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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
CDY CDY '2-CHLORODIDEOXYADENOSINE ' non-polymer 30 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CDY
#
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
CDY CL CL CL 0.000 0.000 0.000 0.000
CDY C2 C CR6 0.000 -1.362 0.047 -1.076
CDY N1 N NRD6 0.000 -1.142 0.154 -2.375
CDY C6 C CR6 0.000 -2.149 0.193 -3.240
CDY N6 N NH2 0.000 -1.911 0.305 -4.599
CDY HN62 H H 0.000 -2.684 0.334 -5.257
CDY HN61 H H 0.000 -0.961 0.358 -4.953
CDY C5 C CR56 0.000 -3.463 0.125 -2.745
CDY N7 N NRD5 0.000 -4.695 0.130 -3.308
CDY C8 C CR15 0.000 -5.597 0.034 -2.376
CDY HC8 H H 0.000 -6.667 0.019 -2.546
CDY N3 N NRD6 0.000 -2.575 -0.025 -0.567
CDY C4 C CR56 0.000 -3.643 0.007 -1.357
CDY N9 N NR5 0.000 -4.998 -0.045 -1.155
CDY "C1'" C CH1 0.000 -5.678 -0.162 0.138
CDY "H1'" H H 0.000 -5.054 -0.734 0.838
CDY "O4'" O O2 0.000 -6.947 -0.816 -0.035
CDY "C2'" C CH2 0.000 -5.960 1.239 0.711
CDY HC21 H H 0.000 -5.652 2.031 0.026
CDY HC22 H H 0.000 -5.478 1.389 1.679
CDY "C3'" C CH2 0.000 -7.498 1.275 0.887
CDY HC31 H H 0.000 -8.012 1.753 0.051
CDY HC32 H H 0.000 -7.809 1.746 1.821
CDY "C4'" C CH1 0.000 -7.856 -0.232 0.922
CDY "H4'" H H 0.000 -7.683 -0.649 1.925
CDY "C5'" C CH2 0.000 -9.307 -0.449 0.491
CDY HC51 H H 0.000 -9.444 -0.075 -0.525
CDY HC52 H H 0.000 -9.972 0.089 1.169
CDY "O5'" O OH1 0.000 -9.611 -1.846 0.531
CDY HO5 H H 0.000 -10.528 -1.983 0.258
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
CDY CL n/a C2 START
CDY C2 CL N3 .
CDY N1 C2 C6 .
CDY C6 N1 C5 .
CDY N6 C6 HN61 .
CDY HN62 N6 . .
CDY HN61 N6 . .
CDY C5 C6 N7 .
CDY N7 C5 C8 .
CDY C8 N7 HC8 .
CDY HC8 C8 . .
CDY N3 C2 C4 .
CDY C4 N3 N9 .
CDY N9 C4 "C1'" .
CDY "C1'" N9 "C2'" .
CDY "H1'" "C1'" . .
CDY "O4'" "C1'" . .
CDY "C2'" "C1'" "C3'" .
CDY HC21 "C2'" . .
CDY HC22 "C2'" . .
CDY "C3'" "C2'" "C4'" .
CDY HC31 "C3'" . .
CDY HC32 "C3'" . .
CDY "C4'" "C3'" "C5'" .
CDY "H4'" "C4'" . .
CDY "C5'" "C4'" "O5'" .
CDY HC51 "C5'" . .
CDY HC52 "C5'" . .
CDY "O5'" "C5'" HO5 .
CDY HO5 "O5'" . END
CDY "C4'" "O4'" . ADD
CDY N9 C8 . ADD
CDY C5 C4 . 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
CDY "O5'" "C5'" single 1.432 0.020
CDY HO5 "O5'" single 0.967 0.020
CDY "C5'" "C4'" single 1.524 0.020
CDY HC51 "C5'" single 1.092 0.020
CDY HC52 "C5'" single 1.092 0.020
CDY "C4'" "O4'" single 1.426 0.020
CDY "C4'" "C3'" single 1.524 0.020
CDY "H4'" "C4'" single 1.099 0.020
CDY "O4'" "C1'" single 1.426 0.020
CDY "C3'" "C2'" single 1.524 0.020
CDY HC31 "C3'" single 1.092 0.020
CDY HC32 "C3'" single 1.092 0.020
CDY "C2'" "C1'" single 1.524 0.020
CDY HC21 "C2'" single 1.092 0.020
CDY HC22 "C2'" single 1.092 0.020
CDY "C1'" N9 single 1.485 0.020
CDY "H1'" "C1'" single 1.099 0.020
CDY N9 C8 single 1.337 0.020
CDY N9 C4 single 1.337 0.020
CDY C8 N7 double 1.350 0.020
CDY HC8 C8 single 1.083 0.020
CDY N7 C5 single 1.350 0.020
CDY C5 C4 double 1.490 0.020
CDY C5 C6 single 1.490 0.020
CDY C4 N3 single 1.355 0.020
CDY N3 C2 double 1.350 0.020
CDY C2 CL single 1.795 0.020
CDY N1 C2 single 1.350 0.020
CDY C6 N1 double 1.350 0.020
CDY N6 C6 single 1.355 0.020
CDY HN61 N6 single 1.010 0.020
CDY HN62 N6 single 1.010 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
CDY CL C2 N1 120.000 3.000
CDY CL C2 N3 120.000 3.000
CDY N1 C2 N3 120.000 3.000
CDY C2 N1 C6 120.000 3.000
CDY N1 C6 N6 120.000 3.000
CDY N1 C6 C5 120.000 3.000
CDY N6 C6 C5 120.000 3.000
CDY C6 N6 HN62 120.000 3.000
CDY C6 N6 HN61 120.000 3.000
CDY HN62 N6 HN61 120.000 3.000
CDY C6 C5 N7 132.000 3.000
CDY C6 C5 C4 120.000 3.000
CDY N7 C5 C4 108.000 3.000
CDY C5 N7 C8 108.000 3.000
CDY N7 C8 HC8 126.000 3.000
CDY N7 C8 N9 108.000 3.000
CDY HC8 C8 N9 126.000 3.000
CDY C2 N3 C4 120.000 3.000
CDY N3 C4 N9 132.000 3.000
CDY N3 C4 C5 120.000 3.000
CDY N9 C4 C5 108.000 3.000
CDY C4 N9 "C1'" 126.000 3.000
CDY C4 N9 C8 108.000 3.000
CDY "C1'" N9 C8 126.000 3.000
CDY N9 "C1'" "H1'" 109.470 3.000
CDY N9 "C1'" "O4'" 109.470 3.000
CDY N9 "C1'" "C2'" 109.470 3.000
CDY "H1'" "C1'" "O4'" 109.470 3.000
CDY "H1'" "C1'" "C2'" 108.340 3.000
CDY "O4'" "C1'" "C2'" 109.470 3.000
CDY "C1'" "O4'" "C4'" 111.800 3.000
CDY "C1'" "C2'" HC21 109.470 3.000
CDY "C1'" "C2'" HC22 109.470 3.000
CDY "C1'" "C2'" "C3'" 111.000 3.000
CDY HC21 "C2'" HC22 107.900 3.000
CDY HC21 "C2'" "C3'" 109.470 3.000
CDY HC22 "C2'" "C3'" 109.470 3.000
CDY "C2'" "C3'" HC31 109.470 3.000
CDY "C2'" "C3'" HC32 109.470 3.000
CDY "C2'" "C3'" "C4'" 111.000 3.000
CDY HC31 "C3'" HC32 107.900 3.000
CDY HC31 "C3'" "C4'" 109.470 3.000
CDY HC32 "C3'" "C4'" 109.470 3.000
CDY "C3'" "C4'" "H4'" 108.340 3.000
CDY "C3'" "C4'" "C5'" 109.470 3.000
CDY "C3'" "C4'" "O4'" 109.470 3.000
CDY "H4'" "C4'" "C5'" 108.340 3.000
CDY "H4'" "C4'" "O4'" 109.470 3.000
CDY "C5'" "C4'" "O4'" 109.470 3.000
CDY "C4'" "C5'" HC51 109.470 3.000
CDY "C4'" "C5'" HC52 109.470 3.000
CDY "C4'" "C5'" "O5'" 109.470 3.000
CDY HC51 "C5'" HC52 107.900 3.000
CDY HC51 "C5'" "O5'" 109.470 3.000
CDY HC52 "C5'" "O5'" 109.470 3.000
CDY "C5'" "O5'" HO5 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
CDY CONST_1 CL C2 N1 C6 180.000 0.000 0
CDY CONST_2 C2 N1 C6 C5 0.000 0.000 0
CDY CONST_3 N1 C6 N6 HN61 -0.015 0.000 0
CDY CONST_4 N1 C6 C5 N7 180.000 0.000 0
CDY CONST_5 C6 C5 C4 N3 0.000 0.000 0
CDY CONST_6 C6 C5 N7 C8 180.000 0.000 0
CDY CONST_7 C5 N7 C8 N9 0.000 0.000 0
CDY CONST_8 CL C2 N3 C4 180.000 0.000 0
CDY CONST_9 C2 N3 C4 N9 180.000 0.000 0
CDY CONST_10 N3 C4 N9 "C1'" 0.000 0.000 0
CDY CONST_11 C4 N9 C8 N7 0.000 0.000 0
CDY var_1 C4 N9 "C1'" "C2'" 89.985 20.000 1
CDY var_2 N9 "C1'" "O4'" "C4'" -150.000 20.000 1
CDY var_3 N9 "C1'" "C2'" "C3'" 120.000 20.000 3
CDY var_4 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
CDY var_5 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
CDY var_6 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
CDY var_7 "C3'" "C4'" "C5'" "O5'" 179.954 20.000 3
CDY var_8 "C4'" "C5'" "O5'" HO5 -179.985 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
CDY chir_01 "C4'" "C5'" "O4'" "C3'" negativ
CDY chir_02 "C1'" "O4'" "C2'" N9 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
CDY plan-1 N9 0.020
CDY plan-1 "C1'" 0.020
CDY plan-1 C8 0.020
CDY plan-1 C4 0.020
CDY plan-1 N7 0.020
CDY plan-1 HC8 0.020
CDY plan-1 C5 0.020
CDY plan-1 C6 0.020
CDY plan-1 N3 0.020
CDY plan-1 C2 0.020
CDY plan-1 N1 0.020
CDY plan-1 CL 0.020
CDY plan-1 N6 0.020
CDY plan-1 HN62 0.020
CDY plan-1 HN61 0.020
CDY plan-2 N6 0.020
CDY plan-2 C6 0.020
CDY plan-2 HN61 0.020
CDY plan-2 HN62 0.020
# ------------------------------------------------------
|
