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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
GDR GDR 'GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE ' non-polymer 61 38 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GDR
#
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
GDR O6 O O 0.000 0.000 0.000 0.000
GDR C6 C CR6 0.000 -0.728 -0.481 0.851
GDR N1 N NR16 0.000 -0.222 -1.249 1.840
GDR HN1 H H 0.000 0.801 -1.435 1.880
GDR C2 C CR6 0.000 -1.045 -1.782 2.787
GDR N2 N NH2 0.000 -0.503 -2.560 3.780
GDR HN22 H H 0.000 0.495 -2.733 3.807
GDR HN21 H H 0.000 -1.097 -2.966 4.494
GDR N3 N NRD6 0.000 -2.343 -1.574 2.776
GDR C5 C CR56 0.000 -2.123 -0.248 0.828
GDR C4 C CR56 0.000 -2.914 -0.818 1.832
GDR N7 N NRD5 0.000 -2.950 0.450 0.011
GDR C8 C CR15 0.000 -4.173 0.340 0.442
GDR H8 H H 0.000 -5.039 0.797 -0.020
GDR N9 N NR5 0.000 -4.200 -0.439 1.563
GDR C1D C CH1 0.000 -5.389 -0.794 2.340
GDR "H1'" H H 0.000 -5.251 -1.766 2.834
GDR O4D O O2 0.000 -6.560 -0.817 1.496
GDR C2D C CH1 0.000 -5.715 0.305 3.381
GDR "H2'" H H 0.000 -5.517 1.305 2.970
GDR O2D O OH1 0.000 -4.983 0.097 4.591
GDR HO2A H H 0.000 -5.202 0.794 5.224
GDR C3D C CH1 0.000 -7.234 0.094 3.613
GDR "H3'" H H 0.000 -7.749 1.062 3.689
GDR O3D O OH1 0.000 -7.458 -0.684 4.791
GDR HO3A H H 0.000 -7.104 -0.214 5.558
GDR C4D C CH1 0.000 -7.702 -0.667 2.357
GDR "H4'" H H 0.000 -8.088 -1.656 2.642
GDR C5D C CH2 0.000 -8.793 0.130 1.641
GDR "H5'" H H 0.000 -8.399 1.106 1.351
GDR "H5''" H H 0.000 -9.643 0.267 2.312
GDR O5D O O2 0.000 -9.214 -0.581 0.475
GDR PA P P 0.000 -10.357 0.310 -0.225
GDR O1A O OP -0.500 -9.797 1.634 -0.589
GDR O2A O OP -0.500 -11.487 0.494 0.717
GDR O3A O O2 0.000 -10.880 -0.433 -1.553
GDR PB P P 0.000 -12.015 0.507 -2.199
GDR O1B O OP -0.500 -11.429 1.828 -2.532
GDR O2B O OP -0.500 -13.119 0.688 -1.226
GDR O3B O O2 0.000 -12.585 -0.180 -3.538
GDR "C1'" C CH1 0.000 -13.583 0.699 -4.061
GDR "HC1'" H H 0.000 -14.055 1.249 -3.235
GDR "O5'" O O2 0.000 -12.975 1.624 -4.959
GDR "C5'" C CH1 0.000 -12.226 0.872 -5.911
GDR "HC5'" H H 0.000 -11.551 0.183 -5.384
GDR "C6'" C CH3 0.000 -11.402 1.826 -6.779
GDR HC63 H H 0.000 -10.842 1.268 -7.485
GDR HC62 H H 0.000 -12.051 2.490 -7.290
GDR HC61 H H 0.000 -10.741 2.382 -6.165
GDR "C4'" C CH1 0.000 -13.176 0.069 -6.801
GDR "HC4'" H H 0.000 -13.869 0.753 -7.312
GDR "O4'" O OH1 0.000 -12.423 -0.661 -7.770
GDR "HO4'" H H 0.000 -11.922 -0.044 -8.320
GDR "C3'" C CH1 0.000 -13.971 -0.908 -5.927
GDR "HC3'" H H 0.000 -13.291 -1.658 -5.498
GDR "O3'" O OH1 0.000 -14.967 -1.561 -6.717
GDR "HO3'" H H 0.000 -15.474 -2.167 -6.159
GDR "C2'" C CH1 0.000 -14.644 -0.120 -4.799
GDR "HC2'" H H 0.000 -15.124 -0.817 -4.098
GDR "O2'" O OH1 0.000 -15.629 0.758 -5.349
GDR "HO2'" H H 0.000 -16.047 1.258 -4.635
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
GDR O6 n/a C6 START
GDR C6 O6 C5 .
GDR N1 C6 C2 .
GDR HN1 N1 . .
GDR C2 N1 N3 .
GDR N2 C2 HN21 .
GDR HN22 N2 . .
GDR HN21 N2 . .
GDR N3 C2 . .
GDR C5 C6 N7 .
GDR C4 C5 . .
GDR N7 C5 C8 .
GDR C8 N7 N9 .
GDR H8 C8 . .
GDR N9 C8 C1D .
GDR C1D N9 C2D .
GDR "H1'" C1D . .
GDR O4D C1D . .
GDR C2D C1D C3D .
GDR "H2'" C2D . .
GDR O2D C2D HO2A .
GDR HO2A O2D . .
GDR C3D C2D C4D .
GDR "H3'" C3D . .
GDR O3D C3D HO3A .
GDR HO3A O3D . .
GDR C4D C3D C5D .
GDR "H4'" C4D . .
GDR C5D C4D O5D .
GDR "H5'" C5D . .
GDR "H5''" C5D . .
GDR O5D C5D PA .
GDR PA O5D O3A .
GDR O1A PA . .
GDR O2A PA . .
GDR O3A PA PB .
GDR PB O3A O3B .
GDR O1B PB . .
GDR O2B PB . .
GDR O3B PB "C1'" .
GDR "C1'" O3B "O5'" .
GDR "HC1'" "C1'" . .
GDR "O5'" "C1'" "C5'" .
GDR "C5'" "O5'" "C4'" .
GDR "HC5'" "C5'" . .
GDR "C6'" "C5'" HC61 .
GDR HC63 "C6'" . .
GDR HC62 "C6'" . .
GDR HC61 "C6'" . .
GDR "C4'" "C5'" "C3'" .
GDR "HC4'" "C4'" . .
GDR "O4'" "C4'" "HO4'" .
GDR "HO4'" "O4'" . .
GDR "C3'" "C4'" "C2'" .
GDR "HC3'" "C3'" . .
GDR "O3'" "C3'" "HO3'" .
GDR "HO3'" "O3'" . .
GDR "C2'" "C3'" "O2'" .
GDR "HC2'" "C2'" . .
GDR "O2'" "C2'" "HO2'" .
GDR "HO2'" "O2'" . END
GDR C4D O4D . ADD
GDR N9 C4 . ADD
GDR C4 N3 . ADD
GDR "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
GDR PB O3A single 1.610 0.020
GDR O1B PB deloc 1.510 0.020
GDR O2B PB deloc 1.510 0.020
GDR O3B PB single 1.610 0.020
GDR O3A PA single 1.610 0.020
GDR "C1'" O3B single 1.426 0.020
GDR O1A PA deloc 1.510 0.020
GDR O2A PA deloc 1.510 0.020
GDR PA O5D single 1.610 0.020
GDR O5D C5D single 1.426 0.020
GDR C5D C4D single 1.524 0.020
GDR "H5'" C5D single 1.092 0.020
GDR "H5''" C5D single 1.092 0.020
GDR C4D O4D single 1.426 0.020
GDR C4D C3D single 1.524 0.020
GDR "H4'" C4D single 1.099 0.020
GDR O4D C1D single 1.426 0.020
GDR C1D N9 single 1.485 0.020
GDR C2D C1D single 1.524 0.020
GDR "H1'" C1D single 1.099 0.020
GDR N9 C4 single 1.337 0.020
GDR N9 C8 single 1.337 0.020
GDR C4 N3 single 1.355 0.020
GDR C4 C5 double 1.490 0.020
GDR N3 C2 double 1.350 0.020
GDR N2 C2 single 1.355 0.020
GDR C2 N1 single 1.337 0.020
GDR HN21 N2 single 1.010 0.020
GDR HN22 N2 single 1.010 0.020
GDR N1 C6 single 1.337 0.020
GDR HN1 N1 single 1.040 0.020
GDR C6 O6 double 1.250 0.020
GDR C5 C6 single 1.490 0.020
GDR N7 C5 single 1.350 0.020
GDR C8 N7 double 1.350 0.020
GDR H8 C8 single 1.083 0.020
GDR O2D C2D single 1.432 0.020
GDR C3D C2D single 1.524 0.020
GDR "H2'" C2D single 1.099 0.020
GDR HO2A O2D single 0.967 0.020
GDR O3D C3D single 1.432 0.020
GDR "H3'" C3D single 1.099 0.020
GDR HO3A O3D single 0.967 0.020
GDR "C1'" "C2'" single 1.524 0.020
GDR "O5'" "C1'" single 1.426 0.020
GDR "HC1'" "C1'" single 1.099 0.020
GDR "O2'" "C2'" single 1.432 0.020
GDR "C2'" "C3'" single 1.524 0.020
GDR "HC2'" "C2'" single 1.099 0.020
GDR "HO2'" "O2'" single 0.967 0.020
GDR "O3'" "C3'" single 1.432 0.020
GDR "C3'" "C4'" single 1.524 0.020
GDR "HC3'" "C3'" single 1.099 0.020
GDR "HO3'" "O3'" single 0.967 0.020
GDR "O4'" "C4'" single 1.432 0.020
GDR "C4'" "C5'" single 1.524 0.020
GDR "HC4'" "C4'" single 1.099 0.020
GDR "HO4'" "O4'" single 0.967 0.020
GDR "C5'" "O5'" single 1.426 0.020
GDR "C6'" "C5'" single 1.524 0.020
GDR "HC5'" "C5'" single 1.099 0.020
GDR HC61 "C6'" single 1.059 0.020
GDR HC62 "C6'" single 1.059 0.020
GDR HC63 "C6'" 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
GDR O6 C6 N1 120.000 3.000
GDR O6 C6 C5 120.000 3.000
GDR N1 C6 C5 120.000 3.000
GDR C6 N1 HN1 120.000 3.000
GDR C6 N1 C2 120.000 3.000
GDR HN1 N1 C2 120.000 3.000
GDR N1 C2 N2 120.000 3.000
GDR N1 C2 N3 120.000 3.000
GDR N2 C2 N3 120.000 3.000
GDR C2 N2 HN22 120.000 3.000
GDR C2 N2 HN21 120.000 3.000
GDR HN22 N2 HN21 120.000 3.000
GDR C2 N3 C4 120.000 3.000
GDR C6 C5 C4 120.000 3.000
GDR C6 C5 N7 132.000 3.000
GDR C4 C5 N7 108.000 3.000
GDR C5 C4 N9 108.000 3.000
GDR C5 C4 N3 120.000 3.000
GDR N9 C4 N3 132.000 3.000
GDR C5 N7 C8 108.000 3.000
GDR N7 C8 H8 126.000 3.000
GDR N7 C8 N9 108.000 3.000
GDR H8 C8 N9 126.000 3.000
GDR C8 N9 C1D 126.000 3.000
GDR C8 N9 C4 108.000 3.000
GDR C1D N9 C4 126.000 3.000
GDR N9 C1D "H1'" 109.470 3.000
GDR N9 C1D O4D 109.470 3.000
GDR N9 C1D C2D 109.470 3.000
GDR "H1'" C1D O4D 109.470 3.000
GDR "H1'" C1D C2D 108.340 3.000
GDR O4D C1D C2D 109.470 3.000
GDR C1D O4D C4D 111.800 3.000
GDR C1D C2D "H2'" 108.340 3.000
GDR C1D C2D O2D 109.470 3.000
GDR C1D C2D C3D 111.000 3.000
GDR "H2'" C2D O2D 109.470 3.000
GDR "H2'" C2D C3D 108.340 3.000
GDR O2D C2D C3D 109.470 3.000
GDR C2D O2D HO2A 109.470 3.000
GDR C2D C3D "H3'" 108.340 3.000
GDR C2D C3D O3D 109.470 3.000
GDR C2D C3D C4D 111.000 3.000
GDR "H3'" C3D O3D 109.470 3.000
GDR "H3'" C3D C4D 108.340 3.000
GDR O3D C3D C4D 109.470 3.000
GDR C3D O3D HO3A 109.470 3.000
GDR C3D C4D "H4'" 108.340 3.000
GDR C3D C4D C5D 111.000 3.000
GDR C3D C4D O4D 109.470 3.000
GDR "H4'" C4D C5D 108.340 3.000
GDR "H4'" C4D O4D 109.470 3.000
GDR C5D C4D O4D 109.470 3.000
GDR C4D C5D "H5'" 109.470 3.000
GDR C4D C5D "H5''" 109.470 3.000
GDR C4D C5D O5D 109.470 3.000
GDR "H5'" C5D "H5''" 107.900 3.000
GDR "H5'" C5D O5D 109.470 3.000
GDR "H5''" C5D O5D 109.470 3.000
GDR C5D O5D PA 120.500 3.000
GDR O5D PA O1A 108.200 3.000
GDR O5D PA O2A 108.200 3.000
GDR O5D PA O3A 102.600 3.000
GDR O1A PA O2A 119.900 3.000
GDR O1A PA O3A 108.200 3.000
GDR O2A PA O3A 108.200 3.000
GDR PA O3A PB 120.500 3.000
GDR O3A PB O1B 108.200 3.000
GDR O3A PB O2B 108.200 3.000
GDR O3A PB O3B 102.600 3.000
GDR O1B PB O2B 119.900 3.000
GDR O1B PB O3B 108.200 3.000
GDR O2B PB O3B 108.200 3.000
GDR PB O3B "C1'" 120.500 3.000
GDR O3B "C1'" "HC1'" 109.470 3.000
GDR O3B "C1'" "O5'" 109.470 3.000
GDR O3B "C1'" "C2'" 109.470 3.000
GDR "HC1'" "C1'" "O5'" 109.470 3.000
GDR "HC1'" "C1'" "C2'" 108.340 3.000
GDR "O5'" "C1'" "C2'" 109.470 3.000
GDR "C1'" "O5'" "C5'" 111.800 3.000
GDR "O5'" "C5'" "HC5'" 109.470 3.000
GDR "O5'" "C5'" "C6'" 109.470 3.000
GDR "O5'" "C5'" "C4'" 109.470 3.000
GDR "HC5'" "C5'" "C6'" 108.340 3.000
GDR "HC5'" "C5'" "C4'" 108.340 3.000
GDR "C6'" "C5'" "C4'" 111.000 3.000
GDR "C5'" "C6'" HC63 109.470 3.000
GDR "C5'" "C6'" HC62 109.470 3.000
GDR "C5'" "C6'" HC61 109.470 3.000
GDR HC63 "C6'" HC62 109.470 3.000
GDR HC63 "C6'" HC61 109.470 3.000
GDR HC62 "C6'" HC61 109.470 3.000
GDR "C5'" "C4'" "HC4'" 108.340 3.000
GDR "C5'" "C4'" "O4'" 109.470 3.000
GDR "C5'" "C4'" "C3'" 111.000 3.000
GDR "HC4'" "C4'" "O4'" 109.470 3.000
GDR "HC4'" "C4'" "C3'" 108.340 3.000
GDR "O4'" "C4'" "C3'" 109.470 3.000
GDR "C4'" "O4'" "HO4'" 109.470 3.000
GDR "C4'" "C3'" "HC3'" 108.340 3.000
GDR "C4'" "C3'" "O3'" 109.470 3.000
GDR "C4'" "C3'" "C2'" 111.000 3.000
GDR "HC3'" "C3'" "O3'" 109.470 3.000
GDR "HC3'" "C3'" "C2'" 108.340 3.000
GDR "O3'" "C3'" "C2'" 109.470 3.000
GDR "C3'" "O3'" "HO3'" 109.470 3.000
GDR "C3'" "C2'" "HC2'" 108.340 3.000
GDR "C3'" "C2'" "O2'" 109.470 3.000
GDR "C3'" "C2'" "C1'" 111.000 3.000
GDR "HC2'" "C2'" "O2'" 109.470 3.000
GDR "HC2'" "C2'" "C1'" 108.340 3.000
GDR "O2'" "C2'" "C1'" 109.470 3.000
GDR "C2'" "O2'" "HO2'" 109.470 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
GDR CONST_1 O6 C6 N1 C2 180.000 0.000 0
GDR CONST_2 C6 N1 C2 N3 0.000 0.000 0
GDR CONST_3 N1 C2 N2 HN21 -179.974 0.000 0
GDR CONST_4 N1 C2 N3 C4 0.000 0.000 0
GDR CONST_5 O6 C6 C5 N7 0.000 0.000 0
GDR CONST_6 C6 C5 C4 N9 180.000 0.000 0
GDR CONST_7 C5 C4 N3 C2 0.000 0.000 0
GDR CONST_8 C6 C5 N7 C8 180.000 0.000 0
GDR CONST_9 C5 N7 C8 N9 0.000 0.000 0
GDR CONST_10 N7 C8 N9 C1D 180.000 0.000 0
GDR CONST_11 C8 N9 C4 C5 0.000 0.000 0
GDR var_1 C8 N9 C1D C2D -85.603 20.000 1
GDR var_2 N9 C1D O4D C4D -150.000 20.000 1
GDR var_3 N9 C1D C2D C3D 150.000 20.000 3
GDR var_4 C1D C2D O2D HO2A 179.956 20.000 1
GDR var_5 C1D C2D C3D C4D -30.000 20.000 3
GDR var_6 C2D C3D O3D HO3A 61.446 20.000 1
GDR var_7 C2D C3D C4D C5D -120.000 20.000 3
GDR var_8 C3D C4D O4D C1D 30.000 20.000 1
GDR var_9 C3D C4D C5D O5D 179.717 20.000 3
GDR var_10 C4D C5D O5D PA 179.981 20.000 1
GDR var_11 C5D O5D PA O3A 179.958 20.000 1
GDR var_12 O5D PA O3A PB 179.991 20.000 1
GDR var_13 PA O3A PB O3B -179.988 20.000 1
GDR var_14 O3A PB O3B "C1'" -179.994 20.000 1
GDR var_15 PB O3B "C1'" "O5'" 89.990 20.000 1
GDR var_16 O3B "C1'" "C2'" "C3'" -60.000 20.000 3
GDR var_17 O3B "C1'" "O5'" "C5'" 60.000 20.000 1
GDR var_18 "C1'" "O5'" "C5'" "C4'" 60.000 20.000 1
GDR var_19 "O5'" "C5'" "C6'" HC61 59.822 20.000 3
GDR var_20 "O5'" "C5'" "C4'" "C3'" -60.000 20.000 3
GDR var_21 "C5'" "C4'" "O4'" "HO4'" -60.539 20.000 1
GDR var_22 "C5'" "C4'" "C3'" "C2'" 60.000 20.000 3
GDR var_23 "C4'" "C3'" "O3'" "HO3'" -179.237 20.000 1
GDR var_24 "C4'" "C3'" "C2'" "O2'" 60.000 20.000 3
GDR var_25 "C3'" "C2'" "O2'" "HO2'" -179.611 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
GDR chir_01 C4D C5D O4D C3D negativ
GDR chir_02 C1D O4D N9 C2D negativ
GDR chir_03 C2D C1D O2D C3D positiv
GDR chir_04 C3D C4D C2D O3D positiv
GDR chir_05 "C1'" O3B "C2'" "O5'" positiv
GDR chir_06 "C2'" "C1'" "O2'" "C3'" negativ
GDR chir_07 "C3'" "C2'" "O3'" "C4'" negativ
GDR chir_08 "C4'" "C3'" "O4'" "C5'" positiv
GDR chir_09 "C5'" "C4'" "O5'" "C6'" 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
GDR plan-1 N9 0.020
GDR plan-1 C1D 0.020
GDR plan-1 C4 0.020
GDR plan-1 C8 0.020
GDR plan-1 N7 0.020
GDR plan-1 N3 0.020
GDR plan-1 C5 0.020
GDR plan-1 C2 0.020
GDR plan-1 N1 0.020
GDR plan-1 C6 0.020
GDR plan-1 N2 0.020
GDR plan-1 HN1 0.020
GDR plan-1 O6 0.020
GDR plan-1 H8 0.020
GDR plan-1 HN22 0.020
GDR plan-1 HN21 0.020
GDR plan-2 N2 0.020
GDR plan-2 C2 0.020
GDR plan-2 HN21 0.020
GDR plan-2 HN22 0.020
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