! Filename = dud_O_refi_dict.txt ! Created by XPLO2D V. 050802/3.3.2 at Fri Feb 29 17:08:17 2008 for A. Nonymous ! Auto-generated by XPLO2D from file dud_msd.pdb ! !!!!! ADD THIS FILE TO YOUR .bonds_angles DATABLOCK !!!!! !!!!! THEN UPDATE THE .bonds_angles DATABLOCK HEADER !!!!! ! ! -------------------------------------------------------- ! residue DUD ! centre N1 ! atom N1 C2 N3 C4 C5 C6 O2 O4 C1' C2' \ C3' C4' O4' O3' C5' O5' PA O1A O2A O3A \ PB O1B O2B O3B ! fragment_all N1 C2 N3 C4 C5 C6 O2 O4 C1' C2' \ C3' C4' O4' O3' C5' O5' PA O1A O2A O3A \ PB O1B O2B O3B ! fragment_sc N1 C2 N3 C4 C5 C6 O2 O4 C1' C2' \ C3' C4' O4' O3' C5' O5' PA O1A O2A O3A \ PB O1B O2B O3B ! side-chain N1 C2 N3 C4 C5 C6 O2 O4 C1' C2' \ C3' C4' O4' O3' C5' O5' PA O1A O2A O3A \ PB O1B O2B O3B ! ! connectivity ! connect_all N1 C2 N3 C4 C5 C6 N1 C1' C2' C3' C4' O4' connect_all C2 O2 connect_all C4 O4 connect_all C1' O4' connect_all C3' O3' connect_all C4' C5' O5' PA O1A connect_all PA O2A connect_all PA O3A PB O1B connect_all PB O2B connect_all PB O3B ! ! torsion-angle definitions ! note: only the first 12 torsions can be used in O ! torsion tor1 C2' C1' N1 C2 C2 N3 C4 C5 C6 O2 O4 torsion tor2 O4' C4' C5' O5' O5' PA O1A O2A O3A PB O1B O2B O3B torsion tor3 C5' O5' PA O1A O1A O2A O3A PB O1B O2B O3B torsion tor4 O1A PA O3A PB PB O1B O2B O3B torsion tor5 PA O3A PB O1B O1B O2B O3B ! ! bond lengths ! bond_distance N1 C2 1.345 0.020 bond_distance N1 C6 1.368 0.020 bond_distance N1 C1' 1.464 0.020 bond_distance C2 N3 1.347 0.020 bond_distance C2 O2 1.216 0.020 bond_distance N3 C4 1.348 0.020 bond_distance C4 C5 1.415 0.020 bond_distance C4 O4 1.218 0.020 bond_distance C5 C6 1.351 0.020 bond_distance C1' C2' 1.543 0.020 bond_distance C1' O4' 1.445 0.020 bond_distance C2' C3' 1.545 0.020 bond_distance C3' C4' 1.545 0.020 bond_distance C3' O3' 1.429 0.020 bond_distance C4' O4' 1.446 0.020 bond_distance C4' C5' 1.529 0.020 bond_distance C5' O5' 1.429 0.020 bond_distance O5' PA 1.609 0.020 bond_distance PA O1A 1.480 0.020 bond_distance PA O2A 1.609 0.020 bond_distance PA O3A 1.609 0.020 bond_distance O3A PB 1.610 0.020 bond_distance PB O1B 1.479 0.020 bond_distance PB O2B 1.610 0.020 bond_distance PB O3B 1.609 0.020 ! ! bond angles ! bond_angle C2 N1 C6 120.62 2.00 bond_angle C2 N1 C1' 119.65 2.00 bond_angle C6 N1 C1' 119.73 2.00 bond_angle N1 C2 N3 120.93 2.00 bond_angle N1 C2 O2 119.59 2.00 bond_angle N3 C2 O2 119.48 2.00 bond_angle C2 N3 C4 120.24 2.00 bond_angle N3 C4 C5 119.43 2.00 bond_angle N3 C4 O4 120.30 2.00 bond_angle C5 C4 O4 120.27 2.00 bond_angle C4 C5 C6 119.07 2.00 bond_angle N1 C6 C5 119.71 2.00 bond_angle N1 C1' C2' 110.40 2.00 bond_angle N1 C1' O4' 110.50 2.00 bond_angle C2' C1' O4' 104.83 2.00 bond_angle C1' C2' C3' 104.10 2.00 bond_angle C2' C3' C4' 104.13 2.00 bond_angle C2' C3' O3' 110.54 2.00 bond_angle C4' C3' O3' 110.56 2.00 bond_angle C3' C4' O4' 104.74 2.00 bond_angle C3' C4' C5' 110.69 2.00 bond_angle O4' C4' C5' 110.37 2.00 bond_angle C1' O4' C4' 105.36 2.00 bond_angle C4' C5' O5' 109.53 2.00 bond_angle C5' O5' PA 106.84 2.00 bond_angle O5' PA O1A 109.44 2.00 bond_angle O5' PA O2A 109.48 2.00 bond_angle O5' PA O3A 109.48 2.00 bond_angle O1A PA O2A 109.48 2.00 bond_angle O1A PA O3A 109.49 2.00 bond_angle O2A PA O3A 109.45 2.00 bond_angle PA O3A PB 106.83 2.00 bond_angle O3A PB O1B 109.46 2.00 bond_angle O3A PB O2B 109.50 2.00 bond_angle O3A PB O3B 109.48 2.00 bond_angle O1B PB O2B 109.44 2.00 bond_angle O1B PB O3B 109.50 2.00 bond_angle O2B PB O3B 109.45 2.00 ! ! dihedral angles (fixed and flexible) ! torsion_fixed C6 N1 C2 N3 0.00 2.00 ! CIS torsion - Actual value : -0.60 torsion_fixed C6 N1 C2 O2 180.00 2.00 ! TRANS torsion - Actual value : -179.99 torsion_fixed C1' N1 C2 N3 180.00 2.00 ! TRANS torsion - Actual value : 179.73 torsion_fixed C1' N1 C2 O2 0.00 2.00 ! CIS torsion - Actual value : 0.35 torsion_fixed C2 N1 C6 C5 0.00 2.00 ! CIS torsion - Actual value : 0.28 torsion_fixed C1' N1 C6 C5 180.00 2.00 ! TRANS torsion - Actual value : 179.94 torsion_flexible C2 N1 C1' C2' -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.35 torsion_flexible C2 N1 C1' O4' 60.00 20.00 ! 60/90/120 torsion - Actual value : 55.15 torsion_flexible C6 N1 C1' C2' 120.00 20.00 ! 60/90/120 torsion - Actual value : 119.98 torsion_flexible C6 N1 C1' O4' -120.00 20.00 ! 60/90/120 torsion - Actual value : -124.51 torsion_fixed N1 C2 N3 C4 0.00 2.00 ! CIS torsion - Actual value : 0.62 torsion_fixed O2 C2 N3 C4 180.00 2.00 ! TRANS torsion - Actual value : -180.00 torsion_fixed C2 N3 C4 C5 0.00 2.00 ! CIS torsion - Actual value : -0.31 torsion_fixed C2 N3 C4 O4 180.00 2.00 ! TRANS torsion - Actual value : 179.70 torsion_fixed N3 C4 C5 C6 0.00 2.00 ! CIS torsion - Actual value : 0.00 torsion_fixed O4 C4 C5 C6 180.00 2.00 ! TRANS torsion - Actual value : 179.99 torsion_fixed C4 C5 C6 N1 0.00 2.00 ! CIS torsion - Actual value : 0.02 torsion_flexible N1 C1' C2' C3' 143.00 20.00 ! Descriptive torsion - Actual value : 142.97 torsion_flexible O4' C1' C2' C3' 24.00 20.00 ! Descriptive torsion - Actual value : 23.96 torsion_flexible N1 C1' O4' C4' -159.00 20.00 ! Descriptive torsion - Actual value : -159.33 torsion_flexible C2' C1' O4' C4' -40.00 20.00 ! Descriptive torsion - Actual value : -40.39 torsion_fixed C1' C2' C3' C4' 0.00 2.00 ! CIS torsion - Actual value : -0.09 torsion_flexible C1' C2' C3' O3' 120.00 20.00 ! 60/90/120 torsion - Actual value : 118.67 torsion_flexible C2' C3' C4' O4' -24.00 20.00 ! Descriptive torsion - Actual value : -23.78 torsion_flexible C2' C3' C4' C5' -143.00 20.00 ! Descriptive torsion - Actual value : -142.73 torsion_flexible O3' C3' C4' O4' -143.00 20.00 ! Descriptive torsion - Actual value : -142.53 torsion_flexible O3' C3' C4' C5' 90.00 20.00 ! 60/90/120 torsion - Actual value : 98.52 torsion_flexible C3' C4' O4' C1' 40.00 20.00 ! Descriptive torsion - Actual value : 40.28 torsion_flexible C5' C4' O4' C1' 159.00 20.00 ! Descriptive torsion - Actual value : 159.45 torsion_fixed C3' C4' C5' O5' 180.00 2.00 ! TRANS torsion - Actual value : 176.91 torsion_flexible O4' C4' C5' O5' 60.00 20.00 ! 60/90/120 torsion - Actual value : 61.43 torsion_fixed C4' C5' O5' PA 180.00 2.00 ! TRANS torsion - Actual value : 179.98 torsion_flexible C5' O5' PA O1A 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.00 torsion_flexible C5' O5' PA O2A -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.00 torsion_fixed C5' O5' PA O3A 180.00 2.00 ! TRANS torsion - Actual value : -179.99 torsion_fixed O5' PA O3A PB 180.00 2.00 ! TRANS torsion - Actual value : -179.98 torsion_flexible O1A PA O3A PB -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.00 torsion_flexible O2A PA O3A PB 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.01 torsion_flexible PA O3A PB O1B 60.00 20.00 ! 60/90/120 torsion - Actual value : 60.01 torsion_fixed PA O3A PB O2B 180.00 2.00 ! TRANS torsion - Actual value : 179.98 torsion_flexible PA O3A PB O3B -60.00 20.00 ! 60/90/120 torsion - Actual value : -60.02 ! ! improper torsion angles ! torsion_fixed N1 C2 C6 C1' 0.00 2.00 ! Actual value : 0.20 torsion_fixed C2 N1 N3 O2 0.00 2.00 ! Actual value : 0.35 torsion_fixed C4 N3 C5 O4 0.00 2.00 ! Actual value : 0.01 torsion_fixed C1' N1 C2' O4' -35.00 2.00 ! Actual value : -36.91 torsion_fixed C3' C2' C4' O3' -35.00 2.00 ! Actual value : -33.59 torsion_fixed C4' C3' O4' C5' 35.00 2.00 ! Actual value : 34.97 torsion_fixed PA O5' O1A O2A 35.00 2.00 ! Actual value : 35.84 torsion_fixed PB O3A O1B O2B -35.00 2.00 ! Actual value : -35.86 !