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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
GPD GPD '(2R,3S,5S,6R)-5-amino-3-hydroxy-6-me' non-polymer 61 37 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GPD
#
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
GPD O6 O O 0.000 0.000 0.000 0.000
GPD C6 C CR6 0.000 -0.653 -0.554 -0.867
GPD C5 C CR56 0.000 -1.992 -0.943 -0.629
GPD N7 N NRD5 0.000 -2.829 -0.847 0.433
GPD C8 C CR15 0.000 -3.978 -1.370 0.126
GPD H8 H H 0.000 -4.833 -1.428 0.788
GPD N1 N NR16 0.000 -0.115 -0.813 -2.079
GPD HN1 H H 0.000 0.863 -0.526 -2.283
GPD C2 C CR6 0.000 -0.849 -1.450 -3.036
GPD N2 N NH2 0.000 -0.275 -1.707 -4.255
GPD HN2A H H 0.000 0.685 -1.436 -4.436
GPD HN2 H H 0.000 -0.807 -2.169 -4.984
GPD N3 N NRD6 0.000 -2.096 -1.811 -2.828
GPD C4 C CR56 0.000 -2.697 -1.582 -1.656
GPD N9 N NR5 0.000 -3.947 -1.835 -1.157
GPD "C1'" C CH1 0.000 -5.046 -2.491 -1.869
GPD "H1'" H H 0.000 -5.019 -2.240 -2.939
GPD "O4'" O O2 0.000 -6.317 -2.122 -1.293
GPD "C2'" C CH1 0.000 -4.991 -4.031 -1.668
GPD "H2'" H H 0.000 -4.672 -4.281 -0.647
GPD "O2'" O OH1 0.000 -4.134 -4.643 -2.634
GPD "HO2'" H H 0.000 -4.187 -5.605 -2.549
GPD "C3'" C CH1 0.000 -6.466 -4.440 -1.900
GPD "H3'" H H 0.000 -6.769 -5.211 -1.177
GPD "O3'" O OH1 0.000 -6.653 -4.908 -3.237
GPD "HO3'" H H 0.000 -6.150 -5.724 -3.365
GPD "C4'" C CH1 0.000 -7.260 -3.140 -1.667
GPD "H4'" H H 0.000 -7.778 -2.848 -2.591
GPD "C5'" C CH2 0.000 -8.277 -3.346 -0.543
GPD "H5'" H H 0.000 -7.749 -3.537 0.394
GPD "H5'A" H H 0.000 -8.914 -4.200 -0.781
GPD "O5'" O O2 0.000 -9.081 -2.173 -0.407
GPD P P P 0.000 -10.258 -2.038 0.682
GPD O1P O OP -0.500 -11.332 -3.014 0.375
GPD O2P O OP -0.500 -9.714 -2.311 2.034
GPD OPP O O2 0.000 -10.862 -0.546 0.639
GPD P2 P P 0.000 -11.715 0.346 1.672
GPD O3P O OP -0.500 -12.731 -0.506 2.338
GPD O4P O OP -0.500 -10.809 0.925 2.693
GPD O1G O O2 0.000 -12.453 1.534 0.874
GPD C1G C CH1 0.000 -13.371 2.437 1.494
GPD H1G H H 0.000 -13.883 1.928 2.322
GPD O5G O O2 0.000 -12.659 3.569 1.997
GPD C5G C CH1 0.000 -11.932 4.292 1.002
GPD H5G H H 0.000 -11.208 3.622 0.518
GPD C6G C CH3 0.000 -11.190 5.458 1.658
GPD H6GB H H 0.000 -10.516 5.085 2.385
GPD H6GA H H 0.000 -10.652 5.995 0.921
GPD H6G H H 0.000 -11.888 6.104 2.125
GPD C2G C CH1 0.000 -14.403 2.903 0.464
GPD H2G H H 0.000 -14.921 2.030 0.043
GPD O2G O OH1 0.000 -15.353 3.763 1.096
GPD HO2G H H 0.000 -15.804 3.281 1.802
GPD C3G C CH2 0.000 -13.688 3.663 -0.656
GPD H3G H H 0.000 -14.423 4.046 -1.367
GPD H3GA H H 0.000 -12.998 2.993 -1.173
GPD C4G C CH1 0.000 -12.908 4.832 -0.047
GPD H4G H H 0.000 -13.607 5.534 0.428
GPD N4A N NH2 0.000 -12.158 5.525 -1.104
GPD HN4B H H 0.000 -11.147 5.584 -1.059
GPD HN4A H H 0.000 -12.646 5.948 -1.884
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
GPD O6 n/a C6 START
GPD C6 O6 N1 .
GPD C5 C6 N7 .
GPD N7 C5 C8 .
GPD C8 N7 H8 .
GPD H8 C8 . .
GPD N1 C6 C2 .
GPD HN1 N1 . .
GPD C2 N1 N3 .
GPD N2 C2 HN2 .
GPD HN2A N2 . .
GPD HN2 N2 . .
GPD N3 C2 C4 .
GPD C4 N3 N9 .
GPD N9 C4 "C1'" .
GPD "C1'" N9 "C2'" .
GPD "H1'" "C1'" . .
GPD "O4'" "C1'" . .
GPD "C2'" "C1'" "C3'" .
GPD "H2'" "C2'" . .
GPD "O2'" "C2'" "HO2'" .
GPD "HO2'" "O2'" . .
GPD "C3'" "C2'" "C4'" .
GPD "H3'" "C3'" . .
GPD "O3'" "C3'" "HO3'" .
GPD "HO3'" "O3'" . .
GPD "C4'" "C3'" "C5'" .
GPD "H4'" "C4'" . .
GPD "C5'" "C4'" "O5'" .
GPD "H5'" "C5'" . .
GPD "H5'A" "C5'" . .
GPD "O5'" "C5'" P .
GPD P "O5'" OPP .
GPD O1P P . .
GPD O2P P . .
GPD OPP P P2 .
GPD P2 OPP O1G .
GPD O3P P2 . .
GPD O4P P2 . .
GPD O1G P2 C1G .
GPD C1G O1G C2G .
GPD H1G C1G . .
GPD O5G C1G C5G .
GPD C5G O5G C6G .
GPD H5G C5G . .
GPD C6G C5G H6G .
GPD H6GB C6G . .
GPD H6GA C6G . .
GPD H6G C6G . .
GPD C2G C1G C3G .
GPD H2G C2G . .
GPD O2G C2G HO2G .
GPD HO2G O2G . .
GPD C3G C2G C4G .
GPD H3G C3G . .
GPD H3GA C3G . .
GPD C4G C3G N4A .
GPD H4G C4G . .
GPD N4A C4G HN4A .
GPD HN4B N4A . .
GPD HN4A N4A . END
GPD C4G C5G . ADD
GPD "C4'" "O4'" . ADD
GPD N9 C8 . ADD
GPD C4 C5 . 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
GPD N4A C4G single 1.450 0.020
GPD HN4A N4A single 1.010 0.020
GPD HN4B N4A single 1.010 0.020
GPD C4G C3G single 1.524 0.020
GPD C4G C5G single 1.524 0.020
GPD H4G C4G single 1.099 0.020
GPD C5G O5G single 1.426 0.020
GPD C6G C5G single 1.524 0.020
GPD H5G C5G single 1.099 0.020
GPD H6G C6G single 1.059 0.020
GPD H6GA C6G single 1.059 0.020
GPD H6GB C6G single 1.059 0.020
GPD O5G C1G single 1.426 0.020
GPD C3G C2G single 1.524 0.020
GPD H3G C3G single 1.092 0.020
GPD H3GA C3G single 1.092 0.020
GPD O2G C2G single 1.432 0.020
GPD C2G C1G single 1.524 0.020
GPD H2G C2G single 1.099 0.020
GPD HO2G O2G single 0.967 0.020
GPD C1G O1G single 1.426 0.020
GPD H1G C1G single 1.099 0.020
GPD O1G P2 single 1.610 0.020
GPD P2 OPP single 1.610 0.020
GPD O3P P2 deloc 1.510 0.020
GPD O4P P2 deloc 1.510 0.020
GPD OPP P single 1.610 0.020
GPD P "O5'" single 1.610 0.020
GPD O2P P deloc 1.510 0.020
GPD O1P P deloc 1.510 0.020
GPD "O5'" "C5'" single 1.426 0.020
GPD "C5'" "C4'" single 1.524 0.020
GPD "H5'" "C5'" single 1.092 0.020
GPD "H5'A" "C5'" single 1.092 0.020
GPD "C4'" "O4'" single 1.426 0.020
GPD "C4'" "C3'" single 1.524 0.020
GPD "H4'" "C4'" single 1.099 0.020
GPD "O4'" "C1'" single 1.426 0.020
GPD "C3'" "C2'" single 1.524 0.020
GPD "O3'" "C3'" single 1.432 0.020
GPD "H3'" "C3'" single 1.099 0.020
GPD "HO3'" "O3'" single 0.967 0.020
GPD "O2'" "C2'" single 1.432 0.020
GPD "C2'" "C1'" single 1.524 0.020
GPD "H2'" "C2'" single 1.099 0.020
GPD "HO2'" "O2'" single 0.967 0.020
GPD "C1'" N9 single 1.485 0.020
GPD "H1'" "C1'" single 1.099 0.020
GPD N9 C4 single 1.337 0.020
GPD N9 C8 single 1.337 0.020
GPD C8 N7 double 1.350 0.020
GPD H8 C8 single 1.083 0.020
GPD N7 C5 single 1.350 0.020
GPD C4 N3 single 1.355 0.020
GPD C4 C5 double 1.490 0.020
GPD C5 C6 single 1.490 0.020
GPD N1 C6 single 1.337 0.020
GPD C6 O6 double 1.250 0.020
GPD N3 C2 double 1.350 0.020
GPD N2 C2 single 1.355 0.020
GPD C2 N1 single 1.337 0.020
GPD HN1 N1 single 1.040 0.020
GPD HN2 N2 single 1.010 0.020
GPD HN2A N2 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
GPD O6 C6 C5 120.000 3.000
GPD O6 C6 N1 120.000 3.000
GPD C5 C6 N1 120.000 3.000
GPD C6 C5 N7 132.000 3.000
GPD C6 C5 C4 120.000 3.000
GPD N7 C5 C4 108.000 3.000
GPD C5 N7 C8 108.000 3.000
GPD N7 C8 H8 126.000 3.000
GPD N7 C8 N9 108.000 3.000
GPD H8 C8 N9 126.000 3.000
GPD C6 N1 HN1 120.000 3.000
GPD C6 N1 C2 120.000 3.000
GPD HN1 N1 C2 120.000 3.000
GPD N1 C2 N2 120.000 3.000
GPD N1 C2 N3 120.000 3.000
GPD N2 C2 N3 120.000 3.000
GPD C2 N2 HN2A 120.000 3.000
GPD C2 N2 HN2 120.000 3.000
GPD HN2A N2 HN2 120.000 3.000
GPD C2 N3 C4 120.000 3.000
GPD N3 C4 N9 132.000 3.000
GPD N3 C4 C5 120.000 3.000
GPD N9 C4 C5 108.000 3.000
GPD C4 N9 "C1'" 126.000 3.000
GPD C4 N9 C8 108.000 3.000
GPD "C1'" N9 C8 126.000 3.000
GPD N9 "C1'" "H1'" 109.470 3.000
GPD N9 "C1'" "O4'" 109.470 3.000
GPD N9 "C1'" "C2'" 109.470 3.000
GPD "H1'" "C1'" "O4'" 109.470 3.000
GPD "H1'" "C1'" "C2'" 108.340 3.000
GPD "O4'" "C1'" "C2'" 109.470 3.000
GPD "C1'" "O4'" "C4'" 111.800 3.000
GPD "C1'" "C2'" "H2'" 108.340 3.000
GPD "C1'" "C2'" "O2'" 109.470 3.000
GPD "C1'" "C2'" "C3'" 111.000 3.000
GPD "H2'" "C2'" "O2'" 109.470 3.000
GPD "H2'" "C2'" "C3'" 108.340 3.000
GPD "O2'" "C2'" "C3'" 109.470 3.000
GPD "C2'" "O2'" "HO2'" 109.470 3.000
GPD "C2'" "C3'" "H3'" 108.340 3.000
GPD "C2'" "C3'" "O3'" 109.470 3.000
GPD "C2'" "C3'" "C4'" 111.000 3.000
GPD "H3'" "C3'" "O3'" 109.470 3.000
GPD "H3'" "C3'" "C4'" 108.340 3.000
GPD "O3'" "C3'" "C4'" 109.470 3.000
GPD "C3'" "O3'" "HO3'" 109.470 3.000
GPD "C3'" "C4'" "H4'" 108.340 3.000
GPD "C3'" "C4'" "C5'" 111.000 3.000
GPD "C3'" "C4'" "O4'" 109.470 3.000
GPD "H4'" "C4'" "C5'" 108.340 3.000
GPD "H4'" "C4'" "O4'" 109.470 3.000
GPD "C5'" "C4'" "O4'" 109.470 3.000
GPD "C4'" "C5'" "H5'" 109.470 3.000
GPD "C4'" "C5'" "H5'A" 109.470 3.000
GPD "C4'" "C5'" "O5'" 109.470 3.000
GPD "H5'" "C5'" "H5'A" 107.900 3.000
GPD "H5'" "C5'" "O5'" 109.470 3.000
GPD "H5'A" "C5'" "O5'" 109.470 3.000
GPD "C5'" "O5'" P 120.500 3.000
GPD "O5'" P O1P 108.200 3.000
GPD "O5'" P O2P 108.200 3.000
GPD "O5'" P OPP 102.600 3.000
GPD O1P P O2P 119.900 3.000
GPD O1P P OPP 108.200 3.000
GPD O2P P OPP 108.200 3.000
GPD P OPP P2 120.500 3.000
GPD OPP P2 O3P 108.200 3.000
GPD OPP P2 O4P 108.200 3.000
GPD OPP P2 O1G 102.600 3.000
GPD O3P P2 O4P 119.900 3.000
GPD O3P P2 O1G 108.200 3.000
GPD O4P P2 O1G 108.200 3.000
GPD P2 O1G C1G 120.500 3.000
GPD O1G C1G H1G 109.470 3.000
GPD O1G C1G O5G 109.470 3.000
GPD O1G C1G C2G 109.470 3.000
GPD H1G C1G O5G 109.470 3.000
GPD H1G C1G C2G 108.340 3.000
GPD O5G C1G C2G 109.470 3.000
GPD C1G O5G C5G 111.800 3.000
GPD O5G C5G H5G 109.470 3.000
GPD O5G C5G C6G 109.470 3.000
GPD O5G C5G C4G 109.470 3.000
GPD H5G C5G C6G 108.340 3.000
GPD H5G C5G C4G 108.340 3.000
GPD C6G C5G C4G 111.000 3.000
GPD C5G C6G H6GB 109.470 3.000
GPD C5G C6G H6GA 109.470 3.000
GPD C5G C6G H6G 109.470 3.000
GPD H6GB C6G H6GA 109.470 3.000
GPD H6GB C6G H6G 109.470 3.000
GPD H6GA C6G H6G 109.470 3.000
GPD C1G C2G H2G 108.340 3.000
GPD C1G C2G O2G 109.470 3.000
GPD C1G C2G C3G 111.000 3.000
GPD H2G C2G O2G 109.470 3.000
GPD H2G C2G C3G 108.340 3.000
GPD O2G C2G C3G 109.470 3.000
GPD C2G O2G HO2G 109.470 3.000
GPD C2G C3G H3G 109.470 3.000
GPD C2G C3G H3GA 109.470 3.000
GPD C2G C3G C4G 111.000 3.000
GPD H3G C3G H3GA 107.900 3.000
GPD H3G C3G C4G 109.470 3.000
GPD H3GA C3G C4G 109.470 3.000
GPD C3G C4G H4G 108.340 3.000
GPD C3G C4G N4A 109.470 3.000
GPD C3G C4G C5G 111.000 3.000
GPD H4G C4G N4A 109.470 3.000
GPD H4G C4G C5G 108.340 3.000
GPD N4A C4G C5G 109.470 3.000
GPD C4G N4A HN4B 120.000 3.000
GPD C4G N4A HN4A 120.000 3.000
GPD HN4B N4A HN4A 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
GPD CONST_1 O6 C6 C5 N7 0.000 0.000 0
GPD CONST_2 C6 C5 N7 C8 180.000 0.000 0
GPD CONST_3 C5 N7 C8 N9 0.000 0.000 0
GPD CONST_4 O6 C6 N1 C2 180.000 0.000 0
GPD CONST_5 C6 N1 C2 N3 0.000 0.000 0
GPD CONST_6 N1 C2 N2 HN2 -179.276 0.000 0
GPD CONST_7 N1 C2 N3 C4 0.000 0.000 0
GPD CONST_8 C2 N3 C4 N9 180.000 0.000 0
GPD CONST_9 N3 C4 C5 C6 0.000 0.000 0
GPD CONST_10 N3 C4 N9 "C1'" 0.000 0.000 0
GPD CONST_11 C4 N9 C8 N7 0.000 0.000 0
GPD var_1 C4 N9 "C1'" "C2'" 89.126 20.000 1
GPD var_2 N9 "C1'" "O4'" "C4'" -150.000 20.000 1
GPD var_3 N9 "C1'" "C2'" "C3'" 150.000 20.000 3
GPD var_4 "C1'" "C2'" "O2'" "HO2'" -174.148 20.000 1
GPD var_5 "C1'" "C2'" "C3'" "C4'" -30.000 20.000 3
GPD var_6 "C2'" "C3'" "O3'" "HO3'" 65.223 20.000 1
GPD var_7 "C2'" "C3'" "C4'" "C5'" -120.000 20.000 3
GPD var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
GPD var_9 "C3'" "C4'" "C5'" "O5'" -175.313 20.000 3
GPD var_10 "C4'" "C5'" "O5'" P 179.972 20.000 1
GPD var_11 "C5'" "O5'" P OPP 174.999 20.000 1
GPD var_12 "O5'" P OPP P2 -159.951 20.000 1
GPD var_13 P OPP P2 O1G -159.995 20.000 1
GPD var_14 OPP P2 O1G C1G 174.987 20.000 1
GPD var_15 P2 O1G C1G C2G -150.093 20.000 1
GPD var_16 O1G C1G O5G C5G 60.000 20.000 1
GPD var_17 C1G O5G C5G C6G 180.000 20.000 1
GPD var_18 O5G C5G C6G H6G -59.971 20.000 3
GPD var_19 O1G C1G C2G C3G -60.000 20.000 3
GPD var_20 C1G C2G O2G HO2G -60.314 20.000 1
GPD var_21 C1G C2G C3G C4G -60.000 20.000 3
GPD var_22 C2G C3G C4G N4A 180.000 20.000 3
GPD var_23 C3G C4G C5G O5G -60.000 20.000 3
GPD var_24 C3G C4G N4A HN4A 60.378 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
GPD chir_01 C4G N4A C5G C3G positiv
GPD chir_02 C5G C4G C6G O5G negativ
GPD chir_03 C2G C3G O2G C1G positiv
GPD chir_04 C1G O5G C2G O1G negativ
GPD chir_05 "C4'" "C5'" "O4'" "C3'" negativ
GPD chir_06 "C3'" "C4'" "O3'" "C2'" negativ
GPD chir_07 "C2'" "C3'" "O2'" "C1'" negativ
GPD chir_08 "C1'" "O4'" "C2'" N9 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
GPD plan-1 N4A 0.020
GPD plan-1 C4G 0.020
GPD plan-1 HN4A 0.020
GPD plan-1 HN4B 0.020
GPD plan-2 N9 0.020
GPD plan-2 "C1'" 0.020
GPD plan-2 C8 0.020
GPD plan-2 C4 0.020
GPD plan-2 N7 0.020
GPD plan-2 H8 0.020
GPD plan-2 C5 0.020
GPD plan-2 N3 0.020
GPD plan-2 C6 0.020
GPD plan-2 C2 0.020
GPD plan-2 N1 0.020
GPD plan-2 O6 0.020
GPD plan-2 N2 0.020
GPD plan-2 HN1 0.020
GPD plan-2 HN2A 0.020
GPD plan-2 HN2 0.020
GPD plan-3 N2 0.020
GPD plan-3 C2 0.020
GPD plan-3 HN2 0.020
GPD plan-3 HN2A 0.020
# ------------------------------------------------------
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