! Filename = r88_O_refi_dict.txt ! Created by XPLO2D V. 050802/3.3.2 at Sun Mar 2 16:03:04 2008 for A. Nonymous ! Auto-generated by XPLO2D from file r88_msd.pdb ! !!!!! ADD THIS FILE TO YOUR .bonds_angles DATABLOCK !!!!! !!!!! THEN UPDATE THE .bonds_angles DATABLOCK HEADER !!!!! ! ! -------------------------------------------------------- ! residue R88 ! centre C1 ! atom C1A C1 O2 C1B C6B C5B C4B C2C C3C C4C \ C5C N1D C1F C1E C2E C3B C2B C6A C5A C4A \ O1C C3E BR23 C3A C2A ! fragment_all C1A C1 O2 C1B C6B C5B C4B C2C C3C C4C \ C5C N1D C1F C1E C2E C3B C2B C6A C5A C4A \ O1C C3E BR23 C3A C2A ! fragment_sc C1A C1 O2 C1B C6B C5B C4B C2C C3C C4C \ C5C N1D C1F C1E C2E C3B C2B C6A C5A C4A \ O1C C3E BR23 C3A C2A ! side-chain C1A C1 O2 C1B C6B C5B C4B C2C C3C C4C \ C5C N1D C1F C1E C2E C3B C2B C6A C5A C4A \ O1C C3E BR23 C3A C2A ! ! connectivity ! connect_all C1A C1 O2 connect_all C1A C6A C5A C4A BR23 connect_all C1A C2A C3A C4A connect_all C1 C1B C6B C5B C4B C3B C2B C1B connect_all C4B O1C C2C C3C C4C C5C N1D C1F connect_all N1D C1E C2E C3E C1E ! ! torsion-angle definitions ! note: only the first 12 torsions can be used in O ! torsion tor1 C6B C1B C1 C1A C1A O2 C6A C5A C4A BR23 C3A C2A torsion tor2 O1C C2C C3C C4C C4C C5C N1D C1F C1E C2E C3E torsion tor3 C3C C4C C5C N1D N1D C1F C1E C2E C3E torsion tor4 C4C C5C N1D C1F C1F C1E C2E C3E torsion tor5 C5C N1D C1E C3E C2E C3E ! ! bond lengths ! bond_distance C1A C1 1.477 0.020 bond_distance C1A C6A 1.397 0.020 bond_distance C1A C2A 1.397 0.020 bond_distance C1 O2 1.216 0.020 bond_distance C1 C1B 1.475 0.020 bond_distance C1B C6B 1.398 0.020 bond_distance C1B C2B 1.399 0.020 bond_distance C6B C5B 1.375 0.020 bond_distance C5B C4B 1.391 0.020 bond_distance C4B C3B 1.391 0.020 bond_distance C4B O1C 1.357 0.020 bond_distance C2C C3C 1.507 0.020 bond_distance C2C O1C 1.429 0.020 bond_distance C3C C4C 1.310 0.020 bond_distance C4C C5C 1.507 0.020 bond_distance C5C N1D 1.469 0.020 bond_distance N1D C1F 1.467 0.020 bond_distance N1D C1E 1.468 0.020 bond_distance C1E C2E 1.531 0.020 bond_distance C1E C3E 1.530 0.020 bond_distance C2E C3E 1.531 0.020 bond_distance C3B C2B 1.376 0.020 bond_distance C6A C5A 1.379 0.020 bond_distance C5A C4A 1.383 0.020 bond_distance C4A BR23 1.891 0.020 bond_distance C4A C3A 1.385 0.020 bond_distance C3A C2A 1.378 0.020 ! ! bond angles ! bond_angle C1 C1A C6A 120.14 2.00 bond_angle C1 C1A C2A 120.13 2.00 bond_angle C6A C1A C2A 119.73 2.00 bond_angle C1A C1 O2 119.99 2.00 bond_angle C1A C1 C1B 120.02 2.00 bond_angle O2 C1 C1B 119.99 2.00 bond_angle C1 C1B C6B 120.14 2.00 bond_angle C1 C1B C2B 120.10 2.00 bond_angle C6B C1B C2B 119.76 2.00 bond_angle C1B C6B C5B 119.94 2.00 bond_angle C6B C5B C4B 120.11 2.00 bond_angle C5B C4B C3B 120.18 2.00 bond_angle C5B C4B O1C 119.94 2.00 bond_angle C3B C4B O1C 119.88 2.00 bond_angle C3C C2C O1C 109.42 2.00 bond_angle C2C C3C C4C 120.01 2.00 bond_angle C3C C4C C5C 120.09 2.00 bond_angle C4C C5C N1D 109.50 2.00 bond_angle C5C N1D C1F 106.74 2.00 bond_angle C5C N1D C1E 106.71 2.00 bond_angle C1F N1D C1E 106.76 2.00 bond_angle N1D C1E C2E 117.51 2.00 bond_angle N1D C1E C3E 117.52 2.00 ! >>> WARNING - next angle less than 80 degrees : 60.019 bond_angle C2E C1E C3E 60.02 2.00 ! >>> WARNING - next angle less than 80 degrees : 59.980 bond_angle C1E C2E C3E 59.98 2.00 bond_angle C4B C3B C2B 120.06 2.00 bond_angle C1B C2B C3B 119.95 2.00 bond_angle C1A C6A C5A 119.82 2.00 bond_angle C6A C5A C4A 120.17 2.00 bond_angle C5A C4A BR23 119.87 2.00 bond_angle C5A C4A C3A 120.28 2.00 bond_angle BR23 C4A C3A 119.85 2.00 bond_angle C4B O1C C2C 106.79 2.00 ! >>> WARNING - next angle less than 80 degrees : 60.001 bond_angle C1E C3E C2E 60.00 2.00 bond_angle C4A C3A C2A 120.18 2.00 bond_angle C1A C2A C3A 119.81 2.00 ! ! dihedral angles (fixed and flexible) ! torsion_fixed C6A C1A C1 O2 0.00 2.00 ! CIS torsion - Actual value : -7.62 torsion_fixed C6A C1A C1 C1B 180.00 2.00 ! TRANS torsion - Actual value : 172.40 torsion_fixed C2A C1A C1 O2 180.00 2.00 ! TRANS torsion - Actual value : 172.20 torsion_fixed C2A C1A C1 C1B 0.00 2.00 ! CIS torsion - Actual value : -7.79 torsion_fixed C1 C1A C6A C5A 180.00 2.00 ! TRANS torsion - Actual value : -179.99 torsion_fixed C2A C1A C6A C5A 0.00 2.00 ! CIS torsion - Actual value : 0.19 torsion_fixed C1 C1A C2A C3A 180.00 2.00 ! TRANS torsion - Actual value : 179.72 torsion_fixed C6A C1A C2A C3A 0.00 2.00 ! CIS torsion - Actual value : -0.46 torsion_flexible C1A C1 C1B C6B 146.00 20.00 ! Descriptive torsion - Actual value : 146.03 torsion_flexible C1A C1 C1B C2B -34.00 20.00 ! Descriptive torsion - Actual value : -34.00 torsion_flexible O2 C1 C1B C6B -34.00 20.00 ! Descriptive torsion - Actual value : -33.95 torsion_flexible O2 C1 C1B C2B 146.00 20.00 ! Descriptive torsion - Actual value : 146.02 torsion_fixed C1 C1B C6B C5B 180.00 2.00 ! TRANS torsion - Actual value : 179.98 torsion_fixed C2B C1B C6B C5B 0.00 2.00 ! CIS torsion - Actual value : 0.00 torsion_fixed C1 C1B C2B C3B 180.00 2.00 ! TRANS torsion - Actual value : 179.76 torsion_fixed C6B C1B C2B C3B 0.00 2.00 ! CIS torsion - Actual value : -0.27 torsion_fixed C1B C6B C5B C4B 0.00 2.00 ! CIS torsion - Actual value : 0.02 torsion_fixed C6B C5B C4B C3B 0.00 2.00 ! CIS torsion - Actual value : 0.23 torsion_fixed C6B C5B C4B O1C 180.00 2.00 ! TRANS torsion - Actual value : 179.99 torsion_fixed C5B C4B C3B C2B 0.00 2.00 ! CIS torsion - Actual value : -0.50 torsion_fixed O1C C4B C3B C2B 180.00 2.00 ! TRANS torsion - Actual value : 179.74 torsion_fixed C5B C4B O1C C2C 180.00 2.00 ! TRANS torsion - Actual value : 179.96 torsion_fixed C3B C4B O1C C2C 0.00 2.00 ! CIS torsion - Actual value : -0.28 torsion_flexible O1C C2C C3C C4C 120.00 20.00 ! 60/90/120 torsion - Actual value : 120.04 torsion_fixed C3C C2C O1C C4B 180.00 2.00 ! TRANS torsion - Actual value : 179.97 torsion_fixed C2C C3C C4C C5C 180.00 2.00 ! TRANS torsion - Actual value : 179.97 torsion_flexible C3C C4C C5C N1D 120.00 20.00 ! 60/90/120 torsion - Actual value : 119.94 torsion_flexible C4C C5C N1D C1F -60.00 20.00 ! 60/90/120 torsion - Actual value : -66.10 torsion_fixed C4C C5C N1D C1E 180.00 2.00 ! TRANS torsion - Actual value : -179.98 torsion_fixed C5C N1D C1E C2E 180.00 2.00 ! TRANS torsion - Actual value : -179.96 torsion_flexible C5C N1D C1E C3E -120.00 20.00 ! 60/90/120 torsion - Actual value : -111.31 torsion_flexible C1F N1D C1E C2E 60.00 20.00 ! 60/90/120 torsion - Actual value : 66.17 torsion_flexible C1F N1D C1E C3E 135.00 20.00 ! Descriptive torsion - Actual value : 134.83 torsion_flexible N1D C1E C2E C3E 108.00 20.00 ! Descriptive torsion - Actual value : 107.52 torsion_flexible N1D C1E C3E C2E -107.00 20.00 ! Descriptive torsion - Actual value : -107.50 torsion_fixed C4B C3B C2B C1B 0.00 2.00 ! CIS torsion - Actual value : 0.52 torsion_fixed C1A C6A C5A C4A 0.00 2.00 ! CIS torsion - Actual value : 0.04 torsion_fixed C6A C5A C4A BR23 180.00 2.00 ! TRANS torsion - Actual value : 179.93 torsion_fixed C6A C5A C4A C3A 0.00 2.00 ! CIS torsion - Actual value : 0.00 torsion_fixed C5A C4A C3A C2A 0.00 2.00 ! CIS torsion - Actual value : -0.27 torsion_fixed BR23 C4A C3A C2A 180.00 2.00 ! TRANS torsion - Actual value : 179.80 torsion_fixed C4A C3A C2A C1A 0.00 2.00 ! CIS torsion - Actual value : 0.50 ! ! improper torsion angles ! torsion_fixed C1A C1 C6A C2A 0.00 2.00 ! Actual value : -0.11 torsion_fixed C1 C1A O2 C1B 0.00 2.00 ! Actual value : 0.01 torsion_fixed C1B C1 C6B C2B 0.00 2.00 ! Actual value : -0.02 torsion_fixed C4B C5B C3B O1C 0.00 2.00 ! Actual value : -0.14 torsion_fixed N1D C5C C1F C1E 35.00 2.00 ! Actual value : 39.06 torsion_fixed C1E N1D C2E C3E -35.00 2.00 ! Actual value : -59.90 torsion_fixed C4A C5A BR23 C3A 0.00 2.00 ! Actual value : 0.04 !