! Filename = hmd_O_refi_dict.txt ! Created by XPLO2D V. 050802/3.3.2 at Sat Mar 1 06:52:00 2008 for A. Nonymous ! Auto-generated by XPLO2D from file hmd_msd.pdb ! !!!!! ADD THIS FILE TO YOUR .bonds_angles DATABLOCK !!!!! !!!!! THEN UPDATE THE .bonds_angles DATABLOCK HEADER !!!!! ! ! -------------------------------------------------------- ! residue HMD ! centre C1 ! atom BR1 O1 O2 N1 N2 N3 N4 N5 C1 C2 \ C3 C4 C5 C6 C7 C8 C9 C10 C11 ! fragment_all BR1 O1 O2 N1 N2 N3 N4 N5 C1 C2 \ C3 C4 C5 C6 C7 C8 C9 C10 C11 ! fragment_sc BR1 O1 O2 N1 N2 N3 N4 N5 C1 C2 \ C3 C4 C5 C6 C7 C8 C9 C10 C11 ! side-chain BR1 O1 O2 N1 N2 N3 N4 N5 C1 C2 \ C3 C4 C5 C6 C7 C8 C9 C10 C11 ! ! connectivity ! connect_all BR1 C1 N1 C4 C3 C2 C1 connect_all O1 C5 N2 C6 C7 C8 C3 connect_all O2 C10 N3 C11 N4 C9 C8 connect_all N5 C11 connect_all C4 C5 connect_all C9 C10 ! ! torsion-angle definitions ! note: only the first 12 torsions can be used in O ! torsion tor1 C3 C8 C9 N4 O2 N3 N4 N5 C10 C11 ! ! bond lengths ! bond_distance BR1 C1 1.891 0.020 bond_distance O1 C5 1.216 0.020 bond_distance O2 C10 1.214 0.020 bond_distance N1 C1 1.340 0.020 bond_distance N1 C4 1.298 0.020 bond_distance N2 C5 1.340 0.020 bond_distance N2 C6 1.407 0.020 bond_distance N3 C10 1.349 0.020 bond_distance N3 C11 1.322 0.020 bond_distance N4 C9 1.299 0.020 bond_distance N4 C11 1.369 0.020 bond_distance N5 C11 1.359 0.020 bond_distance C1 C2 1.340 0.020 bond_distance C2 C3 1.512 0.020 bond_distance C3 C4 1.498 0.020 bond_distance C3 C8 1.539 0.020 bond_distance C4 C5 1.467 0.020 bond_distance C6 C7 1.507 0.020 bond_distance C7 C8 1.539 0.020 bond_distance C8 C9 1.507 0.020 bond_distance C9 C10 1.504 0.020 ! ! bond angles ! bond_angle C1 N1 C4 112.95 2.00 bond_angle C5 N2 C6 123.83 2.00 bond_angle C10 N3 C11 108.38 2.00 bond_angle C9 N4 C11 109.27 2.00 bond_angle BR1 C1 N1 123.77 2.00 bond_angle BR1 C1 C2 123.76 2.00 bond_angle N1 C1 C2 112.46 2.00 bond_angle C1 C2 C3 104.54 2.00 bond_angle C2 C3 C4 103.21 2.00 bond_angle C2 C3 C8 110.78 2.00 bond_angle C4 C3 C8 111.05 2.00 bond_angle N1 C4 C3 106.50 2.00 bond_angle N1 C4 C5 128.65 2.00 bond_angle C3 C4 C5 124.84 2.00 bond_angle O1 C5 N2 120.75 2.00 bond_angle O1 C5 C4 120.74 2.00 bond_angle N2 C5 C4 118.52 2.00 bond_angle N2 C6 C7 124.81 2.00 bond_angle C6 C7 C8 112.32 2.00 bond_angle C3 C8 C7 109.70 2.00 bond_angle C3 C8 C9 109.41 2.00 bond_angle C7 C8 C9 109.44 2.00 bond_angle N4 C9 C8 127.09 2.00 bond_angle N4 C9 C10 105.81 2.00 bond_angle C8 C9 C10 127.10 2.00 bond_angle O2 C10 N3 127.29 2.00 bond_angle O2 C10 C9 127.22 2.00 bond_angle N3 C10 C9 105.49 2.00 bond_angle N3 C11 N4 111.05 2.00 bond_angle N3 C11 N5 124.46 2.00 bond_angle N4 C11 N5 124.49 2.00 ! ! dihedral angles (fixed and flexible) ! torsion_fixed C4 N1 C1 BR1 180.00 2.00 ! TRANS torsion - Actual value : -177.13 torsion_fixed C4 N1 C1 C2 0.00 2.00 ! CIS torsion - Actual value : 2.96 torsion_fixed C1 N1 C4 C3 0.00 2.00 ! CIS torsion - Actual value : -5.57 torsion_fixed C1 N1 C4 C5 180.00 2.00 ! TRANS torsion - Actual value : 173.37 torsion_flexible C6 N2 C5 O1 -167.00 20.00 ! Descriptive torsion - Actual value : -166.84 torsion_flexible C6 N2 C5 C4 13.00 20.00 ! Descriptive torsion - Actual value : 13.18 torsion_flexible C5 N2 C6 C7 -27.00 20.00 ! Descriptive torsion - Actual value : -26.94 torsion_fixed C11 N3 C10 O2 180.00 2.00 ! TRANS torsion - Actual value : -179.95 torsion_fixed C11 N3 C10 C9 0.00 2.00 ! CIS torsion - Actual value : 0.05 torsion_fixed C10 N3 C11 N4 0.00 2.00 ! CIS torsion - Actual value : 0.23 torsion_fixed C10 N3 C11 N5 180.00 2.00 ! TRANS torsion - Actual value : -179.95 torsion_fixed C11 N4 C9 C8 180.00 2.00 ! TRANS torsion - Actual value : -179.82 torsion_fixed C11 N4 C9 C10 0.00 2.00 ! CIS torsion - Actual value : 0.45 torsion_fixed C9 N4 C11 N3 0.00 2.00 ! CIS torsion - Actual value : -0.45 torsion_fixed C9 N4 C11 N5 180.00 2.00 ! TRANS torsion - Actual value : 179.73 torsion_fixed BR1 C1 C2 C3 180.00 2.00 ! TRANS torsion - Actual value : -178.79 torsion_fixed N1 C1 C2 C3 0.00 2.00 ! CIS torsion - Actual value : 1.12 torsion_fixed C1 C2 C3 C4 0.00 2.00 ! CIS torsion - Actual value : -4.09 torsion_flexible C1 C2 C3 C8 -120.00 20.00 ! 60/90/120 torsion - Actual value : -123.02 torsion_fixed C2 C3 C4 N1 0.00 2.00 ! CIS torsion - Actual value : 5.80 torsion_fixed C2 C3 C4 C5 180.00 2.00 ! TRANS torsion - Actual value : -173.19 torsion_flexible C8 C3 C4 N1 120.00 20.00 ! 60/90/120 torsion - Actual value : 124.54 torsion_flexible C8 C3 C4 C5 -60.00 20.00 ! 60/90/120 torsion - Actual value : -54.45 torsion_flexible C2 C3 C8 C7 90.00 20.00 ! 60/90/120 torsion - Actual value : 83.41 torsion_flexible C2 C3 C8 C9 -37.00 20.00 ! Descriptive torsion - Actual value : -36.65 torsion_flexible C4 C3 C8 C7 -31.00 20.00 ! Descriptive torsion - Actual value : -30.66 torsion_flexible C4 C3 C8 C9 -151.00 20.00 ! Descriptive torsion - Actual value : -150.73 torsion_flexible N1 C4 C5 O1 60.00 20.00 ! 60/90/120 torsion - Actual value : 61.42 torsion_flexible N1 C4 C5 N2 -120.00 20.00 ! 60/90/120 torsion - Actual value : -118.59 torsion_flexible C3 C4 C5 O1 -120.00 20.00 ! 60/90/120 torsion - Actual value : -119.82 torsion_flexible C3 C4 C5 N2 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.17 torsion_flexible N2 C6 C7 C8 -40.00 20.00 ! Descriptive torsion - Actual value : -40.07 torsion_flexible C6 C7 C8 C3 90.00 20.00 ! 60/90/120 torsion - Actual value : 82.94 torsion_flexible C6 C7 C8 C9 -157.00 20.00 ! Descriptive torsion - Actual value : -157.01 torsion_flexible C3 C8 C9 N4 120.00 20.00 ! 60/90/120 torsion - Actual value : 114.94 torsion_flexible C3 C8 C9 C10 -60.00 20.00 ! 60/90/120 torsion - Actual value : -65.38 torsion_fixed C7 C8 C9 N4 0.00 2.00 ! CIS torsion - Actual value : -5.29 torsion_fixed C7 C8 C9 C10 180.00 2.00 ! TRANS torsion - Actual value : 174.39 torsion_fixed N4 C9 C10 O2 180.00 2.00 ! TRANS torsion - Actual value : 179.68 torsion_fixed N4 C9 C10 N3 0.00 2.00 ! CIS torsion - Actual value : -0.31 torsion_fixed C8 C9 C10 O2 0.00 2.00 ! CIS torsion - Actual value : -0.05 torsion_fixed C8 C9 C10 N3 180.00 2.00 ! TRANS torsion - Actual value : 179.95 ! ! improper torsion angles ! torsion_fixed C1 BR1 N1 C2 0.00 2.00 ! Actual value : -0.05 torsion_fixed C3 C2 C4 C8 35.00 2.00 ! Actual value : 34.69 torsion_fixed C4 N1 C3 C5 0.00 2.00 ! Actual value : -0.53 torsion_fixed C5 O1 N2 C4 0.00 2.00 ! Actual value : -0.01 torsion_fixed C8 C3 C7 C9 35.00 2.00 ! Actual value : 35.00 torsion_fixed C9 N4 C8 C10 0.00 2.00 ! Actual value : 0.18 torsion_fixed C10 O2 N3 C9 0.00 2.00 ! Actual value : 0.00 torsion_fixed C11 N3 N4 N5 0.00 2.00 ! Actual value : -0.10 !