! Filename = da5_O_refi_dict.txt ! Created by XPLO2D V. 050802/3.3.2 at Fri Feb 29 11:32:53 2008 for A. Nonymous ! Auto-generated by XPLO2D from file da5_msd.pdb ! !!!!! ADD THIS FILE TO YOUR .bonds_angles DATABLOCK !!!!! !!!!! THEN UPDATE THE .bonds_angles DATABLOCK HEADER !!!!! ! ! -------------------------------------------------------- ! residue DA5 ! centre C1 ! atom C1 C2 C3 C4 C5 C6 C7 C8 C9 N9 \ N10 C11 C12 C13 C14 BR CD1 OD1 ND1 CD2 \ CD3 ND2 CD7 CD8 ! fragment_all C1 C2 C3 C4 C5 C6 C7 C8 C9 N9 \ N10 C11 C12 C13 C14 BR CD1 OD1 ND1 CD2 \ CD3 ND2 CD7 CD8 ! fragment_sc C1 C2 C3 C4 C5 C6 C7 C8 C9 N9 \ N10 C11 C12 C13 C14 BR CD1 OD1 ND1 CD2 \ CD3 ND2 CD7 CD8 ! side-chain C1 C2 C3 C4 C5 C6 C7 C8 C9 N9 \ N10 C11 C12 C13 C14 BR CD1 OD1 ND1 CD2 \ CD3 ND2 CD7 CD8 ! ! connectivity ! connect_all C1 C2 C3 C4 C12 N10 C14 C5 C6 C7 C8 C13 connect_all C1 C11 C9 N9 connect_all C4 CD1 OD1 connect_all C5 BR connect_all C9 C13 C14 connect_all C11 C12 connect_all CD1 ND1 CD2 CD3 ND2 CD7 connect_all ND2 CD8 ! ! torsion-angle definitions ! note: only the first 12 torsions can be used in O ! torsion tor1 CD2 CD3 ND2 CD7 CD7 CD8 ! ! bond lengths ! bond_distance C1 C2 1.360 0.020 bond_distance C1 C11 1.408 0.020 bond_distance C2 C3 1.388 0.020 bond_distance C3 C4 1.387 0.020 bond_distance C4 C12 1.466 0.020 bond_distance C4 CD1 1.472 0.020 bond_distance C5 C6 1.359 0.020 bond_distance C5 C14 1.411 0.020 bond_distance C5 BR 1.891 0.020 bond_distance C6 C7 1.394 0.020 bond_distance C7 C8 1.359 0.020 bond_distance C8 C13 1.410 0.020 bond_distance C9 N9 1.398 0.020 bond_distance C9 C11 1.397 0.020 bond_distance C9 C13 1.398 0.020 bond_distance N10 C12 1.324 0.020 bond_distance N10 C14 1.330 0.020 bond_distance C11 C12 1.466 0.020 bond_distance C13 C14 1.466 0.020 bond_distance CD1 OD1 1.216 0.020 bond_distance CD1 ND1 1.347 0.020 bond_distance ND1 CD2 1.466 0.020 bond_distance CD2 CD3 1.530 0.020 bond_distance CD3 ND2 1.470 0.020 bond_distance ND2 CD7 1.469 0.020 bond_distance ND2 CD8 1.469 0.020 ! ! bond angles ! bond_angle C2 C1 C11 120.52 2.00 bond_angle C1 C2 C3 122.41 2.00 bond_angle C2 C3 C4 121.42 2.00 bond_angle C3 C4 C12 118.55 2.00 bond_angle C3 C4 CD1 120.73 2.00 bond_angle C12 C4 CD1 120.72 2.00 bond_angle C6 C5 C14 119.58 2.00 bond_angle C6 C5 BR 120.22 2.00 bond_angle C14 C5 BR 120.20 2.00 bond_angle C5 C6 C7 121.83 2.00 bond_angle C6 C7 C8 121.58 2.00 bond_angle C7 C8 C13 119.50 2.00 bond_angle N9 C9 C11 121.09 2.00 bond_angle N9 C9 C13 121.09 2.00 bond_angle C11 C9 C13 117.82 2.00 bond_angle C12 N10 C14 121.46 2.00 bond_angle C1 C11 C9 121.40 2.00 bond_angle C1 C11 C12 119.08 2.00 bond_angle C9 C11 C12 119.51 2.00 bond_angle C4 C12 N10 121.06 2.00 bond_angle C4 C12 C11 118.01 2.00 bond_angle N10 C12 C11 120.92 2.00 bond_angle C8 C13 C9 121.35 2.00 bond_angle C8 C13 C14 119.04 2.00 bond_angle C9 C13 C14 119.61 2.00 bond_angle C5 C14 N10 120.86 2.00 bond_angle C5 C14 C13 118.47 2.00 bond_angle N10 C14 C13 120.67 2.00 bond_angle C4 CD1 OD1 120.03 2.00 bond_angle C4 CD1 ND1 119.98 2.00 bond_angle OD1 CD1 ND1 119.99 2.00 bond_angle CD1 ND1 CD2 120.00 2.00 bond_angle ND1 CD2 CD3 109.47 2.00 bond_angle CD2 CD3 ND2 109.44 2.00 bond_angle CD3 ND2 CD7 106.66 2.00 bond_angle CD3 ND2 CD8 106.68 2.00 bond_angle CD7 ND2 CD8 106.74 2.00 ! ! dihedral angles (fixed and flexible) ! torsion_fixed C11 C1 C2 C3 0.00 2.00 ! CIS torsion - Actual value : 0.04 torsion_fixed C2 C1 C11 C9 180.00 2.00 ! TRANS torsion - Actual value : 179.98 torsion_fixed C2 C1 C11 C12 0.00 2.00 ! CIS torsion - Actual value : -0.31 torsion_fixed C1 C2 C3 C4 0.00 2.00 ! CIS torsion - Actual value : -0.04 torsion_fixed C2 C3 C4 C12 0.00 2.00 ! CIS torsion - Actual value : 0.30 torsion_fixed C2 C3 C4 CD1 180.00 2.00 ! TRANS torsion - Actual value : 179.98 torsion_fixed C3 C4 C12 N10 180.00 2.00 ! TRANS torsion - Actual value : -179.73 torsion_fixed C3 C4 C12 C11 0.00 2.00 ! CIS torsion - Actual value : -0.54 torsion_fixed CD1 C4 C12 N10 0.00 2.00 ! CIS torsion - Actual value : 0.60 torsion_fixed CD1 C4 C12 C11 180.00 2.00 ! TRANS torsion - Actual value : 179.78 torsion_fixed C3 C4 CD1 OD1 180.00 2.00 ! TRANS torsion - Actual value : 174.29 torsion_fixed C3 C4 CD1 ND1 0.00 2.00 ! CIS torsion - Actual value : -5.63 torsion_fixed C12 C4 CD1 OD1 0.00 2.00 ! CIS torsion - Actual value : -6.04 torsion_fixed C12 C4 CD1 ND1 180.00 2.00 ! TRANS torsion - Actual value : 174.04 torsion_fixed C14 C5 C6 C7 0.00 2.00 ! CIS torsion - Actual value : -0.04 torsion_fixed BR C5 C6 C7 180.00 2.00 ! TRANS torsion - Actual value : 179.95 torsion_fixed C6 C5 C14 N10 180.00 2.00 ! TRANS torsion - Actual value : 179.96 torsion_fixed C6 C5 C14 C13 0.00 2.00 ! CIS torsion - Actual value : 0.06 torsion_fixed BR C5 C14 N10 0.00 2.00 ! CIS torsion - Actual value : -0.03 torsion_fixed BR C5 C14 C13 180.00 2.00 ! TRANS torsion - Actual value : -179.93 torsion_fixed C5 C6 C7 C8 0.00 2.00 ! CIS torsion - Actual value : 0.01 torsion_fixed C6 C7 C8 C13 0.00 2.00 ! CIS torsion - Actual value : -0.01 torsion_fixed C7 C8 C13 C9 180.00 2.00 ! TRANS torsion - Actual value : -179.97 torsion_fixed C7 C8 C13 C14 0.00 2.00 ! CIS torsion - Actual value : 0.03 torsion_fixed N9 C9 C11 C1 0.00 2.00 ! CIS torsion - Actual value : -0.01 torsion_fixed N9 C9 C11 C12 180.00 2.00 ! TRANS torsion - Actual value : -179.73 torsion_fixed C13 C9 C11 C1 180.00 2.00 ! TRANS torsion - Actual value : 179.96 torsion_fixed C13 C9 C11 C12 0.00 2.00 ! CIS torsion - Actual value : 0.24 torsion_fixed N9 C9 C13 C8 0.00 2.00 ! CIS torsion - Actual value : -0.04 torsion_fixed N9 C9 C13 C14 180.00 2.00 ! TRANS torsion - Actual value : 179.96 torsion_fixed C11 C9 C13 C8 180.00 2.00 ! TRANS torsion - Actual value : 179.99 torsion_fixed C11 C9 C13 C14 0.00 2.00 ! CIS torsion - Actual value : -0.01 torsion_fixed C14 N10 C12 C4 180.00 2.00 ! TRANS torsion - Actual value : 179.76 torsion_fixed C14 N10 C12 C11 0.00 2.00 ! CIS torsion - Actual value : 0.60 torsion_fixed C12 N10 C14 C5 180.00 2.00 ! TRANS torsion - Actual value : 179.75 torsion_fixed C12 N10 C14 C13 0.00 2.00 ! CIS torsion - Actual value : -0.35 torsion_fixed C1 C11 C12 C4 0.00 2.00 ! CIS torsion - Actual value : 0.55 torsion_fixed C1 C11 C12 N10 180.00 2.00 ! TRANS torsion - Actual value : 179.73 torsion_fixed C9 C11 C12 C4 180.00 2.00 ! TRANS torsion - Actual value : -179.73 torsion_fixed C9 C11 C12 N10 0.00 2.00 ! CIS torsion - Actual value : -0.55 torsion_fixed C8 C13 C14 C5 0.00 2.00 ! CIS torsion - Actual value : -0.06 torsion_fixed C8 C13 C14 N10 180.00 2.00 ! TRANS torsion - Actual value : -179.96 torsion_fixed C9 C13 C14 C5 180.00 2.00 ! TRANS torsion - Actual value : 179.95 torsion_fixed C9 C13 C14 N10 0.00 2.00 ! CIS torsion - Actual value : 0.05 torsion_fixed C4 CD1 ND1 CD2 180.00 2.00 ! TRANS torsion - Actual value : -180.00 torsion_fixed OD1 CD1 ND1 CD2 0.00 2.00 ! CIS torsion - Actual value : 0.09 torsion_fixed CD1 ND1 CD2 CD3 180.00 2.00 ! TRANS torsion - Actual value : 179.96 torsion_fixed ND1 CD2 CD3 ND2 180.00 2.00 ! TRANS torsion - Actual value : 179.96 torsion_flexible CD2 CD3 ND2 CD7 170.00 20.00 ! Descriptive torsion - Actual value : 169.99 torsion_flexible CD2 CD3 ND2 CD8 -76.00 20.00 ! Descriptive torsion - Actual value : -76.22 ! ! improper torsion angles ! torsion_fixed C4 C3 C12 CD1 0.00 2.00 ! Actual value : -0.19 torsion_fixed C5 C6 C14 BR 0.00 2.00 ! Actual value : -0.01 torsion_fixed C9 N9 C11 C13 0.00 2.00 ! Actual value : 0.02 torsion_fixed C11 C1 C9 C12 0.00 2.00 ! Actual value : -0.17 torsion_fixed C12 C4 N10 C11 0.00 2.00 ! Actual value : -0.49 torsion_fixed C13 C8 C9 C14 0.00 2.00 ! Actual value : 0.00 torsion_fixed C14 C5 N10 C13 0.00 2.00 ! Actual value : 0.06 torsion_fixed CD1 C4 OD1 ND1 0.00 2.00 ! Actual value : 0.05 torsion_fixed ND2 CD3 CD7 CD8 -35.00 2.00 ! Actual value : -39.10 !