! Filename = ph9_O_refi_dict.txt ! Created by XPLO2D V. 050802/3.3.2 at Sun Mar 2 10:37:08 2008 for A. Nonymous ! Auto-generated by XPLO2D from file ph9_msd.pdb ! !!!!! ADD THIS FILE TO YOUR .bonds_angles DATABLOCK !!!!! !!!!! THEN UPDATE THE .bonds_angles DATABLOCK HEADER !!!!! ! ! -------------------------------------------------------- ! residue PH9 ! centre C1 ! atom CB2 CB3 CB4 CB6 CB5 CB1 C2 C1 N C \ CO2 O OC1 OC2 OAB CA1 CA2 CA3 CA4 CA5 \ CA6 BRA2 CC4 CC3 CC5 CC2 CC6 CC1 C10 CC8 \ CC9 CC7 ! fragment_all CB2 CB3 CB4 CB6 CB5 CB1 C2 C1 N C \ CO2 O OC1 OC2 OAB CA1 CA2 CA3 CA4 CA5 \ CA6 BRA2 CC4 CC3 CC5 CC2 CC6 CC1 C10 CC8 \ CC9 CC7 ! fragment_sc CB2 CB3 CB4 CB6 CB5 CB1 C2 C1 N C \ CO2 O OC1 OC2 OAB CA1 CA2 CA3 CA4 CA5 \ CA6 BRA2 CC4 CC3 CC5 CC2 CC6 CC1 C10 CC8 \ CC9 CC7 ! side-chain CB2 CB3 CB4 CB6 CB5 CB1 C2 C1 N C \ CO2 O OC1 OC2 OAB CA1 CA2 CA3 CA4 CA5 \ CA6 BRA2 CC4 CC3 CC5 CC2 CC6 CC1 C10 CC8 \ CC9 CC7 ! ! connectivity ! connect_all CB2 CB3 CB4 CB6 CB5 CB1 CB2 C1 C2 N C O connect_all CB6 OAB CA1 CA2 CA3 CA4 CA5 CA6 CA1 connect_all C2 CO2 OC1 connect_all C CC1 CC2 CC5 CC4 CC3 CC6 CC1 CC7 CC8 C10 CC5 connect_all CO2 OC2 connect_all CA2 BRA2 connect_all CC3 CC9 CC8 ! ! torsion-angle definitions ! note: only the first 12 torsions can be used in O ! torsion tor1 CB4 CB6 OAB CA1 CA1 CA2 CA3 CA4 CA5 CA6 BRA2 torsion tor2 N C2 C1 CB2 CB2 CB3 CB4 CB6 CB5 CB1 OAB CA1 CA2 \ CA3 CA4 CA5 CA6 BRA2 torsion tor3 C1 C2 N C C O CC4 CC3 CC5 CC2 CC6 CC1 C10 CC8 CC9 \ CC7 torsion tor4 C1 C2 CO2 OC1 OC1 OC2 torsion tor5 C2 C1 CB2 CB3 CB3 CB4 CB6 CB5 CB1 OAB CA1 CA2 CA3 \ CA4 CA5 CA6 BRA2 torsion tor6 N C CC1 CC6 CC4 CC3 CC5 CC2 CC6 C10 CC8 CC9 CC7 ! ! bond lengths ! bond_distance CB2 CB3 1.383 0.020 bond_distance CB2 CB1 1.383 0.020 bond_distance CB2 C1 1.506 0.020 bond_distance CB3 CB4 1.381 0.020 bond_distance CB4 CB6 1.387 0.020 bond_distance CB6 CB5 1.388 0.020 bond_distance CB6 OAB 1.359 0.020 bond_distance CB5 CB1 1.381 0.020 bond_distance C2 C1 1.530 0.020 bond_distance C2 N 1.466 0.020 bond_distance C2 CO2 1.507 0.020 bond_distance N C 1.348 0.020 bond_distance C O 1.212 0.020 bond_distance C CC1 1.507 0.020 bond_distance CO2 OC1 1.208 0.020 bond_distance CO2 OC2 1.342 0.020 bond_distance OAB CA1 1.359 0.020 bond_distance CA1 CA2 1.388 0.020 bond_distance CA1 CA6 1.387 0.020 bond_distance CA2 CA3 1.382 0.020 bond_distance CA2 BRA2 1.891 0.020 bond_distance CA3 CA4 1.382 0.020 bond_distance CA4 CA5 1.383 0.020 bond_distance CA5 CA6 1.382 0.020 bond_distance CC4 CC3 1.531 0.020 bond_distance CC4 CC5 1.530 0.020 bond_distance CC3 CC6 1.530 0.020 bond_distance CC3 CC9 1.530 0.020 bond_distance CC5 CC2 1.530 0.020 bond_distance CC5 C10 1.531 0.020 bond_distance CC2 CC1 1.531 0.020 bond_distance CC6 CC1 1.529 0.020 bond_distance CC1 CC7 1.530 0.020 bond_distance C10 CC8 1.529 0.020 bond_distance CC8 CC9 1.530 0.020 bond_distance CC8 CC7 1.530 0.020 ! ! bond angles ! bond_angle CB3 CB2 CB1 120.07 2.00 bond_angle CB3 CB2 C1 119.93 2.00 bond_angle CB1 CB2 C1 120.00 2.00 bond_angle CB2 CB3 CB4 120.07 2.00 bond_angle CB3 CB4 CB6 119.97 2.00 bond_angle CB4 CB6 CB5 119.87 2.00 bond_angle CB4 CB6 OAB 120.09 2.00 bond_angle CB5 CB6 OAB 120.04 2.00 bond_angle CB6 CB5 CB1 119.94 2.00 bond_angle CB2 CB1 CB5 120.08 2.00 bond_angle C1 C2 N 109.45 2.00 bond_angle C1 C2 CO2 109.49 2.00 bond_angle N C2 CO2 109.48 2.00 bond_angle CB2 C1 C2 109.49 2.00 bond_angle C2 N C 119.96 2.00 bond_angle N C O 120.03 2.00 bond_angle N C CC1 119.94 2.00 bond_angle O C CC1 120.03 2.00 bond_angle C2 CO2 OC1 119.97 2.00 bond_angle C2 CO2 OC2 119.98 2.00 bond_angle OC1 CO2 OC2 120.05 2.00 bond_angle CB6 OAB CA1 106.78 2.00 bond_angle OAB CA1 CA2 120.02 2.00 bond_angle OAB CA1 CA6 120.04 2.00 bond_angle CA2 CA1 CA6 119.94 2.00 bond_angle CA1 CA2 CA3 119.90 2.00 bond_angle CA1 CA2 BRA2 120.06 2.00 bond_angle CA3 CA2 BRA2 120.03 2.00 bond_angle CA2 CA3 CA4 120.05 2.00 bond_angle CA3 CA4 CA5 120.13 2.00 bond_angle CA4 CA5 CA6 120.09 2.00 bond_angle CA1 CA6 CA5 119.90 2.00 bond_angle CC3 CC4 CC5 109.50 2.00 bond_angle CC4 CC3 CC6 109.44 2.00 bond_angle CC4 CC3 CC9 109.45 2.00 bond_angle CC6 CC3 CC9 109.48 2.00 bond_angle CC4 CC5 CC2 109.46 2.00 bond_angle CC4 CC5 C10 109.46 2.00 bond_angle CC2 CC5 C10 109.44 2.00 bond_angle CC5 CC2 CC1 109.49 2.00 bond_angle CC3 CC6 CC1 109.51 2.00 bond_angle C CC1 CC2 109.44 2.00 bond_angle C CC1 CC6 109.50 2.00 bond_angle C CC1 CC7 109.49 2.00 bond_angle CC2 CC1 CC6 109.47 2.00 bond_angle CC2 CC1 CC7 109.45 2.00 bond_angle CC6 CC1 CC7 109.48 2.00 bond_angle CC5 C10 CC8 109.47 2.00 bond_angle C10 CC8 CC9 109.52 2.00 bond_angle C10 CC8 CC7 109.48 2.00 bond_angle CC9 CC8 CC7 109.46 2.00 bond_angle CC3 CC9 CC8 109.46 2.00 bond_angle CC1 CC7 CC8 109.47 2.00 ! ! dihedral angles (fixed and flexible) ! torsion_fixed CB1 CB2 CB3 CB4 0.00 2.00 ! CIS torsion - Actual value : 0.31 torsion_fixed C1 CB2 CB3 CB4 180.00 2.00 ! TRANS torsion - Actual value : 179.99 torsion_fixed CB3 CB2 CB1 CB5 0.00 2.00 ! CIS torsion - Actual value : -0.55 torsion_fixed C1 CB2 CB1 CB5 180.00 2.00 ! TRANS torsion - Actual value : 179.77 torsion_flexible CB3 CB2 C1 C2 90.00 20.00 ! 60/90/120 torsion - Actual value : 90.04 torsion_flexible CB1 CB2 C1 C2 -90.00 20.00 ! 60/90/120 torsion - Actual value : -90.28 torsion_fixed CB2 CB3 CB4 CB6 0.00 2.00 ! CIS torsion - Actual value : -0.06 torsion_fixed CB3 CB4 CB6 CB5 0.00 2.00 ! CIS torsion - Actual value : 0.05 torsion_fixed CB3 CB4 CB6 OAB 180.00 2.00 ! TRANS torsion - Actual value : -179.96 torsion_fixed CB4 CB6 CB5 CB1 0.00 2.00 ! CIS torsion - Actual value : -0.29 torsion_fixed OAB CB6 CB5 CB1 180.00 2.00 ! TRANS torsion - Actual value : 179.72 torsion_flexible CB4 CB6 OAB CA1 90.00 20.00 ! 60/90/120 torsion - Actual value : 89.38 torsion_flexible CB5 CB6 OAB CA1 -90.00 20.00 ! 60/90/120 torsion - Actual value : -90.63 torsion_fixed CB6 CB5 CB1 CB2 0.00 2.00 ! CIS torsion - Actual value : 0.54 torsion_flexible N C2 C1 CB2 60.00 20.00 ! 60/90/120 torsion - Actual value : 64.95 torsion_fixed CO2 C2 C1 CB2 180.00 2.00 ! TRANS torsion - Actual value : -175.04 torsion_flexible C1 C2 N C -155.00 20.00 ! Descriptive torsion - Actual value : -154.97 torsion_flexible CO2 C2 N C 90.00 20.00 ! 60/90/120 torsion - Actual value : 85.01 torsion_flexible C1 C2 CO2 OC1 -120.00 20.00 ! 60/90/120 torsion - Actual value : -120.02 torsion_flexible C1 C2 CO2 OC2 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.00 torsion_fixed N C2 CO2 OC1 0.00 2.00 ! CIS torsion - Actual value : -0.03 torsion_fixed N C2 CO2 OC2 180.00 2.00 ! TRANS torsion - Actual value : 179.99 torsion_fixed C2 N C O 0.00 2.00 ! CIS torsion - Actual value : 0.00 torsion_fixed C2 N C CC1 180.00 2.00 ! TRANS torsion - Actual value : -180.00 torsion_fixed N C CC1 CC2 180.00 2.00 ! TRANS torsion - Actual value : 179.99 torsion_flexible N C CC1 CC6 -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.02 torsion_flexible N C CC1 CC7 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.02 torsion_fixed O C CC1 CC2 0.00 2.00 ! CIS torsion - Actual value : -0.01 torsion_flexible O C CC1 CC6 120.00 20.00 ! 60/90/120 torsion - Actual value : 119.98 torsion_flexible O C CC1 CC7 -120.00 20.00 ! 60/90/120 torsion - Actual value : -119.98 torsion_fixed CB6 OAB CA1 CA2 180.00 2.00 ! TRANS torsion - Actual value : -178.74 torsion_fixed CB6 OAB CA1 CA6 0.00 2.00 ! CIS torsion - Actual value : 1.55 torsion_fixed OAB CA1 CA2 CA3 180.00 2.00 ! TRANS torsion - Actual value : 179.74 torsion_fixed OAB CA1 CA2 BRA2 0.00 2.00 ! CIS torsion - Actual value : 0.31 torsion_fixed CA6 CA1 CA2 CA3 0.00 2.00 ! CIS torsion - Actual value : -0.55 torsion_fixed CA6 CA1 CA2 BRA2 180.00 2.00 ! TRANS torsion - Actual value : -179.98 torsion_fixed OAB CA1 CA6 CA5 180.00 2.00 ! TRANS torsion - Actual value : 179.99 torsion_fixed CA2 CA1 CA6 CA5 0.00 2.00 ! CIS torsion - Actual value : 0.28 torsion_fixed CA1 CA2 CA3 CA4 0.00 2.00 ! CIS torsion - Actual value : 0.58 torsion_fixed BRA2 CA2 CA3 CA4 180.00 2.00 ! TRANS torsion - Actual value : -180.00 torsion_fixed CA2 CA3 CA4 CA5 0.00 2.00 ! CIS torsion - Actual value : -0.33 torsion_fixed CA3 CA4 CA5 CA6 0.00 2.00 ! CIS torsion - Actual value : 0.06 torsion_fixed CA4 CA5 CA6 CA1 0.00 2.00 ! CIS torsion - Actual value : -0.03 torsion_flexible CC5 CC4 CC3 CC6 -60.00 20.00 ! 60/90/120 torsion - Actual value : -59.97 torsion_flexible CC5 CC4 CC3 CC9 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.01 torsion_flexible CC3 CC4 CC5 CC2 60.00 20.00 ! 60/90/120 torsion - Actual value : 59.97 torsion_flexible CC3 CC4 CC5 C10 -60.00 20.00 ! 60/90/120 torsion - Actual value : -59.97 torsion_flexible CC4 CC3 CC6 CC1 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.00 torsion_flexible CC9 CC3 CC6 CC1 -60.00 20.00 ! 60/90/120 torsion - Actual value : -59.96 torsion_flexible CC4 CC3 CC9 CC8 -60.00 20.00 ! 60/90/120 torsion - Actual value : -59.99 torsion_flexible CC6 CC3 CC9 CC8 60.00 20.00 ! 60/90/120 torsion - Actual value : 59.96 torsion_flexible CC4 CC5 CC2 CC1 -60.00 20.00 ! 60/90/120 torsion - Actual value : -59.97 torsion_flexible C10 CC5 CC2 CC1 60.00 20.00 ! 60/90/120 torsion - Actual value : 59.99 torsion_flexible CC4 CC5 C10 CC8 60.00 20.00 ! 60/90/120 torsion - Actual value : 59.95 torsion_flexible CC2 CC5 C10 CC8 -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.01 torsion_fixed CC5 CC2 CC1 C 180.00 2.00 ! TRANS torsion - Actual value : -179.99 torsion_flexible CC5 CC2 CC1 CC6 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.00 torsion_flexible CC5 CC2 CC1 CC7 -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.00 torsion_fixed CC3 CC6 CC1 C 180.00 2.00 ! TRANS torsion - Actual value : -179.99 torsion_flexible CC3 CC6 CC1 CC2 -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.02 torsion_flexible CC3 CC6 CC1 CC7 60.00 20.00 ! 60/90/120 torsion - Actual value : 59.96 torsion_fixed C CC1 CC7 CC8 180.00 2.00 ! TRANS torsion - Actual value : 179.95 torsion_flexible CC2 CC1 CC7 CC8 60.00 20.00 ! 60/90/120 torsion - Actual value : 59.99 torsion_flexible CC6 CC1 CC7 CC8 -60.00 20.00 ! 60/90/120 torsion - Actual value : -59.99 torsion_flexible CC5 C10 CC8 CC9 -60.00 20.00 ! 60/90/120 torsion - Actual value : -59.99 torsion_flexible CC5 C10 CC8 CC7 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.03 torsion_flexible C10 CC8 CC9 CC3 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.02 torsion_flexible CC7 CC8 CC9 CC3 -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.01 torsion_flexible C10 CC8 CC7 CC1 -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.04 torsion_flexible CC9 CC8 CC7 CC1 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.02 ! ! improper torsion angles ! torsion_fixed CB2 CB3 CB1 C1 0.00 2.00 ! Actual value : -0.19 torsion_fixed CB6 CB4 CB5 OAB 0.00 2.00 ! Actual value : 0.00 torsion_fixed C2 C1 N CO2 -35.00 2.00 ! Actual value : -35.34 torsion_fixed C N O CC1 0.00 2.00 ! Actual value : 0.00 torsion_fixed CO2 C2 OC1 OC2 0.00 2.00 ! Actual value : 0.01 torsion_fixed CA1 OAB CA2 CA6 0.00 2.00 ! Actual value : 0.17 torsion_fixed CA2 CA1 CA3 BRA2 0.00 2.00 ! Actual value : 0.36 torsion_fixed CC3 CC4 CC6 CC9 -35.00 2.00 ! Actual value : -35.27 torsion_fixed CC5 CC4 CC2 C10 35.00 2.00 ! Actual value : 35.30 torsion_fixed CC1 C CC2 CC6 -35.00 2.00 ! Actual value : -35.35 torsion_fixed CC8 C10 CC9 CC7 -35.00 2.00 ! Actual value : -35.26 !