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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
CDP CDP 'CYTIDINE-5'-DIPHOSPHATE ' non-polymer 37 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CDP
#
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
CDP O2 O O 0.000 0.000 0.000 0.000
CDP C2 C CR6 0.000 0.527 0.304 -1.058
CDP N3 N NRD6 0.000 1.468 1.247 -1.073
CDP C4 C CR6 0.000 2.056 1.597 -2.210
CDP N4 N NH2 0.000 3.027 2.571 -2.214
CDP H4N2 H H 0.000 3.478 2.841 -3.081
CDP H4N1 H H 0.000 3.299 3.027 -1.350
CDP C5 C CR16 0.000 1.681 0.964 -3.413
CDP H5 H H 0.000 2.150 1.242 -4.349
CDP C6 C CR16 0.000 0.726 0.004 -3.379
CDP H6 H H 0.000 0.427 -0.502 -4.289
CDP N1 N NR6 0.000 0.147 -0.318 -2.189
CDP "C1'" C CH1 0.000 -0.890 -1.351 -2.139
CDP "H1'" H H 0.000 -1.125 -1.713 -3.150
CDP "O4'" O O2 0.000 -2.078 -0.848 -1.490
CDP "C2'" C CH1 0.000 -0.449 -2.525 -1.229
CDP "H2'" H H 0.000 0.108 -2.155 -0.357
CDP "O2'" O OH1 0.000 0.325 -3.476 -1.962
CDP HB H H 0.000 0.510 -4.241 -1.400
CDP "C3'" C CH1 0.000 -1.808 -3.131 -0.799
CDP "H3'" H H 0.000 -1.784 -3.417 0.262
CDP "O3'" O OH1 0.000 -2.133 -4.258 -1.614
CDP HA H H 0.000 -1.490 -4.963 -1.459
CDP "C4'" C CH1 0.000 -2.819 -1.990 -1.028
CDP "H4'" H H 0.000 -3.556 -2.290 -1.786
CDP "C5'" C CH2 0.000 -3.529 -1.654 0.284
CDP "H5'1" H H 0.000 -2.802 -1.268 1.002
CDP "H5'2" H H 0.000 -3.994 -2.556 0.688
CDP "O5'" O O2 0.000 -4.533 -0.666 0.043
CDP PA P P 0.000 -5.479 -0.075 1.205
CDP O1A O OP -0.500 -6.168 -1.190 1.896
CDP O2A O OP -0.500 -4.652 0.677 2.180
CDP O3A O O2 0.000 -6.573 0.912 0.555
CDP PB P P 0.000 -7.949 1.559 1.085
CDP O3B O OP -0.666 -7.640 2.757 1.956
CDP O1B O OP -0.666 -8.713 0.532 1.891
CDP O2B O OP -0.666 -8.786 1.998 -0.096
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
CDP O2 n/a C2 START
CDP C2 O2 N3 .
CDP N3 C2 C4 .
CDP C4 N3 C5 .
CDP N4 C4 H4N1 .
CDP H4N2 N4 . .
CDP H4N1 N4 . .
CDP C5 C4 C6 .
CDP H5 C5 . .
CDP C6 C5 N1 .
CDP H6 C6 . .
CDP N1 C6 "C1'" .
CDP "C1'" N1 "C2'" .
CDP "H1'" "C1'" . .
CDP "O4'" "C1'" . .
CDP "C2'" "C1'" "C3'" .
CDP "H2'" "C2'" . .
CDP "O2'" "C2'" HB .
CDP HB "O2'" . .
CDP "C3'" "C2'" "C4'" .
CDP "H3'" "C3'" . .
CDP "O3'" "C3'" HA .
CDP HA "O3'" . .
CDP "C4'" "C3'" "C5'" .
CDP "H4'" "C4'" . .
CDP "C5'" "C4'" "O5'" .
CDP "H5'1" "C5'" . .
CDP "H5'2" "C5'" . .
CDP "O5'" "C5'" PA .
CDP PA "O5'" O3A .
CDP O1A PA . .
CDP O2A PA . .
CDP O3A PA PB .
CDP PB O3A O2B .
CDP O3B PB . .
CDP O1B PB . .
CDP O2B PB . END
CDP "C4'" "O4'" . ADD
CDP 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
CDP O3B PB deloc 1.510 0.020
CDP O1B PB deloc 1.510 0.020
CDP O2B PB deloc 1.510 0.020
CDP PB O3A single 1.610 0.020
CDP O3A PA single 1.610 0.020
CDP O1A PA deloc 1.510 0.020
CDP O2A PA deloc 1.510 0.020
CDP PA "O5'" single 1.610 0.020
CDP "O5'" "C5'" single 1.426 0.020
CDP "C5'" "C4'" single 1.524 0.020
CDP "H5'1" "C5'" single 1.092 0.020
CDP "H5'2" "C5'" single 1.092 0.020
CDP "C4'" "O4'" single 1.426 0.020
CDP "C4'" "C3'" single 1.524 0.020
CDP "H4'" "C4'" single 1.099 0.020
CDP "O4'" "C1'" single 1.426 0.020
CDP "O3'" "C3'" single 1.432 0.020
CDP "C3'" "C2'" single 1.524 0.020
CDP "H3'" "C3'" single 1.099 0.020
CDP HA "O3'" single 0.967 0.020
CDP "O2'" "C2'" single 1.432 0.020
CDP "C2'" "C1'" single 1.524 0.020
CDP "H2'" "C2'" single 1.099 0.020
CDP HB "O2'" single 0.967 0.020
CDP "C1'" N1 single 1.465 0.020
CDP "H1'" "C1'" single 1.099 0.020
CDP N1 C2 single 1.410 0.020
CDP N1 C6 single 1.337 0.020
CDP C2 O2 double 1.250 0.020
CDP N3 C2 single 1.350 0.020
CDP C4 N3 double 1.350 0.020
CDP N4 C4 single 1.355 0.020
CDP C5 C4 single 1.390 0.020
CDP H4N1 N4 single 1.010 0.020
CDP H4N2 N4 single 1.010 0.020
CDP C6 C5 double 1.390 0.020
CDP H5 C5 single 1.083 0.020
CDP 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
CDP O2 C2 N3 120.000 3.000
CDP O2 C2 N1 120.000 3.000
CDP N3 C2 N1 120.000 3.000
CDP C2 N3 C4 120.000 3.000
CDP N3 C4 N4 120.000 3.000
CDP N3 C4 C5 120.000 3.000
CDP N4 C4 C5 120.000 3.000
CDP C4 N4 H4N2 120.000 3.000
CDP C4 N4 H4N1 120.000 3.000
CDP H4N2 N4 H4N1 120.000 3.000
CDP C4 C5 H5 120.000 3.000
CDP C4 C5 C6 120.000 3.000
CDP H5 C5 C6 120.000 3.000
CDP C5 C6 H6 120.000 3.000
CDP C5 C6 N1 120.000 3.000
CDP H6 C6 N1 120.000 3.000
CDP C6 N1 "C1'" 120.000 3.000
CDP C6 N1 C2 120.000 3.000
CDP "C1'" N1 C2 120.000 3.000
CDP N1 "C1'" "H1'" 109.470 3.000
CDP N1 "C1'" "O4'" 109.470 3.000
CDP N1 "C1'" "C2'" 109.470 3.000
CDP "H1'" "C1'" "O4'" 109.470 3.000
CDP "H1'" "C1'" "C2'" 108.340 3.000
CDP "O4'" "C1'" "C2'" 109.470 3.000
CDP "C1'" "O4'" "C4'" 111.800 3.000
CDP "C1'" "C2'" "H2'" 108.340 3.000
CDP "C1'" "C2'" "O2'" 109.470 3.000
CDP "C1'" "C2'" "C3'" 111.000 3.000
CDP "H2'" "C2'" "O2'" 109.470 3.000
CDP "H2'" "C2'" "C3'" 108.340 3.000
CDP "O2'" "C2'" "C3'" 109.470 3.000
CDP "C2'" "O2'" HB 109.470 3.000
CDP "C2'" "C3'" "H3'" 108.340 3.000
CDP "C2'" "C3'" "O3'" 109.470 3.000
CDP "C2'" "C3'" "C4'" 111.000 3.000
CDP "H3'" "C3'" "O3'" 109.470 3.000
CDP "H3'" "C3'" "C4'" 108.340 3.000
CDP "O3'" "C3'" "C4'" 109.470 3.000
CDP "C3'" "O3'" HA 109.470 3.000
CDP "C3'" "C4'" "H4'" 108.340 3.000
CDP "C3'" "C4'" "C5'" 111.000 3.000
CDP "C3'" "C4'" "O4'" 109.470 3.000
CDP "H4'" "C4'" "C5'" 108.340 3.000
CDP "H4'" "C4'" "O4'" 109.470 3.000
CDP "C5'" "C4'" "O4'" 109.470 3.000
CDP "C4'" "C5'" "H5'1" 109.470 3.000
CDP "C4'" "C5'" "H5'2" 109.470 3.000
CDP "C4'" "C5'" "O5'" 109.470 3.000
CDP "H5'1" "C5'" "H5'2" 107.900 3.000
CDP "H5'1" "C5'" "O5'" 109.470 3.000
CDP "H5'2" "C5'" "O5'" 109.470 3.000
CDP "C5'" "O5'" PA 120.500 3.000
CDP "O5'" PA O1A 108.200 3.000
CDP "O5'" PA O2A 108.200 3.000
CDP "O5'" PA O3A 102.600 3.000
CDP O1A PA O2A 119.900 3.000
CDP O1A PA O3A 108.200 3.000
CDP O2A PA O3A 108.200 3.000
CDP PA O3A PB 120.500 3.000
CDP O3A PB O3B 108.200 3.000
CDP O3A PB O1B 108.200 3.000
CDP O3A PB O2B 108.200 3.000
CDP O3B PB O1B 119.900 3.000
CDP O3B PB O2B 119.900 3.000
CDP O1B PB O2B 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
CDP CONST_1 O2 C2 N3 C4 180.000 0.000 0
CDP CONST_2 C2 N3 C4 C5 0.000 0.000 0
CDP CONST_3 N3 C4 N4 H4N1 -0.012 0.000 0
CDP CONST_4 N3 C4 C5 C6 0.000 0.000 0
CDP CONST_5 C4 C5 C6 N1 0.000 0.000 0
CDP CONST_6 C5 C6 N1 "C1'" 180.000 0.000 0
CDP CONST_7 C6 N1 C2 O2 180.000 0.000 0
CDP var_1 C6 N1 "C1'" "C2'" 119.214 20.000 1
CDP var_2 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
CDP var_3 N1 "C1'" "C2'" "C3'" 150.000 20.000 3
CDP var_4 "C1'" "C2'" "O2'" HB -174.146 20.000 1
CDP var_5 "C1'" "C2'" "C3'" "C4'" -30.000 20.000 3
CDP var_6 "C2'" "C3'" "O3'" HA 65.262 20.000 1
CDP var_7 "C2'" "C3'" "C4'" "C5'" -120.000 20.000 3
CDP var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
CDP var_9 "C3'" "C4'" "C5'" "O5'" -175.715 20.000 3
CDP var_10 "C4'" "C5'" "O5'" PA -179.959 20.000 1
CDP var_11 "C5'" "O5'" PA O3A -174.972 20.000 1
CDP var_12 "O5'" PA O3A PB 164.987 20.000 1
CDP var_13 PA O3A PB O2B -160.031 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
CDP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
CDP chir_02 "C3'" "C4'" "O3'" "C2'" negativ
CDP chir_03 "C2'" "C3'" "O2'" "C1'" negativ
CDP chir_04 "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
CDP plan-1 N1 0.020
CDP plan-1 "C1'" 0.020
CDP plan-1 C2 0.020
CDP plan-1 C6 0.020
CDP plan-1 N3 0.020
CDP plan-1 C4 0.020
CDP plan-1 C5 0.020
CDP plan-1 O2 0.020
CDP plan-1 N4 0.020
CDP plan-1 H5 0.020
CDP plan-1 H6 0.020
CDP plan-1 H4N2 0.020
CDP plan-1 H4N1 0.020
CDP plan-2 N4 0.020
CDP plan-2 C4 0.020
CDP plan-2 H4N1 0.020
CDP plan-2 H4N2 0.020
# ------------------------------------------------------
|
