################################################################################ # # File:  # Date: 08-Dec-97 13:25:40 # # 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_cyt # _chem_comp.type base _chem_comp.id cyt _chem_comp.parent cyt _chem_comp.name cytosine _chem_comp.formula 'H4 C5 N3 O1 ' _chem_comp.formula_weight 122.11 _chem_comp.number_atoms_all 13 _chem_comp.number_atoms_nh 9 _chem_comp.model_details 'Model constructed for cytosine 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 cyt N1 N base 0 -0.6349 0.6660 2.2475 cyt C2 C base 0 0.5951 0.0051 2.2119 cyt N3 N base 0 1.6514 0.5405 2.8698 cyt C4 C base 0 1.5043 1.6751 3.5611 cyt C5 C base 0 0.2574 2.3612 3.6174 cyt C6 C base 0 -0.7738 1.8280 2.9506 cyt O2 O base 0 0.6876 -1.0537 1.5765 cyt N4 N base 0 2.5651 2.1627 4.2040 cyt C1* C base 0 -1.7694 0.0843 1.5131 cyt H4A H base 0 . . . cyt H4B H base 0 . . . cyt H5 H base 0 . . . cyt 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 cyt N1 C2 sing 1.3967 0.0096 cyt C2 N3 sing 1.3546 0.0099 cyt N3 C4 doub 1.3367 0.0100 cyt C4 C5 sing 1.4243 0.0088 cyt C5 C6 doub 1.3389 0.0087 cyt C6 N1 sing 1.3653 0.0070 cyt C2 O2 doub 1.2383 0.0089 cyt C4 N4 sing 1.3328 0.0097 cyt N1 C1* sing 1.4713 0.0169 cyt N4 H4A sing . . cyt N4 H4B sing . . cyt C5 H5 sing . . cyt 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 cyt C6 N1 C2 120.32 0.52 2.40 0.01 cyt N1 C2 N3 119.12 0.65 2.37 0.01 cyt C2 N3 C4 120.02 0.46 2.33 0.02 cyt N3 C4 C5 121.68 0.70 2.41 0.01 cyt C4 C5 C6 117.53 0.73 2.36 0.01 cyt C5 C6 N1 121.12 0.51 2.35 0.01 cyt N1 C2 O2 118.93 0.71 2.27 0.01 cyt N3 C2 O2 121.95 0.67 2.27 0.01 cyt N3 C4 N4 118.21 0.92 2.29 0.01 cyt C5 C4 N4 120.11 0.73 2.39 0.01 cyt C6 N1 C1* 120.96 1.24 2.47 0.02 cyt C2 N1 C1* 118.59 1.30 2.47 0.02 # 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 cyt N1-C2-N3-C4 N1 C2 N3 C4 cyt C2-N3-C4-C5 C2 N3 C4 C5 cyt N3-C4-C5-C6 N3 C4 C5 C6 cyt C4-C5-C6-N1 C4 C5 C6 N1 cyt C5-C6-N1-C2 C5 C6 N1 C2 cyt C6-N1-C2-N3 C6 N1 C2 N3 cyt C6-N1-C2-O2 C6 N1 C2 O2 cyt C4-N3-C2-O2 C4 N3 C2 O2 cyt C2-N3-C4-N4 C2 N3 C4 N4 cyt C6-C5-C4-N4 C6 C5 C4 N4 cyt C5-C6-N1-C1* C5 C6 N1 C1* cyt O2-C2-N1-C1* O2 C2 N1 C1* cyt N3-C2-N1-C1* 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 cyt N1-C2-N3-C4 1.13 3.09 2.70 0.01 cyt C2-N3-C4-C5 359.21 2.66 2.76 0.01 cyt N3-C4-C5-C6 0.06 3.62 2.75 0.01 cyt C4-C5-C6-N1 0.28 2.05 2.70 0.01 cyt C5-C6-N1-C2 0.09 2.67 2.76 0.01 cyt C6-N1-C2-N3 359.20 4.32 2.75 0.01 cyt C6-N1-C2-O2 179.31 3.98 3.51 0.01 cyt C4-N3-C2-O2 181.02 2.75 3.47 0.01 cyt C2-N3-C4-N4 179.42 2.48 3.54 0.02 cyt C6-C5-C4-N4 179.86 3.56 3.58 0.01 cyt C5-C6-N1-C1* 180.14 4.19 3.70 0.02 cyt O2-C2-N1-C1* 359.25 5.35 2.71 0.04 cyt N3-C2-N1-C1* 179.14 5.67 3.71 0.02 #