################################################################################ # # File:  # Date: 08-Dec-97 13:27:46 # # 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_thy # _chem_comp.type base _chem_comp.id thy _chem_comp.parent thy _chem_comp.name thymine _chem_comp.formula 'H5 C6 N2 O2 ' _chem_comp.formula_weight 137.12 _chem_comp.number_atoms_all 15 _chem_comp.number_atoms_nh 10 _chem_comp.model_details 'Model constructed for thymine 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 thy N1 N base 0 0.7932 1.5843 3.7985 thy C2 C base 0 -0.2743 0.9925 3.1603 thy N3 N base 0 0.0344 -0.1609 2.4816 thy C4 C base 0 1.2731 -0.7657 2.3799 thy C5 C base 0 2.3472 -0.0871 3.0675 thy C6 C base 0 2.0583 1.0381 3.7333 thy O2 O base 0 -1.4050 1.4469 3.1910 thy O4 O base 0 1.3929 -1.8045 1.7357 thy C5M C base 0 3.7276 -0.6647 3.0061 thy C1* C base 0 0.5520 2.8279 4.5486 thy H3 H base 0 . . . thy H6 H base 0 . . . thy HC5MA H base 0 . . . thy HC5MB H base 0 . . . thy HC5MC 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 thy N1 C2 sing 1.3773 0.0086 thy C2 N3 sing 1.3734 0.0079 thy N3 C4 sing 1.3821 0.0084 thy C4 C5 sing 1.4446 0.0088 thy C5 C6 doub 1.3390 0.0064 thy C6 N1 sing 1.3796 0.0072 thy C2 O2 doub 1.2190 0.0079 thy C4 O4 doub 1.2282 0.0090 thy C5 C5M sing 1.4977 0.0071 thy N3 H3 sing . . thy C6 H6 sing . . thy N1 C1* sing 1.4721 0.0133 thy C5M HC5MA sing . . thy C5M HC5MB sing . . thy C5M HC5MC 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 thy C6 N1 C2 121.22 0.51 2.40 0.01 thy N1 C2 N3 114.54 0.59 2.31 0.01 thy C2 N3 C4 127.22 0.53 2.47 0.01 thy N3 C4 C5 115.18 0.61 2.39 0.01 thy C4 C5 C6 118.08 0.51 2.39 0.01 thy C5 C6 N1 123.63 0.56 2.40 0.01 thy N1 C2 O2 123.17 0.83 2.28 0.01 thy N3 C2 O2 122.28 0.63 2.27 0.01 thy N3 C4 O4 119.75 0.65 2.26 0.01 thy C5 C4 O4 125.07 0.74 2.37 0.01 thy C4 C5 C5M 118.99 0.57 2.54 0.01 thy C6 C5 C5M 122.91 0.60 2.49 0.01 thy C6 N1 C1* 120.52 1.53 2.48 0.03 thy C2 N1 C1* 118.11 1.57 2.44 0.02 # 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 thy N1 C2 N3 C4 C2-N3-C4-C5 thy C2 N3 C4 C5 N3-C4-C5-C6 thy N3 C4 C5 C6 C4-C5-C6-N1 thy C4 C5 C6 N1 C5-C6-N1-C2 thy C5 C6 N1 C2 C6-N1-C2-N3 thy C6 N1 C2 N3 C6-N1-C2-O2 thy C6 N1 C2 O2 C4-N3-C2-O2 thy C4 N3 C2 O2 C2-N3-C4-O4 thy C2 N3 C4 O4 C6-C5-C4-O4 thy C6 C5 C4 O4 O4-C4-C5-C5M thy O4 C4 C5 C5M N3-C4-C5-C5M thy N3 C4 C5 C5M N1-C6-C5-C5M thy N1 C6 C5 C5M C5-C6-N1-C1* thy C5 C6 N1 C1* O2-C2-N1-C1* thy O2 C2 N1 C1* N3-C2-N1-C1* thy 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 thy N1-C2-N3-C4 359.98 2.89 2.79 0.01 thy C2-N3-C4-C5 359.70 3.25 2.84 0.01 thy N3-C4-C5-C6 0.30 2.52 2.66 0.01 thy C4-C5-C6-N1 359.99 1.37 2.79 0.01 thy C5-C6-N1-C2 359.67 2.27 2.84 0.01 thy C6-N1-C2-N3 0.33 2.74 2.66 0.01 thy C6-N1-C2-O2 180.25 2.64 3.53 0.01 thy C4-N3-C2-O2 180.07 2.74 3.57 0.01 thy C2-N3-C4-O4 179.80 2.86 3.55 0.01 thy C6-C5-C4-O4 180.19 2.21 3.54 0.01 thy O4-C4-C5-C5M 0.26 2.16 2.89 0.02 thy N3-C4-C5-C5M 180.37 2.35 3.76 0.01 thy N1-C6-C5-C5M 179.92 1.53 3.78 0.01 thy C5-C6-N1-C1* 180.14 4.18 3.73 0.02 thy O2-C2-N1-C1* 359.79 3.90 2.75 0.04 thy N3-C2-N1-C1* 179.88 3.85 3.67 0.02 #