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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
CTD CTD '3-DEAZACYTIDINE ' non-polymer 31 17 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CTD
#
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
CTD O2 O O 0.000 0.000 0.000 0.000
CTD C2 C CR6 0.000 -0.606 0.879 -0.593
CTD C3 C CR16 0.000 0.032 2.087 -0.889
CTD H3 H H 0.000 1.062 2.250 -0.595
CTD C4 C CR6 0.000 -0.670 3.073 -1.562
CTD N4 N NH2 0.000 -0.068 4.280 -1.868
CTD HN42 H H 0.000 0.896 4.457 -1.604
CTD HN41 H H 0.000 -0.584 5.002 -2.361
CTD C5 C CR16 0.000 -2.012 2.827 -1.924
CTD H5 H H 0.000 -2.582 3.587 -2.443
CTD C6 C CR16 0.000 -2.582 1.642 -1.621
CTD H6 H H 0.000 -3.610 1.455 -1.907
CTD N1 N NR6 0.000 -1.885 0.681 -0.961
CTD "C1'" C CH1 0.000 -2.537 -0.590 -0.643
CTD "H1'" H H 0.000 -1.837 -1.259 -0.123
CTD "O4'" O O2 0.000 -3.029 -1.217 -1.846
CTD "C4'" C CH1 0.000 -4.041 -2.148 -1.404
CTD "H4'" H H 0.000 -3.575 -3.057 -1.000
CTD "C5'" C CH2 0.000 -4.981 -2.500 -2.559
CTD "H5'1" H H 0.000 -5.448 -1.589 -2.938
CTD "H5'2" H H 0.000 -5.755 -3.183 -2.202
CTD "O5'" O OH1 0.000 -4.238 -3.127 -3.605
CTD "HO5'" H H 0.000 -4.833 -3.349 -4.334
CTD "C3'" C CH1 0.000 -4.808 -1.398 -0.294
CTD "H3'" H H 0.000 -5.697 -0.902 -0.707
CTD "O3'" O OH1 0.000 -5.177 -2.297 0.754
CTD "HO3'" H H 0.000 -5.763 -2.980 0.400
CTD "C2'" C CH1 0.000 -3.793 -0.350 0.222
CTD "H2'" H H 0.000 -4.178 0.667 0.065
CTD "O2'" O OH1 0.000 -3.507 -0.569 1.605
CTD "HO2'" H H 0.000 -4.319 -0.472 2.120
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
CTD O2 n/a C2 START
CTD C2 O2 C3 .
CTD C3 C2 C4 .
CTD H3 C3 . .
CTD C4 C3 C5 .
CTD N4 C4 HN41 .
CTD HN42 N4 . .
CTD HN41 N4 . .
CTD C5 C4 C6 .
CTD H5 C5 . .
CTD C6 C5 N1 .
CTD H6 C6 . .
CTD N1 C6 "C1'" .
CTD "C1'" N1 "O4'" .
CTD "H1'" "C1'" . .
CTD "O4'" "C1'" "C4'" .
CTD "C4'" "O4'" "C3'" .
CTD "H4'" "C4'" . .
CTD "C5'" "C4'" "O5'" .
CTD "H5'1" "C5'" . .
CTD "H5'2" "C5'" . .
CTD "O5'" "C5'" "HO5'" .
CTD "HO5'" "O5'" . .
CTD "C3'" "C4'" "C2'" .
CTD "H3'" "C3'" . .
CTD "O3'" "C3'" "HO3'" .
CTD "HO3'" "O3'" . .
CTD "C2'" "C3'" "O2'" .
CTD "H2'" "C2'" . .
CTD "O2'" "C2'" "HO2'" .
CTD "HO2'" "O2'" . END
CTD N1 C2 . ADD
CTD "C1'" "C2'" . 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
CTD N1 C2 single 1.410 0.020
CTD N1 C6 single 1.337 0.020
CTD "C1'" N1 single 1.465 0.020
CTD C3 C2 single 1.390 0.020
CTD C2 O2 double 1.250 0.020
CTD C4 C3 double 1.390 0.020
CTD H3 C3 single 1.083 0.020
CTD C5 C4 single 1.390 0.020
CTD N4 C4 single 1.355 0.020
CTD C6 C5 double 1.390 0.020
CTD H5 C5 single 1.083 0.020
CTD H6 C6 single 1.083 0.020
CTD HN41 N4 single 1.010 0.020
CTD HN42 N4 single 1.010 0.020
CTD "C1'" "C2'" single 1.524 0.020
CTD "O4'" "C1'" single 1.426 0.020
CTD "H1'" "C1'" single 1.099 0.020
CTD "O2'" "C2'" single 1.432 0.020
CTD "C2'" "C3'" single 1.524 0.020
CTD "H2'" "C2'" single 1.099 0.020
CTD "HO2'" "O2'" single 0.967 0.020
CTD "C3'" "C4'" single 1.524 0.020
CTD "O3'" "C3'" single 1.432 0.020
CTD "H3'" "C3'" single 1.099 0.020
CTD "C4'" "O4'" single 1.426 0.020
CTD "C5'" "C4'" single 1.524 0.020
CTD "H4'" "C4'" single 1.099 0.020
CTD "HO3'" "O3'" single 0.967 0.020
CTD "O5'" "C5'" single 1.432 0.020
CTD "H5'1" "C5'" single 1.092 0.020
CTD "H5'2" "C5'" single 1.092 0.020
CTD "HO5'" "O5'" 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
CTD O2 C2 C3 120.000 3.000
CTD O2 C2 N1 120.000 3.000
CTD C3 C2 N1 120.000 3.000
CTD C2 C3 H3 120.000 3.000
CTD C2 C3 C4 120.000 3.000
CTD H3 C3 C4 120.000 3.000
CTD C3 C4 N4 120.000 3.000
CTD C3 C4 C5 120.000 3.000
CTD N4 C4 C5 120.000 3.000
CTD C4 N4 HN42 120.000 3.000
CTD C4 N4 HN41 120.000 3.000
CTD HN42 N4 HN41 120.000 3.000
CTD C4 C5 H5 120.000 3.000
CTD C4 C5 C6 120.000 3.000
CTD H5 C5 C6 120.000 3.000
CTD C5 C6 H6 120.000 3.000
CTD C5 C6 N1 120.000 3.000
CTD H6 C6 N1 120.000 3.000
CTD C6 N1 "C1'" 120.000 3.000
CTD C6 N1 C2 120.000 3.000
CTD "C1'" N1 C2 120.000 3.000
CTD N1 "C1'" "H1'" 109.470 3.000
CTD N1 "C1'" "O4'" 109.470 3.000
CTD N1 "C1'" "C2'" 109.470 3.000
CTD "H1'" "C1'" "O4'" 109.470 3.000
CTD "H1'" "C1'" "C2'" 108.340 3.000
CTD "O4'" "C1'" "C2'" 109.470 3.000
CTD "C1'" "O4'" "C4'" 111.800 3.000
CTD "O4'" "C4'" "H4'" 109.470 3.000
CTD "O4'" "C4'" "C5'" 109.470 3.000
CTD "O4'" "C4'" "C3'" 109.470 3.000
CTD "H4'" "C4'" "C5'" 108.340 3.000
CTD "H4'" "C4'" "C3'" 108.340 3.000
CTD "C5'" "C4'" "C3'" 111.000 3.000
CTD "C4'" "C5'" "H5'1" 109.470 3.000
CTD "C4'" "C5'" "H5'2" 109.470 3.000
CTD "C4'" "C5'" "O5'" 109.470 3.000
CTD "H5'1" "C5'" "H5'2" 107.900 3.000
CTD "H5'1" "C5'" "O5'" 109.470 3.000
CTD "H5'2" "C5'" "O5'" 109.470 3.000
CTD "C5'" "O5'" "HO5'" 109.470 3.000
CTD "C4'" "C3'" "H3'" 108.340 3.000
CTD "C4'" "C3'" "O3'" 109.470 3.000
CTD "C4'" "C3'" "C2'" 111.000 3.000
CTD "H3'" "C3'" "O3'" 109.470 3.000
CTD "H3'" "C3'" "C2'" 108.340 3.000
CTD "O3'" "C3'" "C2'" 109.470 3.000
CTD "C3'" "O3'" "HO3'" 109.470 3.000
CTD "C3'" "C2'" "H2'" 108.340 3.000
CTD "C3'" "C2'" "O2'" 109.470 3.000
CTD "C3'" "C2'" "C1'" 111.000 3.000
CTD "H2'" "C2'" "O2'" 109.470 3.000
CTD "H2'" "C2'" "C1'" 108.340 3.000
CTD "O2'" "C2'" "C1'" 109.470 3.000
CTD "C2'" "O2'" "HO2'" 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
CTD CONST_1 O2 C2 C3 C4 180.000 0.000 0
CTD CONST_2 C2 C3 C4 C5 0.000 0.000 0
CTD CONST_3 C3 C4 N4 HN41 -179.973 0.000 0
CTD CONST_4 C3 C4 C5 C6 0.000 0.000 0
CTD CONST_5 C4 C5 C6 N1 0.000 0.000 0
CTD CONST_6 C5 C6 N1 "C1'" 180.000 0.000 0
CTD CONST_7 C6 N1 C2 O2 180.000 0.000 0
CTD var_1 C6 N1 "C1'" "O4'" 57.069 20.000 1
CTD var_2 N1 "C1'" "C2'" "C3'" 150.000 20.000 3
CTD var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
CTD var_4 "C1'" "O4'" "C4'" "C3'" 30.000 20.000 1
CTD var_5 "O4'" "C4'" "C5'" "O5'" 61.429 20.000 3
CTD var_6 "C4'" "C5'" "O5'" "HO5'" -179.985 20.000 1
CTD var_7 "O4'" "C4'" "C3'" "C2'" -30.000 20.000 3
CTD var_8 "C4'" "C3'" "O3'" "HO3'" -61.421 20.000 1
CTD var_9 "C4'" "C3'" "C2'" "O2'" -120.000 20.000 3
CTD var_10 "C3'" "C2'" "O2'" "HO2'" -61.462 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
CTD chir_01 "C1'" N1 "C2'" "O4'" negativ
CTD chir_02 "C2'" "C1'" "O2'" "C3'" positiv
CTD chir_03 "C3'" "C2'" "C4'" "O3'" negativ
CTD chir_04 "C4'" "C3'" "O4'" "C5'" 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
CTD plan-1 N1 0.020
CTD plan-1 C2 0.020
CTD plan-1 C6 0.020
CTD plan-1 "C1'" 0.020
CTD plan-1 C3 0.020
CTD plan-1 C4 0.020
CTD plan-1 C5 0.020
CTD plan-1 O2 0.020
CTD plan-1 H3 0.020
CTD plan-1 N4 0.020
CTD plan-1 H5 0.020
CTD plan-1 H6 0.020
CTD plan-1 HN42 0.020
CTD plan-1 HN41 0.020
CTD plan-2 N4 0.020
CTD plan-2 C4 0.020
CTD plan-2 HN41 0.020
CTD plan-2 HN42 0.020
# ------------------------------------------------------
|
