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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
PUY PUY 'PUROMYCIN ' non-polymer 63 34 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PUY
#
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
PUY O O O 0.000 0.000 0.000 0.000
PUY C C C 0.000 -0.742 0.904 -0.319
PUY CA C CH1 0.000 -0.172 2.203 -0.827
PUY HA H H 0.000 -0.749 3.042 -0.415
PUY CB C CH2 0.000 -0.251 2.231 -2.355
PUY HB1 H H 0.000 -1.281 2.054 -2.669
PUY HB2 H H 0.000 0.393 1.451 -2.767
PUY CG C CR6 0.000 0.205 3.578 -2.857
PUY CD2 C CR16 0.000 -0.712 4.600 -3.020
PUY HD2 H H 0.000 -1.757 4.431 -2.792
PUY CE2 C CR16 0.000 -0.296 5.836 -3.475
PUY HE2 H H 0.000 -1.013 6.639 -3.595
PUY CZ C CR6 0.000 1.041 6.049 -3.777
PUY OM O O2 0.000 1.451 7.263 -4.230
PUY CMZ C CH3 0.000 0.292 8.094 -4.292
PUY HMZ3 H H 0.000 -0.415 7.667 -4.955
PUY HMZ2 H H 0.000 -0.136 8.178 -3.327
PUY HMZ1 H H 0.000 0.565 9.056 -4.641
PUY CE1 C CR16 0.000 1.959 5.022 -3.612
PUY HE1 H H 0.000 3.004 5.187 -3.844
PUY CD1 C CR16 0.000 1.539 3.789 -3.151
PUY HD1 H H 0.000 2.256 2.987 -3.021
PUY N N NH2 0.000 1.231 2.320 -0.407
PUY HN2 H H 0.000 1.527 3.094 0.176
PUY HN1 H H 0.000 1.911 1.628 -0.697
PUY "N3'" N NH1 0.000 -2.077 0.747 -0.220
PUY H3 H H 0.000 -2.695 1.500 -0.485
PUY "C3'" C CH1 0.000 -2.631 -0.517 0.274
PUY "H3'" H H 0.000 -1.974 -0.953 1.039
PUY "C4'" C CH1 0.000 -2.837 -1.509 -0.891
PUY "H4'" H H 0.000 -2.939 -0.967 -1.842
PUY "C5'" C CH2 0.000 -1.673 -2.501 -0.967
PUY "H5'1" H H 0.000 -1.632 -3.083 -0.044
PUY "H5''" H H 0.000 -0.737 -1.954 -1.092
PUY "O5'" O OH1 0.000 -1.867 -3.378 -2.077
PUY "H5'" H H 0.000 -1.132 -4.004 -2.125
PUY "C2'" C CH1 0.000 -4.051 -0.299 0.842
PUY "H2'" H H 0.000 -4.102 -0.628 1.889
PUY "O2'" O OH1 0.000 -4.430 1.074 0.730
PUY H1 H H 0.000 -5.320 1.192 1.089
PUY "C1'" C CH1 0.000 -4.951 -1.186 -0.048
PUY "H1'" H H 0.000 -5.381 -0.593 -0.868
PUY "O4'" O O2 0.000 -4.066 -2.201 -0.571
PUY N9 N NR5 0.000 -6.015 -1.797 0.751
PUY C8 C CR15 0.000 -5.990 -3.037 1.317
PUY H8 H H 0.000 -5.166 -3.736 1.244
PUY N7 N NRD5 0.000 -7.101 -3.257 1.958
PUY C5 C CR56 0.000 -7.908 -2.175 1.843
PUY C4 C CR56 0.000 -7.220 -1.224 1.073
PUY C6 C CR6 0.000 -9.192 -1.848 2.311
PUY N6 N NT 0.000 -9.917 -2.743 3.079
PUY C10 C CH3 0.000 -10.228 -3.887 2.211
PUY H103 H H 0.000 -10.784 -4.603 2.757
PUY H102 H H 0.000 -10.796 -3.556 1.381
PUY H101 H H 0.000 -9.327 -4.326 1.869
PUY C9 C CH3 0.000 -11.195 -2.091 3.393
PUY H93 H H 0.000 -11.012 -1.197 3.930
PUY H92 H H 0.000 -11.707 -1.866 2.494
PUY H91 H H 0.000 -11.787 -2.742 3.983
PUY N1 N NRD6 0.000 -9.695 -0.658 1.999
PUY C2 C CR16 0.000 -9.012 0.203 1.267
PUY H2 H H 0.000 -9.459 1.162 1.036
PUY N3 N NRD6 0.000 -7.806 -0.061 0.807
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
PUY O n/a C START
PUY C O "N3'" .
PUY CA C N .
PUY HA CA . .
PUY CB CA CG .
PUY HB1 CB . .
PUY HB2 CB . .
PUY CG CB CD2 .
PUY CD2 CG CE2 .
PUY HD2 CD2 . .
PUY CE2 CD2 CZ .
PUY HE2 CE2 . .
PUY CZ CE2 CE1 .
PUY OM CZ CMZ .
PUY CMZ OM HMZ1 .
PUY HMZ3 CMZ . .
PUY HMZ2 CMZ . .
PUY HMZ1 CMZ . .
PUY CE1 CZ CD1 .
PUY HE1 CE1 . .
PUY CD1 CE1 HD1 .
PUY HD1 CD1 . .
PUY N CA HN1 .
PUY HN2 N . .
PUY HN1 N . .
PUY "N3'" C "C3'" .
PUY H3 "N3'" . .
PUY "C3'" "N3'" "C2'" .
PUY "H3'" "C3'" . .
PUY "C4'" "C3'" "C5'" .
PUY "H4'" "C4'" . .
PUY "C5'" "C4'" "O5'" .
PUY "H5'1" "C5'" . .
PUY "H5''" "C5'" . .
PUY "O5'" "C5'" "H5'" .
PUY "H5'" "O5'" . .
PUY "C2'" "C3'" "C1'" .
PUY "H2'" "C2'" . .
PUY "O2'" "C2'" H1 .
PUY H1 "O2'" . .
PUY "C1'" "C2'" N9 .
PUY "H1'" "C1'" . .
PUY "O4'" "C1'" . .
PUY N9 "C1'" C8 .
PUY C8 N9 N7 .
PUY H8 C8 . .
PUY N7 C8 C5 .
PUY C5 N7 C6 .
PUY C4 C5 . .
PUY C6 C5 N1 .
PUY N6 C6 C9 .
PUY C10 N6 H101 .
PUY H103 C10 . .
PUY H102 C10 . .
PUY H101 C10 . .
PUY C9 N6 H91 .
PUY H93 C9 . .
PUY H92 C9 . .
PUY H91 C9 . .
PUY N1 C6 C2 .
PUY C2 N1 N3 .
PUY H2 C2 . .
PUY N3 C2 . END
PUY CG CD1 . ADD
PUY "C4'" "O4'" . ADD
PUY N9 C4 . ADD
PUY C4 N3 . 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
PUY N CA single 1.450 0.020
PUY HN1 N single 1.010 0.020
PUY HN2 N single 1.010 0.020
PUY CB CA single 1.524 0.020
PUY CA C single 1.500 0.020
PUY HA CA single 1.099 0.020
PUY CG CB single 1.511 0.020
PUY HB1 CB single 1.092 0.020
PUY HB2 CB single 1.092 0.020
PUY CG CD1 double 1.390 0.020
PUY CD2 CG single 1.390 0.020
PUY CD1 CE1 single 1.390 0.020
PUY HD1 CD1 single 1.083 0.020
PUY CE2 CD2 double 1.390 0.020
PUY HD2 CD2 single 1.083 0.020
PUY CE1 CZ double 1.390 0.020
PUY HE1 CE1 single 1.083 0.020
PUY CZ CE2 single 1.390 0.020
PUY HE2 CE2 single 1.083 0.020
PUY OM CZ single 1.370 0.020
PUY C O double 1.220 0.020
PUY CMZ OM single 1.426 0.020
PUY HMZ1 CMZ single 1.059 0.020
PUY HMZ2 CMZ single 1.059 0.020
PUY HMZ3 CMZ single 1.059 0.020
PUY "N3'" C single 1.330 0.020
PUY "O5'" "C5'" single 1.432 0.020
PUY "H5'" "O5'" single 0.967 0.020
PUY "C5'" "C4'" single 1.524 0.020
PUY "H5'1" "C5'" single 1.092 0.020
PUY "H5''" "C5'" single 1.092 0.020
PUY "C4'" "O4'" single 1.426 0.020
PUY "C4'" "C3'" single 1.524 0.020
PUY "H4'" "C4'" single 1.099 0.020
PUY "O4'" "C1'" single 1.426 0.020
PUY N9 "C1'" single 1.485 0.020
PUY "C1'" "C2'" single 1.524 0.020
PUY "H1'" "C1'" single 1.099 0.020
PUY N9 C4 single 1.337 0.020
PUY C8 N9 single 1.337 0.020
PUY C4 N3 double 1.355 0.020
PUY C4 C5 single 1.490 0.020
PUY N3 C2 single 1.337 0.020
PUY C2 N1 double 1.337 0.020
PUY H2 C2 single 1.083 0.020
PUY N1 C6 single 1.350 0.020
PUY N6 C6 single 1.405 0.020
PUY C6 C5 double 1.490 0.020
PUY C9 N6 single 1.469 0.020
PUY C10 N6 single 1.469 0.020
PUY H91 C9 single 1.059 0.020
PUY H92 C9 single 1.059 0.020
PUY H93 C9 single 1.059 0.020
PUY H101 C10 single 1.059 0.020
PUY H102 C10 single 1.059 0.020
PUY H103 C10 single 1.059 0.020
PUY C5 N7 single 1.350 0.020
PUY N7 C8 double 1.350 0.020
PUY H8 C8 single 1.083 0.020
PUY "O2'" "C2'" single 1.432 0.020
PUY "C2'" "C3'" single 1.524 0.020
PUY "H2'" "C2'" single 1.099 0.020
PUY H1 "O2'" single 0.967 0.020
PUY "C3'" "N3'" single 1.450 0.020
PUY "H3'" "C3'" single 1.099 0.020
PUY H3 "N3'" single 1.010 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
PUY O C CA 120.500 3.000
PUY O C "N3'" 123.000 3.000
PUY CA C "N3'" 116.500 3.000
PUY C CA HA 108.810 3.000
PUY C CA CB 109.470 3.000
PUY C CA N 109.470 3.000
PUY HA CA CB 108.340 3.000
PUY HA CA N 109.470 3.000
PUY CB CA N 109.470 3.000
PUY CA CB HB1 109.470 3.000
PUY CA CB HB2 109.470 3.000
PUY CA CB CG 109.470 3.000
PUY HB1 CB HB2 107.900 3.000
PUY HB1 CB CG 109.470 3.000
PUY HB2 CB CG 109.470 3.000
PUY CB CG CD2 120.000 3.000
PUY CB CG CD1 120.000 3.000
PUY CD2 CG CD1 120.000 3.000
PUY CG CD2 HD2 120.000 3.000
PUY CG CD2 CE2 120.000 3.000
PUY HD2 CD2 CE2 120.000 3.000
PUY CD2 CE2 HE2 120.000 3.000
PUY CD2 CE2 CZ 120.000 3.000
PUY HE2 CE2 CZ 120.000 3.000
PUY CE2 CZ OM 120.000 3.000
PUY CE2 CZ CE1 120.000 3.000
PUY OM CZ CE1 120.000 3.000
PUY CZ OM CMZ 120.000 3.000
PUY OM CMZ HMZ3 109.470 3.000
PUY OM CMZ HMZ2 109.470 3.000
PUY OM CMZ HMZ1 109.470 3.000
PUY HMZ3 CMZ HMZ2 109.470 3.000
PUY HMZ3 CMZ HMZ1 109.470 3.000
PUY HMZ2 CMZ HMZ1 109.470 3.000
PUY CZ CE1 HE1 120.000 3.000
PUY CZ CE1 CD1 120.000 3.000
PUY HE1 CE1 CD1 120.000 3.000
PUY CE1 CD1 HD1 120.000 3.000
PUY CE1 CD1 CG 120.000 3.000
PUY HD1 CD1 CG 120.000 3.000
PUY CA N HN2 120.000 3.000
PUY CA N HN1 120.000 3.000
PUY HN2 N HN1 120.000 3.000
PUY C "N3'" H3 120.000 3.000
PUY C "N3'" "C3'" 121.500 3.000
PUY H3 "N3'" "C3'" 118.500 3.000
PUY "N3'" "C3'" "H3'" 108.550 3.000
PUY "N3'" "C3'" "C4'" 110.000 3.000
PUY "N3'" "C3'" "C2'" 110.000 3.000
PUY "H3'" "C3'" "C4'" 108.340 3.000
PUY "H3'" "C3'" "C2'" 108.340 3.000
PUY "C4'" "C3'" "C2'" 111.000 3.000
PUY "C3'" "C4'" "H4'" 108.340 3.000
PUY "C3'" "C4'" "C5'" 111.000 3.000
PUY "C3'" "C4'" "O4'" 109.470 3.000
PUY "H4'" "C4'" "C5'" 108.340 3.000
PUY "H4'" "C4'" "O4'" 109.470 3.000
PUY "C5'" "C4'" "O4'" 109.470 3.000
PUY "C4'" "C5'" "H5'1" 109.470 3.000
PUY "C4'" "C5'" "H5''" 109.470 3.000
PUY "C4'" "C5'" "O5'" 109.470 3.000
PUY "H5'1" "C5'" "H5''" 107.900 3.000
PUY "H5'1" "C5'" "O5'" 109.470 3.000
PUY "H5''" "C5'" "O5'" 109.470 3.000
PUY "C5'" "O5'" "H5'" 109.470 3.000
PUY "C3'" "C2'" "H2'" 108.340 3.000
PUY "C3'" "C2'" "O2'" 109.470 3.000
PUY "C3'" "C2'" "C1'" 111.000 3.000
PUY "H2'" "C2'" "O2'" 109.470 3.000
PUY "H2'" "C2'" "C1'" 108.340 3.000
PUY "O2'" "C2'" "C1'" 109.470 3.000
PUY "C2'" "O2'" H1 109.470 3.000
PUY "C2'" "C1'" "H1'" 108.340 3.000
PUY "C2'" "C1'" "O4'" 109.470 3.000
PUY "C2'" "C1'" N9 109.470 3.000
PUY "H1'" "C1'" "O4'" 109.470 3.000
PUY "H1'" "C1'" N9 109.470 3.000
PUY "O4'" "C1'" N9 109.470 3.000
PUY "C1'" "O4'" "C4'" 111.800 3.000
PUY "C1'" N9 C8 126.000 3.000
PUY "C1'" N9 C4 126.000 3.000
PUY C8 N9 C4 108.000 3.000
PUY N9 C8 H8 126.000 3.000
PUY N9 C8 N7 108.000 3.000
PUY H8 C8 N7 126.000 3.000
PUY C8 N7 C5 108.000 3.000
PUY N7 C5 C4 108.000 3.000
PUY N7 C5 C6 132.000 3.000
PUY C4 C5 C6 120.000 3.000
PUY C5 C4 N9 108.000 3.000
PUY C5 C4 N3 120.000 3.000
PUY N9 C4 N3 132.000 3.000
PUY C5 C6 N6 120.000 3.000
PUY C5 C6 N1 120.000 3.000
PUY N6 C6 N1 120.000 3.000
PUY C6 N6 C10 109.500 3.000
PUY C6 N6 C9 109.500 3.000
PUY C10 N6 C9 109.470 3.000
PUY N6 C10 H103 109.470 3.000
PUY N6 C10 H102 109.470 3.000
PUY N6 C10 H101 109.470 3.000
PUY H103 C10 H102 109.470 3.000
PUY H103 C10 H101 109.470 3.000
PUY H102 C10 H101 109.470 3.000
PUY N6 C9 H93 109.470 3.000
PUY N6 C9 H92 109.470 3.000
PUY N6 C9 H91 109.470 3.000
PUY H93 C9 H92 109.470 3.000
PUY H93 C9 H91 109.470 3.000
PUY H92 C9 H91 109.470 3.000
PUY C6 N1 C2 120.000 3.000
PUY N1 C2 H2 120.000 3.000
PUY N1 C2 N3 120.000 3.000
PUY H2 C2 N3 120.000 3.000
PUY C2 N3 C4 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
PUY var_1 O C CA N -19.996 20.000 3
PUY var_2 C CA CB CG 175.027 20.000 3
PUY var_3 CA CB CG CD2 -89.972 20.000 2
PUY CONST_1 CB CG CD1 CE1 180.000 0.000 0
PUY CONST_2 CB CG CD2 CE2 180.000 0.000 0
PUY CONST_3 CG CD2 CE2 CZ 0.000 0.000 0
PUY CONST_4 CD2 CE2 CZ CE1 0.000 0.000 0
PUY var_4 CE2 CZ OM CMZ -0.272 20.000 1
PUY var_5 CZ OM CMZ HMZ1 179.985 20.000 1
PUY CONST_5 CE2 CZ CE1 CD1 0.000 0.000 0
PUY CONST_6 CZ CE1 CD1 CG 0.000 0.000 0
PUY var_6 C CA N HN1 60.002 20.000 1
PUY CONST_7 O C "N3'" "C3'" 0.000 0.000 0
PUY var_7 C "N3'" "C3'" "C2'" 156.906 20.000 3
PUY var_8 "N3'" "C3'" "C4'" "C5'" 90.000 20.000 3
PUY var_9 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
PUY var_10 "C3'" "C4'" "C5'" "O5'" -178.135 20.000 3
PUY var_11 "C4'" "C5'" "O5'" "H5'" 179.984 20.000 1
PUY var_12 "N3'" "C3'" "C2'" "C1'" 120.000 20.000 3
PUY var_13 "C3'" "C2'" "O2'" H1 179.965 20.000 1
PUY var_14 "C3'" "C2'" "C1'" N9 150.000 20.000 3
PUY var_15 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
PUY var_16 "C2'" "C1'" N9 C8 -95.014 20.000 1
PUY CONST_8 "C1'" N9 C4 C5 180.000 0.000 0
PUY CONST_9 "C1'" N9 C8 N7 180.000 0.000 0
PUY CONST_10 N9 C8 N7 C5 0.000 0.000 0
PUY CONST_11 C8 N7 C5 C6 180.000 0.000 0
PUY CONST_12 N7 C5 C4 N9 0.000 0.000 0
PUY CONST_13 C5 C4 N3 C2 0.000 0.000 0
PUY CONST_14 N7 C5 C6 N1 180.000 0.000 0
PUY var_17 C5 C6 N6 C9 179.992 20.000 1
PUY var_18 C6 N6 C10 H101 59.982 20.000 1
PUY var_19 C6 N6 C9 H91 -179.987 20.000 1
PUY CONST_15 C5 C6 N1 C2 0.000 0.000 0
PUY CONST_16 C6 N1 C2 N3 0.000 0.000 0
PUY CONST_17 N1 C2 N3 C4 0.000 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
PUY chir_01 CA N CB C negativ
PUY chir_02 "C4'" "C5'" "O4'" "C3'" negativ
PUY chir_03 "C1'" "O4'" N9 "C2'" negativ
PUY chir_04 N6 C6 C9 C10 negativ
PUY chir_05 "C2'" "C1'" "O2'" "C3'" positiv
PUY chir_06 "C3'" "C4'" "C2'" "N3'" 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
PUY plan-1 N 0.020
PUY plan-1 CA 0.020
PUY plan-1 HN1 0.020
PUY plan-1 HN2 0.020
PUY plan-2 CG 0.020
PUY plan-2 CB 0.020
PUY plan-2 CD1 0.020
PUY plan-2 CD2 0.020
PUY plan-2 CE1 0.020
PUY plan-2 CE2 0.020
PUY plan-2 CZ 0.020
PUY plan-2 HD1 0.020
PUY plan-2 HD2 0.020
PUY plan-2 HE1 0.020
PUY plan-2 HE2 0.020
PUY plan-2 OM 0.020
PUY plan-3 C 0.020
PUY plan-3 CA 0.020
PUY plan-3 O 0.020
PUY plan-3 "N3'" 0.020
PUY plan-3 H3 0.020
PUY plan-4 N9 0.020
PUY plan-4 "C1'" 0.020
PUY plan-4 C4 0.020
PUY plan-4 C8 0.020
PUY plan-4 N7 0.020
PUY plan-4 N3 0.020
PUY plan-4 C5 0.020
PUY plan-4 C2 0.020
PUY plan-4 N1 0.020
PUY plan-4 C6 0.020
PUY plan-4 H2 0.020
PUY plan-4 N6 0.020
PUY plan-4 H8 0.020
PUY plan-5 "N3'" 0.020
PUY plan-5 C 0.020
PUY plan-5 "C3'" 0.020
PUY plan-5 H3 0.020
# ------------------------------------------------------
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