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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
ATM ATM '3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPH' non-polymer 35 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_ATM
#
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
ATM O4 O O 0.000 0.000 0.000 0.000
ATM C4 C CR6 0.000 -1.140 -0.245 -0.354
ATM N3 N NR16 0.000 -2.143 -0.264 0.548
ATM HN3 H H 0.000 -1.942 -0.070 1.550
ATM C2 C CR6 0.000 -3.402 -0.534 0.157
ATM O2 O O 0.000 -4.295 -0.553 0.982
ATM C5 C CR6 0.000 -1.426 -0.502 -1.716
ATM C5A C CH3 0.000 -0.325 -0.483 -2.744
ATM H53 H H 0.000 0.587 -0.773 -2.291
ATM H52 H H 0.000 -0.560 -1.158 -3.526
ATM H51 H H 0.000 -0.228 0.495 -3.139
ATM C6 C CR16 0.000 -2.698 -0.772 -2.080
ATM H6 H H 0.000 -2.935 -0.976 -3.117
ATM N1 N NR6 0.000 -3.685 -0.786 -1.134
ATM "C1'" C CH1 0.000 -5.066 -1.078 -1.530
ATM "H1'" H H 0.000 -5.133 -1.156 -2.624
ATM "O4'" O O2 0.000 -5.939 -0.036 -1.061
ATM "C2'" C CH2 0.000 -5.530 -2.396 -0.881
ATM "H2'" H H 0.000 -4.769 -2.817 -0.220
ATM "H2''" H H 0.000 -5.815 -3.141 -1.626
ATM "C3'" C CH1 0.000 -6.772 -1.993 -0.049
ATM "H3'" H H 0.000 -6.502 -1.829 1.003
ATM "N3'" N N 0.000 -7.828 -3.002 -0.166
ATM "N4'" N N 1.000 -7.674 -4.030 0.260
ATM "N5'" N NS -1.000 -7.518 -5.058 0.687
ATM "C4'" C CH1 0.000 -7.197 -0.665 -0.724
ATM "H4'" H H 0.000 -7.784 -0.863 -1.632
ATM "C5'" C CH2 0.000 -7.993 0.204 0.251
ATM "H5''" H H 0.000 -7.348 0.504 1.080
ATM "H5'" H H 0.000 -8.839 -0.367 0.639
ATM "O5'" O O2 0.000 -8.472 1.367 -0.428
ATM P P P 0.000 -9.296 2.231 0.653
ATM OP3 O OP -0.666 -10.518 1.455 1.092
ATM OP1 O OP -0.666 -8.417 2.509 1.852
ATM OP2 O OP -0.666 -9.727 3.540 0.028
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
ATM O4 n/a C4 START
ATM C4 O4 C5 .
ATM N3 C4 C2 .
ATM HN3 N3 . .
ATM C2 N3 O2 .
ATM O2 C2 . .
ATM C5 C4 C6 .
ATM C5A C5 H51 .
ATM H53 C5A . .
ATM H52 C5A . .
ATM H51 C5A . .
ATM C6 C5 N1 .
ATM H6 C6 . .
ATM N1 C6 "C1'" .
ATM "C1'" N1 "C2'" .
ATM "H1'" "C1'" . .
ATM "O4'" "C1'" . .
ATM "C2'" "C1'" "C3'" .
ATM "H2'" "C2'" . .
ATM "H2''" "C2'" . .
ATM "C3'" "C2'" "C4'" .
ATM "H3'" "C3'" . .
ATM "N3'" "C3'" "N4'" .
ATM "N4'" "N3'" "N5'" .
ATM "N5'" "N4'" . .
ATM "C4'" "C3'" "C5'" .
ATM "H4'" "C4'" . .
ATM "C5'" "C4'" "O5'" .
ATM "H5''" "C5'" . .
ATM "H5'" "C5'" . .
ATM "O5'" "C5'" P .
ATM P "O5'" OP2 .
ATM OP3 P . .
ATM OP1 P . .
ATM OP2 P . END
ATM "C4'" "O4'" . ADD
ATM 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
ATM OP1 P deloc 1.510 0.020
ATM OP2 P deloc 1.510 0.020
ATM OP3 P deloc 1.510 0.020
ATM P "O5'" single 1.610 0.020
ATM "O5'" "C5'" single 1.426 0.020
ATM "C5'" "C4'" single 1.524 0.020
ATM "H5'" "C5'" single 1.092 0.020
ATM "H5''" "C5'" single 1.092 0.020
ATM "C4'" "O4'" single 1.426 0.020
ATM "C4'" "C3'" single 1.524 0.020
ATM "H4'" "C4'" single 1.099 0.020
ATM "O4'" "C1'" single 1.426 0.020
ATM "N3'" "C3'" single 1.455 0.020
ATM "C3'" "C2'" single 1.524 0.020
ATM "H3'" "C3'" single 1.099 0.020
ATM "N4'" "N3'" double 1.240 0.020
ATM "N5'" "N4'" double 1.295 0.020
ATM "C2'" "C1'" single 1.524 0.020
ATM "H2'" "C2'" single 1.092 0.020
ATM "H2''" "C2'" single 1.092 0.020
ATM "C1'" N1 single 1.465 0.020
ATM "H1'" "C1'" single 1.099 0.020
ATM N1 C2 single 1.410 0.020
ATM N1 C6 single 1.337 0.020
ATM O2 C2 double 1.250 0.020
ATM C2 N3 single 1.337 0.020
ATM N3 C4 single 1.337 0.020
ATM HN3 N3 single 1.040 0.020
ATM C4 O4 double 1.250 0.020
ATM C5 C4 single 1.487 0.020
ATM C5A C5 single 1.506 0.020
ATM C6 C5 double 1.390 0.020
ATM H51 C5A single 1.059 0.020
ATM H52 C5A single 1.059 0.020
ATM H53 C5A single 1.059 0.020
ATM 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
ATM O4 C4 N3 120.000 3.000
ATM O4 C4 C5 120.000 3.000
ATM N3 C4 C5 120.000 3.000
ATM C4 N3 HN3 120.000 3.000
ATM C4 N3 C2 120.000 3.000
ATM HN3 N3 C2 120.000 3.000
ATM N3 C2 O2 120.000 3.000
ATM N3 C2 N1 120.000 3.000
ATM O2 C2 N1 120.000 3.000
ATM C4 C5 C5A 120.000 3.000
ATM C4 C5 C6 120.000 3.000
ATM C5A C5 C6 120.000 3.000
ATM C5 C5A H53 109.470 3.000
ATM C5 C5A H52 109.470 3.000
ATM C5 C5A H51 109.470 3.000
ATM H53 C5A H52 109.470 3.000
ATM H53 C5A H51 109.470 3.000
ATM H52 C5A H51 109.470 3.000
ATM C5 C6 H6 120.000 3.000
ATM C5 C6 N1 120.000 3.000
ATM H6 C6 N1 120.000 3.000
ATM C6 N1 "C1'" 120.000 3.000
ATM C6 N1 C2 120.000 3.000
ATM "C1'" N1 C2 120.000 3.000
ATM N1 "C1'" "H1'" 109.470 3.000
ATM N1 "C1'" "O4'" 109.470 3.000
ATM N1 "C1'" "C2'" 109.470 3.000
ATM "H1'" "C1'" "O4'" 109.470 3.000
ATM "H1'" "C1'" "C2'" 108.340 3.000
ATM "O4'" "C1'" "C2'" 109.470 3.000
ATM "C1'" "O4'" "C4'" 111.800 3.000
ATM "C1'" "C2'" "H2'" 109.470 3.000
ATM "C1'" "C2'" "H2''" 109.470 3.000
ATM "C1'" "C2'" "C3'" 111.000 3.000
ATM "H2'" "C2'" "H2''" 107.900 3.000
ATM "H2'" "C2'" "C3'" 109.470 3.000
ATM "H2''" "C2'" "C3'" 109.470 3.000
ATM "C2'" "C3'" "H3'" 108.340 3.000
ATM "C2'" "C3'" "N3'" 105.000 3.000
ATM "C2'" "C3'" "C4'" 111.000 3.000
ATM "H3'" "C3'" "N3'" 109.470 3.000
ATM "H3'" "C3'" "C4'" 108.340 3.000
ATM "N3'" "C3'" "C4'" 105.000 3.000
ATM "C3'" "N3'" "N4'" 120.000 3.000
ATM "N3'" "N4'" "N5'" 120.000 3.000
ATM "C3'" "C4'" "H4'" 108.340 3.000
ATM "C3'" "C4'" "C5'" 111.000 3.000
ATM "C3'" "C4'" "O4'" 109.470 3.000
ATM "H4'" "C4'" "C5'" 108.340 3.000
ATM "H4'" "C4'" "O4'" 109.470 3.000
ATM "C5'" "C4'" "O4'" 109.470 3.000
ATM "C4'" "C5'" "H5''" 109.470 3.000
ATM "C4'" "C5'" "H5'" 109.470 3.000
ATM "C4'" "C5'" "O5'" 109.470 3.000
ATM "H5''" "C5'" "H5'" 107.900 3.000
ATM "H5''" "C5'" "O5'" 109.470 3.000
ATM "H5'" "C5'" "O5'" 109.470 3.000
ATM "C5'" "O5'" P 120.500 3.000
ATM "O5'" P OP3 108.200 3.000
ATM "O5'" P OP1 108.200 3.000
ATM "O5'" P OP2 108.200 3.000
ATM OP3 P OP1 119.900 3.000
ATM OP3 P OP2 119.900 3.000
ATM 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
ATM CONST_1 O4 C4 N3 C2 180.000 0.000 0
ATM CONST_2 C4 N3 C2 O2 180.000 0.000 0
ATM CONST_3 O4 C4 C5 C6 180.000 0.000 0
ATM var_1 C4 C5 C5A H51 -90.230 20.000 1
ATM CONST_4 C4 C5 C6 N1 0.000 0.000 0
ATM CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
ATM CONST_6 C6 N1 C2 N3 0.000 0.000 0
ATM var_2 C6 N1 "C1'" "C2'" 115.307 20.000 1
ATM var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
ATM var_4 N1 "C1'" "C2'" "C3'" 120.000 20.000 3
ATM var_5 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
ATM var_6 "C2'" "C3'" "N3'" "N4'" 66.453 20.000 3
ATM CONST_7 "C3'" "N3'" "N4'" "N5'" 7.315 0.000 0
ATM var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
ATM var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
ATM var_9 "C3'" "C4'" "C5'" "O5'" -174.967 20.000 3
ATM var_10 "C4'" "C5'" "O5'" P -179.976 20.000 1
ATM var_11 "C5'" "O5'" P OP2 174.990 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
ATM chir_01 "C4'" "C5'" "O4'" "C3'" negativ
ATM chir_02 "C3'" "C4'" "N3'" "C2'" negativ
ATM 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
ATM plan-1 "N3'" 0.020
ATM plan-1 "C3'" 0.020
ATM plan-1 "N4'" 0.020
ATM plan-1 "N5'" 0.020
ATM plan-2 N1 0.020
ATM plan-2 "C1'" 0.020
ATM plan-2 C2 0.020
ATM plan-2 C6 0.020
ATM plan-2 N3 0.020
ATM plan-2 C4 0.020
ATM plan-2 C5 0.020
ATM plan-2 O2 0.020
ATM plan-2 HN3 0.020
ATM plan-2 O4 0.020
ATM plan-2 C5A 0.020
ATM plan-2 H6 0.020
# ------------------------------------------------------
|
