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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
CDC CDC '[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETH' non-polymer 56 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CDC
#
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
CDC O3B O OP -0.500 0.000 0.000 0.000
CDC PB P P 0.000 -0.659 1.039 -0.828
CDC O2B O OP -0.500 -0.733 2.308 -0.064
CDC O1B O O2 0.000 0.193 1.272 -2.174
CDC C14 C CH2 0.000 1.456 1.809 -1.775
CDC H141 H H 0.000 1.960 1.101 -1.114
CDC H142 H H 0.000 1.300 2.751 -1.245
CDC C15 C CH2 0.000 2.320 2.056 -3.013
CDC H151 H H 0.000 2.364 1.144 -3.612
CDC H152 H H 0.000 3.329 2.335 -2.703
CDC N11 N NT 1.000 1.733 3.141 -3.812
CDC C18 C CH3 0.000 2.621 3.454 -4.939
CDC H183 H H 0.000 2.739 2.593 -5.545
CDC H182 H H 0.000 2.198 4.236 -5.515
CDC H181 H H 0.000 3.566 3.759 -4.570
CDC C17 C CH3 0.000 0.422 2.718 -4.323
CDC H173 H H 0.000 0.512 1.768 -4.783
CDC H172 H H 0.000 -0.267 2.658 -3.521
CDC H171 H H 0.000 0.076 3.423 -5.034
CDC C16 C CH3 0.000 1.569 4.333 -2.971
CDC H163 H H 0.000 2.514 4.638 -2.602
CDC H162 H H 0.000 1.146 5.115 -3.546
CDC H161 H H 0.000 0.930 4.107 -2.158
CDC O3A O O2 0.000 -2.146 0.557 -1.212
CDC PA P P 0.000 -3.076 0.850 0.069
CDC O1A O OP -0.500 -2.331 0.515 1.307
CDC O2A O OP -0.500 -3.450 2.285 0.090
CDC "O5'" O O2 0.000 -4.408 -0.051 -0.016
CDC "C5'" C CH2 0.000 -5.130 0.164 1.197
CDC "H5'1" H H 0.000 -5.382 1.222 1.287
CDC "H5'2" H H 0.000 -4.512 -0.136 2.046
CDC "C4'" C CH1 0.000 -6.414 -0.668 1.180
CDC "H4'" H H 0.000 -6.993 -0.444 0.273
CDC "C3'" C CH1 0.000 -7.258 -0.355 2.431
CDC "H3'" H H 0.000 -6.730 0.356 3.082
CDC "O3'" O OH1 0.000 -8.539 0.162 2.062
CDC H3T H H 0.000 -9.073 0.295 2.857
CDC "C2'" C CH1 0.000 -7.410 -1.728 3.137
CDC "H2'" H H 0.000 -6.666 -1.841 3.938
CDC "O2'" O OH1 0.000 -8.735 -1.896 3.645
CDC "HO'2" H H 0.000 -8.886 -1.268 4.364
CDC "O4'" O O2 0.000 -6.090 -2.068 1.219
CDC "C1'" C CH1 0.000 -7.131 -2.720 1.980
CDC "H1'" H H 0.000 -8.031 -2.858 1.364
CDC N1 N NR6 0.000 -6.661 -4.006 2.500
CDC C6 C CR16 0.000 -7.374 -5.140 2.253
CDC H6 H H 0.000 -8.289 -5.095 1.674
CDC C5 C CR16 0.000 -6.929 -6.322 2.739
CDC H5 H H 0.000 -7.480 -7.236 2.554
CDC C4 C CR6 0.000 -5.736 -6.346 3.490
CDC N4 N NH2 0.000 -5.260 -7.534 3.997
CDC H42 H H 0.000 -4.403 -7.554 4.537
CDC H41 H H 0.000 -5.764 -8.399 3.835
CDC N3 N NRD6 0.000 -5.074 -5.217 3.706
CDC C2 C CR6 0.000 -5.522 -4.062 3.216
CDC O2 O O 0.000 -4.896 -3.037 3.429
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
CDC O3B n/a PB START
CDC PB O3B O3A .
CDC O2B PB . .
CDC O1B PB C14 .
CDC C14 O1B C15 .
CDC H141 C14 . .
CDC H142 C14 . .
CDC C15 C14 N11 .
CDC H151 C15 . .
CDC H152 C15 . .
CDC N11 C15 C16 .
CDC C18 N11 H181 .
CDC H183 C18 . .
CDC H182 C18 . .
CDC H181 C18 . .
CDC C17 N11 H171 .
CDC H173 C17 . .
CDC H172 C17 . .
CDC H171 C17 . .
CDC C16 N11 H161 .
CDC H163 C16 . .
CDC H162 C16 . .
CDC H161 C16 . .
CDC O3A PB PA .
CDC PA O3A "O5'" .
CDC O1A PA . .
CDC O2A PA . .
CDC "O5'" PA "C5'" .
CDC "C5'" "O5'" "C4'" .
CDC "H5'1" "C5'" . .
CDC "H5'2" "C5'" . .
CDC "C4'" "C5'" "O4'" .
CDC "H4'" "C4'" . .
CDC "C3'" "C4'" "C2'" .
CDC "H3'" "C3'" . .
CDC "O3'" "C3'" H3T .
CDC H3T "O3'" . .
CDC "C2'" "C3'" "O2'" .
CDC "H2'" "C2'" . .
CDC "O2'" "C2'" "HO'2" .
CDC "HO'2" "O2'" . .
CDC "O4'" "C4'" "C1'" .
CDC "C1'" "O4'" N1 .
CDC "H1'" "C1'" . .
CDC N1 "C1'" C6 .
CDC C6 N1 C5 .
CDC H6 C6 . .
CDC C5 C6 C4 .
CDC H5 C5 . .
CDC C4 C5 N3 .
CDC N4 C4 H41 .
CDC H42 N4 . .
CDC H41 N4 . .
CDC N3 C4 C2 .
CDC C2 N3 O2 .
CDC O2 C2 . END
CDC N1 C2 . ADD
CDC "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
CDC N1 C2 single 1.410 0.020
CDC C6 N1 single 1.337 0.020
CDC N1 "C1'" single 1.465 0.020
CDC C2 N3 single 1.350 0.020
CDC O2 C2 double 1.250 0.020
CDC N3 C4 double 1.350 0.020
CDC C4 C5 single 1.390 0.020
CDC N4 C4 single 1.355 0.020
CDC C5 C6 double 1.390 0.020
CDC H5 C5 single 1.083 0.020
CDC H6 C6 single 1.083 0.020
CDC H41 N4 single 1.010 0.020
CDC H42 N4 single 1.010 0.020
CDC "C1'" "C2'" single 1.524 0.020
CDC "C1'" "O4'" single 1.426 0.020
CDC "H1'" "C1'" single 1.099 0.020
CDC "O2'" "C2'" single 1.432 0.020
CDC "C2'" "C3'" single 1.524 0.020
CDC "H2'" "C2'" single 1.099 0.020
CDC "HO'2" "O2'" single 0.967 0.020
CDC "C3'" "C4'" single 1.524 0.020
CDC "O3'" "C3'" single 1.432 0.020
CDC "H3'" "C3'" single 1.099 0.020
CDC "O4'" "C4'" single 1.426 0.020
CDC "C4'" "C5'" single 1.524 0.020
CDC "H4'" "C4'" single 1.099 0.020
CDC H3T "O3'" single 0.967 0.020
CDC "C5'" "O5'" single 1.426 0.020
CDC "H5'1" "C5'" single 1.092 0.020
CDC "H5'2" "C5'" single 1.092 0.020
CDC "O5'" PA single 1.610 0.020
CDC O1A PA deloc 1.510 0.020
CDC O2A PA deloc 1.510 0.020
CDC PA O3A single 1.610 0.020
CDC O3A PB single 1.610 0.020
CDC O1B PB single 1.610 0.020
CDC O2B PB deloc 1.510 0.020
CDC PB O3B deloc 1.510 0.020
CDC C14 O1B single 1.426 0.020
CDC C15 C14 single 1.524 0.020
CDC H141 C14 single 1.092 0.020
CDC H142 C14 single 1.092 0.020
CDC N11 C15 single 1.469 0.020
CDC H151 C15 single 1.092 0.020
CDC H152 C15 single 1.092 0.020
CDC C16 N11 single 1.469 0.020
CDC C17 N11 single 1.469 0.020
CDC C18 N11 single 1.469 0.020
CDC H161 C16 single 1.059 0.020
CDC H162 C16 single 1.059 0.020
CDC H163 C16 single 1.059 0.020
CDC H171 C17 single 1.059 0.020
CDC H172 C17 single 1.059 0.020
CDC H173 C17 single 1.059 0.020
CDC H181 C18 single 1.059 0.020
CDC H182 C18 single 1.059 0.020
CDC H183 C18 single 1.059 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
CDC O3B PB O2B 119.900 3.000
CDC O3B PB O1B 108.200 3.000
CDC O3B PB O3A 108.200 3.000
CDC O2B PB O1B 108.200 3.000
CDC O2B PB O3A 108.200 3.000
CDC O1B PB O3A 102.600 3.000
CDC PB O1B C14 120.500 3.000
CDC O1B C14 H141 109.470 3.000
CDC O1B C14 H142 109.470 3.000
CDC O1B C14 C15 109.470 3.000
CDC H141 C14 H142 107.900 3.000
CDC H141 C14 C15 109.470 3.000
CDC H142 C14 C15 109.470 3.000
CDC C14 C15 H151 109.470 3.000
CDC C14 C15 H152 109.470 3.000
CDC C14 C15 N11 109.470 3.000
CDC H151 C15 H152 107.900 3.000
CDC H151 C15 N11 109.470 3.000
CDC H152 C15 N11 109.470 3.000
CDC C15 N11 C18 109.470 3.000
CDC C15 N11 C17 109.470 3.000
CDC C15 N11 C16 109.470 3.000
CDC C18 N11 C17 109.470 3.000
CDC C18 N11 C16 109.470 3.000
CDC C17 N11 C16 109.470 3.000
CDC N11 C18 H183 109.470 3.000
CDC N11 C18 H182 109.470 3.000
CDC N11 C18 H181 109.470 3.000
CDC H183 C18 H182 109.470 3.000
CDC H183 C18 H181 109.470 3.000
CDC H182 C18 H181 109.470 3.000
CDC N11 C17 H173 109.470 3.000
CDC N11 C17 H172 109.470 3.000
CDC N11 C17 H171 109.470 3.000
CDC H173 C17 H172 109.470 3.000
CDC H173 C17 H171 109.470 3.000
CDC H172 C17 H171 109.470 3.000
CDC N11 C16 H163 109.470 3.000
CDC N11 C16 H162 109.470 3.000
CDC N11 C16 H161 109.470 3.000
CDC H163 C16 H162 109.470 3.000
CDC H163 C16 H161 109.470 3.000
CDC H162 C16 H161 109.470 3.000
CDC PB O3A PA 120.500 3.000
CDC O3A PA O1A 108.200 3.000
CDC O3A PA O2A 108.200 3.000
CDC O3A PA "O5'" 102.600 3.000
CDC O1A PA O2A 119.900 3.000
CDC O1A PA "O5'" 108.200 3.000
CDC O2A PA "O5'" 108.200 3.000
CDC PA "O5'" "C5'" 120.500 3.000
CDC "O5'" "C5'" "H5'1" 109.470 3.000
CDC "O5'" "C5'" "H5'2" 109.470 3.000
CDC "O5'" "C5'" "C4'" 109.470 3.000
CDC "H5'1" "C5'" "H5'2" 107.900 3.000
CDC "H5'1" "C5'" "C4'" 109.470 3.000
CDC "H5'2" "C5'" "C4'" 109.470 3.000
CDC "C5'" "C4'" "H4'" 108.340 3.000
CDC "C5'" "C4'" "C3'" 111.000 3.000
CDC "C5'" "C4'" "O4'" 109.470 3.000
CDC "H4'" "C4'" "C3'" 108.340 3.000
CDC "H4'" "C4'" "O4'" 109.470 3.000
CDC "C3'" "C4'" "O4'" 109.470 3.000
CDC "C4'" "C3'" "H3'" 108.340 3.000
CDC "C4'" "C3'" "O3'" 109.470 3.000
CDC "C4'" "C3'" "C2'" 111.000 3.000
CDC "H3'" "C3'" "O3'" 109.470 3.000
CDC "H3'" "C3'" "C2'" 108.340 3.000
CDC "O3'" "C3'" "C2'" 109.470 3.000
CDC "C3'" "O3'" H3T 109.470 3.000
CDC "C3'" "C2'" "H2'" 108.340 3.000
CDC "C3'" "C2'" "O2'" 109.470 3.000
CDC "C3'" "C2'" "C1'" 111.000 3.000
CDC "H2'" "C2'" "O2'" 109.470 3.000
CDC "H2'" "C2'" "C1'" 108.340 3.000
CDC "O2'" "C2'" "C1'" 109.470 3.000
CDC "C2'" "O2'" "HO'2" 109.470 3.000
CDC "C4'" "O4'" "C1'" 111.800 3.000
CDC "O4'" "C1'" "H1'" 109.470 3.000
CDC "O4'" "C1'" N1 109.470 3.000
CDC "O4'" "C1'" "C2'" 109.470 3.000
CDC "H1'" "C1'" N1 109.470 3.000
CDC "H1'" "C1'" "C2'" 108.340 3.000
CDC N1 "C1'" "C2'" 109.470 3.000
CDC "C1'" N1 C6 120.000 3.000
CDC "C1'" N1 C2 120.000 3.000
CDC C6 N1 C2 120.000 3.000
CDC N1 C6 H6 120.000 3.000
CDC N1 C6 C5 120.000 3.000
CDC H6 C6 C5 120.000 3.000
CDC C6 C5 H5 120.000 3.000
CDC C6 C5 C4 120.000 3.000
CDC H5 C5 C4 120.000 3.000
CDC C5 C4 N4 120.000 3.000
CDC C5 C4 N3 120.000 3.000
CDC N4 C4 N3 120.000 3.000
CDC C4 N4 H42 120.000 3.000
CDC C4 N4 H41 120.000 3.000
CDC H42 N4 H41 120.000 3.000
CDC C4 N3 C2 120.000 3.000
CDC N3 C2 O2 120.000 3.000
CDC N3 C2 N1 120.000 3.000
CDC 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
CDC var_1 O3B PB O1B C14 -65.002 20.000 1
CDC var_2 PB O1B C14 C15 -179.992 20.000 1
CDC var_3 O1B C14 C15 N11 67.636 20.000 3
CDC var_4 C14 C15 N11 C16 55.222 20.000 1
CDC var_5 C15 N11 C18 H181 -60.040 20.000 1
CDC var_6 C15 N11 C17 H171 -170.017 20.000 1
CDC var_7 C15 N11 C16 H161 -59.950 20.000 1
CDC var_8 O3B PB O3A PA 80.007 20.000 1
CDC var_9 PB O3A PA "O5'" -159.983 20.000 1
CDC var_10 O3A PA "O5'" "C5'" 174.994 20.000 1
CDC var_11 PA "O5'" "C5'" "C4'" -179.998 20.000 1
CDC var_12 "O5'" "C5'" "C4'" "O4'" 66.696 20.000 3
CDC var_13 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
CDC var_14 "C4'" "C3'" "O3'" H3T 176.135 20.000 1
CDC var_15 "C4'" "C3'" "C2'" "O2'" -150.000 20.000 3
CDC var_16 "C3'" "C2'" "O2'" "HO'2" -67.326 20.000 1
CDC var_17 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
CDC var_18 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
CDC var_19 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
CDC var_20 "O4'" "C1'" N1 C6 -126.466 20.000 1
CDC CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
CDC CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
CDC CONST_3 N1 C6 C5 C4 0.000 0.000 0
CDC CONST_4 C6 C5 C4 N3 0.000 0.000 0
CDC CONST_5 C5 C4 N4 H41 -0.014 0.000 0
CDC CONST_6 C5 C4 N3 C2 0.000 0.000 0
CDC 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
CDC chir_01 "C1'" N1 "C2'" "O4'" negativ
CDC chir_02 "C2'" "C1'" "O2'" "C3'" positiv
CDC chir_03 "C3'" "C2'" "C4'" "O3'" negativ
CDC chir_04 "C4'" "C3'" "O4'" "C5'" positiv
CDC chir_05 N11 C15 C16 C17 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
CDC plan-1 N1 0.020
CDC plan-1 C2 0.020
CDC plan-1 C6 0.020
CDC plan-1 "C1'" 0.020
CDC plan-1 N3 0.020
CDC plan-1 C4 0.020
CDC plan-1 C5 0.020
CDC plan-1 O2 0.020
CDC plan-1 N4 0.020
CDC plan-1 H5 0.020
CDC plan-1 H6 0.020
CDC plan-1 H42 0.020
CDC plan-1 H41 0.020
CDC plan-2 N4 0.020
CDC plan-2 C4 0.020
CDC plan-2 H41 0.020
CDC plan-2 H42 0.020
# ------------------------------------------------------
|
