################################################################################ # # File:  # Date: 08-Dec-97 13:28:49 # # 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_ura # _chem_comp.type base _chem_comp.id ura _chem_comp.parent ura _chem_comp.name uracil _chem_comp.formula 'H3 C5 N2 O2 ' _chem_comp.formula_weight 123.09 _chem_comp.number_atoms_all 12 _chem_comp.number_atoms_nh 9 _chem_comp.model_details 'Model constructed for uracil with an N1-glycosidic linkage.' # 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 ura N1 N base 0 -1.5487 1.1551 4.2340 ura C2 C base 0 -2.9015 1.0118 4.4650 ura N3 N base 0 -3.2653 -0.1704 5.0626 ura C4 C base 0 -2.4274 -1.1962 5.4538 ura C5 C base 0 -1.0426 -0.9698 5.1766 ura C6 C base 0 -0.6608 0.1685 4.5884 ura O2 O base 0 -3.7174 1.8660 4.1655 ura O4 O base 0 -2.9045 -2.1980 5.9877 ura C1* C base 0 -1.0952 2.3979 3.5889 ura H3 H base 0 . . . ura H5 H base 0 . . . ura H6 H base 0 . . . # 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 ura N1 C2 sing 1.3798 0.0096 ura C2 N3 sing 1.3737 0.0081 ura N3 C4 sing 1.3810 0.0102 ura C4 C5 sing 1.4304 0.0098 ura C5 C6 doub 1.3370 0.0090 ura C6 N1 sing 1.3737 0.0088 ura C2 O2 doub 1.2186 0.0081 ura C4 O4 doub 1.2314 0.0113 ura N1 C1* sing 1.4719 0.0148 ura N3 H3 sing . . ura C5 H5 sing . . ura C6 H6 sing . . # 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 ura C6 N1 C2 121.03 0.51 2.40 0.01 ura N1 C2 N3 114.92 0.70 2.32 0.01 ura C2 N3 C4 126.96 0.88 2.46 0.01 ura N3 C4 C5 114.50 0.87 2.36 0.01 ura C4 C5 C6 119.75 0.74 2.39 0.01 ura C5 C6 N1 122.69 0.53 2.38 0.01 ura N1 C2 O2 122.86 0.71 2.28 0.01 ura N3 C2 O2 122.21 0.79 2.27 0.01 ura N3 C4 O4 119.48 0.78 2.26 0.01 ura C5 C4 O4 126.01 0.67 2.37 0.01 ura C6 N1 C1* 121.30 1.42 2.48 0.02 ura C2 N1 C1* 117.54 1.32 2.44 0.01 # loop_ _chem_comp_tor.id _chem_comp_tor.comp_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 N1-C2-N3-C4 ura N1 C2 N3 C4 C2-N3-C4-C5 ura C2 N3 C4 C5 N3-C4-C5-C6 ura N3 C4 C5 C6 C4-C5-C6-N1 ura C4 C5 C6 N1 C5-C6-N1-C2 ura C5 C6 N1 C2 C6-N1-C2-N3 ura C6 N1 C2 N3 C6-N1-C2-O2 ura C6 N1 C2 O2 C4-N3-C2-O2 ura C4 N3 C2 O2 C2-N3-C4-O4 ura C2 N3 C4 O4 C6-C5-C4-O4 ura C6 C5 C4 O4 C5-C6-N1-C1* ura C5 C6 N1 C1* O2-C2-N1-C1* ura O2 C2 N1 C1* N3-C2-N1-C1* ura N3 C2 N1 C1* # 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 ura N1-C2-N3-C4 0.58 3.18 2.79 0.01 ura C2-N3-C4-C5 359.31 2.81 2.81 0.01 ura N3-C4-C5-C6 0.24 2.58 2.67 0.01 ura C4-C5-C6-N1 0.28 1.31 2.79 0.01 ura C5-C6-N1-C2 359.59 2.42 2.81 0.01 ura C6-N1-C2-N3 360.00 3.54 2.67 0.01 ura C6-N1-C2-O2 179.92 3.05 3.52 0.01 ura C4-N3-C2-O2 180.66 2.90 3.56 0.01 ura C2-N3-C4-O4 179.58 2.85 3.55 0.01 ura C6-C5-C4-O4 179.95 2.82 3.55 0.01 ura C5-C6-N1-C1* 179.92 4.33 3.72 0.02 ura O2-C2-N1-C1* 359.59 4.32 2.74 0.03 ura N3-C2-N1-C1* 179.67 4.57 3.67 0.01 #