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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
DCM DCM '2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE ' non-polymer 32 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DCM
#
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
DCM O3P O OP -0.666 0.000 0.000 0.000
DCM P P P 0.000 -0.792 -0.461 1.204
DCM O1P O OP -0.666 -1.040 0.713 2.125
DCM O2P O OP -0.666 -0.011 -1.525 1.944
DCM "O5'" O O2 0.000 -2.202 -1.071 0.719
DCM "C5'" C CH2 0.000 -2.888 -0.024 0.033
DCM "H5'1" H H 0.000 -2.291 0.303 -0.821
DCM "H5'2" H H 0.000 -3.041 0.817 0.712
DCM "C4'" C CH1 0.000 -4.243 -0.539 -0.458
DCM "H4'" H H 0.000 -4.111 -1.418 -1.103
DCM "C3'" C CH1 0.000 -5.013 0.577 -1.208
DCM "H3'" H H 0.000 -4.852 1.553 -0.730
DCM "O3'" O OH1 0.000 -4.637 0.617 -2.587
DCM "HO3'" H H 0.000 -5.193 1.256 -3.053
DCM "C2'" C CH2 0.000 -6.482 0.121 -1.051
DCM "H2'2" H H 0.000 -6.839 -0.420 -1.929
DCM "H2'1" H H 0.000 -7.151 0.959 -0.844
DCM "O4'" O O2 0.000 -5.106 -0.853 0.658
DCM "C1'" C CH1 0.000 -6.454 -0.829 0.163
DCM "H1'" H H 0.000 -6.758 -1.839 -0.145
DCM N1 N NR6 0.000 -7.358 -0.333 1.204
DCM C6 C CR16 0.000 -8.396 -1.109 1.626
DCM H6 H H 0.000 -8.559 -2.088 1.193
DCM C5 C CR16 0.000 -9.221 -0.642 2.591
DCM H5 H H 0.000 -10.048 -1.245 2.946
DCM C4 C CR6 0.000 -8.989 0.641 3.128
DCM N4 N NH2 0.000 -9.815 1.141 4.108
DCM HN42 H H 0.000 -10.597 0.593 4.447
DCM HN41 H H 0.000 -9.648 2.062 4.498
DCM N3 N NRD6 0.000 -7.966 1.360 2.686
DCM C2 C CR6 0.000 -7.160 0.885 1.738
DCM O2 O O 0.000 -6.225 1.566 1.348
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
DCM O3P n/a P START
DCM P O3P "O5'" .
DCM O1P P . .
DCM O2P P . .
DCM "O5'" P "C5'" .
DCM "C5'" "O5'" "C4'" .
DCM "H5'1" "C5'" . .
DCM "H5'2" "C5'" . .
DCM "C4'" "C5'" "O4'" .
DCM "H4'" "C4'" . .
DCM "C3'" "C4'" "C2'" .
DCM "H3'" "C3'" . .
DCM "O3'" "C3'" "HO3'" .
DCM "HO3'" "O3'" . .
DCM "C2'" "C3'" "H2'1" .
DCM "H2'2" "C2'" . .
DCM "H2'1" "C2'" . .
DCM "O4'" "C4'" "C1'" .
DCM "C1'" "O4'" N1 .
DCM "H1'" "C1'" . .
DCM N1 "C1'" C6 .
DCM C6 N1 C5 .
DCM H6 C6 . .
DCM C5 C6 C4 .
DCM H5 C5 . .
DCM C4 C5 N3 .
DCM N4 C4 HN41 .
DCM HN42 N4 . .
DCM HN41 N4 . .
DCM N3 C4 C2 .
DCM C2 N3 O2 .
DCM O2 C2 . END
DCM N1 C2 . ADD
DCM "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
DCM N1 C2 single 1.410 0.020
DCM C6 N1 single 1.337 0.020
DCM N1 "C1'" single 1.465 0.020
DCM C2 N3 single 1.350 0.020
DCM O2 C2 double 1.250 0.020
DCM N3 C4 double 1.350 0.020
DCM C4 C5 single 1.390 0.020
DCM N4 C4 single 1.355 0.020
DCM C5 C6 double 1.390 0.020
DCM H5 C5 single 1.083 0.020
DCM H6 C6 single 1.083 0.020
DCM HN41 N4 single 1.010 0.020
DCM HN42 N4 single 1.010 0.020
DCM "C1'" "C2'" single 1.524 0.020
DCM "C1'" "O4'" single 1.426 0.020
DCM "H1'" "C1'" single 1.099 0.020
DCM "C2'" "C3'" single 1.524 0.020
DCM "H2'1" "C2'" single 1.092 0.020
DCM "H2'2" "C2'" single 1.092 0.020
DCM "C3'" "C4'" single 1.524 0.020
DCM "O3'" "C3'" single 1.432 0.020
DCM "H3'" "C3'" single 1.099 0.020
DCM "O4'" "C4'" single 1.426 0.020
DCM "C4'" "C5'" single 1.524 0.020
DCM "H4'" "C4'" single 1.099 0.020
DCM "HO3'" "O3'" single 0.967 0.020
DCM "C5'" "O5'" single 1.426 0.020
DCM "H5'1" "C5'" single 1.092 0.020
DCM "H5'2" "C5'" single 1.092 0.020
DCM "O5'" P single 1.610 0.020
DCM O1P P deloc 1.510 0.020
DCM O2P P deloc 1.510 0.020
DCM P O3P deloc 1.510 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
DCM O3P P O1P 119.900 3.000
DCM O3P P O2P 119.900 3.000
DCM O3P P "O5'" 108.200 3.000
DCM O1P P O2P 119.900 3.000
DCM O1P P "O5'" 108.200 3.000
DCM O2P P "O5'" 108.200 3.000
DCM P "O5'" "C5'" 120.500 3.000
DCM "O5'" "C5'" "H5'1" 109.470 3.000
DCM "O5'" "C5'" "H5'2" 109.470 3.000
DCM "O5'" "C5'" "C4'" 109.470 3.000
DCM "H5'1" "C5'" "H5'2" 107.900 3.000
DCM "H5'1" "C5'" "C4'" 109.470 3.000
DCM "H5'2" "C5'" "C4'" 109.470 3.000
DCM "C5'" "C4'" "H4'" 108.340 3.000
DCM "C5'" "C4'" "C3'" 111.000 3.000
DCM "C5'" "C4'" "O4'" 109.470 3.000
DCM "H4'" "C4'" "C3'" 108.340 3.000
DCM "H4'" "C4'" "O4'" 109.470 3.000
DCM "C3'" "C4'" "O4'" 109.470 3.000
DCM "C4'" "C3'" "H3'" 108.340 3.000
DCM "C4'" "C3'" "O3'" 109.470 3.000
DCM "C4'" "C3'" "C2'" 111.000 3.000
DCM "H3'" "C3'" "O3'" 109.470 3.000
DCM "H3'" "C3'" "C2'" 108.340 3.000
DCM "O3'" "C3'" "C2'" 109.470 3.000
DCM "C3'" "O3'" "HO3'" 109.470 3.000
DCM "C3'" "C2'" "H2'2" 109.470 3.000
DCM "C3'" "C2'" "H2'1" 109.470 3.000
DCM "C3'" "C2'" "C1'" 111.000 3.000
DCM "H2'2" "C2'" "H2'1" 107.900 3.000
DCM "H2'2" "C2'" "C1'" 109.470 3.000
DCM "H2'1" "C2'" "C1'" 109.470 3.000
DCM "C4'" "O4'" "C1'" 111.800 3.000
DCM "O4'" "C1'" "H1'" 109.470 3.000
DCM "O4'" "C1'" N1 109.470 3.000
DCM "O4'" "C1'" "C2'" 109.470 3.000
DCM "H1'" "C1'" N1 109.470 3.000
DCM "H1'" "C1'" "C2'" 108.340 3.000
DCM N1 "C1'" "C2'" 109.470 3.000
DCM "C1'" N1 C6 120.000 3.000
DCM "C1'" N1 C2 120.000 3.000
DCM C6 N1 C2 120.000 3.000
DCM N1 C6 H6 120.000 3.000
DCM N1 C6 C5 120.000 3.000
DCM H6 C6 C5 120.000 3.000
DCM C6 C5 H5 120.000 3.000
DCM C6 C5 C4 120.000 3.000
DCM H5 C5 C4 120.000 3.000
DCM C5 C4 N4 120.000 3.000
DCM C5 C4 N3 120.000 3.000
DCM N4 C4 N3 120.000 3.000
DCM C4 N4 HN42 120.000 3.000
DCM C4 N4 HN41 120.000 3.000
DCM HN42 N4 HN41 120.000 3.000
DCM C4 N3 C2 120.000 3.000
DCM N3 C2 O2 120.000 3.000
DCM N3 C2 N1 120.000 3.000
DCM O2 C2 N1 120.000 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
DCM var_1 O3P P "O5'" "C5'" -60.015 20.000 1
DCM var_2 P "O5'" "C5'" "C4'" 179.972 20.000 1
DCM var_3 "O5'" "C5'" "C4'" "O4'" 65.747 20.000 3
DCM var_4 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
DCM var_5 "C4'" "C3'" "O3'" "HO3'" 174.203 20.000 1
DCM var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
DCM var_7 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DCM var_8 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
DCM var_9 "O4'" "C1'" "C2'" "C3'" 0.000 20.000 3
DCM var_10 "O4'" "C1'" N1 C6 -121.742 20.000 1
DCM CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
DCM CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
DCM CONST_3 N1 C6 C5 C4 0.000 0.000 0
DCM CONST_4 C6 C5 C4 N3 0.000 0.000 0
DCM CONST_5 C5 C4 N4 HN41 179.763 0.000 0
DCM CONST_6 C5 C4 N3 C2 0.000 0.000 0
DCM 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
DCM chir_01 "C1'" N1 "C2'" "O4'" negativ
DCM chir_02 "C3'" "C2'" "C4'" "O3'" negativ
DCM chir_03 "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
DCM plan-1 N1 0.020
DCM plan-1 C2 0.020
DCM plan-1 C6 0.020
DCM plan-1 "C1'" 0.020
DCM plan-1 N3 0.020
DCM plan-1 C4 0.020
DCM plan-1 C5 0.020
DCM plan-1 O2 0.020
DCM plan-1 N4 0.020
DCM plan-1 H5 0.020
DCM plan-1 H6 0.020
DCM plan-1 HN42 0.020
DCM plan-1 HN41 0.020
DCM plan-2 N4 0.020
DCM plan-2 C4 0.020
DCM plan-2 HN41 0.020
DCM plan-2 HN42 0.020
# ------------------------------------------------------
|
