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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
DC DC '2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE ' DNA 32 20 .
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DC
#
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
DC P P P 0.000 0.001 -0.540 0.119
DC OP3 O OP -0.660 0.227 -1.987 0.516
DC OP1 O OP -0.660 0.381 0.441 1.194
DC "O5'" O O2 0.000 -1.613 -0.460 0.002
DC "C5'" C CH2 0.000 -2.412 0.695 -0.366
DC "H5'" H H 0.000 -2.004 1.206 -1.241
DC "H5''" H H 0.000 -2.500 1.405 0.459
DC "C4'" C CH1 0.000 -3.783 0.131 -0.701
DC "H4'" H H 0.000 -3.606 -0.705 -1.391
DC "C3'" C CH1 0.000 -4.862 0.991 -1.350
DC "H3'" H H 0.000 -4.664 2.061 -1.199
DC "O3'" O OH1 0.000 -4.928 0.664 -2.754
DC "HO3'" H H 0.000 -5.661 1.144 -3.165
DC "C2'" C CH2 0.000 -6.185 0.558 -0.660
DC "H2' " H H 0.000 -6.865 0.104 -1.383
DC "H2''" H H 0.000 -6.673 1.415 -0.192
DC "C1'" C CH1 0.000 -5.815 -0.478 0.421
DC "H1'" H H 0.000 -6.089 -1.462 0.015
DC "O4'" O O2 0.000 -4.377 -0.452 0.488
DC N1 N NR6 0.000 -6.434 -0.388 1.735
DC C6 C CR16 0.000 -7.038 -1.463 2.305
DC H6 H H 0.000 -7.005 -2.406 1.774
DC C5 C CR16 0.000 -7.709 -1.424 3.556
DC H5 H H 0.000 -8.160 -2.314 3.979
DC C4 C CR6 0.000 -7.767 -0.214 4.213
DC N4 N NH2 0.000 -8.312 -0.031 5.446
DC H42 H H 0.000 -8.712 -0.813 5.946
DC H41 H H 0.000 -8.318 0.889 5.866
DC N3 N NRD6 0.000 -6.825 0.681 3.769
DC C2 C CR6 0.000 -6.022 0.556 2.670
DC O2 O O 0.000 -4.961 1.193 2.528
DC OP2 O OP -0.660 0.506 -0.216 -1.268
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
DC "O5'" n/a "C5'" START
DC P "O5'" OP2 .
DC OP3 P . .
DC OP1 P . .
DC "C5'" "O5'" "C4'" .
DC "H5'" "C5'" . .
DC "H5''" "C5'" . .
DC "C4'" "C5'" "C3'" .
DC "H4'" "C4'" . .
DC "C3'" "C4'" "C2'" .
DC "H3'" "C3'" . .
DC "O3'" "C3'" "HO3'" .
DC "HO3'" "O3'" . .
DC "C2'" "C3'" "C1'" .
DC "H2' " "C2'" . .
DC "H2''" "C2'" . .
DC "C1'" "C2'" N1 .
DC "H1'" "C1'" . .
DC "O4'" "C1'" . .
DC N1 "C1'" C6 .
DC C6 N1 C5 .
DC H6 C6 . .
DC C5 C6 C4 .
DC H5 C5 . .
DC C4 C5 N3 .
DC N4 C4 H41 .
DC H42 N4 . .
DC H41 N4 . .
DC N3 C4 C2 .
DC C2 N3 O2 .
DC O2 C2 . END
DC OP2 P . .
DC "C4'" "O4'" . ADD
DC N1 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
DC OP3 P deloc 1.485 0.017
DC OP1 P deloc 1.485 0.017
DC OP2 P deloc 1.485 0.017
DC "O5'" P single 1.593 0.010
DC "C5'" "O5'" single 1.440 0.016
DC "C4'" "C5'" single 1.511 0.008
DC "C4'" "O4'" single 1.446 0.011
DC "C3'" "C4'" single 1.528 0.010
DC "O4'" "C1'" single 1.420 0.013
DC "O3'" "C3'" single 1.431 0.013
DC "C2'" "C3'" single 1.518 0.010
DC "C1'" "C2'" single 1.521 0.014
DC N1 "C1'" single 1.470 0.012
DC N1 C2 single 1.397 0.010
DC C6 N1 single 1.367 0.006
DC O2 C2 double 1.240 0.009
DC C2 N3 single 1.353 0.008
DC N3 C4 double 1.335 0.007
DC N4 C4 single 1.335 0.009
DC C4 C5 single 1.425 0.008
DC C5 C6 double 1.339 0.008
DC "H5'" "C5'" single 1.092 0.020
DC "H5''" "C5'" single 1.092 0.020
DC "H4'" "C4'" single 1.099 0.020
DC "H3'" "C3'" single 1.099 0.020
DC "HO3'" "O3'" single 0.967 0.020
DC "H2' " "C2'" single 1.092 0.020
DC "H2''" "C2'" single 1.092 0.020
DC "H1'" "C1'" single 1.099 0.020
DC H41 N4 single 1.010 0.020
DC H42 N4 single 1.010 0.020
DC H5 C5 single 1.083 0.020
DC H6 C6 single 1.083 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
DC OP3 P OP1 107.400 3.200
DC OP3 P "O5'" 104.000 1.900
DC OP1 P "O5'" 108.100 2.900
DC OP3 P OP2 108.300 3.200
DC OP1 P OP2 119.600 1.500
DC "O5'" P OP2 108.300 2.700
DC P "O5'" "C5'" 120.900 1.600
DC "O5'" "C5'" "H5'" 109.470 3.000
DC "O5'" "C5'" "H5''" 109.470 3.000
DC "O5'" "C5'" "C4'" 110.200 1.400
DC "H5'" "C5'" "H5''" 107.900 3.000
DC "H5'" "C5'" "C4'" 109.470 3.000
DC "H5''" "C5'" "C4'" 109.470 3.000
DC "C5'" "C4'" "H4'" 108.340 3.000
DC "C5'" "C4'" "C3'" 114.700 1.500
DC "C5'" "C4'" "O4'" 109.400 1.600
DC "H4'" "C4'" "C3'" 108.340 3.000
DC "H4'" "C4'" "O4'" 109.470 3.000
DC "C3'" "C4'" "O4'" 105.600 1.000
DC "C4'" "C3'" "H3'" 108.340 3.000
DC "C4'" "C3'" "O3'" 110.300 2.200
DC "C4'" "C3'" "C2'" 103.200 1.000
DC "H3'" "C3'" "O3'" 109.470 3.000
DC "H3'" "C3'" "C2'" 108.340 3.000
DC "O3'" "C3'" "C2'" 110.600 2.700
DC "C3'" "O3'" "HO3'" 109.470 3.000
DC "C3'" "C2'" "H2' " 109.470 3.000
DC "C3'" "C2'" "H2''" 109.470 3.000
DC "C3'" "C2'" "C1'" 102.700 1.400
DC "H2' " "C2'" "H2''" 107.900 3.000
DC "H2' " "C2'" "C1'" 109.470 3.000
DC "H2''" "C2'" "C1'" 109.470 3.000
DC "C2'" "C1'" "H1'" 108.340 3.000
DC "C2'" "C1'" "O4'" 106.100 1.100
DC "C2'" "C1'" N1 114.200 1.600
DC "H1'" "C1'" "O4'" 109.470 3.000
DC "H1'" "C1'" N1 109.470 3.000
DC "O4'" "C1'" N1 107.800 0.800
DC "C1'" "O4'" "C4'" 109.700 1.400
DC "C1'" N1 C6 120.800 1.200
DC "C1'" N1 C2 118.800 1.100
DC C6 N1 C2 120.300 0.400
DC N1 C6 H6 120.000 3.000
DC N1 C6 C5 121.000 0.500
DC H6 C6 C5 120.000 3.000
DC C6 C5 H5 120.000 3.000
DC C6 C5 C4 117.400 0.500
DC H5 C5 C4 120.000 3.000
DC C5 C4 N4 120.200 0.700
DC C5 C4 N3 121.900 0.400
DC N4 C4 N3 118.000 0.700
DC C4 N4 H42 120.000 3.000
DC C4 N4 H41 120.000 3.000
DC H42 N4 H41 120.000 3.000
DC C4 N3 C2 119.900 0.500
DC N3 C2 O2 121.900 0.700
DC N3 C2 N1 119.200 0.700
DC O2 C2 N1 118.900 0.600
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
DC var_1 OP2 P "O5'" "C5'" -60.014 20.000 1
DC var_2 P "O5'" "C5'" "C4'" 179.972 20.000 1
DC var_3 "O5'" "C5'" "C4'" "C3'" -179.996 20.000 3
DC var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DC var_5 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
DC var_6 "C4'" "C3'" "O3'" "HO3'" 175.000 20.000 1
DC var_7 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
DC var_8 "C3'" "C2'" "C1'" N1 120.000 20.000 3
DC var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
DC var_10 "C2'" "C1'" N1 C6 120.298 20.000 1
DC CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
DC CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
DC CONST_3 N1 C6 C5 C4 0.000 0.000 0
DC CONST_4 C6 C5 C4 N3 0.000 0.000 0
DC CONST_5 C5 C4 N4 H41 180.000 0.000 0
DC CONST_6 C5 C4 N3 C2 0.000 0.000 0
DC CONST_7 C4 N3 C2 O2 180.000 0.000 0
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
DC chir_01 "C4'" "C5'" "O4'" "C3'" negativ
DC chir_02 "C3'" "C4'" "O3'" "C2'" negativ
DC chir_03 "C1'" "O4'" "C2'" N1 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
DC plan-1 N1 0.020
DC plan-1 "C1'" 0.020
DC plan-1 C2 0.020
DC plan-1 C6 0.020
DC plan-1 N3 0.020
DC plan-1 C4 0.020
DC plan-1 C5 0.020
DC plan-1 O2 0.020
DC plan-1 N4 0.020
DC plan-1 H5 0.020
DC plan-1 H6 0.020
DC plan-1 H42 0.020
DC plan-1 H41 0.020
DC plan-2 N4 0.020
DC plan-2 C4 0.020
DC plan-2 H41 0.020
DC plan-2 H42 0.020
# ------------------------------------------------------
# ------------------------------------------------------
# ------------------------------------------------------
|
