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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
AGS AGS 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE' non-polymer 45 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AGS
#
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
AGS O2A O OP -0.500 0.000 0.000 0.000
AGS PA P P 0.000 -1.127 -0.079 0.961
AGS O1A O OP -0.500 -1.400 1.270 1.514
AGS O3A O O2 0.000 -0.740 -1.081 2.159
AGS PB P P 0.000 0.574 -0.477 2.867
AGS O1B O OP -0.500 0.274 0.877 3.391
AGS O2B O OP -0.500 1.675 -0.392 1.877
AGS O3B O O2 0.000 1.017 -1.437 4.082
AGS PG P P 0.000 2.329 -0.776 4.741
AGS O3G O O 0.000 3.401 -0.687 3.724
AGS O2G O OH1 0.000 2.831 -1.689 5.969
AGS HOG2 H H 0.000 3.613 -1.431 6.475
AGS S1G S SH1 0.000 1.863 1.167 5.448
AGS HSG H H 0.000 0.898 1.096 6.365
AGS "O5'" O O2 0.000 -2.439 -0.625 0.206
AGS "C5'" C CH2 0.000 -2.729 0.303 -0.841
AGS "H5'1" H H 0.000 -1.879 0.355 -1.526
AGS "H5'2" H H 0.000 -2.909 1.291 -0.412
AGS "C4'" C CH1 0.000 -3.972 -0.159 -1.603
AGS "H4'" H H 0.000 -3.799 -1.146 -2.053
AGS "C3'" C CH1 0.000 -4.352 0.869 -2.691
AGS "H3'" H H 0.000 -3.965 1.864 -2.433
AGS "O3'" O OH1 0.000 -3.857 0.455 -3.966
AGS "HO3'" H H 0.000 -4.104 1.108 -4.634
AGS "C2'" C CH1 0.000 -5.899 0.870 -2.684
AGS "H2'" H H 0.000 -6.282 1.866 -2.422
AGS "O2'" O OH1 0.000 -6.406 0.458 -3.955
AGS "HO2'" H H 0.000 -6.113 1.081 -4.634
AGS "C1'" C CH1 0.000 -6.267 -0.155 -1.589
AGS "H1'" H H 0.000 -6.449 -1.143 -2.035
AGS "O4'" O O2 0.000 -5.114 -0.202 -0.721
AGS N9 N NR5 0.000 -7.447 0.293 -0.847
AGS C4 C CR56 0.000 -8.753 -0.012 -1.135
AGS C5 C CR56 0.000 -9.528 0.640 -0.162
AGS N7 N NRD5 0.000 -8.671 1.291 0.660
AGS C8 C CR15 0.000 -7.449 1.091 0.258
AGS H8 H H 0.000 -6.565 1.499 0.731
AGS N3 N NRD6 0.000 -9.363 -0.734 -2.070
AGS C2 C CR16 0.000 -10.675 -0.842 -2.083
AGS H2 H H 0.000 -11.141 -1.438 -2.859
AGS N1 N NRD6 0.000 -11.444 -0.252 -1.187
AGS C6 C CR6 0.000 -10.925 0.489 -0.215
AGS N6 N NH2 0.000 -11.739 1.103 0.720
AGS HN62 H H 0.000 -11.337 1.669 1.462
AGS HN61 H H 0.000 -12.747 0.996 0.676
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
AGS O2A n/a PA START
AGS PA O2A "O5'" .
AGS O1A PA . .
AGS O3A PA PB .
AGS PB O3A O3B .
AGS O1B PB . .
AGS O2B PB . .
AGS O3B PB PG .
AGS PG O3B S1G .
AGS O3G PG . .
AGS O2G PG HOG2 .
AGS HOG2 O2G . .
AGS S1G PG HSG .
AGS HSG S1G . .
AGS "O5'" PA "C5'" .
AGS "C5'" "O5'" "C4'" .
AGS "H5'1" "C5'" . .
AGS "H5'2" "C5'" . .
AGS "C4'" "C5'" "C3'" .
AGS "H4'" "C4'" . .
AGS "C3'" "C4'" "C2'" .
AGS "H3'" "C3'" . .
AGS "O3'" "C3'" "HO3'" .
AGS "HO3'" "O3'" . .
AGS "C2'" "C3'" "C1'" .
AGS "H2'" "C2'" . .
AGS "O2'" "C2'" "HO2'" .
AGS "HO2'" "O2'" . .
AGS "C1'" "C2'" N9 .
AGS "H1'" "C1'" . .
AGS "O4'" "C1'" . .
AGS N9 "C1'" C4 .
AGS C4 N9 N3 .
AGS C5 C4 N7 .
AGS N7 C5 C8 .
AGS C8 N7 H8 .
AGS H8 C8 . .
AGS N3 C4 C2 .
AGS C2 N3 N1 .
AGS H2 C2 . .
AGS N1 C2 C6 .
AGS C6 N1 N6 .
AGS N6 C6 HN61 .
AGS HN62 N6 . .
AGS HN61 N6 . END
AGS "C4'" "O4'" . ADD
AGS N9 C8 . ADD
AGS C5 C6 . 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
AGS S1G PG single 2.075 0.020
AGS O2G PG single 1.610 0.020
AGS O3G PG double 1.480 0.020
AGS PG O3B single 1.610 0.020
AGS HSG S1G single 1.330 0.020
AGS HOG2 O2G single 0.967 0.020
AGS O1B PB deloc 1.510 0.020
AGS O2B PB deloc 1.510 0.020
AGS O3B PB single 1.610 0.020
AGS PB O3A single 1.610 0.020
AGS O1A PA deloc 1.510 0.020
AGS PA O2A deloc 1.510 0.020
AGS O3A PA single 1.610 0.020
AGS "O5'" PA single 1.610 0.020
AGS "C5'" "O5'" single 1.426 0.020
AGS "C4'" "C5'" single 1.524 0.020
AGS "H5'1" "C5'" single 1.092 0.020
AGS "H5'2" "C5'" single 1.092 0.020
AGS "C4'" "O4'" single 1.426 0.020
AGS "C3'" "C4'" single 1.524 0.020
AGS "H4'" "C4'" single 1.099 0.020
AGS "O4'" "C1'" single 1.426 0.020
AGS "O3'" "C3'" single 1.432 0.020
AGS "C2'" "C3'" single 1.524 0.020
AGS "H3'" "C3'" single 1.099 0.020
AGS "HO3'" "O3'" single 0.967 0.020
AGS "O2'" "C2'" single 1.432 0.020
AGS "C1'" "C2'" single 1.524 0.020
AGS "H2'" "C2'" single 1.099 0.020
AGS "HO2'" "O2'" single 0.967 0.020
AGS N9 "C1'" single 1.485 0.020
AGS "H1'" "C1'" single 1.099 0.020
AGS N9 C8 single 1.337 0.020
AGS C4 N9 single 1.337 0.020
AGS C8 N7 double 1.350 0.020
AGS H8 C8 single 1.083 0.020
AGS N7 C5 single 1.350 0.020
AGS C5 C6 single 1.490 0.020
AGS C5 C4 double 1.490 0.020
AGS N6 C6 single 1.355 0.020
AGS C6 N1 double 1.350 0.020
AGS HN61 N6 single 1.010 0.020
AGS HN62 N6 single 1.010 0.020
AGS N1 C2 single 1.337 0.020
AGS C2 N3 double 1.337 0.020
AGS H2 C2 single 1.083 0.020
AGS N3 C4 single 1.355 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
AGS O2A PA O1A 119.900 3.000
AGS O2A PA O3A 108.200 3.000
AGS O2A PA "O5'" 108.200 3.000
AGS O1A PA O3A 108.200 3.000
AGS O1A PA "O5'" 108.200 3.000
AGS O3A PA "O5'" 102.600 3.000
AGS PA O3A PB 120.500 3.000
AGS O3A PB O1B 108.200 3.000
AGS O3A PB O2B 108.200 3.000
AGS O3A PB O3B 102.600 3.000
AGS O1B PB O2B 119.900 3.000
AGS O1B PB O3B 108.200 3.000
AGS O2B PB O3B 108.200 3.000
AGS PB O3B PG 120.500 3.000
AGS O3B PG O3G 109.500 3.000
AGS O3B PG O2G 109.500 3.000
AGS O3B PG S1G 109.500 3.000
AGS O3G PG O2G 109.500 3.000
AGS O3G PG S1G 109.500 3.000
AGS O2G PG S1G 109.500 3.000
AGS PG O2G HOG2 120.000 3.000
AGS PG S1G HSG 109.500 3.000
AGS PA "O5'" "C5'" 120.500 3.000
AGS "O5'" "C5'" "H5'1" 109.470 3.000
AGS "O5'" "C5'" "H5'2" 109.470 3.000
AGS "O5'" "C5'" "C4'" 109.470 3.000
AGS "H5'1" "C5'" "H5'2" 107.900 3.000
AGS "H5'1" "C5'" "C4'" 109.470 3.000
AGS "H5'2" "C5'" "C4'" 109.470 3.000
AGS "C5'" "C4'" "H4'" 108.340 3.000
AGS "C5'" "C4'" "C3'" 111.000 3.000
AGS "C5'" "C4'" "O4'" 109.470 3.000
AGS "H4'" "C4'" "C3'" 108.340 3.000
AGS "H4'" "C4'" "O4'" 109.470 3.000
AGS "C3'" "C4'" "O4'" 109.470 3.000
AGS "C4'" "C3'" "H3'" 108.340 3.000
AGS "C4'" "C3'" "O3'" 109.470 3.000
AGS "C4'" "C3'" "C2'" 111.000 3.000
AGS "H3'" "C3'" "O3'" 109.470 3.000
AGS "H3'" "C3'" "C2'" 108.340 3.000
AGS "O3'" "C3'" "C2'" 109.470 3.000
AGS "C3'" "O3'" "HO3'" 109.470 3.000
AGS "C3'" "C2'" "H2'" 108.340 3.000
AGS "C3'" "C2'" "O2'" 109.470 3.000
AGS "C3'" "C2'" "C1'" 111.000 3.000
AGS "H2'" "C2'" "O2'" 109.470 3.000
AGS "H2'" "C2'" "C1'" 108.340 3.000
AGS "O2'" "C2'" "C1'" 109.470 3.000
AGS "C2'" "O2'" "HO2'" 109.470 3.000
AGS "C2'" "C1'" "H1'" 108.340 3.000
AGS "C2'" "C1'" "O4'" 109.470 3.000
AGS "C2'" "C1'" N9 109.470 3.000
AGS "H1'" "C1'" "O4'" 109.470 3.000
AGS "H1'" "C1'" N9 109.470 3.000
AGS "O4'" "C1'" N9 109.470 3.000
AGS "C1'" "O4'" "C4'" 111.800 3.000
AGS "C1'" N9 C4 126.000 3.000
AGS "C1'" N9 C8 126.000 3.000
AGS C4 N9 C8 108.000 3.000
AGS N9 C4 C5 108.000 3.000
AGS N9 C4 N3 132.000 3.000
AGS C5 C4 N3 120.000 3.000
AGS C4 C5 N7 108.000 3.000
AGS C4 C5 C6 120.000 3.000
AGS N7 C5 C6 132.000 3.000
AGS C5 N7 C8 108.000 3.000
AGS N7 C8 H8 126.000 3.000
AGS N7 C8 N9 108.000 3.000
AGS H8 C8 N9 126.000 3.000
AGS C4 N3 C2 120.000 3.000
AGS N3 C2 H2 120.000 3.000
AGS N3 C2 N1 120.000 3.000
AGS H2 C2 N1 120.000 3.000
AGS C2 N1 C6 120.000 3.000
AGS N1 C6 N6 120.000 3.000
AGS N1 C6 C5 120.000 3.000
AGS N6 C6 C5 120.000 3.000
AGS C6 N6 HN62 120.000 3.000
AGS C6 N6 HN61 120.000 3.000
AGS 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
AGS var_1 O2A PA O3A PB 59.978 20.000 1
AGS var_2 PA O3A PB O3B 179.974 20.000 1
AGS var_3 O3A PB O3B PG -179.991 20.000 1
AGS var_4 PB O3B PG S1G 60.007 20.000 1
AGS var_5 O3B PG O2G HOG2 179.998 20.000 1
AGS var_6 O3B PG S1G HSG 59.997 20.000 1
AGS var_7 O2A PA "O5'" "C5'" -59.978 20.000 1
AGS var_8 PA "O5'" "C5'" "C4'" -179.980 20.000 1
AGS var_9 "O5'" "C5'" "C4'" "C3'" 176.887 20.000 3
AGS var_10 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
AGS var_11 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
AGS var_12 "C4'" "C3'" "O3'" "HO3'" -179.985 20.000 1
AGS var_13 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
AGS var_14 "C3'" "C2'" "O2'" "HO2'" -61.513 20.000 1
AGS var_15 "C3'" "C2'" "C1'" N9 150.000 20.000 3
AGS var_16 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
AGS var_17 "C2'" "C1'" N9 C4 91.417 20.000 1
AGS CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
AGS CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
AGS CONST_3 N9 C4 C5 N7 0.000 0.000 0
AGS CONST_4 C4 C5 C6 N1 0.000 0.000 0
AGS CONST_5 C4 C5 N7 C8 0.000 0.000 0
AGS CONST_6 C5 N7 C8 N9 0.000 0.000 0
AGS CONST_7 N9 C4 N3 C2 180.000 0.000 0
AGS CONST_8 C4 N3 C2 N1 0.000 0.000 0
AGS CONST_9 N3 C2 N1 C6 0.000 0.000 0
AGS CONST_10 C2 N1 C6 N6 180.000 0.000 0
AGS CONST_11 N1 C6 N6 HN61 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
AGS chir_01 "C4'" "C5'" "O4'" "C3'" negativ
AGS chir_02 "C3'" "C4'" "O3'" "C2'" negativ
AGS chir_03 "C2'" "C3'" "O2'" "C1'" negativ
AGS chir_04 "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
AGS plan-1 N9 0.020
AGS plan-1 "C1'" 0.020
AGS plan-1 C8 0.020
AGS plan-1 C4 0.020
AGS plan-1 N7 0.020
AGS plan-1 H8 0.020
AGS plan-1 C5 0.020
AGS plan-1 C6 0.020
AGS plan-1 N1 0.020
AGS plan-1 C2 0.020
AGS plan-1 N3 0.020
AGS plan-1 N6 0.020
AGS plan-1 H2 0.020
AGS plan-1 HN62 0.020
AGS plan-1 HN61 0.020
AGS plan-2 N6 0.020
AGS plan-2 C6 0.020
AGS plan-2 HN61 0.020
AGS plan-2 HN62 0.020
# ------------------------------------------------------
|
