4'C—C4'C—C5'C	111.4 (3)	H5WA—O5W—H5WB	106 (4)
O4'C—C4'C—C3'C	105.9 (3)	H6WA—O6W—H6WB	121 (5)
C5'C—C4'C—C3'C	117.1 (3)	H7WA—O7W—H7WB	104.5
O12P—P1—O5'C—C5'C	179.3 (2)	P1—O5'C—C5'C—C4'C	−174.5 (2)
O11P—P1—O5'C—C5'C	48.2 (3)	O4'C—C4'C—C5'C—O5'C	−73.5 (3)
O3'A—P1—O5'C—C5'C	−63.4 (2)	C3'C—C4'C—C5'C—O5'C	48.4 (4)
O12P—P1—O3'A—C3'A	40.9 (3)	N3A—C4A—C5A—N7A	179.6 (3)
O11P—P1—O3'A—C3'A	171.6 (2)	N9A—C4A—C5A—N7A	−0.1 (4)
O5'C—P1—O3'A—C3'A	−71.9 (2)	N3A—C4A—C5A—C6A	−0.7 (5)
O23P—P2—O5'A—C5'A	−51.3 (3)	N9A—C4A—C5A—C6A	179.6 (3)
O21P—P2—O5'A—C5'A	−178.4 (2)	C8A—N7A—C5A—C4A	−0.1 (4)
O22P—P2—O5'A—C5'A	62.8 (3)	C8A—N7A—C5A—C6A	−179.8 (4)
C4'C—O4'C—C1'C—N1C	−136.5 (3)	N4C—C4C—C5C—C6C	−177.7 (3)
C4'C—O4'C—C1'C—C2'C	−14.1 (3)	N3C—C4C—C5C—C6C	2.3 (5)
C6C—N1C—C1'C—O4'C	57.4 (4)	P1—O3'A—C3'A—C2'A	150.5 (2)
C2C—N1C—C1'C—O4'C	−114.2 (3)	P1—O3'A—C3'A—C4'A	−96.1 (3)
C6C—N1C—C1'C—C2'C	−59.5 (4)	C2A—N1A—C6A—N6A	−179.9 (3)
C2C—N1C—C1'C—C2'C	128.9 (3)	C2A—N1A—C6A—C5A	0.2 (5)
O4'C—C1'C—C2'C—O2'C	150.6 (3)	C4A—C5A—C6A—N6A	−179.5 (3)
N1C—C1'C—C2'C—O2'C	−92.1 (3)	N7A—C5A—C6A—N6A	0.2 (6)
O4'C—C1'C—C2'C—C3'C	29.9 (3)	C4A—C5A—C6A—N1A	0.4 (5)
N1C—C1'C—C2'C—C3'C	147.1 (3)	N7A—C5A—C6A—N1A	−179.9 (3)
C4A—N3A—C2A—N1A	0.4 (5)	C4C—C5C—C6C—N1C	−0.3 (5)
C6A—N1A—C2A—N3A	−0.7 (5)	C2C—N1C—C6C—C5C	−1.6 (5)
C6C—N1C—C2C—O2C	−177.8 (3)	C1'C—N1C—C6C—C5C	−173.0 (3)
C1'C—N1C—C2C—O2C	−6.5 (5)	C1'A—O4'A—C4'A—C5'A	157.8 (3)
C6C—N1C—C2C—N3C	1.4 (5)	C1'A—O4'A—C4'A—C3'A	32.9 (4)
C1'C—N1C—C2C—N3C	172.7 (3)	O3'A—C3'A—C4'A—O4'A	−126.3 (3)
C4C—N3C—C2C—O2C	179.9 (3)	C2'A—C3'A—C4'A—O4'A	−10.8 (3)
C4C—N3C—C2C—N1C	0.7 (5)	O3'A—C3'A—C4'A—C5'A	114.1 (3)
O2'C—C2'C—C3'C—O3'C	−42.2 (4)	C2'A—C3'A—C4'A—C5'A	−130.4 (3)
C1'C—C2'C—C3'C—O3'C	79.7 (3)	P2—O5'A—C5'A—C4'A	160.4 (2)
O2'C—C2'C—C3'C—C4'C	−155.6 (3)	O4'A—C4'A—C5'A—O5'A	−65.8 (3)
C1'C—C2'C—C3'C—C4'C	−33.7 (3)	C3'A—C4'A—C5'A—O5'A	52.8 (4)
C1'C—O4'C—C4'C—C5'C	120.5 (3)	C5A—N7A—C8A—N9A	0.3 (4)
C1'C—O4'C—C4'C—C3'C	−7.8 (3)	C4A—N9A—C8A—N7A	−0.4 (4)
O3'C—C3'C—C4'C—O4'C	−90.6 (3)	C2'A—N9A—C8A—N7A	177.0 (3)
C2'C—C3'C—C4'C—O4'C	26.5 (3)	C4'A—O4'A—C1'A—C2'A	−42.3 (4)
O3'C—C3'C—C4'C—C5'C	144.7 (3)	C8A—N9A—C2'A—C1'A	37.1 (5)
C2'C—C3'C—C4'C—C5'C	−98.3 (3)	C4A—N9A—C2'A—C1'A	−146.0 (3)
C2A—N3A—C4A—N9A	179.8 (3)	C8A—N9A—C2'A—C3'A	−78.3 (4)
C2A—N3A—C4A—C5A	0.2 (5)	C4A—N9A—C2'A—C3'A	98.6 (4)
C8A—N9A—C4A—N3A	−179.4 (3)	O4'A—C1'A—C2'A—N9A	−87.0 (3)
C2'A—N9A—C4A—N3A	3.1 (5)	O4'A—C1'A—C2'A—C3'A	33.6 (3)
C8A—N9A—C4A—C5A	0.3 (4)	O3'A—C3'A—C2'A—N9A	−134.4 (3)
C2'A—N9A—C4A—C5A	−177.2 (3)	C4'A—C3'A—C2'A—N9A	108.3 (3)
C2C—N3C—C4C—N4C	177.4 (3)	O3'A—C3'A—C2'A—C1'A	103.8 (3)
C2C—N3C—C4C—C5C	−2.6 (5)	C4'A—C3'A—C2'A—C1'A	−13.5 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3W—H3WA···O3′C^i	0.85 (2)	1.99 (3)	2.821 (4)	167 (7)
O2′C—H2′O···O23P^ii	0.82	1.82	2.631 (4)	167
O3′C—H3′O···N7A^iii	0.82	2.04	2.767 (4)	147
O23P—H23P···O3W^iv	0.82	2.55	3.227 (6)	141
N1A—H1NA···O11P^v	0.74	1.97	2.692 (4)	166
N3C—H2NC···O1W^vi	0.86	1.79	2.636 (5)	169
N4C—H4AC···O5W^vi	0.86	2.21	2.948 (5)	144
N4C—H4BC···O21P	0.86	1.99	2.822 (5)	163
N6A—H6NA···O2W^vi	0.86	1.93	2.769 (4)	167
N6A—H6NB···O2′C^vii	0.86	2.13	2.967 (4)	163
O1W—H1WA···O3W	0.90 (2)	1.92 (5)	2.686 (6)	142 (6)
O2W—H2WA···O11P^viii	0.82 (2)	2.11 (4)	2.854 (4)	151 (7)
O2W—H2WB···O21P^iv	0.82 (2)	1.97 (2)	2.776 (4)	166 (6)
O3W—H3WB···O21P^iv	0.85 (2)	2.13 (2)	2.978 (5)	172 (6)
O4W—H4WA···O12P^ix	0.80 (2)	1.99 (2)	2.782 (4)	172 (7)
O4W—H4WB···O22P^ix	0.80 (2)	1.88 (2)	2.672 (5)	175 (7)
O5W—H5WA···N4C^x	0.80 (2)	2.45 (6)	2.948 (5)	122 (6)
O5W—H5WA···O1W	0.80 (2)	2.46 (4)	3.195 (5)	153 (7)
O5W—H5WB···O12P^ix	0.82 (2)	1.99 (3)	2.756 (4)	156 (6)
O6W—H6WA···O5W^iv	0.83 (2)	2.10 (3)	2.897 (4)	161 (7)
O6W—H6WB···O23P	0.84 (2)	2.00 (2)	2.833 (5)	172 (7)
O7W—H7WA···O6W	0.80	2.13	2.924 (6)	172
O7W—H7WB···O6W^iv	0.88	2.06	2.924 (6)	166

Symmetry codes: (i) −x+1/2, y+1/2, −z+5/4; (ii) −x+3/2, y−1/2, −z+5/4; (iii) −y+1/2, x−1/2, z+1/4; (iv) y, x, −z+1; (v) −x+1/2, y−1/2, −z+5/4; (vi) x, y−1, z; (vii) y+1/2, −x+1/2, z−1/4; (viii) y−1/2, −x+3/2, z−1/4; (ix) −x+3/2, y+1/2, −z+5/4; (x) x, y+1, z.