################################################################################ # # File:  # Date: 08-Dec-97 19:02:46 # # This file was created by software developed by the # Nucleic Acid Database Project # # H. M. Berman, W. K. Olson, D. L. Beveridge, J. D. Westbrook, A. Gelbin, # T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. Schneider. (1992). # The Nucleic Acid Database: A Comprehensive Relational Database of # Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, 751-759. # # Questions or comments should be directed to: # # # ndbadmin@ndbserver.rutgers.edu # ################################################################################ data_G_deoxyriboseC3endo_O3H_O5P_anti_+sc # _chem_comp.id G_deoxyriboseC3endo_O3H_O5P_anti_+sc _chem_comp.name '2'-deoxyguanosine-5'-phosphate' _chem_comp.type 'DNA linking' _chem_comp.model_details ;Model constructed for 2'-deoxyguanosine-5'-phosphate from subcomponents for 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. ; _chem_comp.parent . _chem_comp.formula 'H10 C10 N5 O7 P1 ' _chem_comp.formula_weight 343.22 _chem_comp.number_atoms_all 33 _chem_comp.number_atoms_nh 23 # loop_ _chem_comp_link.link_id _chem_comp_link.type_comp_1 _chem_comp_link.type_comp_2 all_ribose_purine sugar base ribose_O5_PO4 sugar phosphate # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.substruct_code _chem_comp_atom.charge _chem_comp_atom.model_cartn_x _chem_comp_atom.model_cartn_y _chem_comp_atom.model_cartn_z G_deoxyriboseC3endo_O3H_O5P_anti_+sc N1 N base 0 6.3172 6.5940 2.8379 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2 C base 0 6.2836 5.9376 1.6346 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N3 N base 0 5.8290 4.7053 1.4782 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4 C base 0 5.3880 4.1777 2.6418 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5 C base 0 5.3733 4.7527 3.8964 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6 C base 0 5.8777 6.0682 4.0486 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N7 N base 0 4.6843 3.9519 4.7945 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C8 C base 0 4.3009 2.9246 4.0860 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N9 N base 0 4.6974 2.9951 2.7732 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N2 N base 0 6.7496 6.6194 0.5789 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O6 O base 0 5.9524 6.7470 5.0810 G_deoxyriboseC3endo_O3H_O5P_anti_+sc H8 H base 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc HA2 H base 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc HB2 H base 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1* C sugar 0 4.7289 1.8925 1.7985 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2* C sugar 0 6.0208 1.0965 1.8722 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3* C sugar 0 5.6670 -0.0316 2.8251 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4* C sugar 0 4.2063 -0.2909 2.4899 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5* C sugar 0 3.3672 -0.8679 3.6078 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O3* O sugar 0 6.4850 -1.1757 2.6463 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4* O sugar 0 3.6765 1.0036 2.1108 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O5* O sugar 0 3.4786 -0.0816 4.8065 G_deoxyriboseC3endo_O3H_O5P_anti_+sc HA1* H sugar 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc HA2* H sugar 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc HB2* H sugar 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc HA3* H sugar 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc HA4* H sugar 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc HA5* H sugar 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc HB5* H sugar 0 . . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc P P phosphate 0 2.2639 0.8206 5.3051 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O1P O phosphate 0 1.2308 -0.0191 5.9630 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O2P O phosphate -1 2.7691 2.0276 6.0072 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O O phosphate -1 1.6622 1.3183 4.0419 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id _chem_comp_chir.number_atoms_all _chem_comp_chir.number_atoms_nh _chem_comp_chir.volume_flag _chem_comp_chir.volume_three _chem_comp_chir.volume_three_esd G_deoxyriboseC3endo_O3H_O5P_anti_+sc 1 C1* 4 3 sign 2.49 0.03 G_deoxyriboseC3endo_O3H_O5P_anti_+sc 2 C3* 4 3 sign -2.51 0.10 G_deoxyriboseC3endo_O3H_O5P_anti_+sc 3 C4* 4 3 sign 2.50 0.04 # loop_ _chem_comp_chir_atom.chir_id _chem_comp_chir_atom.enum _chem_comp_chir_atom.comp_id _chem_comp_chir_atom.atom_id 1 1 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4* 1 2 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2* 1 3 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N 2 1 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2* 2 2 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4* 2 3 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O3* 3 1 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3* 3 2 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4* 3 3 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5* # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd G_deoxyriboseC3endo_O3H_O5P_anti_+sc N1 C2 sing 1.3717 0.0089 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2 N3 doub 1.3232 0.0096 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N3 C4 sing 1.3512 0.0084 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4 C5 doub 1.3792 0.0073 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5 C6 sing 1.4166 0.0092 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6 N1 sing 1.3916 0.0081 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5 N7 sing 1.3867 0.0067 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N7 C8 doub 1.3063 0.0077 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C8 N9 sing 1.3736 0.0082 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N9 C4 sing 1.3751 0.0083 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2 N2 sing 1.3403 0.0096 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6 O6 doub 1.2379 0.0090 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C8 H8 sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc N2 HA2 sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc N2 HB2 sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1* C2* sing 1.5192 0.0069 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2* C3* sing 1.5186 0.0110 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3* C4* sing 1.5212 0.0081 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4* O4* sing 1.4492 0.0060 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4* C1* sing 1.4123 0.0065 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3* O3* sing 1.4178 0.0067 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4* C5* sing 1.5120 0.0117 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5* O5* sing 1.4379 0.0099 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1* HA1* sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2* HA2* sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2* HB2* sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3* HA3* sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4* HA4* sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5* HA5* sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5* HB5* sing . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc P O1P doub 1.485 0.017 G_deoxyriboseC3endo_O3H_O5P_anti_+sc P O2P sing 1.485 0.017 G_deoxyriboseC3endo_O3H_O5P_anti_+sc P O sing 1.485 0.017 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1* N9 2 1.4722 0.0124 G_deoxyriboseC3endo_O3H_O5P_anti_+sc P O5* sing 1.593 0.010 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd _chem_comp_angle.value_dist _chem_comp_angle.value_dist_esd G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6 N1 C2 125.09 0.66 2.45 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N1 C2 N3 123.93 0.56 2.38 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2 N3 C4 111.87 0.61 2.22 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N3 C4 C5 128.61 0.66 2.46 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4 C5 C6 118.80 0.68 2.41 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5 C6 N1 111.60 0.61 2.32 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4 C5 N7 110.76 0.51 2.28 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5 N7 C8 104.36 0.59 2.13 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N7 C8 N9 113.12 0.67 2.24 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C8 N9 C4 106.33 0.49 2.20 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N9 C4 C5 105.41 0.42 2.19 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N3 C4 N9 125.96 0.79 2.43 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6 C5 N7 130.42 0.66 2.54 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N1 C2 N2 116.07 0.91 2.30 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6 C2 N2 143.71 0.76 3.62 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N1 C6 O6 120.01 0.73 2.28 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5 C6 O6 128.36 0.66 2.39 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1* C2* C3* 102.80 0.51 2.37 0.02 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2* C3* C4* 102.26 0.57 2.37 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3* C4* O4* 104.79 0.66 2.35 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4* O4* C1* 110.21 0.61 2.35 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4* C1* C2* 107.01 0.63 2.36 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2* C3* O3* 112.71 2.71 2.44 0.04 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4* C3* O3* 112.97 1.78 2.45 0.03 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5* C4* C3* 115.64 1.14 2.57 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5* C4* O4* 109.36 0.32 2.42 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O5* C5* C4* 111.28 1.54 2.42 0.02 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O1P P O2P 119.6 1.5 . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc O1P P O 108.3 3.2 . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc O2P P O 107.3 3.2 . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4 N9 C1* 125.591 1.165644 2.528 0.015 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C8 N9 C1* 127.981 1.182104 2.554 0.019 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N9 C1* C2* 112.573 1.208603 2.499 0.019 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N9 C1* O4* 108.12 0.9 2.325 0.011 G_deoxyriboseC3endo_O3H_O5P_anti_+sc P O5* C5* 120.9 1.6 . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc O1P P O5* 110.7 1.2 . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc O2P P O5* 110.7 1.2 . . G_deoxyriboseC3endo_O3H_O5P_anti_+sc O P O5* 104.0 1.9 . . # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N1-C2-N3-C4 N1 C2 N3 C4 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2-N3-C4-C5 C2 N3 C4 C5 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N3-C4-C5-C6 N3 C4 C5 C6 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4-C5-C6-N1 C4 C5 C6 N1 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5-C6-N1-C2 C5 C6 N1 C2 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6-N1-C2-N3 C6 N1 C2 N3 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N9-C4-C5-N7 N9 C4 C5 N7 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4-C5-N7-C8 C4 C5 N7 C8 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5-N7-C8-N9 C5 N7 C8 N9 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N7-C8-N9-C4 N7 C8 N9 C4 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C8-N9-C4-C5 C8 N9 C4 C5 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6-N1-C2-N2 C6 N1 C2 N2 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2-N1-C6-O6 C2 N1 C6 O6 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4*-O4*-C1*-C2* C4* O4* C1* C2* G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4*-C1*-C2*-C3* O4* C1* C2* C3* G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1*-C2*-C3*-C4* C1* C2* C3* C4* G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2*-C3*-C4*-O4* C2* C3* C4* O4* G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3*-C4*-O4*-C1* C3* C4* O4* C1* G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2*-C3*-C4*-C5* C2* C3* C4* C5* G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3*-C4*-C5*-O5* C3* C4* C5* O5* G_deoxyriboseC3endo_O3H_O5P_anti_+sc O3*-C3*-C4*-C5* O3* C3* C4* C5* G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4*-C4*-C3*-O3* O4* C4* C3* O3* G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4*-C4*-C5*-O5* O4* C4* C5* O5* G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5*-C4*-O4*-C1* C5* C4* O4* C1* G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1*-C2*-C3*-O3* C1* C2* C3* O3* G_deoxyriboseC3endo_O3H_O5P_anti_+sc chi_anti_C3endo_purine O4* C1* N9 C4 # loop_ _chem_comp_tor_value.comp_id _chem_comp_tor_value.tor_id _chem_comp_tor_value.angle _chem_comp_tor_value.angle_esd _chem_comp_tor_value.dist _chem_comp_tor_value.dist_esd G_deoxyriboseC3endo_O3H_O5P_anti_+sc N1-C2-N3-C4 0.69 1.98 2.60 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2-N3-C4-C5 359.60 1.63 2.71 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N3-C4-C5-C6 359.84 1.97 2.91 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4-C5-C6-N1 0.43 1.95 2.60 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5-C6-N1-C2 359.81 2.66 2.71 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6-N1-C2-N3 359.56 3.03 2.91 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N9-C4-C5-N7 359.75 1.10 2.24 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4-C5-N7-C8 0.08 0.93 2.20 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5-N7-C8-N9 0.13 0.75 2.19 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc N7-C8-N9-C4 359.71 0.86 2.28 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C8-N9-C4-C5 0.31 1.00 2.13 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C6-N1-C2-N2 179.75 2.47 3.62 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2-N1-C6-O6 179.98 2.41 3.56 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C4*-O4*-C1*-C2* 4.17 7.07 2.37 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4*-C1*-C2*-C3* 335.52 5.35 2.35 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1*-C2*-C3*-C4* 34.16 2.49 2.35 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2*-C3*-C4*-O4* 327.62 3.09 2.36 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3*-C4*-O4*-C1* 18.00 6.18 2.37 0.02 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C2*-C3*-C4*-C5* 207.16 3.23 3.73 0.01 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C3*-C4*-C5*-O5* 52.19 4.95 2.93 0.07 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O3*-C3*-C4*-C5* 85.70 4.91 3.28 0.06 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4*-C4*-C3*-O3* 206.16 5.02 3.59 0.02 G_deoxyriboseC3endo_O3H_O5P_anti_+sc O4*-C4*-C5*-O5* 293.22 4.75 2.91 0.07 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C5*-C4*-O4*-C1* 142.55 6.60 3.57 0.03 G_deoxyriboseC3endo_O3H_O5P_anti_+sc C1*-C2*-C3*-O3* 155.80 4.77 3.63 0.02 G_deoxyriboseC3endo_O3H_O5P_anti_+sc chi_anti_C3endo_purine 193.3 14.0 . . #