################################################################################ # # File:  # Date: 08-Dec-97 13:26:37 # # 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_pro # _chem_comp.type base _chem_comp.id cyt_pro _chem_comp.parent cyt _chem_comp.name 'protonated 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 protonated 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_pro N1 N base 0 4.2132 0.0760 0.5473 cyt_pro C2 C base 0 4.8783 0.6935 -0.4921 cyt_pro N3 N base 1 6.0912 0.1439 -0.8365 cyt_pro C4 C base 0 6.6277 -0.9472 -0.2464 cyt_pro C5 C base 0 5.9118 -1.5493 0.8128 cyt_pro C6 C base 0 4.7322 -1.0243 1.1715 cyt_pro O2 O base 0 4.4255 1.6595 -1.0779 cyt_pro N4 N base 0 7.7867 -1.3968 -0.6721 cyt_pro C1* C base 0 2.8954 0.6181 0.9360 cyt_pro H4A H base 0 . . . cyt_pro H4B H base 0 . . . cyt_pro H5 H base 0 . . . cyt_pro 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_pro N1 C2 sing 1.3798 0.0117 cyt_pro C2 N3 sing 1.3755 0.0161 cyt_pro N3 C4 doub 1.3515 0.0082 cyt_pro C4 C5 sing 1.4131 0.0072 cyt_pro C5 C6 doub 1.3401 0.0101 cyt_pro C6 N1 sing 1.3673 0.0094 cyt_pro C2 O2 doub 1.2171 0.0128 cyt_pro C4 N4 sing 1.3140 0.0127 cyt_pro N1 C1* sing 1.4771 0.0215 cyt_pro N4 H4A sing . . cyt_pro N4 H4B sing . . cyt_pro C5 H5 sing . . cyt_pro 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_pro C6 N1 C2 121.38 0.82 2.40 0.02 cyt_pro N1 C2 N3 115.77 1.99 2.33 0.02 cyt_pro C2 N3 C4 124.27 2.11 2.41 0.04 cyt_pro N3 C4 C5 118.03 1.57 2.37 0.02 cyt_pro C4 C5 C6 118.65 0.86 2.37 0.01 cyt_pro C5 C6 N1 121.81 0.84 2.37 0.02 cyt_pro N1 C2 O2 122.57 1.72 2.28 0.01 cyt_pro N3 C2 O2 121.64 0.79 2.26 0.01 cyt_pro N3 C4 N4 119.01 0.99 2.30 0.01 cyt_pro C5 C4 N4 122.95 1.23 2.40 0.01 cyt_pro C6 N1 C1* 120.88 1.03 2.47 0.03 cyt_pro C2 N1 C1* 117.57 1.45 2.44 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_pro N1-C2-N3-C4 N1 C2 N3 C4 cyt_pro C2-N3-C4-C5 C2 N3 C4 C5 cyt_pro N3-C4-C5-C6 N3 C4 C5 C6 cyt_pro C4-C5-C6-N1 C4 C5 C6 N1 cyt_pro C5-C6-N1-C2 C5 C6 N1 C2 cyt_pro C6-N1-C2-N3 C6 N1 C2 N3 cyt_pro C6-N1-C2-O2 C6 N1 C2 O2 cyt_pro C4-N3-C2-O2 C4 N3 C2 O2 cyt_pro C2-N3-C4-N4 C2 N3 C4 N4 cyt_pro C6-C5-C4-N4 C6 C5 C4 N4 cyt_pro C5-C6-N1-C1* C5 C6 N1 C1* cyt_pro O2-C2-N1-C1* O2 C2 N1 C1* cyt_pro 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_pro N1-C2-N3-C4 1.42 2.24 2.74 0.02 cyt_pro C2-N3-C4-C5 358.63 2.10 2.79 0.03 cyt_pro N3-C4-C5-C6 0.80 2.11 2.69 0.03 cyt_pro C4-C5-C6-N1 359.60 1.10 2.74 0.02 cyt_pro C5-C6-N1-C2 0.48 1.66 2.79 0.03 cyt_pro C6-N1-C2-N3 359.07 2.58 2.69 0.03 cyt_pro C6-N1-C2-O2 178.69 2.43 3.51 0.01 cyt_pro C4-N3-C2-O2 181.78 2.33 3.51 0.02 cyt_pro C2-N3-C4-N4 178.99 2.06 3.59 0.03 cyt_pro C6-C5-C4-N4 180.44 2.01 3.59 0.01 cyt_pro C5-C6-N1-C1* 178.48 4.54 3.71 0.04 cyt_pro O2-C2-N1-C1* 0.67 4.19 2.73 0.03 cyt_pro N3-C2-N1-C1* 181.04 4.67 3.68 0.02 #