################################################################################ # # File:  # Date: 08-Dec-97 13:23:17 # # 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_ade_pro # _chem_comp.id ade_pro _chem_comp.name 'protonated adenine' _chem_comp.type base _chem_comp.parent ade_pro _chem_comp.formula 'H4 C6 N5 ' _chem_comp.formula_weight 146.14 _chem_comp.number_atoms_all 15 _chem_comp.number_atoms_nh 11 _chem_comp.model_details 'Model constructed for protonated adenine with an N9-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 ade_pro N1 N base 1 2.0987 1.0947 -1.8269 ade_pro C2 C base 0 2.1960 2.0139 -2.8213 ade_pro N3 N base 0 3.2551 2.7086 -3.1208 ade_pro C4 C base 0 4.2955 2.4139 -2.3036 ade_pro C5 C base 0 4.3072 1.5099 -1.2656 ade_pro C6 C base 0 3.1358 0.7872 -1.0000 ade_pro N7 N base 0 5.5499 1.4578 -0.6711 ade_pro C8 C base 0 6.2567 2.3204 -1.3590 ade_pro N9 N base 0 5.5512 2.9318 -2.3637 ade_pro N6 N base 0 2.9895 -0.1185 -0.0579 ade_pro C1* C base 0 6.0373 3.9341 -3.3146 ade_pro H2 H base 0 . . . ade_pro H8 H base 0 . . . ade_pro HA6 H base 0 . . . ade_pro HB6 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 ade_pro N1 C2 sing 1.3577 0.0088 ade_pro C2 N3 doub 1.3015 0.0058 ade_pro N3 C4 sing 1.3554 0.0047 ade_pro C4 C5 doub 1.3764 0.0076 ade_pro C5 C6 sing 1.4018 0.0079 ade_pro C6 N1 doub 1.3616 0.0089 ade_pro C5 N7 sing 1.3786 0.0044 ade_pro N7 C8 doub 1.3103 0.0055 ade_pro C8 N9 sing 1.3715 0.0088 ade_pro N9 C4 sing 1.3596 0.0066 ade_pro C6 N6 sing 1.3150 0.0084 ade_pro N9 C1* sing 1.4646 0.0105 ade_pro C2 H2 sing . . ade_pro C8 H8 sing . . ade_pro N6 HA6 sing . . ade_pro N6 HB6 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 ade_pro C6 N1 C2 122.88 0.94 2.39 0.01 ade_pro N1 C2 N3 126.02 0.50 2.37 0.01 ade_pro C2 N3 C4 111.70 0.42 2.20 0.00 ade_pro N3 C4 C5 127.15 0.64 2.45 0.01 ade_pro C4 C5 C6 118.31 0.76 2.39 0.01 ade_pro C5 C6 N1 113.88 0.43 2.32 0.01 ade_pro C4 C5 N7 110.96 0.34 2.27 0.01 ade_pro C5 N7 C8 103.59 0.31 2.11 0.01 ade_pro N7 C8 N9 113.61 0.40 2.24 0.00 ade_pro C8 N9 C4 105.83 0.42 2.18 0.01 ade_pro N9 C4 C5 106.00 0.50 2.19 0.01 ade_pro N3 C4 N9 126.84 0.45 2.43 0.01 ade_pro C6 C5 N7 130.71 0.57 2.53 0.01 ade_pro N1 C6 N6 120.39 0.71 2.32 0.01 ade_pro C5 C6 N6 125.72 0.52 2.42 0.01 ade_pro C8 N9 C1* 127.56 1.65 2.54 0.02 ade_pro C4 N9 C1* 126.55 1.71 2.52 0.01 # 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 ade_pro N1-C2-N3-C4 N1 C2 N3 C4 ade_pro C2-N3-C4-C5 C2 N3 C4 C5 ade_pro N3-C4-C5-C6 N3 C4 C5 C6 ade_pro C4-C5-C6-N1 C4 C5 C6 N1 ade_pro C5-C6-N1-C2 C5 C6 N1 C2 ade_pro C6-N1-C2-N3 C6 N1 C2 N3 ade_pro N9-C4-C5-N7 N9 C4 C5 N7 ade_pro C4-C5-N7-C8 C4 C5 N7 C8 ade_pro C5-N7-C8-N9 C5 N7 C8 N9 ade_pro N7-C8-N9-C4 N7 C8 N9 C4 ade_pro C8-N9-C4-C5 C8 N9 C4 C5 ade_pro C2-N1-C6-N6 C2 N1 C6 N6 ade_pro N7-C8-N9-C1* N7 C8 N9 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 ade_pro N1-C2-N3-C4 359.80 0.80 2.61 0.01 ade_pro C2-N3-C4-C5 359.87 1.33 2.67 0.01 ade_pro N3-C4-C5-C6 0.53 1.74 2.86 0.01 ade_pro C4-C5-C6-N1 359.43 1.76 2.61 0.01 ade_pro C5-C6-N1-C2 0.30 2.25 2.67 0.01 ade_pro C6-N1-C2-N3 0.11 2.01 2.86 0.01 ade_pro N9-C4-C5-N7 0.25 0.78 2.24 0.00 ade_pro C4-C5-N7-C8 359.81 0.58 2.18 0.01 ade_pro C5-N7-C8-N9 0.06 0.74 2.19 0.01 ade_pro N7-C8-N9-C4 0.09 0.99 2.27 0.01 ade_pro C8-N9-C4-C5 359.80 0.93 2.11 0.01 ade_pro C2-N1-C6-N6 180.46 2.17 3.58 0.01 ade_pro N7-C8-N9-C1* 180.24 2.10 3.65 0.02 #