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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
RBY RBY 'METHYLENE ADP-BETA-XYLOSE ' non-polymer 61 36 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_RBY
#
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
RBY O2A O O 0.000 0.000 0.000 0.000
RBY PA P P 0.000 -0.991 1.086 0.168
RBY O1A O OH1 0.000 -0.340 2.484 -0.294
RBY HO1A H H 0.000 -0.859 3.299 -0.247
RBY CX C CH2 0.000 -2.458 0.733 -0.854
RBY HX1 H H 0.000 -3.190 1.534 -0.728
RBY HX2 H H 0.000 -2.900 -0.215 -0.539
RBY PB P P 0.000 -1.968 0.625 -2.606
RBY OR5 O O2 0.000 -3.263 0.312 -3.509
RBY CR5 C CH2 0.000 -3.192 0.066 -4.914
RBY HR51 H H 0.000 -2.562 -0.807 -5.099
RBY HR52 H H 0.000 -2.762 0.936 -5.415
RBY CR4 C CH1 0.000 -4.598 -0.194 -5.459
RBY HR4 H H 0.000 -5.094 -0.984 -4.876
RBY CR3 C CH1 0.000 -4.533 -0.586 -6.951
RBY HR3 H H 0.000 -4.588 -1.678 -7.066
RBY OR3 O OH1 0.000 -3.339 -0.080 -7.551
RBY HOR3 H H 0.000 -3.314 -0.334 -8.483
RBY CR2 C CH1 0.000 -5.778 0.088 -7.571
RBY HR2 H H 0.000 -5.480 0.813 -8.341
RBY OR2 O OH1 0.000 -6.657 -0.895 -8.122
RBY HOR2 H H 0.000 -7.429 -0.458 -8.505
RBY CR1 C CH1 0.000 -6.448 0.807 -6.380
RBY HR1 H H 0.000 -7.231 0.173 -5.940
RBY OR1 O OH1 0.000 -6.997 2.057 -6.800
RBY HOR1 H H 0.000 -7.368 2.519 -6.036
RBY OR4 O O2 0.000 -5.381 1.019 -5.430
RBY O2B O OH1 0.000 -1.316 2.023 -3.068
RBY HO2B H H 0.000 -1.835 2.837 -3.021
RBY O1B O O 0.000 -0.976 -0.462 -2.774
RBY "O5'" O O2 0.000 -1.425 1.183 1.715
RBY "C5'" C CH2 0.000 -0.485 1.347 2.778
RBY "H5'1" H H 0.000 0.070 2.276 2.632
RBY "H5'2" H H 0.000 0.211 0.506 2.781
RBY "C4'" C CH1 0.000 -1.229 1.400 4.114
RBY "H4'" H H 0.000 -1.998 2.184 4.083
RBY "C3'" C CH1 0.000 -0.235 1.684 5.257
RBY "H3'" H H 0.000 0.792 1.737 4.870
RBY "O3'" O OH1 0.000 -0.580 2.897 5.929
RBY "HO3'" H H 0.000 0.016 3.030 6.679
RBY "C2'" C CH1 0.000 -0.393 0.473 6.208
RBY "H2'" H H 0.000 0.385 -0.279 6.018
RBY "O2'" O OH1 0.000 -0.374 0.891 7.574
RBY "HO2'" H H 0.000 0.476 1.308 7.771
RBY "C1'" C CH1 0.000 -1.793 -0.067 5.814
RBY "H1'" H H 0.000 -2.585 0.512 6.310
RBY "O4'" O O2 0.000 -1.839 0.127 4.385
RBY N9 N NR5 0.000 -1.909 -1.489 6.147
RBY C4 C CR56 0.000 -2.265 -2.013 7.364
RBY C5 C CR56 0.000 -2.243 -3.409 7.206
RBY N7 N NRD5 0.000 -1.872 -3.660 5.928
RBY C8 C CR15 0.000 -1.676 -2.536 5.304
RBY H8 H H 0.000 -1.372 -2.444 4.269
RBY N3 N NRD6 0.000 -2.608 -1.501 8.541
RBY C2 C CR16 0.000 -2.914 -2.287 9.552
RBY H2 H H 0.000 -3.184 -1.837 10.499
RBY N1 N NRD6 0.000 -2.902 -3.604 9.454
RBY C6 C CR6 0.000 -2.577 -4.207 8.314
RBY N6 N NH2 0.000 -2.567 -5.587 8.221
RBY HN62 H H 0.000 -2.809 -6.159 9.024
RBY HN61 H H 0.000 -2.317 -6.043 7.349
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
RBY O2A n/a PA START
RBY PA O2A "O5'" .
RBY O1A PA HO1A .
RBY HO1A O1A . .
RBY CX PA PB .
RBY HX1 CX . .
RBY HX2 CX . .
RBY PB CX O1B .
RBY OR5 PB CR5 .
RBY CR5 OR5 CR4 .
RBY HR51 CR5 . .
RBY HR52 CR5 . .
RBY CR4 CR5 CR3 .
RBY HR4 CR4 . .
RBY CR3 CR4 CR2 .
RBY HR3 CR3 . .
RBY OR3 CR3 HOR3 .
RBY HOR3 OR3 . .
RBY CR2 CR3 CR1 .
RBY HR2 CR2 . .
RBY OR2 CR2 HOR2 .
RBY HOR2 OR2 . .
RBY CR1 CR2 OR4 .
RBY HR1 CR1 . .
RBY OR1 CR1 HOR1 .
RBY HOR1 OR1 . .
RBY OR4 CR1 . .
RBY O2B PB HO2B .
RBY HO2B O2B . .
RBY O1B PB . .
RBY "O5'" PA "C5'" .
RBY "C5'" "O5'" "C4'" .
RBY "H5'1" "C5'" . .
RBY "H5'2" "C5'" . .
RBY "C4'" "C5'" "C3'" .
RBY "H4'" "C4'" . .
RBY "C3'" "C4'" "C2'" .
RBY "H3'" "C3'" . .
RBY "O3'" "C3'" "HO3'" .
RBY "HO3'" "O3'" . .
RBY "C2'" "C3'" "C1'" .
RBY "H2'" "C2'" . .
RBY "O2'" "C2'" "HO2'" .
RBY "HO2'" "O2'" . .
RBY "C1'" "C2'" N9 .
RBY "H1'" "C1'" . .
RBY "O4'" "C1'" . .
RBY N9 "C1'" C4 .
RBY C4 N9 N3 .
RBY C5 C4 N7 .
RBY N7 C5 C8 .
RBY C8 N7 H8 .
RBY H8 C8 . .
RBY N3 C4 C2 .
RBY C2 N3 N1 .
RBY H2 C2 . .
RBY N1 C2 C6 .
RBY C6 N1 N6 .
RBY N6 C6 HN61 .
RBY HN62 N6 . .
RBY HN61 N6 . END
RBY "C4'" "O4'" . ADD
RBY N9 C8 . ADD
RBY C5 C6 . ADD
RBY CR4 OR4 . 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
RBY "O3'" "C3'" single 1.432 0.020
RBY "C2'" "C3'" single 1.524 0.020
RBY "C3'" "C4'" single 1.524 0.020
RBY "O2'" "C2'" single 1.432 0.020
RBY "C4'" "C5'" single 1.524 0.020
RBY "C5'" "O5'" single 1.426 0.020
RBY "C1'" "C2'" single 1.524 0.020
RBY "C4'" "O4'" single 1.426 0.020
RBY "O5'" PA single 1.610 0.020
RBY PA O2A double 1.480 0.020
RBY "O4'" "C1'" single 1.426 0.020
RBY N9 "C1'" single 1.485 0.020
RBY CX PA single 1.812 0.020
RBY O1A PA single 1.610 0.020
RBY C4 N9 single 1.337 0.020
RBY N9 C8 single 1.337 0.020
RBY N3 C4 double 1.355 0.020
RBY C2 N3 single 1.337 0.020
RBY O1B PB double 1.480 0.020
RBY O2B PB single 1.610 0.020
RBY C5 C4 single 1.490 0.020
RBY PB CX single 1.812 0.020
RBY C8 N7 double 1.350 0.020
RBY N1 C2 double 1.337 0.020
RBY OR5 PB single 1.610 0.020
RBY N7 C5 single 1.350 0.020
RBY C5 C6 double 1.490 0.020
RBY C6 N1 single 1.350 0.020
RBY N6 C6 single 1.355 0.020
RBY CR5 OR5 single 1.426 0.020
RBY CR4 CR5 single 1.524 0.020
RBY OR3 CR3 single 1.432 0.020
RBY CR3 CR4 single 1.524 0.020
RBY CR4 OR4 single 1.426 0.020
RBY CR2 CR3 single 1.524 0.020
RBY OR4 CR1 single 1.426 0.020
RBY CR1 CR2 single 1.524 0.020
RBY OR2 CR2 single 1.432 0.020
RBY OR1 CR1 single 1.432 0.020
RBY "H5'1" "C5'" single 1.092 0.020
RBY "H5'2" "C5'" single 1.092 0.020
RBY "H4'" "C4'" single 1.099 0.020
RBY "H3'" "C3'" single 1.099 0.020
RBY "HO3'" "O3'" single 0.967 0.020
RBY "H2'" "C2'" single 1.099 0.020
RBY "HO2'" "O2'" single 0.967 0.020
RBY "H1'" "C1'" single 1.099 0.020
RBY H8 C8 single 1.083 0.020
RBY HN61 N6 single 1.010 0.020
RBY HN62 N6 single 1.010 0.020
RBY H2 C2 single 1.083 0.020
RBY HX1 CX single 1.092 0.020
RBY HX2 CX single 1.092 0.020
RBY HR51 CR5 single 1.092 0.020
RBY HR52 CR5 single 1.092 0.020
RBY HOR3 OR3 single 0.967 0.020
RBY HR2 CR2 single 1.099 0.020
RBY HOR2 OR2 single 0.967 0.020
RBY HR1 CR1 single 1.099 0.020
RBY HOR1 OR1 single 0.967 0.020
RBY HO2B O2B single 0.967 0.020
RBY HO1A O1A single 0.967 0.020
RBY HR3 CR3 single 1.099 0.020
RBY HR4 CR4 single 1.099 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
RBY O2A PA O1A 109.500 3.000
RBY O2A PA CX 109.500 3.000
RBY O2A PA "O5'" 109.500 3.000
RBY O1A PA CX 109.500 3.000
RBY O1A PA "O5'" 109.500 3.000
RBY CX PA "O5'" 109.500 3.000
RBY PA O1A HO1A 120.000 3.000
RBY PA CX HX1 109.500 3.000
RBY PA CX HX2 109.500 3.000
RBY PA CX PB 109.500 3.000
RBY HX1 CX HX2 107.900 3.000
RBY HX1 CX PB 109.500 3.000
RBY HX2 CX PB 109.500 3.000
RBY CX PB OR5 109.500 3.000
RBY CX PB O2B 109.500 3.000
RBY CX PB O1B 109.500 3.000
RBY OR5 PB O2B 109.500 3.000
RBY OR5 PB O1B 109.500 3.000
RBY O2B PB O1B 109.500 3.000
RBY PB OR5 CR5 120.500 3.000
RBY OR5 CR5 HR51 109.470 3.000
RBY OR5 CR5 HR52 109.470 3.000
RBY OR5 CR5 CR4 109.470 3.000
RBY HR51 CR5 HR52 107.900 3.000
RBY HR51 CR5 CR4 109.470 3.000
RBY HR52 CR5 CR4 109.470 3.000
RBY CR5 CR4 HR4 108.340 3.000
RBY CR5 CR4 CR3 111.000 3.000
RBY CR5 CR4 OR4 109.470 3.000
RBY HR4 CR4 CR3 108.340 3.000
RBY HR4 CR4 OR4 109.470 3.000
RBY CR3 CR4 OR4 109.470 3.000
RBY CR4 CR3 HR3 108.340 3.000
RBY CR4 CR3 OR3 109.470 3.000
RBY CR4 CR3 CR2 111.000 3.000
RBY HR3 CR3 OR3 109.470 3.000
RBY HR3 CR3 CR2 108.340 3.000
RBY OR3 CR3 CR2 109.470 3.000
RBY CR3 OR3 HOR3 109.470 3.000
RBY CR3 CR2 HR2 108.340 3.000
RBY CR3 CR2 OR2 109.470 3.000
RBY CR3 CR2 CR1 111.000 3.000
RBY HR2 CR2 OR2 109.470 3.000
RBY HR2 CR2 CR1 108.340 3.000
RBY OR2 CR2 CR1 109.470 3.000
RBY CR2 OR2 HOR2 109.470 3.000
RBY CR2 CR1 HR1 108.340 3.000
RBY CR2 CR1 OR1 109.470 3.000
RBY CR2 CR1 OR4 109.470 3.000
RBY HR1 CR1 OR1 109.470 3.000
RBY HR1 CR1 OR4 109.470 3.000
RBY OR1 CR1 OR4 109.470 3.000
RBY CR1 OR1 HOR1 109.470 3.000
RBY CR1 OR4 CR4 111.800 3.000
RBY PB O2B HO2B 120.000 3.000
RBY PA "O5'" "C5'" 120.500 3.000
RBY "O5'" "C5'" "H5'1" 109.470 3.000
RBY "O5'" "C5'" "H5'2" 109.470 3.000
RBY "O5'" "C5'" "C4'" 109.470 3.000
RBY "H5'1" "C5'" "H5'2" 107.900 3.000
RBY "H5'1" "C5'" "C4'" 109.470 3.000
RBY "H5'2" "C5'" "C4'" 109.470 3.000
RBY "C5'" "C4'" "H4'" 108.340 3.000
RBY "C5'" "C4'" "C3'" 111.000 3.000
RBY "C5'" "C4'" "O4'" 109.470 3.000
RBY "H4'" "C4'" "C3'" 108.340 3.000
RBY "H4'" "C4'" "O4'" 109.470 3.000
RBY "C3'" "C4'" "O4'" 109.470 3.000
RBY "C4'" "C3'" "H3'" 108.340 3.000
RBY "C4'" "C3'" "O3'" 109.470 3.000
RBY "C4'" "C3'" "C2'" 111.000 3.000
RBY "H3'" "C3'" "O3'" 109.470 3.000
RBY "H3'" "C3'" "C2'" 108.340 3.000
RBY "O3'" "C3'" "C2'" 109.470 3.000
RBY "C3'" "O3'" "HO3'" 109.470 3.000
RBY "C3'" "C2'" "H2'" 108.340 3.000
RBY "C3'" "C2'" "O2'" 109.470 3.000
RBY "C3'" "C2'" "C1'" 111.000 3.000
RBY "H2'" "C2'" "O2'" 109.470 3.000
RBY "H2'" "C2'" "C1'" 108.340 3.000
RBY "O2'" "C2'" "C1'" 109.470 3.000
RBY "C2'" "O2'" "HO2'" 109.470 3.000
RBY "C2'" "C1'" "H1'" 108.340 3.000
RBY "C2'" "C1'" "O4'" 109.470 3.000
RBY "C2'" "C1'" N9 109.470 3.000
RBY "H1'" "C1'" "O4'" 109.470 3.000
RBY "H1'" "C1'" N9 109.470 3.000
RBY "O4'" "C1'" N9 109.470 3.000
RBY "C1'" "O4'" "C4'" 111.800 3.000
RBY "C1'" N9 C4 126.000 3.000
RBY "C1'" N9 C8 126.000 3.000
RBY C4 N9 C8 108.000 3.000
RBY N9 C4 C5 108.000 3.000
RBY N9 C4 N3 132.000 3.000
RBY C5 C4 N3 120.000 3.000
RBY C4 C5 N7 108.000 3.000
RBY C4 C5 C6 120.000 3.000
RBY N7 C5 C6 132.000 3.000
RBY C5 N7 C8 108.000 3.000
RBY N7 C8 H8 126.000 3.000
RBY N7 C8 N9 108.000 3.000
RBY H8 C8 N9 126.000 3.000
RBY C4 N3 C2 120.000 3.000
RBY N3 C2 H2 120.000 3.000
RBY N3 C2 N1 120.000 3.000
RBY H2 C2 N1 120.000 3.000
RBY C2 N1 C6 120.000 3.000
RBY N1 C6 N6 120.000 3.000
RBY N1 C6 C5 120.000 3.000
RBY N6 C6 C5 120.000 3.000
RBY C6 N6 HN62 120.000 3.000
RBY C6 N6 HN61 120.000 3.000
RBY HN62 N6 HN61 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
RBY var_1 O2A PA O1A HO1A 179.977 20.000 1
RBY var_2 O2A PA CX PB -60.036 20.000 1
RBY var_3 PA CX PB O1B 59.995 20.000 1
RBY var_4 CX PB OR5 CR5 -174.995 20.000 1
RBY var_5 PB OR5 CR5 CR4 -179.992 20.000 1
RBY var_6 OR5 CR5 CR4 CR3 -175.010 20.000 3
RBY var_7 CR5 CR4 OR4 CR1 150.000 20.000 1
RBY var_8 CR5 CR4 CR3 CR2 -150.000 20.000 3
RBY var_9 CR4 CR3 OR3 HOR3 179.950 20.000 1
RBY var_10 CR4 CR3 CR2 CR1 0.000 20.000 3
RBY var_11 CR3 CR2 OR2 HOR2 179.998 20.000 1
RBY var_12 CR3 CR2 CR1 OR4 30.000 20.000 3
RBY var_13 CR2 CR1 OR1 HOR1 -176.815 20.000 1
RBY var_14 CR2 CR1 OR4 CR4 -30.000 20.000 1
RBY var_15 CX PB O2B HO2B -60.034 20.000 1
RBY var_16 O2A PA "O5'" "C5'" 54.985 20.000 1
RBY var_17 PA "O5'" "C5'" "C4'" -179.943 20.000 1
RBY var_18 "O5'" "C5'" "C4'" "C3'" -175.721 20.000 3
RBY var_19 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
RBY var_20 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
RBY var_21 "C4'" "C3'" "O3'" "HO3'" 176.230 20.000 1
RBY var_22 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
RBY var_23 "C3'" "C2'" "O2'" "HO2'" -61.485 20.000 1
RBY var_24 "C3'" "C2'" "C1'" N9 150.000 20.000 3
RBY var_25 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
RBY var_26 "C2'" "C1'" N9 C4 84.938 20.000 1
RBY CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
RBY CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
RBY CONST_3 N9 C4 C5 N7 0.000 0.000 0
RBY CONST_4 C4 C5 C6 N1 0.000 0.000 0
RBY CONST_5 C4 C5 N7 C8 0.000 0.000 0
RBY CONST_6 C5 N7 C8 N9 0.000 0.000 0
RBY CONST_7 N9 C4 N3 C2 180.000 0.000 0
RBY CONST_8 C4 N3 C2 N1 0.000 0.000 0
RBY CONST_9 N3 C2 N1 C6 0.000 0.000 0
RBY CONST_10 C2 N1 C6 N6 180.000 0.000 0
RBY CONST_11 N1 C6 N6 HN61 -179.947 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
RBY chir_01 "C4'" "C5'" "O4'" "C3'" negativ
RBY chir_02 "C3'" "C4'" "O3'" "C2'" negativ
RBY chir_03 "C2'" "C3'" "O2'" "C1'" negativ
RBY chir_04 "C1'" "O4'" "C2'" N9 positiv
RBY chir_05 CR4 CR5 OR4 CR3 negativ
RBY chir_06 CR3 CR4 OR3 CR2 positiv
RBY chir_07 CR2 CR3 OR2 CR1 negativ
RBY chir_08 CR1 OR4 CR2 OR1 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
RBY plan-1 N9 0.020
RBY plan-1 "C1'" 0.020
RBY plan-1 C8 0.020
RBY plan-1 C4 0.020
RBY plan-1 N7 0.020
RBY plan-1 H8 0.020
RBY plan-1 C5 0.020
RBY plan-1 C6 0.020
RBY plan-1 N1 0.020
RBY plan-1 C2 0.020
RBY plan-1 N3 0.020
RBY plan-1 N6 0.020
RBY plan-1 H2 0.020
RBY plan-1 HN62 0.020
RBY plan-1 HN61 0.020
RBY plan-2 N6 0.020
RBY plan-2 C6 0.020
RBY plan-2 HN61 0.020
RBY plan-2 HN62 0.020
# ------------------------------------------------------
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