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global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
KDD KDD '2,6-anhydro-3,5-dideoxy-D-ribo-oct-2' non-polymer 25 14 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_KDD
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
KDD O1B O OC -0.500 0.000 0.000 0.000
KDD C1 C C 0.000 -0.940 -0.821 0.088
KDD O1A O OC -0.500 -0.698 -2.049 0.110
KDD C2 C C 0.000 -2.331 -0.343 0.157
KDD C3 C C1 0.000 -3.304 -1.239 0.239
KDD H3 H H 0.000 -3.047 -2.285 0.252
KDD C4 C CH1 0.000 -4.755 -0.845 0.312
KDD H4 H H 0.000 -5.265 -1.463 1.064
KDD O61 O OH1 0.000 -5.363 -1.047 -0.965
KDD H12 H H 0.000 -5.293 -1.980 -1.211
KDD C5 C CH2 0.000 -4.865 0.632 0.703
KDD H5 H H 0.000 -4.609 0.761 1.756
KDD H5A H H 0.000 -5.883 0.989 0.531
KDD C6 C CH1 0.000 -3.886 1.434 -0.166
KDD H6 H H 0.000 -4.106 1.259 -1.228
KDD O6 O O2 0.000 -2.558 0.993 0.131
KDD C7 C CH1 0.000 -4.017 2.924 0.150
KDD H7 H H 0.000 -3.808 3.092 1.216
KDD O7 O OH1 0.000 -5.346 3.359 -0.148
KDD HO7 H H 0.000 -5.530 3.211 -1.085
KDD C8 C CH2 0.000 -3.020 3.716 -0.697
KDD H8 H H 0.000 -3.282 3.619 -1.753
KDD H8A H H 0.000 -2.014 3.323 -0.536
KDD O8 O OH1 0.000 -3.060 5.093 -0.319
KDD HO8 H H 0.000 -2.430 5.593 -0.855
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
KDD O1B n/a C1 START
KDD C1 O1B C2 .
KDD O1A C1 . .
KDD C2 C1 C3 .
KDD C3 C2 C4 .
KDD H3 C3 . .
KDD C4 C3 C5 .
KDD H4 C4 . .
KDD O61 C4 H12 .
KDD H12 O61 . .
KDD C5 C4 C6 .
KDD H5 C5 . .
KDD H5A C5 . .
KDD C6 C5 C7 .
KDD H6 C6 . .
KDD O6 C6 . .
KDD C7 C6 C8 .
KDD H7 C7 . .
KDD O7 C7 HO7 .
KDD HO7 O7 . .
KDD C8 C7 O8 .
KDD H8 C8 . .
KDD H8A C8 . .
KDD O8 C8 HO8 .
KDD HO8 O8 . END
KDD C2 O6 . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
KDD O1A C1 deloc 1.250 0.020
KDD C1 O1B deloc 1.250 0.020
KDD C2 C1 single 1.460 0.020
KDD C2 O6 single 1.454 0.020
KDD O6 C6 single 1.426 0.020
KDD C7 C6 single 1.524 0.020
KDD H6 C6 single 1.099 0.020
KDD C8 C7 single 1.524 0.020
KDD H7 C7 single 1.099 0.020
KDD O8 C8 single 1.432 0.020
KDD H8 C8 single 1.092 0.020
KDD H8A C8 single 1.092 0.020
KDD HO8 O8 single 0.967 0.020
KDD O7 C7 single 1.432 0.020
KDD HO7 O7 single 0.967 0.020
KDD C6 C5 single 1.524 0.020
KDD H5 C5 single 1.092 0.020
KDD H5A C5 single 1.092 0.020
KDD C3 C2 double 1.340 0.020
KDD H3 C3 single 1.077 0.020
KDD C5 C4 single 1.524 0.020
KDD C4 C3 single 1.510 0.020
KDD O61 C4 single 1.432 0.020
KDD H4 C4 single 1.099 0.020
KDD H12 O61 single 0.967 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
KDD O1B C1 O1A 123.000 3.000
KDD O1B C1 C2 120.000 3.000
KDD O1A C1 C2 120.000 3.000
KDD C1 C2 C3 120.000 3.000
KDD C1 C2 O6 120.000 3.000
KDD C3 C2 O6 120.000 3.000
KDD C2 C3 H3 120.000 3.000
KDD C2 C3 C4 120.500 3.000
KDD H3 C3 C4 120.000 3.000
KDD C3 C4 H4 108.810 3.000
KDD C3 C4 O61 109.470 3.000
KDD C3 C4 C5 109.470 3.000
KDD H4 C4 O61 109.470 3.000
KDD H4 C4 C5 108.340 3.000
KDD O61 C4 C5 109.470 3.000
KDD C4 O61 H12 109.470 3.000
KDD C4 C5 H5 109.470 3.000
KDD C4 C5 H5A 109.470 3.000
KDD C4 C5 C6 111.000 3.000
KDD H5 C5 H5A 107.900 3.000
KDD H5 C5 C6 109.470 3.000
KDD H5A C5 C6 109.470 3.000
KDD C5 C6 H6 108.340 3.000
KDD C5 C6 O6 109.470 3.000
KDD C5 C6 C7 111.000 3.000
KDD H6 C6 O6 109.470 3.000
KDD H6 C6 C7 108.340 3.000
KDD O6 C6 C7 109.470 3.000
KDD C6 O6 C2 111.800 3.000
KDD C6 C7 H7 108.340 3.000
KDD C6 C7 O7 109.470 3.000
KDD C6 C7 C8 111.000 3.000
KDD H7 C7 O7 109.470 3.000
KDD H7 C7 C8 108.340 3.000
KDD O7 C7 C8 109.470 3.000
KDD C7 O7 HO7 109.470 3.000
KDD C7 C8 H8 109.470 3.000
KDD C7 C8 H8A 109.470 3.000
KDD C7 C8 O8 109.470 3.000
KDD H8 C8 H8A 107.900 3.000
KDD H8 C8 O8 109.470 3.000
KDD H8A C8 O8 109.470 3.000
KDD C8 O8 HO8 109.470 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
KDD var_1 O1B C1 C2 C3 179.438 20.000 1
KDD var_2 C1 C2 O6 C6 150.000 20.000 1
KDD var_3 C1 C2 C3 C4 180.000 20.000 1
KDD var_4 C2 C3 C4 C5 -30.000 20.000 1
KDD var_5 C3 C4 O61 H12 60.039 20.000 1
KDD var_6 C3 C4 C5 C6 60.000 20.000 3
KDD var_7 C4 C5 C6 C7 180.000 20.000 3
KDD var_8 C5 C6 O6 C2 60.000 20.000 1
KDD var_9 C5 C6 C7 C8 178.849 20.000 3
KDD var_10 C6 C7 O7 HO7 -60.015 20.000 1
KDD var_11 C6 C7 C8 O8 -175.007 20.000 3
KDD var_12 C7 C8 O8 HO8 179.989 20.000 1
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
KDD chir_01 C6 O6 C7 C5 positiv
KDD chir_02 C7 C6 C8 O7 negativ
KDD chir_03 C4 C5 C3 O61 positiv
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
KDD plan-1 C1 0.020
KDD plan-1 O1A 0.020
KDD plan-1 O1B 0.020
KDD plan-1 C2 0.020
KDD plan-2 C2 0.020
KDD plan-2 C1 0.020
KDD plan-2 O6 0.020
KDD plan-2 C3 0.020
KDD plan-2 H3 0.020
KDD plan-3 C3 0.020
KDD plan-3 C2 0.020
KDD plan-3 C4 0.020
KDD plan-3 H3 0.020
# ------------------------------------------------------
|
