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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
YYY YYY 'DEOXYCYTIDINE DIPHOSPHATE ' non-polymer 36 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_YYY
#
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
YYY O2 O O 0.000 0.000 0.000 0.000
YYY C2 C CR6 0.000 -0.713 -1.002 0.079
YYY N3 N NRD6 0.000 -0.329 -2.180 -0.539
YYY C4 C CR6 0.000 -1.072 -3.254 -0.466
YYY N4 N NH2 0.000 -0.673 -4.414 -1.087
YYY H4N2 H H 0.000 0.036 -4.390 -1.812
YYY H4N1 H H 0.000 -1.083 -5.303 -0.826
YYY C5 C CR16 0.000 -2.357 -3.263 0.280
YYY H5 H H 0.000 -2.975 -4.151 0.342
YYY C6 C CR16 0.000 -2.708 -2.121 0.867
YYY H6 H H 0.000 -3.638 -2.086 1.421
YYY N1 N NR6 0.000 -1.932 -0.975 0.799
YYY "C1'" C CH1 0.000 -2.395 0.207 1.465
YYY "H1'" H H 0.000 -1.530 0.821 1.752
YYY "O4'" O O2 0.000 -3.118 -0.165 2.646
YYY "C2'" C CH2 0.000 -3.331 1.040 0.604
YYY "H2'1" H H 0.000 -3.903 0.437 -0.105
YYY "H2'2" H H 0.000 -2.815 1.838 0.067
YYY "C3'" C CH1 0.000 -4.267 1.640 1.627
YYY "H3'" H H 0.000 -5.250 1.861 1.187
YYY "O3'" O OH1 0.000 -3.678 2.810 2.190
YYY HA H H 0.000 -4.241 3.574 2.006
YYY "C4'" C CH1 0.000 -4.368 0.550 2.684
YYY "H4'" H H 0.000 -4.510 1.003 3.676
YYY "C5'" C CH2 0.000 -5.485 -0.446 2.405
YYY "H5'1" H H 0.000 -5.316 -0.930 1.441
YYY "H5'2" H H 0.000 -6.446 0.073 2.386
YYY "O5'" O O2 0.000 -5.495 -1.424 3.431
YYY PA P P 0.000 -6.584 -2.620 3.398
YYY O1A O OP -0.500 -6.489 -3.577 4.526
YYY O2A O OP -0.500 -7.891 -1.927 3.292
YYY O3A O O2 0.000 -6.403 -3.295 1.940
YYY PB P P 0.000 -7.252 -4.448 1.193
YYY O3B O OP -0.666 -6.989 -5.673 2.042
YYY O1B O OP -0.666 -8.712 -4.117 0.974
YYY O2B O OP -0.666 -6.453 -4.712 -0.064
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
YYY O2 n/a C2 START
YYY C2 O2 N3 .
YYY N3 C2 C4 .
YYY C4 N3 C5 .
YYY N4 C4 H4N1 .
YYY H4N2 N4 . .
YYY H4N1 N4 . .
YYY C5 C4 C6 .
YYY H5 C5 . .
YYY C6 C5 N1 .
YYY H6 C6 . .
YYY N1 C6 "C1'" .
YYY "C1'" N1 "C2'" .
YYY "H1'" "C1'" . .
YYY "O4'" "C1'" . .
YYY "C2'" "C1'" "C3'" .
YYY "H2'1" "C2'" . .
YYY "H2'2" "C2'" . .
YYY "C3'" "C2'" "C4'" .
YYY "H3'" "C3'" . .
YYY "O3'" "C3'" HA .
YYY HA "O3'" . .
YYY "C4'" "C3'" "C5'" .
YYY "H4'" "C4'" . .
YYY "C5'" "C4'" "O5'" .
YYY "H5'1" "C5'" . .
YYY "H5'2" "C5'" . .
YYY "O5'" "C5'" PA .
YYY PA "O5'" O3A .
YYY O1A PA . .
YYY O2A PA . .
YYY O3A PA PB .
YYY PB O3A O2B .
YYY O3B PB . .
YYY O1B PB . .
YYY O2B PB . END
YYY "C4'" "O4'" . ADD
YYY 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
YYY O3B PB deloc 1.510 0.020
YYY O1B PB deloc 1.510 0.020
YYY O2B PB deloc 1.510 0.020
YYY PB O3A single 1.610 0.020
YYY O3A PA single 1.610 0.020
YYY O1A PA deloc 1.510 0.020
YYY O2A PA deloc 1.510 0.020
YYY PA "O5'" single 1.610 0.020
YYY "O5'" "C5'" single 1.426 0.020
YYY "C5'" "C4'" single 1.524 0.020
YYY "H5'1" "C5'" single 1.092 0.020
YYY "H5'2" "C5'" single 1.092 0.020
YYY "C4'" "O4'" single 1.426 0.020
YYY "C4'" "C3'" single 1.524 0.020
YYY "H4'" "C4'" single 1.099 0.020
YYY "O4'" "C1'" single 1.426 0.020
YYY "O3'" "C3'" single 1.432 0.020
YYY "C3'" "C2'" single 1.524 0.020
YYY "H3'" "C3'" single 1.099 0.020
YYY HA "O3'" single 0.967 0.020
YYY "C2'" "C1'" single 1.524 0.020
YYY "H2'1" "C2'" single 1.092 0.020
YYY "H2'2" "C2'" single 1.092 0.020
YYY "C1'" N1 single 1.465 0.020
YYY "H1'" "C1'" single 1.099 0.020
YYY N1 C2 single 1.410 0.020
YYY N1 C6 single 1.337 0.020
YYY C2 O2 double 1.250 0.020
YYY N3 C2 single 1.350 0.020
YYY C4 N3 double 1.350 0.020
YYY N4 C4 single 1.355 0.020
YYY C5 C4 single 1.390 0.020
YYY H4N1 N4 single 1.010 0.020
YYY H4N2 N4 single 1.010 0.020
YYY C6 C5 double 1.390 0.020
YYY H5 C5 single 1.083 0.020
YYY 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
YYY O2 C2 N3 120.000 3.000
YYY O2 C2 N1 120.000 3.000
YYY N3 C2 N1 120.000 3.000
YYY C2 N3 C4 120.000 3.000
YYY N3 C4 N4 120.000 3.000
YYY N3 C4 C5 120.000 3.000
YYY N4 C4 C5 120.000 3.000
YYY C4 N4 H4N2 120.000 3.000
YYY C4 N4 H4N1 120.000 3.000
YYY H4N2 N4 H4N1 120.000 3.000
YYY C4 C5 H5 120.000 3.000
YYY C4 C5 C6 120.000 3.000
YYY H5 C5 C6 120.000 3.000
YYY C5 C6 H6 120.000 3.000
YYY C5 C6 N1 120.000 3.000
YYY H6 C6 N1 120.000 3.000
YYY C6 N1 "C1'" 120.000 3.000
YYY C6 N1 C2 120.000 3.000
YYY "C1'" N1 C2 120.000 3.000
YYY N1 "C1'" "H1'" 109.470 3.000
YYY N1 "C1'" "O4'" 109.470 3.000
YYY N1 "C1'" "C2'" 109.470 3.000
YYY "H1'" "C1'" "O4'" 109.470 3.000
YYY "H1'" "C1'" "C2'" 108.340 3.000
YYY "O4'" "C1'" "C2'" 109.470 3.000
YYY "C1'" "O4'" "C4'" 111.800 3.000
YYY "C1'" "C2'" "H2'1" 109.470 3.000
YYY "C1'" "C2'" "H2'2" 109.470 3.000
YYY "C1'" "C2'" "C3'" 111.000 3.000
YYY "H2'1" "C2'" "H2'2" 107.900 3.000
YYY "H2'1" "C2'" "C3'" 109.470 3.000
YYY "H2'2" "C2'" "C3'" 109.470 3.000
YYY "C2'" "C3'" "H3'" 108.340 3.000
YYY "C2'" "C3'" "O3'" 109.470 3.000
YYY "C2'" "C3'" "C4'" 111.000 3.000
YYY "H3'" "C3'" "O3'" 109.470 3.000
YYY "H3'" "C3'" "C4'" 108.340 3.000
YYY "O3'" "C3'" "C4'" 109.470 3.000
YYY "C3'" "O3'" HA 109.470 3.000
YYY "C3'" "C4'" "H4'" 108.340 3.000
YYY "C3'" "C4'" "C5'" 111.000 3.000
YYY "C3'" "C4'" "O4'" 109.470 3.000
YYY "H4'" "C4'" "C5'" 108.340 3.000
YYY "H4'" "C4'" "O4'" 109.470 3.000
YYY "C5'" "C4'" "O4'" 109.470 3.000
YYY "C4'" "C5'" "H5'1" 109.470 3.000
YYY "C4'" "C5'" "H5'2" 109.470 3.000
YYY "C4'" "C5'" "O5'" 109.470 3.000
YYY "H5'1" "C5'" "H5'2" 107.900 3.000
YYY "H5'1" "C5'" "O5'" 109.470 3.000
YYY "H5'2" "C5'" "O5'" 109.470 3.000
YYY "C5'" "O5'" PA 120.500 3.000
YYY "O5'" PA O1A 108.200 3.000
YYY "O5'" PA O2A 108.200 3.000
YYY "O5'" PA O3A 102.600 3.000
YYY O1A PA O2A 119.900 3.000
YYY O1A PA O3A 108.200 3.000
YYY O2A PA O3A 108.200 3.000
YYY PA O3A PB 120.500 3.000
YYY O3A PB O3B 108.200 3.000
YYY O3A PB O1B 108.200 3.000
YYY O3A PB O2B 108.200 3.000
YYY O3B PB O1B 119.900 3.000
YYY O3B PB O2B 119.900 3.000
YYY 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
YYY CONST_1 O2 C2 N3 C4 180.000 0.000 0
YYY CONST_2 C2 N3 C4 C5 0.000 0.000 0
YYY CONST_3 N3 C4 N4 H4N1 162.324 0.000 0
YYY CONST_4 N3 C4 C5 C6 0.000 0.000 0
YYY CONST_5 C4 C5 C6 N1 0.000 0.000 0
YYY CONST_6 C5 C6 N1 "C1'" 180.000 0.000 0
YYY CONST_7 C6 N1 C2 O2 180.000 0.000 0
YYY var_1 C6 N1 "C1'" "C2'" -86.507 20.000 1
YYY var_2 N1 "C1'" "O4'" "C4'" -120.000 20.000 1
YYY var_3 N1 "C1'" "C2'" "C3'" 150.000 20.000 3
YYY var_4 "C1'" "C2'" "C3'" "C4'" -30.000 20.000 3
YYY var_5 "C2'" "C3'" "O3'" HA 119.295 20.000 1
YYY var_6 "C2'" "C3'" "C4'" "C5'" -90.000 20.000 3
YYY var_7 "C3'" "C4'" "O4'" "C1'" 0.000 20.000 1
YYY var_8 "C3'" "C4'" "C5'" "O5'" 179.531 20.000 3
YYY var_9 "C4'" "C5'" "O5'" PA 179.977 20.000 1
YYY var_10 "C5'" "O5'" PA O3A 54.131 20.000 1
YYY var_11 "O5'" PA O3A PB -173.802 20.000 1
YYY var_12 PA O3A PB O2B -173.656 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
YYY chir_01 "C4'" "C5'" "O4'" "C3'" negativ
YYY chir_02 "C3'" "C4'" "O3'" "C2'" negativ
YYY 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
YYY plan-1 N1 0.020
YYY plan-1 "C1'" 0.020
YYY plan-1 C2 0.020
YYY plan-1 C6 0.020
YYY plan-1 N3 0.020
YYY plan-1 C4 0.020
YYY plan-1 C5 0.020
YYY plan-1 O2 0.020
YYY plan-1 N4 0.020
YYY plan-1 H5 0.020
YYY plan-1 H6 0.020
YYY plan-1 H4N2 0.020
YYY plan-1 H4N1 0.020
YYY plan-2 N4 0.020
YYY plan-2 C4 0.020
YYY plan-2 H4N1 0.020
YYY plan-2 H4N2 0.020
# ------------------------------------------------------
|
