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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
0C 0C 'L-CYTIDINE-5'-MONOPHOSPHATE ' non-polymer 33 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_0C
#
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
0C O2 O O 0.000 0.000 0.000 0.000
0C C2 C CR6 0.000 -0.761 0.927 -0.226
0C N3 N NRD6 0.000 -0.273 2.076 -0.690
0C C4 C CR6 0.000 -1.078 3.100 -0.944
0C N4 N NH2 0.000 -0.563 4.282 -1.423
0C H42 H H 0.000 -1.175 5.066 -1.619
0C H41 H H 0.000 0.433 4.379 -1.584
0C C5 C CR16 0.000 -2.464 2.968 -0.722
0C H5 H H 0.000 -3.134 3.796 -0.920
0C C6 C CR16 0.000 -2.945 1.791 -0.257
0C H6 H H 0.000 -4.007 1.663 -0.088
0C N1 N NR6 0.000 -2.079 0.770 -0.005
0C "C1'" C CH1 0.000 -2.585 -0.506 0.504
0C "H1'" H H 0.000 -2.121 -0.744 1.471
0C "O4'" O O2 0.000 -4.023 -0.461 0.634
0C "C2'" C CH1 0.000 -2.316 -1.637 -0.514
0C "H2'" H H 0.000 -2.214 -1.225 -1.528
0C "O2'" O OH1 0.000 -1.145 -2.370 -0.150
0C "HO2'" H H 0.000 -1.026 -3.110 -0.761
0C "C3'" C CH1 0.000 -3.570 -2.535 -0.418
0C "H3'" H H 0.000 -4.093 -2.572 -1.383
0C "O3'" O OH1 0.000 -3.211 -3.851 0.009
0C "HO3'" H H 0.000 -2.663 -4.270 -0.668
0C "C4'" C CH1 0.000 -4.447 -1.841 0.648
0C "H4'" H H 0.000 -4.271 -2.286 1.637
0C "C5'" C CH2 0.000 -5.926 -1.948 0.271
0C "H5'" H H 0.000 -6.201 -3.000 0.173
0C "H5''" H H 0.000 -6.097 -1.438 -0.680
0C "O5'" O O2 0.000 -6.723 -1.339 1.289
0C P P P 0.000 -8.329 -1.268 1.220
0C OP3 O OP -0.666 -8.863 -0.672 2.505
0C OP1 O OP -0.666 -8.889 -2.662 1.040
0C OP2 O OP -0.666 -8.747 -0.402 0.051
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
0C O2 n/a C2 START
0C C2 O2 N3 .
0C N3 C2 C4 .
0C C4 N3 C5 .
0C N4 C4 H41 .
0C H42 N4 . .
0C H41 N4 . .
0C C5 C4 C6 .
0C H5 C5 . .
0C C6 C5 N1 .
0C H6 C6 . .
0C N1 C6 "C1'" .
0C "C1'" N1 "C2'" .
0C "H1'" "C1'" . .
0C "O4'" "C1'" . .
0C "C2'" "C1'" "C3'" .
0C "H2'" "C2'" . .
0C "O2'" "C2'" "HO2'" .
0C "HO2'" "O2'" . .
0C "C3'" "C2'" "C4'" .
0C "H3'" "C3'" . .
0C "O3'" "C3'" "HO3'" .
0C "HO3'" "O3'" . .
0C "C4'" "C3'" "C5'" .
0C "H4'" "C4'" . .
0C "C5'" "C4'" "O5'" .
0C "H5'" "C5'" . .
0C "H5''" "C5'" . .
0C "O5'" "C5'" P .
0C P "O5'" OP2 .
0C OP3 P . .
0C OP1 P . .
0C OP2 P . END
0C "C4'" "O4'" . ADD
0C 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
0C OP3 P deloc 1.510 0.020
0C OP1 P deloc 1.510 0.020
0C OP2 P deloc 1.510 0.020
0C P "O5'" single 1.610 0.020
0C "O5'" "C5'" single 1.426 0.020
0C "C5'" "C4'" single 1.524 0.020
0C "H5'" "C5'" single 1.092 0.020
0C "H5''" "C5'" single 1.092 0.020
0C "C4'" "O4'" single 1.426 0.020
0C "C4'" "C3'" single 1.524 0.020
0C "H4'" "C4'" single 1.099 0.020
0C "O4'" "C1'" single 1.426 0.020
0C "O3'" "C3'" single 1.432 0.020
0C "C3'" "C2'" single 1.524 0.020
0C "H3'" "C3'" single 1.099 0.020
0C "HO3'" "O3'" single 0.967 0.020
0C "O2'" "C2'" single 1.432 0.020
0C "C2'" "C1'" single 1.524 0.020
0C "H2'" "C2'" single 1.099 0.020
0C "HO2'" "O2'" single 0.967 0.020
0C "C1'" N1 single 1.465 0.020
0C "H1'" "C1'" single 1.099 0.020
0C N1 C2 single 1.410 0.020
0C N1 C6 single 1.337 0.020
0C C2 O2 double 1.250 0.020
0C N3 C2 single 1.350 0.020
0C C4 N3 double 1.350 0.020
0C N4 C4 single 1.355 0.020
0C C5 C4 single 1.390 0.020
0C H41 N4 single 1.010 0.020
0C H42 N4 single 1.010 0.020
0C C6 C5 double 1.390 0.020
0C H5 C5 single 1.083 0.020
0C 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
0C O2 C2 N3 120.000 3.000
0C O2 C2 N1 120.000 3.000
0C N3 C2 N1 120.000 3.000
0C C2 N3 C4 120.000 3.000
0C N3 C4 N4 120.000 3.000
0C N3 C4 C5 120.000 3.000
0C N4 C4 C5 120.000 3.000
0C C4 N4 H42 120.000 3.000
0C C4 N4 H41 120.000 3.000
0C H42 N4 H41 120.000 3.000
0C C4 C5 H5 120.000 3.000
0C C4 C5 C6 120.000 3.000
0C H5 C5 C6 120.000 3.000
0C C5 C6 H6 120.000 3.000
0C C5 C6 N1 120.000 3.000
0C H6 C6 N1 120.000 3.000
0C C6 N1 "C1'" 120.000 3.000
0C C6 N1 C2 120.000 3.000
0C "C1'" N1 C2 120.000 3.000
0C N1 "C1'" "H1'" 109.470 3.000
0C N1 "C1'" "O4'" 109.470 3.000
0C N1 "C1'" "C2'" 109.470 3.000
0C "H1'" "C1'" "O4'" 109.470 3.000
0C "H1'" "C1'" "C2'" 108.340 3.000
0C "O4'" "C1'" "C2'" 109.470 3.000
0C "C1'" "O4'" "C4'" 111.800 3.000
0C "C1'" "C2'" "H2'" 108.340 3.000
0C "C1'" "C2'" "O2'" 109.470 3.000
0C "C1'" "C2'" "C3'" 111.000 3.000
0C "H2'" "C2'" "O2'" 109.470 3.000
0C "H2'" "C2'" "C3'" 108.340 3.000
0C "O2'" "C2'" "C3'" 109.470 3.000
0C "C2'" "O2'" "HO2'" 109.470 3.000
0C "C2'" "C3'" "H3'" 108.340 3.000
0C "C2'" "C3'" "O3'" 109.470 3.000
0C "C2'" "C3'" "C4'" 111.000 3.000
0C "H3'" "C3'" "O3'" 109.470 3.000
0C "H3'" "C3'" "C4'" 108.340 3.000
0C "O3'" "C3'" "C4'" 109.470 3.000
0C "C3'" "O3'" "HO3'" 109.470 3.000
0C "C3'" "C4'" "H4'" 108.340 3.000
0C "C3'" "C4'" "C5'" 111.000 3.000
0C "C3'" "C4'" "O4'" 109.470 3.000
0C "H4'" "C4'" "C5'" 108.340 3.000
0C "H4'" "C4'" "O4'" 109.470 3.000
0C "C5'" "C4'" "O4'" 109.470 3.000
0C "C4'" "C5'" "H5'" 109.470 3.000
0C "C4'" "C5'" "H5''" 109.470 3.000
0C "C4'" "C5'" "O5'" 109.470 3.000
0C "H5'" "C5'" "H5''" 107.900 3.000
0C "H5'" "C5'" "O5'" 109.470 3.000
0C "H5''" "C5'" "O5'" 109.470 3.000
0C "C5'" "O5'" P 120.500 3.000
0C "O5'" P OP3 108.200 3.000
0C "O5'" P OP1 108.200 3.000
0C "O5'" P OP2 108.200 3.000
0C OP3 P OP1 119.900 3.000
0C OP3 P OP2 119.900 3.000
0C OP1 P OP2 119.900 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
0C CONST_1 O2 C2 N3 C4 180.000 0.000 0
0C CONST_2 C2 N3 C4 C5 0.000 0.000 0
0C CONST_3 N3 C4 N4 H41 -0.045 0.000 0
0C CONST_4 N3 C4 C5 C6 0.000 0.000 0
0C CONST_5 C4 C5 C6 N1 0.000 0.000 0
0C CONST_6 C5 C6 N1 "C1'" 180.000 0.000 0
0C CONST_7 C6 N1 C2 O2 180.000 0.000 0
0C var_1 C6 N1 "C1'" "C2'" 116.548 20.000 1
0C var_2 N1 "C1'" "O4'" "C4'" 150.000 20.000 1
0C var_3 N1 "C1'" "C2'" "C3'" -150.000 20.000 3
0C var_4 "C1'" "C2'" "O2'" "HO2'" 176.072 20.000 1
0C var_5 "C1'" "C2'" "C3'" "C4'" 0.000 20.000 3
0C var_6 "C2'" "C3'" "O3'" "HO3'" -65.359 20.000 1
0C var_7 "C2'" "C3'" "C4'" "C5'" 150.000 20.000 3
0C var_8 "C3'" "C4'" "O4'" "C1'" -30.000 20.000 1
0C var_9 "C3'" "C4'" "C5'" "O5'" 178.143 20.000 3
0C var_10 "C4'" "C5'" "O5'" P 179.954 20.000 1
0C var_11 "C5'" "O5'" P OP2 -64.984 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
0C chir_01 "C4'" "C5'" "O4'" "C3'" positiv
0C chir_02 "C3'" "C4'" "O3'" "C2'" positiv
0C chir_03 "C2'" "C3'" "O2'" "C1'" positiv
0C chir_04 "C1'" "O4'" "C2'" N1 negativ
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
0C plan-1 N1 0.020
0C plan-1 "C1'" 0.020
0C plan-1 C2 0.020
0C plan-1 C6 0.020
0C plan-1 N3 0.020
0C plan-1 C4 0.020
0C plan-1 C5 0.020
0C plan-1 O2 0.020
0C plan-1 N4 0.020
0C plan-1 H5 0.020
0C plan-1 H6 0.020
0C plan-1 H42 0.020
0C plan-1 H41 0.020
0C plan-2 N4 0.020
0C plan-2 C4 0.020
0C plan-2 H41 0.020
0C plan-2 H42 0.020
# ------------------------------------------------------
|
