! Filename = pnp_O_refi_dict.txt ! Created by XPLO2D V. 050802/3.3.2 at Sun Mar 2 12:14:14 2008 for A. Nonymous ! Auto-generated by XPLO2D from file pnp_msd.pdb ! !!!!! ADD THIS FILE TO YOUR .bonds_angles DATABLOCK !!!!! !!!!! THEN UPDATE THE .bonds_angles DATABLOCK HEADER !!!!! ! ! -------------------------------------------------------- ! residue PNP ! centre P ! atom C1 C2 C3 C4 C5 C6 CM N O1N O2N \ P O1P O2P O3P ! fragment_all C1 C2 C3 C4 C5 C6 CM N O1N O2N \ P O1P O2P O3P ! fragment_sc C1 C2 C3 C4 C5 C6 CM N O1N O2N \ P O1P O2P O3P ! side-chain C1 C2 C3 C4 C5 C6 CM N O1N O2N \ P O1P O2P O3P ! ! connectivity ! connect_all C1 C2 C3 C4 C5 C6 C1 O1P P CM connect_all C4 N O1N connect_all N O2N connect_all P O2P connect_all P O3P ! ! torsion-angle definitions ! note: only the first 12 torsions can be used in O ! torsion tor1 C2 C1 O1P P CM P O2P O3P torsion tor2 C1 O1P P O2P CM O2P O3P ! ! bond lengths ! bond_distance C1 C2 1.392 0.020 bond_distance C1 C6 1.393 0.020 bond_distance C1 O1P 1.355 0.020 bond_distance C2 C3 1.364 0.020 bond_distance C3 C4 1.408 0.020 bond_distance C4 C5 1.407 0.020 bond_distance C4 N 1.340 0.020 bond_distance C5 C6 1.364 0.020 bond_distance CM P 1.822 0.020 bond_distance N O1N 1.216 0.020 bond_distance N O2N 1.218 0.020 bond_distance P O1P 1.609 0.020 bond_distance P O2P 1.481 0.020 bond_distance P O3P 1.609 0.020 ! ! bond angles ! bond_angle C2 C1 C6 120.38 2.00 bond_angle C2 C1 O1P 119.83 2.00 bond_angle C6 C1 O1P 119.79 2.00 bond_angle C1 C2 C3 120.20 2.00 bond_angle C2 C3 C4 119.80 2.00 bond_angle C3 C4 C5 119.65 2.00 bond_angle C3 C4 N 120.16 2.00 bond_angle C5 C4 N 120.20 2.00 bond_angle C4 C5 C6 119.83 2.00 bond_angle C1 C6 C5 120.14 2.00 bond_angle C4 N O1N 119.99 2.00 bond_angle C4 N O2N 120.00 2.00 bond_angle O1N N O2N 120.01 2.00 bond_angle CM P O1P 109.56 2.00 bond_angle CM P O2P 109.47 2.00 bond_angle CM P O3P 109.48 2.00 bond_angle O1P P O2P 109.44 2.00 bond_angle O1P P O3P 109.46 2.00 bond_angle O2P P O3P 109.42 2.00 bond_angle C1 O1P P 106.87 2.00 ! ! dihedral angles (fixed and flexible) ! torsion_fixed C6 C1 C2 C3 0.00 2.00 ! CIS torsion - Actual value : 0.18 torsion_fixed O1P C1 C2 C3 180.00 2.00 ! TRANS torsion - Actual value : 180.00 torsion_fixed C2 C1 C6 C5 0.00 2.00 ! CIS torsion - Actual value : -0.44 torsion_fixed O1P C1 C6 C5 180.00 2.00 ! TRANS torsion - Actual value : 179.73 torsion_flexible C2 C1 O1P P 90.00 20.00 ! 60/90/120 torsion - Actual value : 89.95 torsion_flexible C6 C1 O1P P -90.00 20.00 ! 60/90/120 torsion - Actual value : -90.23 torsion_fixed C1 C2 C3 C4 0.00 2.00 ! CIS torsion - Actual value : 0.01 torsion_fixed C2 C3 C4 C5 0.00 2.00 ! CIS torsion - Actual value : 0.06 torsion_fixed C2 C3 C4 N 180.00 2.00 ! TRANS torsion - Actual value : 179.97 torsion_fixed C3 C4 C5 C6 0.00 2.00 ! CIS torsion - Actual value : -0.32 torsion_fixed N C4 C5 C6 180.00 2.00 ! TRANS torsion - Actual value : 179.77 torsion_fixed C3 C4 N O1N 180.00 2.00 ! TRANS torsion - Actual value : -179.99 torsion_fixed C3 C4 N O2N 0.00 2.00 ! CIS torsion - Actual value : 0.07 torsion_fixed C5 C4 N O1N 0.00 2.00 ! CIS torsion - Actual value : -0.08 torsion_fixed C5 C4 N O2N 180.00 2.00 ! TRANS torsion - Actual value : 179.97 torsion_fixed C4 C5 C6 C1 0.00 2.00 ! CIS torsion - Actual value : 0.51 torsion_fixed CM P O1P C1 180.00 2.00 ! TRANS torsion - Actual value : 180.00 torsion_flexible O2P P O1P C1 60.00 20.00 ! 60/90/120 torsion - Actual value : 59.97 torsion_flexible O3P P O1P C1 -60.00 20.00 ! 60/90/120 torsion - Actual value : -59.95 ! ! improper torsion angles ! torsion_fixed C1 C2 C6 O1P 0.00 2.00 ! Actual value : -0.10 torsion_fixed C4 C3 C5 N 0.00 2.00 ! Actual value : -0.05 torsion_fixed N C4 O1N O2N 0.00 2.00 ! Actual value : 0.03 torsion_fixed P CM O1P O2P -35.00 2.00 ! Actual value : -33.32 !