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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
APC APC 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENO' non-polymer 47 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_APC
#
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
APC O1A O O 0.000 0.000 0.000 0.000
APC PA P P 0.000 -0.903 -1.038 -0.546
APC O2A O OH1 0.000 -0.822 -1.027 -2.154
APC HOA2 H H 0.000 -1.355 -1.648 -2.669
APC C3A C CH2 0.000 -0.396 -2.673 0.075
APC H3A1 H H 0.000 -1.063 -3.438 -0.327
APC H3A2 H H 0.000 -0.452 -2.680 1.166
APC PB P P 0.000 1.315 -3.019 -0.449
APC O1B O O 0.000 2.217 -1.982 0.097
APC O2B O OH1 0.000 1.397 -3.008 -2.056
APC HOB2 H H 0.000 0.865 -3.630 -2.572
APC O3B O O2 0.000 1.763 -4.464 0.101
APC PG P P 0.000 3.276 -4.703 -0.396
APC O3G O OP -0.666 3.321 -4.667 -1.908
APC O2G O OP -0.666 3.759 -6.052 0.090
APC O1G O OP -0.666 4.168 -3.616 0.162
APC "O5'" O O2 0.000 -2.414 -0.730 -0.084
APC "C5'" C CH2 0.000 -2.751 0.558 -0.599
APC "H5'1" H H 0.000 -2.673 0.545 -1.689
APC "H5'2" H H 0.000 -2.062 1.302 -0.195
APC "C4'" C CH1 0.000 -4.183 0.912 -0.193
APC "H4'" H H 0.000 -4.890 0.178 -0.605
APC "C3'" C CH1 0.000 -4.545 2.334 -0.673
APC "H3'" H H 0.000 -3.638 2.940 -0.803
APC "O3'" O OH1 0.000 -5.288 2.277 -1.893
APC "HO3'" H H 0.000 -5.506 3.174 -2.179
APC "C2'" C CH1 0.000 -5.420 2.905 0.468
APC "H2'" H H 0.000 -4.947 3.795 0.906
APC "O2'" O OH1 0.000 -6.728 3.221 -0.014
APC "HO2'" H H 0.000 -6.663 3.897 -0.702
APC "C1'" C CH1 0.000 -5.477 1.761 1.502
APC "H1'" H H 0.000 -6.384 1.157 1.354
APC "O4'" O O2 0.000 -4.298 0.967 1.245
APC N9 N NR5 0.000 -5.443 2.300 2.863
APC C4 C CR56 0.000 -6.528 2.632 3.634
APC C5 C CR56 0.000 -6.010 3.109 4.849
APC N7 N NRD5 0.000 -4.660 3.036 4.763
APC C8 C CR15 0.000 -4.325 2.565 3.597
APC H8 H H 0.000 -3.308 2.406 3.260
APC N3 N NRD6 0.000 -7.846 2.596 3.463
APC C2 C CR16 0.000 -8.657 2.995 4.419
APC H2 H H 0.000 -9.725 2.953 4.248
APC N1 N NRD6 0.000 -8.217 3.445 5.581
APC C6 C CR6 0.000 -6.916 3.518 5.842
APC N6 N NH2 0.000 -6.464 3.990 7.061
APC HN62 H H 0.000 -5.469 4.044 7.258
APC HN61 H H 0.000 -7.123 4.289 7.775
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
APC O1A n/a PA START
APC PA O1A "O5'" .
APC O2A PA HOA2 .
APC HOA2 O2A . .
APC C3A PA PB .
APC H3A1 C3A . .
APC H3A2 C3A . .
APC PB C3A O3B .
APC O1B PB . .
APC O2B PB HOB2 .
APC HOB2 O2B . .
APC O3B PB PG .
APC PG O3B O1G .
APC O3G PG . .
APC O2G PG . .
APC O1G PG . .
APC "O5'" PA "C5'" .
APC "C5'" "O5'" "C4'" .
APC "H5'1" "C5'" . .
APC "H5'2" "C5'" . .
APC "C4'" "C5'" "C3'" .
APC "H4'" "C4'" . .
APC "C3'" "C4'" "C2'" .
APC "H3'" "C3'" . .
APC "O3'" "C3'" "HO3'" .
APC "HO3'" "O3'" . .
APC "C2'" "C3'" "C1'" .
APC "H2'" "C2'" . .
APC "O2'" "C2'" "HO2'" .
APC "HO2'" "O2'" . .
APC "C1'" "C2'" N9 .
APC "H1'" "C1'" . .
APC "O4'" "C1'" . .
APC N9 "C1'" C4 .
APC C4 N9 N3 .
APC C5 C4 N7 .
APC N7 C5 C8 .
APC C8 N7 H8 .
APC H8 C8 . .
APC N3 C4 C2 .
APC C2 N3 N1 .
APC H2 C2 . .
APC N1 C2 C6 .
APC C6 N1 N6 .
APC N6 C6 HN61 .
APC HN62 N6 . .
APC HN61 N6 . END
APC "C4'" "O4'" . ADD
APC N9 C8 . ADD
APC 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
APC O1G PG deloc 1.510 0.020
APC O2G PG deloc 1.510 0.020
APC O3G PG deloc 1.510 0.020
APC PG O3B single 1.610 0.020
APC O1B PB double 1.480 0.020
APC O2B PB single 1.610 0.020
APC O3B PB single 1.610 0.020
APC PB C3A single 1.812 0.020
APC HOB2 O2B single 0.967 0.020
APC PA O1A double 1.480 0.020
APC O2A PA single 1.610 0.020
APC C3A PA single 1.812 0.020
APC "O5'" PA single 1.610 0.020
APC HOA2 O2A single 0.967 0.020
APC H3A1 C3A single 1.092 0.020
APC H3A2 C3A single 1.092 0.020
APC "C5'" "O5'" single 1.426 0.020
APC "C4'" "C5'" single 1.524 0.020
APC "H5'1" "C5'" single 1.092 0.020
APC "H5'2" "C5'" single 1.092 0.020
APC "C4'" "O4'" single 1.426 0.020
APC "C3'" "C4'" single 1.524 0.020
APC "H4'" "C4'" single 1.099 0.020
APC "O4'" "C1'" single 1.426 0.020
APC "O3'" "C3'" single 1.432 0.020
APC "C2'" "C3'" single 1.524 0.020
APC "H3'" "C3'" single 1.099 0.020
APC "HO3'" "O3'" single 0.967 0.020
APC "O2'" "C2'" single 1.432 0.020
APC "C1'" "C2'" single 1.524 0.020
APC "H2'" "C2'" single 1.099 0.020
APC "HO2'" "O2'" single 0.967 0.020
APC N9 "C1'" single 1.485 0.020
APC "H1'" "C1'" single 1.099 0.020
APC N9 C8 single 1.337 0.020
APC C4 N9 single 1.337 0.020
APC C8 N7 double 1.350 0.020
APC H8 C8 single 1.083 0.020
APC N7 C5 single 1.350 0.020
APC C5 C6 single 1.490 0.020
APC C5 C4 double 1.490 0.020
APC N6 C6 single 1.355 0.020
APC C6 N1 double 1.350 0.020
APC HN61 N6 single 1.010 0.020
APC HN62 N6 single 1.010 0.020
APC N1 C2 single 1.337 0.020
APC C2 N3 double 1.337 0.020
APC H2 C2 single 1.083 0.020
APC 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
APC O1A PA O2A 109.500 3.000
APC O1A PA C3A 109.500 3.000
APC O1A PA "O5'" 109.500 3.000
APC O2A PA C3A 109.500 3.000
APC O2A PA "O5'" 109.500 3.000
APC C3A PA "O5'" 109.500 3.000
APC PA O2A HOA2 120.000 3.000
APC PA C3A H3A1 109.500 3.000
APC PA C3A H3A2 109.500 3.000
APC PA C3A PB 109.500 3.000
APC H3A1 C3A H3A2 107.900 3.000
APC H3A1 C3A PB 109.500 3.000
APC H3A2 C3A PB 109.500 3.000
APC C3A PB O1B 109.500 3.000
APC C3A PB O2B 109.500 3.000
APC C3A PB O3B 109.500 3.000
APC O1B PB O2B 109.500 3.000
APC O1B PB O3B 109.500 3.000
APC O2B PB O3B 109.500 3.000
APC PB O2B HOB2 120.000 3.000
APC PB O3B PG 120.500 3.000
APC O3B PG O3G 108.200 3.000
APC O3B PG O2G 108.200 3.000
APC O3B PG O1G 108.200 3.000
APC O3G PG O2G 119.900 3.000
APC O3G PG O1G 119.900 3.000
APC O2G PG O1G 119.900 3.000
APC PA "O5'" "C5'" 120.500 3.000
APC "O5'" "C5'" "H5'1" 109.470 3.000
APC "O5'" "C5'" "H5'2" 109.470 3.000
APC "O5'" "C5'" "C4'" 109.470 3.000
APC "H5'1" "C5'" "H5'2" 107.900 3.000
APC "H5'1" "C5'" "C4'" 109.470 3.000
APC "H5'2" "C5'" "C4'" 109.470 3.000
APC "C5'" "C4'" "H4'" 108.340 3.000
APC "C5'" "C4'" "C3'" 111.000 3.000
APC "C5'" "C4'" "O4'" 109.470 3.000
APC "H4'" "C4'" "C3'" 108.340 3.000
APC "H4'" "C4'" "O4'" 109.470 3.000
APC "C3'" "C4'" "O4'" 109.470 3.000
APC "C4'" "C3'" "H3'" 108.340 3.000
APC "C4'" "C3'" "O3'" 109.470 3.000
APC "C4'" "C3'" "C2'" 111.000 3.000
APC "H3'" "C3'" "O3'" 109.470 3.000
APC "H3'" "C3'" "C2'" 108.340 3.000
APC "O3'" "C3'" "C2'" 109.470 3.000
APC "C3'" "O3'" "HO3'" 109.470 3.000
APC "C3'" "C2'" "H2'" 108.340 3.000
APC "C3'" "C2'" "O2'" 109.470 3.000
APC "C3'" "C2'" "C1'" 111.000 3.000
APC "H2'" "C2'" "O2'" 109.470 3.000
APC "H2'" "C2'" "C1'" 108.340 3.000
APC "O2'" "C2'" "C1'" 109.470 3.000
APC "C2'" "O2'" "HO2'" 109.470 3.000
APC "C2'" "C1'" "H1'" 108.340 3.000
APC "C2'" "C1'" "O4'" 109.470 3.000
APC "C2'" "C1'" N9 109.470 3.000
APC "H1'" "C1'" "O4'" 109.470 3.000
APC "H1'" "C1'" N9 109.470 3.000
APC "O4'" "C1'" N9 109.470 3.000
APC "C1'" "O4'" "C4'" 111.800 3.000
APC "C1'" N9 C4 126.000 3.000
APC "C1'" N9 C8 126.000 3.000
APC C4 N9 C8 108.000 3.000
APC N9 C4 C5 108.000 3.000
APC N9 C4 N3 132.000 3.000
APC C5 C4 N3 120.000 3.000
APC C4 C5 N7 108.000 3.000
APC C4 C5 C6 120.000 3.000
APC N7 C5 C6 132.000 3.000
APC C5 N7 C8 108.000 3.000
APC N7 C8 H8 126.000 3.000
APC N7 C8 N9 108.000 3.000
APC H8 C8 N9 126.000 3.000
APC C4 N3 C2 120.000 3.000
APC N3 C2 H2 120.000 3.000
APC N3 C2 N1 120.000 3.000
APC H2 C2 N1 120.000 3.000
APC C2 N1 C6 120.000 3.000
APC N1 C6 N6 120.000 3.000
APC N1 C6 C5 120.000 3.000
APC N6 C6 C5 120.000 3.000
APC C6 N6 HN62 120.000 3.000
APC C6 N6 HN61 120.000 3.000
APC 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
APC var_1 O1A PA O2A HOA2 -179.965 20.000 1
APC var_2 O1A PA C3A PB -59.989 20.000 1
APC var_3 PA C3A PB O3B 179.976 20.000 1
APC var_4 C3A PB O2B HOB2 -59.973 20.000 1
APC var_5 C3A PB O3B PG -179.986 20.000 1
APC var_6 PB O3B PG O1G 60.003 20.000 1
APC var_7 O1A PA "O5'" "C5'" 59.986 20.000 1
APC var_8 PA "O5'" "C5'" "C4'" 179.978 20.000 1
APC var_9 "O5'" "C5'" "C4'" "C3'" 176.888 20.000 3
APC var_10 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
APC var_11 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
APC var_12 "C4'" "C3'" "O3'" "HO3'" -179.959 20.000 1
APC var_13 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
APC var_14 "C3'" "C2'" "O2'" "HO2'" -61.437 20.000 1
APC var_15 "C3'" "C2'" "C1'" N9 150.000 20.000 3
APC var_16 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
APC var_17 "C2'" "C1'" N9 C4 91.501 20.000 1
APC CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
APC CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
APC CONST_3 N9 C4 C5 N7 0.000 0.000 0
APC CONST_4 C4 C5 C6 N1 0.000 0.000 0
APC CONST_5 C4 C5 N7 C8 0.000 0.000 0
APC CONST_6 C5 N7 C8 N9 0.000 0.000 0
APC CONST_7 N9 C4 N3 C2 180.000 0.000 0
APC CONST_8 C4 N3 C2 N1 0.000 0.000 0
APC CONST_9 N3 C2 N1 C6 0.000 0.000 0
APC CONST_10 C2 N1 C6 N6 180.000 0.000 0
APC CONST_11 N1 C6 N6 HN61 -0.009 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
APC chir_01 "C4'" "C5'" "O4'" "C3'" negativ
APC chir_02 "C3'" "C4'" "O3'" "C2'" negativ
APC chir_03 "C2'" "C3'" "O2'" "C1'" negativ
APC 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
APC plan-1 N9 0.020
APC plan-1 "C1'" 0.020
APC plan-1 C8 0.020
APC plan-1 C4 0.020
APC plan-1 N7 0.020
APC plan-1 H8 0.020
APC plan-1 C5 0.020
APC plan-1 C6 0.020
APC plan-1 N1 0.020
APC plan-1 C2 0.020
APC plan-1 N3 0.020
APC plan-1 N6 0.020
APC plan-1 H2 0.020
APC plan-1 HN62 0.020
APC plan-1 HN61 0.020
APC plan-2 N6 0.020
APC plan-2 C6 0.020
APC plan-2 HN61 0.020
APC plan-2 HN62 0.020
# ------------------------------------------------------
|
