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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
AP7 AP7 '. ' RNA 36 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AP7
#
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
AP7 OP3 O OP -0.666 0.000 0.000 0.000
AP7 P P P 0.000 -1.124 -0.997 -0.179
AP7 OP1 O OP -0.666 -1.340 -1.750 1.115
AP7 OP2 O OP -0.666 -0.762 -1.974 -1.276
AP7 "O5'" O O2 0.000 -2.474 -0.218 -0.579
AP7 "C5'" C CH2 0.000 -3.133 0.698 0.299
AP7 "H5''" H H 0.000 -2.454 1.517 0.546
AP7 "H5'" H H 0.000 -3.424 0.179 1.214
AP7 "C4'" C CH1 0.000 -4.379 1.258 -0.390
AP7 "H4'" H H 0.000 -4.108 1.686 -1.365
AP7 "O4'" O O2 0.000 -5.350 0.212 -0.569
AP7 "C1'" C CH1 0.000 -6.653 0.819 -0.427
AP7 "H1'" H H 0.000 -6.934 1.351 -1.346
AP7 "C2'" C CH1 0.000 -6.463 1.815 0.744
AP7 "H2'" H H 0.000 -6.529 1.298 1.712
AP7 "O2'" O OH1 0.000 -7.414 2.878 0.669
AP7 "HO2'" H H 0.000 -7.276 3.485 1.409
AP7 N9 N NR5 0.000 -7.658 -0.192 -0.087
AP7 C4 C CR56 0.000 -9.017 -0.067 -0.233
AP7 N3 N NRD6 0.000 -9.829 0.888 -0.677
AP7 C2 C CR16 0.000 -11.132 0.704 -0.693
AP7 H2 H H 0.000 -11.766 1.502 -1.060
AP7 C8 C CR15 0.000 -7.415 -1.429 0.431
AP7 H8 H H 0.000 -6.433 -1.825 0.660
AP7 N7 N NRD5 0.000 -8.537 -2.064 0.609
AP7 C5 C CR56 0.000 -9.568 -1.277 0.219
AP7 C6 C CR6 0.000 -10.965 -1.426 0.181
AP7 N6 N NH2 0.000 -11.564 -2.595 0.614
AP7 H62 H H 0.000 -11.002 -3.363 0.966
AP7 H61 H H 0.000 -12.574 -2.698 0.584
AP7 N1 N NR16 1.000 -11.696 -0.416 -0.279
AP7 H1 H H 0.000 -12.732 -0.510 -0.313
AP7 "C3'" C CH1 0.000 -5.028 2.339 0.496
AP7 "H3'" H H 0.000 -4.483 2.436 1.446
AP7 "O3'" O OH1 0.000 -5.065 3.592 -0.191
AP7 "HO3'" H H 0.000 -5.514 4.295 0.298
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
AP7 OP3 n/a P START
AP7 P OP3 "O5'" .
AP7 OP1 P . .
AP7 OP2 P . .
AP7 "O5'" P "C5'" .
AP7 "C5'" "O5'" "C4'" .
AP7 "H5''" "C5'" . .
AP7 "H5'" "C5'" . .
AP7 "C4'" "C5'" "C3'" .
AP7 "H4'" "C4'" . .
AP7 "O4'" "C4'" "C1'" .
AP7 "C1'" "O4'" N9 .
AP7 "H1'" "C1'" . .
AP7 "C2'" "C1'" "O2'" .
AP7 "H2'" "C2'" . .
AP7 "O2'" "C2'" "HO2'" .
AP7 "HO2'" "O2'" . .
AP7 N9 "C1'" C8 .
AP7 C4 N9 N3 .
AP7 N3 C4 C2 .
AP7 C2 N3 H2 .
AP7 H2 C2 . .
AP7 C8 N9 N7 .
AP7 H8 C8 . .
AP7 N7 C8 C5 .
AP7 C5 N7 C6 .
AP7 C6 C5 N1 .
AP7 N6 C6 H61 .
AP7 H62 N6 . .
AP7 H61 N6 . .
AP7 N1 C6 H1 .
AP7 H1 N1 . .
AP7 "C3'" "C4'" "O3'" .
AP7 "H3'" "C3'" . .
AP7 "O3'" "C3'" . END
AP7 "HO3'" "O3'" . .
AP7 N1 C2 . ADD
AP7 C4 C5 . ADD
AP7 "C2'" "C3'" . 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
AP7 N9 "C1'" single 1.485 0.020
AP7 "C2'" "C1'" single 1.524 0.020
AP7 "C1'" "O4'" single 1.426 0.020
AP7 "H1'" "C1'" single 1.099 0.020
AP7 N1 C2 single 1.337 0.020
AP7 N1 C6 double 1.337 0.020
AP7 H1 N1 single 1.040 0.020
AP7 C2 N3 double 1.337 0.020
AP7 H2 C2 single 1.083 0.020
AP7 N3 C4 single 1.355 0.020
AP7 C4 C5 double 1.490 0.020
AP7 C4 N9 single 1.337 0.020
AP7 C6 C5 single 1.490 0.020
AP7 C5 N7 single 1.350 0.020
AP7 N6 C6 single 1.355 0.020
AP7 H61 N6 single 1.010 0.020
AP7 H62 N6 single 1.010 0.020
AP7 N7 C8 double 1.350 0.020
AP7 C8 N9 single 1.337 0.020
AP7 H8 C8 single 1.083 0.020
AP7 "O2'" "C2'" single 1.432 0.020
AP7 "C2'" "C3'" single 1.524 0.020
AP7 "H2'" "C2'" single 1.099 0.020
AP7 "HO2'" "O2'" single 0.967 0.020
AP7 "O3'" "C3'" single 1.432 0.020
AP7 "C3'" "C4'" single 1.524 0.020
AP7 "H3'" "C3'" single 1.099 0.020
AP7 "HO3'" "O3'" single 0.967 0.020
AP7 "O4'" "C4'" single 1.426 0.020
AP7 "C4'" "C5'" single 1.524 0.020
AP7 "H4'" "C4'" single 1.099 0.020
AP7 "C5'" "O5'" single 1.426 0.020
AP7 "H5''" "C5'" single 1.092 0.020
AP7 "H5'" "C5'" single 1.092 0.020
AP7 "O5'" P single 1.610 0.020
AP7 OP1 P deloc 1.510 0.020
AP7 OP2 P deloc 1.510 0.020
AP7 P OP3 deloc 1.510 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
AP7 OP3 P OP1 119.900 3.000
AP7 OP3 P OP2 119.900 3.000
AP7 OP3 P "O5'" 108.200 3.000
AP7 OP1 P OP2 119.900 3.000
AP7 OP1 P "O5'" 108.200 3.000
AP7 OP2 P "O5'" 108.200 3.000
AP7 P "O5'" "C5'" 120.500 3.000
AP7 "O5'" "C5'" "H5''" 109.470 3.000
AP7 "O5'" "C5'" "H5'" 109.470 3.000
AP7 "O5'" "C5'" "C4'" 109.470 3.000
AP7 "H5''" "C5'" "H5'" 107.900 3.000
AP7 "H5''" "C5'" "C4'" 109.470 3.000
AP7 "H5'" "C5'" "C4'" 109.470 3.000
AP7 "C5'" "C4'" "H4'" 108.340 3.000
AP7 "C5'" "C4'" "O4'" 109.470 3.000
AP7 "C5'" "C4'" "C3'" 111.000 3.000
AP7 "H4'" "C4'" "O4'" 109.470 3.000
AP7 "H4'" "C4'" "C3'" 108.340 3.000
AP7 "O4'" "C4'" "C3'" 109.470 3.000
AP7 "C4'" "O4'" "C1'" 111.800 3.000
AP7 "O4'" "C1'" "H1'" 109.470 3.000
AP7 "O4'" "C1'" "C2'" 109.470 3.000
AP7 "O4'" "C1'" N9 109.470 3.000
AP7 "H1'" "C1'" "C2'" 108.340 3.000
AP7 "H1'" "C1'" N9 109.470 3.000
AP7 "C2'" "C1'" N9 109.470 3.000
AP7 "C1'" "C2'" "H2'" 108.340 3.000
AP7 "C1'" "C2'" "O2'" 109.470 3.000
AP7 "C1'" "C2'" "C3'" 111.000 3.000
AP7 "H2'" "C2'" "O2'" 109.470 3.000
AP7 "H2'" "C2'" "C3'" 108.340 3.000
AP7 "O2'" "C2'" "C3'" 109.470 3.000
AP7 "C2'" "O2'" "HO2'" 109.470 3.000
AP7 "C1'" N9 C4 126.000 3.000
AP7 "C1'" N9 C8 126.000 3.000
AP7 C4 N9 C8 108.000 3.000
AP7 N9 C4 N3 132.000 3.000
AP7 N9 C4 C5 108.000 3.000
AP7 N3 C4 C5 120.000 3.000
AP7 C4 N3 C2 120.000 3.000
AP7 N3 C2 H2 120.000 3.000
AP7 N3 C2 N1 120.000 3.000
AP7 H2 C2 N1 120.000 3.000
AP7 N9 C8 H8 126.000 3.000
AP7 N9 C8 N7 108.000 3.000
AP7 H8 C8 N7 126.000 3.000
AP7 C8 N7 C5 108.000 3.000
AP7 N7 C5 C6 132.000 3.000
AP7 N7 C5 C4 108.000 3.000
AP7 C6 C5 C4 120.000 3.000
AP7 C5 C6 N6 120.000 3.000
AP7 C5 C6 N1 120.000 3.000
AP7 N6 C6 N1 120.000 3.000
AP7 C6 N6 H62 120.000 3.000
AP7 C6 N6 H61 120.000 3.000
AP7 H62 N6 H61 120.000 3.000
AP7 C6 N1 H1 120.000 3.000
AP7 C6 N1 C2 120.000 3.000
AP7 H1 N1 C2 120.000 3.000
AP7 "C4'" "C3'" "H3'" 108.340 3.000
AP7 "C4'" "C3'" "O3'" 109.470 3.000
AP7 "C4'" "C3'" "C2'" 111.000 3.000
AP7 "H3'" "C3'" "O3'" 109.470 3.000
AP7 "H3'" "C3'" "C2'" 108.340 3.000
AP7 "O3'" "C3'" "C2'" 109.470 3.000
AP7 "C3'" "O3'" "HO3'" 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
AP7 var_1 OP3 P "O5'" "C5'" -65.012 20.000 1
AP7 var_2 P "O5'" "C5'" "C4'" 179.994 20.000 1
AP7 var_3 "O5'" "C5'" "C4'" "C3'" -174.990 20.000 3
AP7 var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
AP7 var_5 "C4'" "O4'" "C1'" N9 -150.000 20.000 1
AP7 var_6 "O4'" "C1'" "C2'" "O2'" 150.000 20.000 3
AP7 var_7 "C1'" "C2'" "C3'" "C4'" -30.000 20.000 3
AP7 var_8 "C1'" "C2'" "O2'" "HO2'" 179.993 20.000 1
AP7 var_9 "O4'" "C1'" N9 C8 19.106 20.000 1
AP7 CONST_1 "C1'" N9 C4 N3 0.000 0.000 0
AP7 CONST_2 N9 C4 C5 N7 0.000 0.000 0
AP7 CONST_3 N9 C4 N3 C2 180.000 0.000 0
AP7 CONST_4 C4 N3 C2 N1 0.000 0.000 0
AP7 CONST_5 "C1'" N9 C8 N7 180.000 0.000 0
AP7 CONST_6 N9 C8 N7 C5 0.000 0.000 0
AP7 CONST_7 C8 N7 C5 C6 180.000 0.000 0
AP7 CONST_8 N7 C5 C6 N1 180.000 0.000 0
AP7 CONST_9 C5 C6 N6 H61 179.983 0.000 0
AP7 CONST_10 C5 C6 N1 C2 0.000 0.000 0
AP7 CONST_11 C6 N1 C2 N3 0.000 0.000 0
AP7 var_10 "C5'" "C4'" "C3'" "O3'" 120.000 20.000 3
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
AP7 chir_01 "C2'" "O2'" "C3'" "C1'" positiv
AP7 chir_02 "C3'" "C2'" "O3'" "C4'" positiv
AP7 chir_03 "C4'" "C3'" "O4'" "C5'" positiv
AP7 chir_04 "C1'" N9 "C2'" "O4'" negativ
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
AP7 plan-1 N1 0.020
AP7 plan-1 C2 0.020
AP7 plan-1 C6 0.020
AP7 plan-1 H1 0.020
AP7 plan-1 N3 0.020
AP7 plan-1 H2 0.020
AP7 plan-1 C4 0.020
AP7 plan-1 C5 0.020
AP7 plan-1 N9 0.020
AP7 plan-1 N7 0.020
AP7 plan-1 C8 0.020
AP7 plan-1 N6 0.020
AP7 plan-1 H8 0.020
AP7 plan-1 "C1'" 0.020
AP7 plan-1 H62 0.020
AP7 plan-1 H61 0.020
AP7 plan-2 N6 0.020
AP7 plan-2 C6 0.020
AP7 plan-2 H61 0.020
AP7 plan-2 H62 0.020
# ------------------------------------------------------
|
