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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
P1D P1D '"((2S,3AS,4R,6S)-4-(HYDROXYMETHYL)-6' non-polymer 41 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_P1D
#
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
P1D O6 O O 0.000 0.000 0.000 0.000
P1D C6 C CR6 0.000 -1.103 -0.495 -0.165
P1D C5 C CR56 0.000 -2.267 0.297 -0.091
P1D N7 N NR15 0.000 -2.505 1.631 0.148
P1D HN7 H H 0.000 -1.779 2.352 0.332
P1D C8 C CR15 0.000 -3.847 1.851 0.102
P1D H8 H H 0.000 -4.329 2.809 0.253
P1D N1 N NR16 0.000 -1.238 -1.814 -0.424
P1D HN1 H H 0.000 -0.393 -2.417 -0.484
P1D C2 C CR16 0.000 -2.468 -2.358 -0.607
P1D H2 H H 0.000 -2.546 -3.419 -0.813
P1D N3 N NRD6 0.000 -3.556 -1.649 -0.544
P1D C4 C CR56 0.000 -3.508 -0.320 -0.282
P1D C9 C CR5 0.000 -4.485 0.691 -0.160
P1D "C1'" C CH1 0.000 -5.974 0.506 -0.290
P1D "H1'" H H 0.000 -6.191 -0.248 -1.060
P1D "O4'" O O2 0.000 -6.592 1.755 -0.643
P1D "C4'" C CH1 0.000 -7.896 1.768 -0.026
P1D "H4'" H H 0.000 -8.604 1.161 -0.608
P1D "C5'" C CH2 0.000 -8.408 3.203 0.113
P1D "H5'1" H H 0.000 -7.648 3.814 0.604
P1D "H5'2" H H 0.000 -9.320 3.206 0.714
P1D "O5'" O OH1 0.000 -8.688 3.738 -1.182
P1D "H5'" H H 0.000 -9.012 4.644 -1.092
P1D "C3'" C CH1 0.000 -7.657 1.139 1.367
P1D "H3'" H H 0.000 -7.349 1.868 2.130
P1D "O3'" O O2 0.000 -8.825 0.370 1.740
P1D "C2'" C CH1 0.000 -6.570 0.064 1.059
P1D "H2'" H H 0.000 -5.818 -0.033 1.855
P1D "O2'" O O2 0.000 -7.339 -1.143 0.850
P1D C1 C CH1 0.000 -8.439 -1.013 1.775
P1D H1 H H 0.000 -8.115 -1.290 2.788
P1D C1P C CH2 0.000 -9.604 -1.899 1.333
P1D H1P1 H H 0.000 -10.430 -1.794 2.040
P1D H1P2 H H 0.000 -9.279 -2.942 1.307
P1D P P P 0.000 -10.157 -1.392 -0.329
P1D O2 O O 0.000 -9.008 -1.422 -1.261
P1D O4 O OH1 0.000 -11.295 -2.406 -0.848
P1D HO4 H H 0.000 -11.697 -2.278 -1.718
P1D O3 O OH1 0.000 -10.757 0.101 -0.263
P1D HO3 H H 0.000 -11.517 0.292 0.304
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
P1D O6 n/a C6 START
P1D C6 O6 N1 .
P1D C5 C6 N7 .
P1D N7 C5 C8 .
P1D HN7 N7 . .
P1D C8 N7 H8 .
P1D H8 C8 . .
P1D N1 C6 C2 .
P1D HN1 N1 . .
P1D C2 N1 N3 .
P1D H2 C2 . .
P1D N3 C2 C4 .
P1D C4 N3 C9 .
P1D C9 C4 "C1'" .
P1D "C1'" C9 "C2'" .
P1D "H1'" "C1'" . .
P1D "O4'" "C1'" "C4'" .
P1D "C4'" "O4'" "C3'" .
P1D "H4'" "C4'" . .
P1D "C5'" "C4'" "O5'" .
P1D "H5'1" "C5'" . .
P1D "H5'2" "C5'" . .
P1D "O5'" "C5'" "H5'" .
P1D "H5'" "O5'" . .
P1D "C3'" "C4'" "O3'" .
P1D "H3'" "C3'" . .
P1D "O3'" "C3'" . .
P1D "C2'" "C1'" "O2'" .
P1D "H2'" "C2'" . .
P1D "O2'" "C2'" C1 .
P1D C1 "O2'" C1P .
P1D H1 C1 . .
P1D C1P C1 P .
P1D H1P1 C1P . .
P1D H1P2 C1P . .
P1D P C1P O3 .
P1D O2 P . .
P1D O4 P HO4 .
P1D HO4 O4 . .
P1D O3 P HO3 .
P1D HO3 O3 . END
P1D C1 "O3'" . ADD
P1D "C2'" "C3'" . ADD
P1D C9 C8 . ADD
P1D C5 C4 . 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
P1D O3 P single 1.610 0.020
P1D HO3 O3 single 0.967 0.020
P1D O4 P single 1.610 0.020
P1D O2 P double 1.480 0.020
P1D P C1P single 1.812 0.020
P1D HO4 O4 single 0.967 0.020
P1D C1P C1 single 1.524 0.020
P1D H1P1 C1P single 1.092 0.020
P1D H1P2 C1P single 1.092 0.020
P1D C1 "O3'" single 1.426 0.020
P1D C1 "O2'" single 1.426 0.020
P1D H1 C1 single 1.099 0.020
P1D "O3'" "C3'" single 1.426 0.020
P1D "O2'" "C2'" single 1.426 0.020
P1D "C2'" "C3'" single 1.524 0.020
P1D "C2'" "C1'" single 1.524 0.020
P1D "H2'" "C2'" single 1.099 0.020
P1D "C3'" "C4'" single 1.524 0.020
P1D "H3'" "C3'" single 1.099 0.020
P1D "C5'" "C4'" single 1.524 0.020
P1D "C4'" "O4'" single 1.426 0.020
P1D "H4'" "C4'" single 1.099 0.020
P1D "O5'" "C5'" single 1.432 0.020
P1D "H5'1" "C5'" single 1.092 0.020
P1D "H5'2" "C5'" single 1.092 0.020
P1D "H5'" "O5'" single 0.967 0.020
P1D "O4'" "C1'" single 1.426 0.020
P1D "C1'" C9 single 1.480 0.020
P1D "H1'" "C1'" single 1.099 0.020
P1D C9 C8 double 1.387 0.020
P1D C9 C4 single 1.490 0.020
P1D C8 N7 single 1.350 0.020
P1D H8 C8 single 1.083 0.020
P1D N7 C5 single 1.340 0.020
P1D HN7 N7 single 1.040 0.020
P1D C5 C4 double 1.490 0.020
P1D C5 C6 single 1.490 0.020
P1D C4 N3 single 1.355 0.020
P1D N3 C2 double 1.337 0.020
P1D C2 N1 single 1.337 0.020
P1D H2 C2 single 1.083 0.020
P1D N1 C6 single 1.337 0.020
P1D HN1 N1 single 1.040 0.020
P1D C6 O6 double 1.250 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
P1D O6 C6 C5 120.000 3.000
P1D O6 C6 N1 120.000 3.000
P1D C5 C6 N1 120.000 3.000
P1D C6 C5 N7 132.000 3.000
P1D C6 C5 C4 120.000 3.000
P1D N7 C5 C4 108.000 3.000
P1D C5 N7 HN7 126.000 3.000
P1D C5 N7 C8 108.000 3.000
P1D HN7 N7 C8 126.000 3.000
P1D N7 C8 H8 126.000 3.000
P1D N7 C8 C9 108.000 3.000
P1D H8 C8 C9 126.000 3.000
P1D C6 N1 HN1 120.000 3.000
P1D C6 N1 C2 120.000 3.000
P1D HN1 N1 C2 120.000 3.000
P1D N1 C2 H2 120.000 3.000
P1D N1 C2 N3 120.000 3.000
P1D H2 C2 N3 120.000 3.000
P1D C2 N3 C4 120.000 3.000
P1D N3 C4 C9 120.000 3.000
P1D N3 C4 C5 120.000 3.000
P1D C9 C4 C5 108.000 3.000
P1D C4 C9 "C1'" 108.000 3.000
P1D C4 C9 C8 108.000 3.000
P1D "C1'" C9 C8 108.000 3.000
P1D C9 "C1'" "H1'" 109.470 3.000
P1D C9 "C1'" "O4'" 109.500 3.000
P1D C9 "C1'" "C2'" 109.470 3.000
P1D "H1'" "C1'" "O4'" 109.470 3.000
P1D "H1'" "C1'" "C2'" 108.340 3.000
P1D "O4'" "C1'" "C2'" 109.470 3.000
P1D "C1'" "O4'" "C4'" 111.800 3.000
P1D "O4'" "C4'" "H4'" 109.470 3.000
P1D "O4'" "C4'" "C5'" 109.470 3.000
P1D "O4'" "C4'" "C3'" 109.470 3.000
P1D "H4'" "C4'" "C5'" 108.340 3.000
P1D "H4'" "C4'" "C3'" 108.340 3.000
P1D "C5'" "C4'" "C3'" 111.000 3.000
P1D "C4'" "C5'" "H5'1" 109.470 3.000
P1D "C4'" "C5'" "H5'2" 109.470 3.000
P1D "C4'" "C5'" "O5'" 109.470 3.000
P1D "H5'1" "C5'" "H5'2" 107.900 3.000
P1D "H5'1" "C5'" "O5'" 109.470 3.000
P1D "H5'2" "C5'" "O5'" 109.470 3.000
P1D "C5'" "O5'" "H5'" 109.470 3.000
P1D "C4'" "C3'" "H3'" 108.340 3.000
P1D "C4'" "C3'" "O3'" 109.470 3.000
P1D "C4'" "C3'" "C2'" 111.000 3.000
P1D "H3'" "C3'" "O3'" 109.470 3.000
P1D "H3'" "C3'" "C2'" 108.340 3.000
P1D "O3'" "C3'" "C2'" 109.470 3.000
P1D "C3'" "O3'" C1 111.800 3.000
P1D "C1'" "C2'" "H2'" 108.340 3.000
P1D "C1'" "C2'" "O2'" 109.470 3.000
P1D "C1'" "C2'" "C3'" 111.000 3.000
P1D "H2'" "C2'" "O2'" 109.470 3.000
P1D "H2'" "C2'" "C3'" 108.340 3.000
P1D "O2'" "C2'" "C3'" 109.470 3.000
P1D "C2'" "O2'" C1 111.800 3.000
P1D "O2'" C1 H1 109.470 3.000
P1D "O2'" C1 C1P 109.470 3.000
P1D "O2'" C1 "O3'" 109.470 3.000
P1D H1 C1 C1P 108.340 3.000
P1D H1 C1 "O3'" 109.470 3.000
P1D C1P C1 "O3'" 109.470 3.000
P1D C1 C1P H1P1 109.470 3.000
P1D C1 C1P H1P2 109.470 3.000
P1D C1 C1P P 109.500 3.000
P1D H1P1 C1P H1P2 107.900 3.000
P1D H1P1 C1P P 109.500 3.000
P1D H1P2 C1P P 109.500 3.000
P1D C1P P O2 109.500 3.000
P1D C1P P O4 109.500 3.000
P1D C1P P O3 109.500 3.000
P1D O2 P O4 109.500 3.000
P1D O2 P O3 109.500 3.000
P1D O4 P O3 109.500 3.000
P1D P O4 HO4 120.000 3.000
P1D P O3 HO3 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
P1D CONST_1 O6 C6 C5 N7 0.000 0.000 0
P1D CONST_2 C6 C5 C4 N3 0.000 0.000 0
P1D CONST_3 C6 C5 N7 C8 180.000 0.000 0
P1D CONST_4 C5 N7 C8 C9 0.000 0.000 0
P1D CONST_5 O6 C6 N1 C2 180.000 0.000 0
P1D CONST_6 C6 N1 C2 N3 0.000 0.000 0
P1D CONST_7 N1 C2 N3 C4 0.000 0.000 0
P1D CONST_8 C2 N3 C4 C9 180.000 0.000 0
P1D CONST_9 N3 C4 C9 "C1'" 0.000 0.000 0
P1D CONST_10 C4 C9 C8 N7 0.000 0.000 0
P1D var_1 C4 C9 "C1'" "C2'" 85.236 20.000 1
P1D var_2 C9 "C1'" "O4'" "C4'" -150.000 20.000 1
P1D var_3 "C1'" "O4'" "C4'" "C3'" 30.000 20.000 1
P1D var_4 "O4'" "C4'" "C5'" "O5'" 68.435 20.000 3
P1D var_5 "C4'" "C5'" "O5'" "H5'" 179.943 20.000 1
P1D var_6 "O4'" "C4'" "C3'" "O3'" -150.000 20.000 3
P1D var_7 "C4'" "C3'" "O3'" C1 120.000 20.000 1
P1D var_8 C9 "C1'" "C2'" "O2'" -120.000 20.000 3
P1D var_9 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
P1D var_10 "C1'" "C2'" "O2'" C1 -150.000 20.000 1
P1D var_11 "C2'" "O2'" C1 C1P 150.000 20.000 1
P1D var_12 "O2'" C1 "O3'" "C3'" -30.000 20.000 1
P1D var_13 "O2'" C1 C1P P -60.028 20.000 3
P1D var_14 C1 C1P P O3 -64.969 20.000 1
P1D var_15 C1P P O4 HO4 -179.964 20.000 1
P1D var_16 C1P P O3 HO3 -59.960 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
P1D chir_01 C1 C1P "O3'" "O2'" positiv
P1D chir_02 "C2'" "O2'" "C3'" "C1'" positiv
P1D chir_03 "C3'" "O3'" "C2'" "C4'" negativ
P1D chir_04 "C4'" "C3'" "C5'" "O4'" negativ
P1D chir_05 "C1'" "C2'" "O4'" C9 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
P1D plan-1 C9 0.020
P1D plan-1 "C1'" 0.020
P1D plan-1 C8 0.020
P1D plan-1 C4 0.020
P1D plan-1 N7 0.020
P1D plan-1 H8 0.020
P1D plan-1 C5 0.020
P1D plan-1 HN7 0.020
P1D plan-1 C6 0.020
P1D plan-1 N3 0.020
P1D plan-1 C2 0.020
P1D plan-1 N1 0.020
P1D plan-1 H2 0.020
P1D plan-1 HN1 0.020
P1D plan-1 O6 0.020
# ------------------------------------------------------
|
