# Supplementary Material (ESI) for Chemical Communications # This journal is (c) The Royal Society of Chemistry 2007 data_global _journal_name_full Chem.Commun. _journal_coden_Cambridge 0182 _publ_contact_author_name 'W. J. Stec' _publ_contact_author_address ; Department of Bioorganic Chemistry Centre of Molecular and Macromolecular Studies PAS Sienkiewicza 112 Lodz 90-363 POLAND ; _publ_contact_author_email WJSTEC@BIO.CBMM.LODZ.PL _publ_section_title ; Stereochemistry of rHint1 Hydrolase Assisted Cleavage of P-N Bond in Nucleoside 5'-O-phosphoramidothioates ; loop_ _publ_author_name W.J.Stec J.Baraniak R.Kaczmarek A.Krakowiak M.Wieczorek data_wie5dc _database_code_depnum_ccdc_archive 'CCDC 614931' _audit_creation_date 2006-07-13T16:27:56-00:00 _audit_creation_method 'WinGX routine CIF_UPDATE' #----------------------------------------------------------------------------# # CHEMICAL INFORMATION # #----------------------------------------------------------------------------# _chemical_name_systematic ; N-(2-thiono-1,3,2-oxathiaphospholanyl)tryptophan methyl ester ; _chemical_formula_moiety 'C14 H17 N2 O3 P S2' _chemical_formula_sum 'C14 H17 N2 O3 P S2' _chemical_formula_weight 356.41 _chemical_absolute_configuration rm #----------------------------------------------------------------------------# # UNIT CELL INFORMATION # #----------------------------------------------------------------------------# _symmetry_cell_setting monoclinic _symmetry_space_group_name_H-M 'P 21' _symmetry_space_group_name_Hall 'P 2yb' loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, y+1/2, -z' _cell_length_a 8.4537(6) _cell_length_b 9.5906(7) _cell_length_c 10.0814(8) _cell_angle_alpha 90 _cell_angle_beta 104.847(6) _cell_angle_gamma 90 _cell_volume 790.07(10) _cell_formula_units_Z 2 _cell_measurement_temperature 110(2) _cell_measurement_reflns_used 5000 _cell_measurement_theta_min 3.53 _cell_measurement_theta_max 28.53 #----------------------------------------------------------------------------# # CRYSTAL INFORMATION # #----------------------------------------------------------------------------# _exptl_crystal_description needle _exptl_crystal_colour colourless _exptl_crystal_size_max 0.65 _exptl_crystal_size_mid 0.55 _exptl_crystal_size_min 0.2 _exptl_crystal_density_diffrn 1.498 _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 372 _exptl_special_details ; ? ; #----------------------------------------------------------------------------# # ABSORPTION CORRECTION # #----------------------------------------------------------------------------# _exptl_absorpt_coefficient_mu 0.451 _exptl_absorpt_correction_type analytical _exptl_absorpt_process_details '(CrysAlis RED; KM4CCD software, 2000)' _exptl_absorpt_correction_T_min 0.758 _exptl_absorpt_correction_T_max 0.9152 #----------------------------------------------------------------------------# # DATA COLLECTION # #----------------------------------------------------------------------------# _diffrn_ambient_temperature 110(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'KUMA KM4 CCD \k-geometry diffractometer' _diffrn_measurement_method \w _diffrn_reflns_av_R_equivalents 0.023 _diffrn_reflns_av_unetI/netI 0.019 _diffrn_reflns_number 5191 _diffrn_reflns_limit_h_min -10 _diffrn_reflns_limit_h_max 10 _diffrn_reflns_limit_k_min -11 _diffrn_reflns_limit_k_max 12 _diffrn_reflns_limit_l_min -8 _diffrn_reflns_limit_l_max 13 _diffrn_reflns_theta_min 3.53 _diffrn_reflns_theta_max 27.5 _diffrn_reflns_theta_full 27.5 _diffrn_measured_fraction_theta_full 0.981 _diffrn_measured_fraction_theta_max 0.981 _reflns_number_total 3383 _reflns_number_gt 3330 _reflns_threshold_expression >2sigma(I) #----------------------------------------------------------------------------# # COMPUTER PROGRAMS USED # #----------------------------------------------------------------------------# _computing_data_collection 'CrysAlis CCD (KM4CCD software, 2000)' _computing_cell_refinement 'CrysAlis RED (KM4CCD software, 2000)' _computing_data_reduction 'CrysAlis RED' _computing_structure_solution 'SHELXS-97 (Sheldrick, 1990)' _computing_structure_refinement 'SHELXL-97 (Sheldrick, 1997)' #----------------------------------------------------------------------------# # REFINEMENT INFORMATION # #----------------------------------------------------------------------------# _refine_special_details ; Refinement of F^2^ against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The threshold expression of F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.0319P)^2^+0.1845P] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_ls_hydrogen_treatment mixed _refine_ls_extinction_method SHELXL _refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^ _refine_ls_extinction_coef 0.021(2) _refine_ls_number_reflns 3383 _refine_ls_number_parameters 268 _refine_ls_number_restraints 1 _refine_ls_R_factor_all 0.0205 _refine_ls_R_factor_gt 0.0201 _refine_ls_wR_factor_ref 0.0527 _refine_ls_wR_factor_gt 0.0524 _refine_ls_goodness_of_fit_ref 1.028 _refine_ls_restrained_S_all 1.028 _refine_ls_shift/su_max 0.001 _refine_ls_shift/su_mean 0 _refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881' _refine_ls_abs_structure_Flack 0.03(4) _refine_diff_density_max 0.206 _refine_diff_density_min -0.219 _refine_diff_density_rms 0.041 #----------------------------------------------------------------------------# # ATOMIC TYPES, COORDINATES AND THERMAL PARAMETERS # #----------------------------------------------------------------------------# loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' H H 0 0 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0106 0.006 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' P P 0.1023 0.0942 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' S S 0.1246 0.1234 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_occupancy _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group P1 P 0.31419(4) 0.13856(4) 0.51866(3) 0.01188(8) Uani 1 d . . . S1 S 0.06394(4) 0.14926(3) 0.42450(3) 0.01602(8) Uani 1 d . . . S2 S 0.36907(5) 0.19891(4) 0.70733(3) 0.02093(9) Uani 1 d . . . O1 O 0.33756(12) -0.02317(10) 0.48582(10) 0.0150(2) Uani 1 d . . . O2 O 0.55766(12) 0.11003(11) 0.13509(10) 0.0186(2) Uani 1 d . . . O3 O 0.68882(13) 0.10452(12) 0.35870(11) 0.0209(2) Uani 1 d . . . N1 N 0.42599(15) 0.21671(14) 0.43264(12) 0.0144(2) Uani 1 d . . . H1N H 0.464(3) 0.279(2) 0.462(2) 0.024(6) Uiso 1 d . . . N2 N 0.01631(17) 0.51314(15) 0.27066(14) 0.0182(3) Uani 1 d . . . H2N H -0.022(2) 0.560(2) 0.305(2) 0.018(5) Uiso 1 d . . . C1 C 0.05011(19) -0.03400(16) 0.37620(17) 0.0206(3) Uani 1 d . . . H11 H -0.052(3) -0.073(2) 0.385(2) 0.027(5) Uiso 1 d . . . H12 H 0.052(3) -0.042(2) 0.282(2) 0.025(5) Uiso 1 d . . . C2 C 0.19165(17) -0.10723(17) 0.47374(17) 0.0197(3) Uani 1 d . . . H21 H 0.175(2) -0.116(2) 0.565(2) 0.021(5) Uiso 1 d . . . H22 H 0.216(3) -0.198(2) 0.431(2) 0.030(5) Uiso 1 d . . . C3 C 0.41394(16) 0.19809(16) 0.28734(13) 0.0133(2) Uani 1 d . . . H31 H 0.328(2) 0.134(2) 0.2495(16) 0.012(4) Uiso 1 d . . . C4 C 0.57024(16) 0.13171(16) 0.26796(13) 0.0142(2) Uani 1 d . . . C5 C 0.38079(17) 0.33826(15) 0.21017(14) 0.0156(3) Uani 1 d . . . H51 H 0.472(2) 0.404(2) 0.2510(19) 0.018(4) Uiso 1 d . . . H52 H 0.386(2) 0.316(2) 0.115(2) 0.019(4) Uiso 1 d . . . C6 C 0.21879(17) 0.39838(15) 0.21098(15) 0.0154(3) Uani 1 d . . . C7 C 0.18169(19) 0.48428(16) 0.30660(15) 0.0180(3) Uani 1 d . . . H71 H 0.252(3) 0.526(2) 0.388(2) 0.029(5) Uiso 1 d . . . C8 C -0.05615(18) 0.44584(15) 0.15042(14) 0.0162(3) Uani 1 d . . . C9 C -0.21752(19) 0.44565(17) 0.07278(16) 0.0198(3) Uani 1 d . . . H91 H -0.298(3) 0.503(2) 0.101(2) 0.033(6) Uiso 1 d . . . C10 C -0.2544(2) 0.36681(17) -0.04617(16) 0.0222(3) Uani 1 d . . . H101 H -0.362(3) 0.364(2) -0.104(2) 0.033(6) Uiso 1 d . . . C11 C -0.1342(2) 0.28909(17) -0.08656(16) 0.0213(3) Uani 1 d . . . H111 H -0.165(2) 0.226(2) -0.169(2) 0.028(5) Uiso 1 d . . . C21 C 0.70033(19) 0.05128(18) 0.10218(16) 0.0210(3) Uani 1 d . . . H211 H 0.676(2) 0.055(3) 0.001(2) 0.029(5) Uiso 1 d . . . H212 H 0.722(3) -0.041(3) 0.137(2) 0.028(5) Uiso 1 d . . . H213 H 0.794(2) 0.108(2) 0.1377(19) 0.023(5) Uiso 1 d . . . C12 C 0.02634(19) 0.29095(16) -0.01026(15) 0.0176(3) Uani 1 d . . . H121 H 0.108(2) 0.233(2) -0.0345(19) 0.018(4) Uiso 1 d . . . C13 C 0.06826(17) 0.37099(16) 0.11017(14) 0.0145(3) Uani 1 d . . . loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 P1 0.01148(15) 0.01096(16) 0.01334(15) 0.00139(12) 0.00345(11) 0.00066(12) S1 0.01124(15) 0.01403(17) 0.02260(16) 0.00166(13) 0.00400(11) 0.00192(13) S2 0.02683(19) 0.02186(18) 0.01431(16) -0.00187(14) 0.00563(13) -0.00255(15) O1 0.0125(5) 0.0111(5) 0.0211(5) 0.0015(4) 0.0036(4) 0.0014(3) O2 0.0168(5) 0.0237(6) 0.0157(5) -0.0017(4) 0.0046(4) 0.0023(4) O3 0.0158(5) 0.0262(6) 0.0192(5) 0.0002(4) 0.0015(4) 0.0043(4) N1 0.0145(6) 0.0136(6) 0.0152(5) -0.0009(5) 0.0039(4) -0.0042(5) N2 0.0219(7) 0.0154(6) 0.0196(6) -0.0041(5) 0.0096(5) 0.0020(5) C1 0.0149(7) 0.0161(7) 0.0286(8) -0.0043(6) 0.0013(6) -0.0011(5) C2 0.0148(7) 0.0128(7) 0.0309(8) 0.0004(5) 0.0049(6) -0.0013(5) C3 0.0125(6) 0.0137(6) 0.0136(6) 0.0009(5) 0.0032(4) -0.0021(5) C4 0.0145(6) 0.0115(6) 0.0164(6) 0.0010(5) 0.0035(5) -0.0018(5) C5 0.0168(7) 0.0142(7) 0.0162(6) 0.0038(5) 0.0051(5) -0.0003(5) C6 0.0165(7) 0.0135(7) 0.0161(7) 0.0035(5) 0.0042(5) 0.0006(5) C7 0.0218(7) 0.0160(7) 0.0155(7) 0.0004(5) 0.0039(5) -0.0003(5) C8 0.0204(7) 0.0122(7) 0.0176(6) 0.0010(5) 0.0075(5) 0.0002(5) C9 0.0174(7) 0.0171(7) 0.0265(7) 0.0010(6) 0.0084(6) 0.0023(6) C10 0.0183(7) 0.0200(8) 0.0259(8) 0.0010(6) 0.0011(6) -0.0024(6) C11 0.0245(8) 0.0191(8) 0.0194(7) -0.0034(6) 0.0038(6) -0.0040(6) C21 0.0222(8) 0.0215(8) 0.0216(7) -0.0025(6) 0.0094(6) 0.0028(6) C12 0.0219(8) 0.0141(7) 0.0185(6) -0.0004(5) 0.0082(5) 0.0004(5) C13 0.0166(6) 0.0123(6) 0.0153(6) 0.0029(5) 0.0052(5) 0.0006(5) #----------------------------------------------------------------------------# # MOLECULAR GEOMETRY # #----------------------------------------------------------------------------# _geom_special_details ; All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag P1 O1 1.6088(11) . ? P1 N1 1.6208(12) . ? P1 S2 1.9277(5) . ? P1 S1 2.0876(5) . ? S1 C1 1.8196(16) . ? O1 C2 1.4523(17) . ? O2 C4 1.3326(17) . ? O2 C21 1.4448(18) . ? O3 C4 1.2000(17) . ? N1 C3 1.4531(17) . ? N1 H1N 0.71(2) . ? N2 C8 1.371(2) . ? N2 C7 1.379(2) . ? N2 H2N 0.69(2) . ? C1 C2 1.513(2) . ? C1 H11 0.96(2) . ? C1 H12 0.95(2) . ? C2 H21 0.97(2) . ? C2 H22 1.01(2) . ? C3 C4 1.5237(18) . ? C3 C5 1.542(2) . ? C3 H31 0.950(18) . ? C5 C6 1.4879(19) . ? C5 H51 1.00(2) . ? C5 H52 0.993(19) . ? C6 C7 1.364(2) . ? C6 C13 1.435(2) . ? C7 H71 0.97(2) . ? C8 C9 1.388(2) . ? C8 C13 1.416(2) . ? C9 C10 1.384(2) . ? C9 H91 0.98(2) . ? C10 C11 1.403(2) . ? C10 H101 0.95(2) . ? C11 C12 1.378(2) . ? C11 H111 1.01(2) . ? C21 H211 0.99(2) . ? C21 H212 0.95(2) . ? C21 H213 0.96(2) . ? C12 C13 1.403(2) . ? C12 H121 0.96(2) . ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag O1 P1 N1 102.51(6) . . ? O1 P1 S2 118.77(4) . . ? N1 P1 S2 111.30(5) . . ? O1 P1 S1 96.74(4) . . ? N1 P1 S1 113.32(5) . . ? S2 P1 S1 113.18(2) . . ? C1 S1 P1 93.57(5) . . ? C2 O1 P1 113.96(9) . . ? C4 O2 C21 115.81(11) . . ? C3 N1 P1 125.64(10) . . ? C3 N1 H1N 115.6(18) . . ? P1 N1 H1N 115.7(18) . . ? C8 N2 C7 109.32(13) . . ? C8 N2 H2N 126.1(16) . . ? C7 N2 H2N 124.3(16) . . ? C2 C1 S1 106.77(11) . . ? C2 C1 H11 109.5(13) . . ? S1 C1 H11 110.4(13) . . ? C2 C1 H12 113.4(12) . . ? S1 C1 H12 109.1(13) . . ? H11 C1 H12 107.7(17) . . ? O1 C2 C1 108.06(13) . . ? O1 C2 H21 107.4(12) . . ? C1 C2 H21 112.0(12) . . ? O1 C2 H22 104.6(13) . . ? C1 C2 H22 109.3(12) . . ? H21 C2 H22 115.0(17) . . ? N1 C3 C4 109.97(11) . . ? N1 C3 C5 110.98(12) . . ? C4 C3 C5 110.54(11) . . ? N1 C3 H31 109.5(10) . . ? C4 C3 H31 105.9(11) . . ? C5 C3 H31 109.8(11) . . ? O3 C4 O2 124.64(13) . . ? O3 C4 C3 125.14(12) . . ? O2 C4 C3 110.22(11) . . ? C6 C5 C3 112.55(11) . . ? C6 C5 H51 111.5(11) . . ? C3 C5 H51 108.7(11) . . ? C6 C5 H52 110.8(12) . . ? C3 C5 H52 104.6(13) . . ? H51 C5 H52 108.4(16) . . ? C7 C6 C13 106.76(13) . . ? C7 C6 C5 128.06(14) . . ? C13 C6 C5 125.15(13) . . ? C6 C7 N2 109.67(14) . . ? C6 C7 H71 130.4(13) . . ? N2 C7 H71 120.0(13) . . ? N2 C8 C9 130.61(14) . . ? N2 C8 C13 107.19(13) . . ? C9 C8 C13 122.19(14) . . ? C10 C9 C8 117.40(14) . . ? C10 C9 H91 122.9(13) . . ? C8 C9 H91 119.6(13) . . ? C9 C10 C11 121.50(14) . . ? C9 C10 H101 121.0(14) . . ? C11 C10 H101 117.5(13) . . ? C12 C11 C10 120.97(14) . . ? C12 C11 H111 118.5(12) . . ? C10 C11 H111 120.5(12) . . ? O2 C21 H211 105.1(12) . . ? O2 C21 H212 111.6(13) . . ? H211 C21 H212 112.4(18) . . ? O2 C21 H213 110.7(12) . . ? H211 C21 H213 107.4(17) . . ? H212 C21 H213 109.5(18) . . ? C11 C12 C13 118.97(14) . . ? C11 C12 H121 121.1(11) . . ? C13 C12 H121 119.7(11) . . ? C12 C13 C8 118.94(13) . . ? C12 C13 C6 134.00(14) . . ? C8 C13 C6 107.06(12) . . ? loop_ _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4 _geom_torsion _geom_torsion_site_symmetry_1 _geom_torsion_site_symmetry_2 _geom_torsion_site_symmetry_3 _geom_torsion_site_symmetry_4 _geom_torsion_publ_flag O1 P1 S1 C1 1.36(7) . . . . ? N1 P1 S1 C1 108.12(8) . . . . ? S2 P1 S1 C1 -123.94(6) . . . . ? N1 P1 O1 C2 -144.14(10) . . . . ? S2 P1 O1 C2 92.75(10) . . . . ? S1 P1 O1 C2 -28.38(10) . . . . ? O1 P1 N1 C3 53.54(13) . . . . ? S2 P1 N1 C3 -178.46(10) . . . . ? S1 P1 N1 C3 -49.56(13) . . . . ? P1 S1 C1 C2 23.42(11) . . . . ? P1 O1 C2 C1 50.04(15) . . . . ? S1 C1 C2 O1 -45.05(15) . . . . ? P1 N1 C3 C4 -114.78(12) . . . . ? P1 N1 C3 C5 122.59(12) . . . . ? C21 O2 C4 O3 -0.9(2) . . . . ? C21 O2 C4 C3 178.12(12) . . . . ? N1 C3 C4 O3 -3.1(2) . . . . ? C5 C3 C4 O3 119.78(15) . . . . ? N1 C3 C4 O2 177.89(12) . . . . ? C5 C3 C4 O2 -59.22(15) . . . . ? N1 C3 C5 C6 -65.06(15) . . . . ? C4 C3 C5 C6 172.64(12) . . . . ? C3 C5 C6 C7 88.30(18) . . . . ? C3 C5 C6 C13 -89.28(17) . . . . ? C13 C6 C7 N2 -0.48(17) . . . . ? C5 C6 C7 N2 -178.41(13) . . . . ? C8 N2 C7 C6 -0.04(18) . . . . ? C7 N2 C8 C9 -178.25(16) . . . . ? C7 N2 C8 C13 0.54(17) . . . . ? N2 C8 C9 C10 179.70(15) . . . . ? C13 C8 C9 C10 1.1(2) . . . . ? C8 C9 C10 C11 0.5(2) . . . . ? C9 C10 C11 C12 -1.4(3) . . . . ? C10 C11 C12 C13 0.7(2) . . . . ? C11 C12 C13 C8 0.8(2) . . . . ? C11 C12 C13 C6 -178.96(16) . . . . ? N2 C8 C13 C12 179.35(13) . . . . ? C9 C8 C13 C12 -1.7(2) . . . . ? N2 C8 C13 C6 -0.82(16) . . . . ? C9 C8 C13 C6 178.10(14) . . . . ? C7 C6 C13 C12 -179.40(16) . . . . ? C5 C6 C13 C12 -1.4(3) . . . . ? C7 C6 C13 C8 0.79(16) . . . . ? C5 C6 C13 C8 178.80(13) . . . . ? loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_site_symmetry_A C5 H52 O2 0.993(19) 2.43(2) 2.8600(18) 105.5(14) . C9 H91 S2 0.98(2) 2.86(2) 3.7297(16) 148.3(17) 2_556 C7 H71 O3 0.97(2) 2.58(2) 3.4671(18) 151.9(17) 2_656 N1 H1N O1 0.71(2) 2.50(2) 3.1706(16) 160(2) 2_656 _chemical_name_common 'N-(2-thiono-1,3,2-oxathiaphospholanyl)tryptophan methyl ester'