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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
PAP PAP '3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHAT' non-polymer 42 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PAP
#
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
PAP O3 O OP -0.666 0.000 0.000 0.000
PAP P P P 0.000 -0.629 1.125 -0.793
PAP O1 O OP -0.666 -1.220 0.572 -2.071
PAP O2 O OP -0.666 0.426 2.156 -1.128
PAP "O3'" O O2 0.000 -1.794 1.811 0.082
PAP "C3'" C CH1 0.000 -2.754 0.793 0.365
PAP "H3'" H H 0.000 -2.421 -0.173 -0.041
PAP "C4'" C CH1 0.000 -4.135 1.174 -0.210
PAP "H4'" H H 0.000 -4.214 2.264 -0.325
PAP "C5'" C CH2 0.000 -4.365 0.480 -1.554
PAP "H5'1" H H 0.000 -4.269 -0.600 -1.426
PAP "H5'2" H H 0.000 -3.621 0.828 -2.274
PAP "O5'" O O2 0.000 -5.674 0.791 -2.033
PAP PA P P 0.000 -5.847 0.033 -3.442
PAP O1A O OP -0.500 -4.813 0.512 -4.391
PAP O2A O OP -0.500 -5.693 -1.428 -3.239
PAP O3A O O2 0.000 -7.310 0.339 -4.041
PAP PB P P 0.000 -7.412 -0.446 -5.443
PAP O3B O OP -0.666 -6.333 0.051 -6.380
PAP O2B O OP -0.666 -8.770 -0.198 -6.061
PAP O1B O OP -0.666 -7.230 -1.929 -5.204
PAP "C2'" C CH1 0.000 -2.998 0.685 1.889
PAP "H2'" H H 0.000 -2.787 -0.334 2.241
PAP "O2'" O OH1 0.000 -2.194 1.633 2.593
PAP "HO2'" H H 0.000 -2.359 1.552 3.542
PAP "C1'" C CH1 0.000 -4.498 1.012 2.050
PAP "H1'" H H 0.000 -4.634 2.077 2.286
PAP "O4'" O O2 0.000 -5.085 0.703 0.768
PAP N9 N NR5 0.000 -5.092 0.178 3.098
PAP C4 C CR56 0.000 -5.199 0.499 4.427
PAP C5 C CR56 0.000 -5.825 -0.597 5.042
PAP N7 N NRD5 0.000 -6.073 -1.511 4.072
PAP C8 C CR15 0.000 -5.640 -1.057 2.931
PAP H8 H H 0.000 -5.705 -1.585 1.988
PAP N3 N NRD6 0.000 -4.852 1.545 5.171
PAP C2 C CR16 0.000 -5.096 1.558 6.465
PAP H2 H H 0.000 -4.801 2.426 7.042
PAP N1 N NRD6 0.000 -5.687 0.554 7.086
PAP C6 C CR6 0.000 -6.070 -0.533 6.424
PAP N6 N NH2 0.000 -6.690 -1.581 7.083
PAP HN62 H H 0.000 -6.980 -2.410 6.574
PAP HN61 H H 0.000 -6.861 -1.533 8.083
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
PAP O3 n/a P START
PAP P O3 "O3'" .
PAP O1 P . .
PAP O2 P . .
PAP "O3'" P "C3'" .
PAP "C3'" "O3'" "C2'" .
PAP "H3'" "C3'" . .
PAP "C4'" "C3'" "C5'" .
PAP "H4'" "C4'" . .
PAP "C5'" "C4'" "O5'" .
PAP "H5'1" "C5'" . .
PAP "H5'2" "C5'" . .
PAP "O5'" "C5'" PA .
PAP PA "O5'" O3A .
PAP O1A PA . .
PAP O2A PA . .
PAP O3A PA PB .
PAP PB O3A O1B .
PAP O3B PB . .
PAP O2B PB . .
PAP O1B PB . .
PAP "C2'" "C3'" "C1'" .
PAP "H2'" "C2'" . .
PAP "O2'" "C2'" "HO2'" .
PAP "HO2'" "O2'" . .
PAP "C1'" "C2'" N9 .
PAP "H1'" "C1'" . .
PAP "O4'" "C1'" . .
PAP N9 "C1'" C4 .
PAP C4 N9 N3 .
PAP C5 C4 N7 .
PAP N7 C5 C8 .
PAP C8 N7 H8 .
PAP H8 C8 . .
PAP N3 C4 C2 .
PAP C2 N3 N1 .
PAP H2 C2 . .
PAP N1 C2 C6 .
PAP C6 N1 N6 .
PAP N6 C6 HN61 .
PAP HN62 N6 . .
PAP HN61 N6 . END
PAP "C4'" "O4'" . ADD
PAP N9 C8 . ADD
PAP 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
PAP O1B PB deloc 1.510 0.020
PAP O2B PB deloc 1.510 0.020
PAP O3B PB deloc 1.510 0.020
PAP PB O3A single 1.610 0.020
PAP O1A PA deloc 1.510 0.020
PAP O2A PA deloc 1.510 0.020
PAP O3A PA single 1.610 0.020
PAP PA "O5'" single 1.610 0.020
PAP "O5'" "C5'" single 1.426 0.020
PAP "C5'" "C4'" single 1.524 0.020
PAP "H5'1" "C5'" single 1.092 0.020
PAP "H5'2" "C5'" single 1.092 0.020
PAP "C4'" "O4'" single 1.426 0.020
PAP "C4'" "C3'" single 1.524 0.020
PAP "H4'" "C4'" single 1.099 0.020
PAP "O4'" "C1'" single 1.426 0.020
PAP "C3'" "O3'" single 1.426 0.020
PAP "C2'" "C3'" single 1.524 0.020
PAP "H3'" "C3'" single 1.099 0.020
PAP "O3'" P single 1.610 0.020
PAP O1 P deloc 1.510 0.020
PAP O2 P deloc 1.510 0.020
PAP P O3 deloc 1.510 0.020
PAP "O2'" "C2'" single 1.432 0.020
PAP "C1'" "C2'" single 1.524 0.020
PAP "H2'" "C2'" single 1.099 0.020
PAP "HO2'" "O2'" single 0.967 0.020
PAP N9 "C1'" single 1.485 0.020
PAP "H1'" "C1'" single 1.099 0.020
PAP N9 C8 single 1.337 0.020
PAP C4 N9 single 1.337 0.020
PAP C8 N7 double 1.350 0.020
PAP H8 C8 single 1.083 0.020
PAP N7 C5 single 1.350 0.020
PAP C5 C6 single 1.490 0.020
PAP C5 C4 double 1.490 0.020
PAP N6 C6 single 1.355 0.020
PAP C6 N1 double 1.350 0.020
PAP HN61 N6 single 1.010 0.020
PAP HN62 N6 single 1.010 0.020
PAP N1 C2 single 1.337 0.020
PAP C2 N3 double 1.337 0.020
PAP H2 C2 single 1.083 0.020
PAP 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
PAP O3 P O1 119.900 3.000
PAP O3 P O2 119.900 3.000
PAP O3 P "O3'" 108.200 3.000
PAP O1 P O2 119.900 3.000
PAP O1 P "O3'" 108.200 3.000
PAP O2 P "O3'" 108.200 3.000
PAP P "O3'" "C3'" 120.500 3.000
PAP "O3'" "C3'" "H3'" 109.470 3.000
PAP "O3'" "C3'" "C4'" 109.470 3.000
PAP "O3'" "C3'" "C2'" 109.470 3.000
PAP "H3'" "C3'" "C4'" 108.340 3.000
PAP "H3'" "C3'" "C2'" 108.340 3.000
PAP "C4'" "C3'" "C2'" 111.000 3.000
PAP "C3'" "C4'" "H4'" 108.340 3.000
PAP "C3'" "C4'" "C5'" 111.000 3.000
PAP "C3'" "C4'" "O4'" 109.470 3.000
PAP "H4'" "C4'" "C5'" 108.340 3.000
PAP "H4'" "C4'" "O4'" 109.470 3.000
PAP "C5'" "C4'" "O4'" 109.470 3.000
PAP "C4'" "C5'" "H5'1" 109.470 3.000
PAP "C4'" "C5'" "H5'2" 109.470 3.000
PAP "C4'" "C5'" "O5'" 109.470 3.000
PAP "H5'1" "C5'" "H5'2" 107.900 3.000
PAP "H5'1" "C5'" "O5'" 109.470 3.000
PAP "H5'2" "C5'" "O5'" 109.470 3.000
PAP "C5'" "O5'" PA 120.500 3.000
PAP "O5'" PA O1A 108.200 3.000
PAP "O5'" PA O2A 108.200 3.000
PAP "O5'" PA O3A 102.600 3.000
PAP O1A PA O2A 119.900 3.000
PAP O1A PA O3A 108.200 3.000
PAP O2A PA O3A 108.200 3.000
PAP PA O3A PB 120.500 3.000
PAP O3A PB O3B 108.200 3.000
PAP O3A PB O2B 108.200 3.000
PAP O3A PB O1B 108.200 3.000
PAP O3B PB O2B 119.900 3.000
PAP O3B PB O1B 119.900 3.000
PAP O2B PB O1B 119.900 3.000
PAP "C3'" "C2'" "H2'" 108.340 3.000
PAP "C3'" "C2'" "O2'" 109.470 3.000
PAP "C3'" "C2'" "C1'" 111.000 3.000
PAP "H2'" "C2'" "O2'" 109.470 3.000
PAP "H2'" "C2'" "C1'" 108.340 3.000
PAP "O2'" "C2'" "C1'" 109.470 3.000
PAP "C2'" "O2'" "HO2'" 109.470 3.000
PAP "C2'" "C1'" "H1'" 108.340 3.000
PAP "C2'" "C1'" "O4'" 109.470 3.000
PAP "C2'" "C1'" N9 109.470 3.000
PAP "H1'" "C1'" "O4'" 109.470 3.000
PAP "H1'" "C1'" N9 109.470 3.000
PAP "O4'" "C1'" N9 109.470 3.000
PAP "C1'" "O4'" "C4'" 111.800 3.000
PAP "C1'" N9 C4 126.000 3.000
PAP "C1'" N9 C8 126.000 3.000
PAP C4 N9 C8 108.000 3.000
PAP N9 C4 C5 108.000 3.000
PAP N9 C4 N3 132.000 3.000
PAP C5 C4 N3 120.000 3.000
PAP C4 C5 N7 108.000 3.000
PAP C4 C5 C6 120.000 3.000
PAP N7 C5 C6 132.000 3.000
PAP C5 N7 C8 108.000 3.000
PAP N7 C8 H8 126.000 3.000
PAP N7 C8 N9 108.000 3.000
PAP H8 C8 N9 126.000 3.000
PAP C4 N3 C2 120.000 3.000
PAP N3 C2 H2 120.000 3.000
PAP N3 C2 N1 120.000 3.000
PAP H2 C2 N1 120.000 3.000
PAP C2 N1 C6 120.000 3.000
PAP N1 C6 N6 120.000 3.000
PAP N1 C6 C5 120.000 3.000
PAP N6 C6 C5 120.000 3.000
PAP C6 N6 HN62 120.000 3.000
PAP C6 N6 HN61 120.000 3.000
PAP 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
PAP var_1 O3 P "O3'" "C3'" -60.028 20.000 1
PAP var_2 P "O3'" "C3'" "C2'" 125.298 20.000 1
PAP var_3 "O3'" "C3'" "C4'" "C5'" 90.000 20.000 3
PAP var_4 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
PAP var_5 "C3'" "C4'" "C5'" "O5'" 176.984 20.000 3
PAP var_6 "C4'" "C5'" "O5'" PA -179.999 20.000 1
PAP var_7 "C5'" "O5'" PA O3A 179.950 20.000 1
PAP var_8 "O5'" PA O3A PB 179.989 20.000 1
PAP var_9 PA O3A PB O1B 60.040 20.000 1
PAP var_10 "O3'" "C3'" "C2'" "C1'" 120.000 20.000 3
PAP var_11 "C3'" "C2'" "O2'" "HO2'" 179.993 20.000 1
PAP var_12 "C3'" "C2'" "C1'" N9 150.000 20.000 3
PAP var_13 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
PAP var_14 "C2'" "C1'" N9 C4 91.564 20.000 1
PAP CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
PAP CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
PAP CONST_3 N9 C4 C5 N7 0.000 0.000 0
PAP CONST_4 C4 C5 C6 N1 0.000 0.000 0
PAP CONST_5 C4 C5 N7 C8 0.000 0.000 0
PAP CONST_6 C5 N7 C8 N9 0.000 0.000 0
PAP CONST_7 N9 C4 N3 C2 180.000 0.000 0
PAP CONST_8 C4 N3 C2 N1 0.000 0.000 0
PAP CONST_9 N3 C2 N1 C6 0.000 0.000 0
PAP CONST_10 C2 N1 C6 N6 180.000 0.000 0
PAP CONST_11 N1 C6 N6 HN61 0.062 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
PAP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
PAP chir_02 "C3'" "C4'" "O3'" "C2'" negativ
PAP chir_03 "C2'" "C3'" "O2'" "C1'" negativ
PAP 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
PAP plan-1 N9 0.020
PAP plan-1 "C1'" 0.020
PAP plan-1 C8 0.020
PAP plan-1 C4 0.020
PAP plan-1 N7 0.020
PAP plan-1 H8 0.020
PAP plan-1 C5 0.020
PAP plan-1 C6 0.020
PAP plan-1 N1 0.020
PAP plan-1 C2 0.020
PAP plan-1 N3 0.020
PAP plan-1 N6 0.020
PAP plan-1 H2 0.020
PAP plan-1 HN62 0.020
PAP plan-1 HN61 0.020
PAP plan-2 N6 0.020
PAP plan-2 C6 0.020
PAP plan-2 HN61 0.020
PAP plan-2 HN62 0.020
# ------------------------------------------------------
|
