! Filename = yol_O_refi_dict.txt ! Created by XPLO2D V. 050802/3.3.2 at Mon Mar 3 11:34:59 2008 for A. Nonymous ! Auto-generated by XPLO2D from file yol_msd.pdb ! !!!!! ADD THIS FILE TO YOUR .bonds_angles DATABLOCK !!!!! !!!!! THEN UPDATE THE .bonds_angles DATABLOCK HEADER !!!!! ! ! -------------------------------------------------------- ! residue YOL ! centre CA ! atom O2A CAA O1A CC5 CC6 CC1 CC2 CC3 CC4 NA \ CA CA1 CA6 CA5 CA4 CA3 CA2 OA FE OB \ CB2 CB3 CB4 CB5 CB6 CB1 CB NB ! fragment_all O2A CAA O1A CC5 CC6 CC1 CC2 CC3 CC4 NA \ CA CA1 CA6 CA5 CA4 CA3 CA2 OA FE OB \ CB2 CB3 CB4 CB5 CB6 CB1 CB NB ! fragment_sc O2A CAA O1A CC5 CC6 CC1 CC2 CC3 CC4 NA \ CA CA1 CA6 CA5 CA4 CA3 CA2 OA FE OB \ CB2 CB3 CB4 CB5 CB6 CB1 CB NB ! side-chain O2A CAA O1A CC5 CC6 CC1 CC2 CC3 CC4 NA \ CA CA1 CA6 CA5 CA4 CA3 CA2 OA FE OB \ CB2 CB3 CB4 CB5 CB6 CB1 CB NB ! ! connectivity ! connect_all O2A CAA O1A connect_all CAA CC5 CC6 CC1 CC2 CC3 CC4 CC5 connect_all CC1 NA CA CA1 CA6 CA5 CA4 CA3 CA2 CA1 connect_all CC2 NB FE NA connect_all CA2 OA FE OB CB2 CB3 CB4 CB5 CB6 CB1 CB2 connect_all CB1 CB NB ! ! torsion-angle definitions ! note: only the first 12 torsions can be used in O ! ! ! bond lengths ! bond_distance O2A CAA 1.347 0.020 bond_distance CAA O1A 1.214 0.020 bond_distance CAA CC5 1.475 0.020 bond_distance CC5 CC6 1.390 0.020 bond_distance CC5 CC4 1.400 0.020 bond_distance CC6 CC1 1.409 0.020 bond_distance CC1 CC2 1.384 0.020 bond_distance CC1 NA 1.373 0.020 bond_distance CC2 CC3 1.416 0.020 bond_distance CC2 NB 1.369 0.020 bond_distance CC3 CC4 1.359 0.020 bond_distance NA CA 1.298 0.020 bond_distance NA FE 1.867 0.020 bond_distance CA CA1 1.458 0.020 bond_distance CA1 CA6 1.404 0.020 bond_distance CA1 CA2 1.397 0.020 bond_distance CA6 CA5 1.376 0.020 bond_distance CA5 CA4 1.385 0.020 bond_distance CA4 CA3 1.378 0.020 bond_distance CA3 CA2 1.396 0.020 bond_distance CA2 OA 1.331 0.020 bond_distance OA FE 1.778 0.020 bond_distance FE OB 1.778 0.020 bond_distance FE NB 1.867 0.020 bond_distance OB CB2 1.330 0.020 bond_distance CB2 CB3 1.397 0.020 bond_distance CB2 CB1 1.397 0.020 bond_distance CB3 CB4 1.378 0.020 bond_distance CB4 CB5 1.386 0.020 bond_distance CB5 CB6 1.375 0.020 bond_distance CB6 CB1 1.404 0.020 bond_distance CB1 CB 1.457 0.020 bond_distance CB NB 1.299 0.020 ! ! bond angles ! bond_angle O2A CAA O1A 120.03 2.00 bond_angle O2A CAA CC5 119.97 2.00 bond_angle O1A CAA CC5 120.00 2.00 bond_angle CAA CC5 CC6 120.02 2.00 bond_angle CAA CC5 CC4 120.05 2.00 bond_angle CC6 CC5 CC4 119.93 2.00 bond_angle CC5 CC6 CC1 120.13 2.00 bond_angle CC6 CC1 CC2 119.41 2.00 bond_angle CC6 CC1 NA 124.72 2.00 bond_angle CC2 CC1 NA 115.87 2.00 bond_angle CC1 CC2 CC3 119.64 2.00 bond_angle CC1 CC2 NB 115.96 2.00 bond_angle CC3 CC2 NB 124.40 2.00 bond_angle CC2 CC3 CC4 120.74 2.00 bond_angle CC5 CC4 CC3 120.15 2.00 bond_angle CC1 NA CA 125.42 2.00 bond_angle CC1 NA FE 110.29 2.00 bond_angle CA NA FE 124.29 2.00 bond_angle NA CA CA1 125.70 2.00 bond_angle CA CA1 CA6 118.78 2.00 bond_angle CA CA1 CA2 121.32 2.00 bond_angle CA6 CA1 CA2 119.90 2.00 bond_angle CA1 CA6 CA5 120.22 2.00 bond_angle CA6 CA5 CA4 119.92 2.00 bond_angle CA5 CA4 CA3 120.42 2.00 bond_angle CA4 CA3 CA2 120.71 2.00 bond_angle CA1 CA2 CA3 118.82 2.00 bond_angle CA1 CA2 OA 123.19 2.00 bond_angle CA3 CA2 OA 117.99 2.00 bond_angle CA2 OA FE 128.95 2.00 bond_angle NA FE OA 96.56 2.00 bond_angle NA FE OB 175.96 2.00 bond_angle NA FE NB 87.50 2.00 ! >>> WARNING - next angle less than 80 degrees : 79.453 bond_angle OA FE OB 79.45 2.00 bond_angle OA FE NB 175.90 2.00 bond_angle OB FE NB 96.48 2.00 bond_angle FE OB CB2 128.97 2.00 bond_angle OB CB2 CB3 117.96 2.00 bond_angle OB CB2 CB1 123.32 2.00 bond_angle CB3 CB2 CB1 118.72 2.00 bond_angle CB2 CB3 CB4 120.76 2.00 bond_angle CB3 CB4 CB5 120.41 2.00 bond_angle CB4 CB5 CB6 119.95 2.00 bond_angle CB5 CB6 CB1 120.19 2.00 bond_angle CB2 CB1 CB6 119.97 2.00 bond_angle CB2 CB1 CB 121.22 2.00 bond_angle CB6 CB1 CB 118.81 2.00 bond_angle CB1 CB NB 125.69 2.00 bond_angle CC2 NB FE 110.37 2.00 bond_angle CC2 NB CB 125.31 2.00 bond_angle FE NB CB 124.32 2.00 ! ! dihedral angles (fixed and flexible) ! torsion_fixed O2A CAA CC5 CC6 180.00 2.00 ! TRANS torsion - Actual value : -179.90 torsion_fixed O2A CAA CC5 CC4 0.00 2.00 ! CIS torsion - Actual value : 0.07 torsion_fixed O1A CAA CC5 CC6 0.00 2.00 ! CIS torsion - Actual value : 0.03 torsion_fixed O1A CAA CC5 CC4 180.00 2.00 ! TRANS torsion - Actual value : 180.00 torsion_fixed CAA CC5 CC6 CC1 180.00 2.00 ! TRANS torsion - Actual value : -179.89 torsion_fixed CC4 CC5 CC6 CC1 0.00 2.00 ! CIS torsion - Actual value : 0.14 torsion_fixed CAA CC5 CC4 CC3 180.00 2.00 ! TRANS torsion - Actual value : 179.81 torsion_fixed CC6 CC5 CC4 CC3 0.00 2.00 ! CIS torsion - Actual value : -0.22 torsion_fixed CC5 CC6 CC1 CC2 0.00 2.00 ! CIS torsion - Actual value : 0.18 torsion_fixed CC5 CC6 CC1 NA 180.00 2.00 ! TRANS torsion - Actual value : -179.90 torsion_fixed CC6 CC1 CC2 CC3 0.00 2.00 ! CIS torsion - Actual value : -0.42 torsion_fixed CC6 CC1 CC2 NB 180.00 2.00 ! TRANS torsion - Actual value : 179.42 torsion_fixed NA CC1 CC2 CC3 180.00 2.00 ! TRANS torsion - Actual value : 179.66 torsion_fixed NA CC1 CC2 NB 0.00 2.00 ! CIS torsion - Actual value : -0.51 torsion_fixed CC6 CC1 NA CA 0.00 2.00 ! CIS torsion - Actual value : 0.21 torsion_fixed CC6 CC1 NA FE 180.00 2.00 ! TRANS torsion - Actual value : -179.81 torsion_fixed CC2 CC1 NA CA 180.00 2.00 ! TRANS torsion - Actual value : -179.87 torsion_fixed CC2 CC1 NA FE 0.00 2.00 ! CIS torsion - Actual value : 0.11 torsion_fixed CC1 CC2 CC3 CC4 0.00 2.00 ! CIS torsion - Actual value : 0.34 torsion_fixed NB CC2 CC3 CC4 180.00 2.00 ! TRANS torsion - Actual value : -179.48 torsion_fixed CC1 CC2 NB FE 0.00 2.00 ! CIS torsion - Actual value : 0.64 torsion_fixed CC1 CC2 NB CB 180.00 2.00 ! TRANS torsion - Actual value : -179.22 torsion_fixed CC3 CC2 NB FE 180.00 2.00 ! TRANS torsion - Actual value : -179.54 torsion_fixed CC3 CC2 NB CB 0.00 2.00 ! CIS torsion - Actual value : 0.61 torsion_fixed CC2 CC3 CC4 CC5 0.00 2.00 ! CIS torsion - Actual value : -0.02 torsion_fixed CC1 NA CA CA1 180.00 2.00 ! TRANS torsion - Actual value : -179.61 torsion_fixed FE NA CA CA1 0.00 2.00 ! CIS torsion - Actual value : 0.41 torsion_fixed CC1 NA FE OA 180.00 2.00 ! TRANS torsion - Actual value : 179.63 torsion_fixed CC1 NA FE OB 180.00 2.00 ! TRANS torsion - Actual value : 170.61 torsion_fixed CC1 NA FE NB 0.00 2.00 ! CIS torsion - Actual value : 0.20 torsion_fixed CA NA FE OA 0.00 2.00 ! CIS torsion - Actual value : -0.39 torsion_fixed CA NA FE OB 0.00 2.00 ! CIS torsion - Actual value : -9.41 torsion_fixed CA NA FE NB 180.00 2.00 ! TRANS torsion - Actual value : -179.82 torsion_fixed NA CA CA1 CA6 180.00 2.00 ! TRANS torsion - Actual value : 179.81 torsion_fixed NA CA CA1 CA2 0.00 2.00 ! CIS torsion - Actual value : -0.19 torsion_fixed CA CA1 CA6 CA5 180.00 2.00 ! TRANS torsion - Actual value : -179.94 torsion_fixed CA2 CA1 CA6 CA5 0.00 2.00 ! CIS torsion - Actual value : 0.05 torsion_fixed CA CA1 CA2 CA3 180.00 2.00 ! TRANS torsion - Actual value : 179.91 torsion_fixed CA CA1 CA2 OA 0.00 2.00 ! CIS torsion - Actual value : 0.02 torsion_fixed CA6 CA1 CA2 CA3 0.00 2.00 ! CIS torsion - Actual value : -0.09 torsion_fixed CA6 CA1 CA2 OA 180.00 2.00 ! TRANS torsion - Actual value : -179.98 torsion_fixed CA1 CA6 CA5 CA4 0.00 2.00 ! CIS torsion - Actual value : -0.01 torsion_fixed CA6 CA5 CA4 CA3 0.00 2.00 ! CIS torsion - Actual value : 0.00 torsion_fixed CA5 CA4 CA3 CA2 0.00 2.00 ! CIS torsion - Actual value : -0.04 torsion_fixed CA4 CA3 CA2 CA1 0.00 2.00 ! CIS torsion - Actual value : 0.08 torsion_fixed CA4 CA3 CA2 OA 180.00 2.00 ! TRANS torsion - Actual value : 179.98 torsion_fixed CA1 CA2 OA FE 0.00 2.00 ! CIS torsion - Actual value : -0.11 torsion_fixed CA3 CA2 OA FE 180.00 2.00 ! TRANS torsion - Actual value : 180.00 torsion_fixed CA2 OA FE NA 0.00 2.00 ! CIS torsion - Actual value : 0.25 torsion_fixed CA2 OA FE OB 180.00 2.00 ! TRANS torsion - Actual value : 179.60 torsion_fixed CA2 OA FE NB 180.00 2.00 ! TRANS torsion - Actual value : 172.35 torsion_fixed NA FE OB CB2 180.00 2.00 ! TRANS torsion - Actual value : -170.21 torsion_fixed OA FE OB CB2 180.00 2.00 ! TRANS torsion - Actual value : -179.33 torsion_fixed NB FE OB CB2 0.00 2.00 ! CIS torsion - Actual value : 0.15 torsion_fixed NA FE NB CC2 0.00 2.00 ! CIS torsion - Actual value : -0.46 torsion_fixed NA FE NB CB 180.00 2.00 ! TRANS torsion - Actual value : 179.40 torsion_fixed OA FE NB CC2 180.00 2.00 ! TRANS torsion - Actual value : -172.60 torsion_fixed OA FE NB CB 0.00 2.00 ! CIS torsion - Actual value : 7.25 torsion_fixed OB FE NB CC2 180.00 2.00 ! TRANS torsion - Actual value : -179.78 torsion_fixed OB FE NB CB 0.00 2.00 ! CIS torsion - Actual value : 0.08 torsion_fixed FE OB CB2 CB3 180.00 2.00 ! TRANS torsion - Actual value : 179.80 torsion_fixed FE OB CB2 CB1 0.00 2.00 ! CIS torsion - Actual value : -0.30 torsion_fixed OB CB2 CB3 CB4 180.00 2.00 ! TRANS torsion - Actual value : 179.97 torsion_fixed CB1 CB2 CB3 CB4 0.00 2.00 ! CIS torsion - Actual value : 0.07 torsion_fixed OB CB2 CB1 CB6 180.00 2.00 ! TRANS torsion - Actual value : -179.90 torsion_fixed OB CB2 CB1 CB 0.00 2.00 ! CIS torsion - Actual value : 0.20 torsion_fixed CB3 CB2 CB1 CB6 0.00 2.00 ! CIS torsion - Actual value : 0.00 torsion_fixed CB3 CB2 CB1 CB 180.00 2.00 ! TRANS torsion - Actual value : -179.90 torsion_fixed CB2 CB3 CB4 CB5 0.00 2.00 ! CIS torsion - Actual value : -0.06 torsion_fixed CB3 CB4 CB5 CB6 0.00 2.00 ! CIS torsion - Actual value : 0.00 torsion_fixed CB4 CB5 CB6 CB1 0.00 2.00 ! CIS torsion - Actual value : 0.06 torsion_fixed CB5 CB6 CB1 CB2 0.00 2.00 ! CIS torsion - Actual value : -0.06 torsion_fixed CB5 CB6 CB1 CB 180.00 2.00 ! TRANS torsion - Actual value : 179.84 torsion_fixed CB2 CB1 CB NB 0.00 2.00 ! CIS torsion - Actual value : 0.03 torsion_fixed CB6 CB1 CB NB 180.00 2.00 ! TRANS torsion - Actual value : -179.86 torsion_fixed CB1 CB NB CC2 180.00 2.00 ! TRANS torsion - Actual value : 179.67 torsion_fixed CB1 CB NB FE 0.00 2.00 ! CIS torsion - Actual value : -0.16 ! ! improper torsion angles ! torsion_fixed CAA O2A O1A CC5 0.00 2.00 ! Actual value : -0.04 torsion_fixed CC5 CAA CC6 CC4 0.00 2.00 ! Actual value : -0.02 torsion_fixed CC1 CC6 CC2 NA 0.00 2.00 ! Actual value : -0.04 torsion_fixed CC2 CC1 CC3 NB 0.00 2.00 ! Actual value : -0.10 torsion_fixed NA CC1 CA FE 0.00 2.00 ! Actual value : -0.01 torsion_fixed CA1 CA CA6 CA2 0.00 2.00 ! Actual value : 0.00 torsion_fixed CA2 CA1 CA3 OA 0.00 2.00 ! Actual value : 0.06 torsion_fixed FE NA OA OB 0.00 2.00 ! Actual value : 0.50 torsion_fixed CB2 OB CB3 CB1 0.00 2.00 ! Actual value : -0.06 torsion_fixed CB1 CB2 CB6 CB 0.00 2.00 ! Actual value : 0.06 torsion_fixed NB CC2 FE CB 0.00 2.00 ! Actual value : 0.07 !