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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
AMP AMP 'ADENOSINE MONOPHOSPHATE ' non-polymer 35 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AMP
#
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
AMP O3P O OP -0.666 0.000 0.000 0.000
AMP P P P 0.000 -1.182 -0.449 -0.831
AMP O1P O OP -0.666 -0.884 -1.801 -1.442
AMP O2P O OP -0.666 -1.435 0.557 -1.932
AMP "O5'" O O2 0.000 -2.486 -0.560 0.107
AMP "C5'" C CH2 0.000 -3.533 -1.098 -0.703
AMP "H5'1" H H 0.000 -3.236 -2.081 -1.074
AMP "H5'2" H H 0.000 -3.716 -0.432 -1.549
AMP "C4'" C CH1 0.000 -4.808 -1.228 0.131
AMP "H4'" H H 0.000 -4.618 -1.836 1.027
AMP "C3'" C CH1 0.000 -5.943 -1.853 -0.710
AMP "H3'" H H 0.000 -5.770 -1.678 -1.781
AMP "O3'" O OH1 0.000 -6.053 -3.253 -0.442
AMP "HO3'" H H 0.000 -6.766 -3.627 -0.976
AMP "C2'" C CH1 0.000 -7.214 -1.109 -0.238
AMP "H2'" H H 0.000 -7.673 -0.563 -1.075
AMP "O2'" O OH1 0.000 -8.149 -2.027 0.333
AMP "HO2'" H H 0.000 -8.416 -2.672 -0.337
AMP "C1'" C CH1 0.000 -6.694 -0.121 0.830
AMP "H1'" H H 0.000 -6.795 -0.556 1.834
AMP "O4'" O O2 0.000 -5.301 0.077 0.505
AMP N9 N NR5 0.000 -7.422 1.148 0.749
AMP C4 C CR56 0.000 -8.607 1.445 1.371
AMP C5 C CR56 0.000 -8.921 2.763 0.999
AMP N7 N NRD5 0.000 -7.924 3.198 0.192
AMP C8 C CR15 0.000 -7.044 2.251 0.041
AMP H8 H H 0.000 -6.145 2.327 -0.558
AMP N3 N NRD6 0.000 -9.436 0.786 2.174
AMP C2 C CR16 0.000 -10.534 1.359 2.622
AMP H2 H H 0.000 -11.188 0.794 3.274
AMP N1 N NRD6 0.000 -10.867 2.597 2.306
AMP C6 C CR6 0.000 -10.100 3.334 1.508
AMP N6 N NH2 0.000 -10.457 4.631 1.182
AMP HN62 H H 0.000 -9.869 5.190 0.572
AMP HN61 H H 0.000 -11.312 5.038 1.549
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
AMP O3P n/a P START
AMP P O3P "O5'" .
AMP O1P P . .
AMP O2P P . .
AMP "O5'" P "C5'" .
AMP "C5'" "O5'" "C4'" .
AMP "H5'1" "C5'" . .
AMP "H5'2" "C5'" . .
AMP "C4'" "C5'" "C3'" .
AMP "H4'" "C4'" . .
AMP "C3'" "C4'" "C2'" .
AMP "H3'" "C3'" . .
AMP "O3'" "C3'" "HO3'" .
AMP "HO3'" "O3'" . .
AMP "C2'" "C3'" "C1'" .
AMP "H2'" "C2'" . .
AMP "O2'" "C2'" "HO2'" .
AMP "HO2'" "O2'" . .
AMP "C1'" "C2'" N9 .
AMP "H1'" "C1'" . .
AMP "O4'" "C1'" . .
AMP N9 "C1'" C4 .
AMP C4 N9 N3 .
AMP C5 C4 N7 .
AMP N7 C5 C8 .
AMP C8 N7 H8 .
AMP H8 C8 . .
AMP N3 C4 C2 .
AMP C2 N3 N1 .
AMP H2 C2 . .
AMP N1 C2 C6 .
AMP C6 N1 N6 .
AMP N6 C6 HN61 .
AMP HN62 N6 . .
AMP HN61 N6 . END
AMP "C4'" "O4'" . ADD
AMP N9 C8 . ADD
AMP 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
AMP O1P P deloc 1.510 0.020
AMP O2P P deloc 1.510 0.020
AMP P O3P deloc 1.510 0.020
AMP "O5'" P single 1.610 0.020
AMP "C5'" "O5'" single 1.426 0.020
AMP "C4'" "C5'" single 1.524 0.020
AMP "H5'1" "C5'" single 1.092 0.020
AMP "H5'2" "C5'" single 1.092 0.020
AMP "C4'" "O4'" single 1.426 0.020
AMP "C3'" "C4'" single 1.524 0.020
AMP "H4'" "C4'" single 1.099 0.020
AMP "O4'" "C1'" single 1.426 0.020
AMP "O3'" "C3'" single 1.432 0.020
AMP "C2'" "C3'" single 1.524 0.020
AMP "H3'" "C3'" single 1.099 0.020
AMP "HO3'" "O3'" single 0.967 0.020
AMP "O2'" "C2'" single 1.432 0.020
AMP "C1'" "C2'" single 1.524 0.020
AMP "H2'" "C2'" single 1.099 0.020
AMP "HO2'" "O2'" single 0.967 0.020
AMP N9 "C1'" single 1.485 0.020
AMP "H1'" "C1'" single 1.099 0.020
AMP N9 C8 single 1.337 0.020
AMP C4 N9 single 1.337 0.020
AMP C8 N7 double 1.350 0.020
AMP H8 C8 single 1.083 0.020
AMP N7 C5 single 1.350 0.020
AMP C5 C6 single 1.490 0.020
AMP C5 C4 double 1.490 0.020
AMP N6 C6 single 1.355 0.020
AMP C6 N1 double 1.350 0.020
AMP HN61 N6 single 1.010 0.020
AMP HN62 N6 single 1.010 0.020
AMP N1 C2 single 1.337 0.020
AMP C2 N3 double 1.337 0.020
AMP H2 C2 single 1.083 0.020
AMP 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
AMP O3P P O1P 119.900 3.000
AMP O3P P O2P 119.900 3.000
AMP O3P P "O5'" 108.200 3.000
AMP O1P P O2P 119.900 3.000
AMP O1P P "O5'" 108.200 3.000
AMP O2P P "O5'" 108.200 3.000
AMP P "O5'" "C5'" 120.500 3.000
AMP "O5'" "C5'" "H5'1" 109.470 3.000
AMP "O5'" "C5'" "H5'2" 109.470 3.000
AMP "O5'" "C5'" "C4'" 109.470 3.000
AMP "H5'1" "C5'" "H5'2" 107.900 3.000
AMP "H5'1" "C5'" "C4'" 109.470 3.000
AMP "H5'2" "C5'" "C4'" 109.470 3.000
AMP "C5'" "C4'" "H4'" 108.340 3.000
AMP "C5'" "C4'" "C3'" 111.000 3.000
AMP "C5'" "C4'" "O4'" 109.470 3.000
AMP "H4'" "C4'" "C3'" 108.340 3.000
AMP "H4'" "C4'" "O4'" 109.470 3.000
AMP "C3'" "C4'" "O4'" 109.470 3.000
AMP "C4'" "C3'" "H3'" 108.340 3.000
AMP "C4'" "C3'" "O3'" 109.470 3.000
AMP "C4'" "C3'" "C2'" 111.000 3.000
AMP "H3'" "C3'" "O3'" 109.470 3.000
AMP "H3'" "C3'" "C2'" 108.340 3.000
AMP "O3'" "C3'" "C2'" 109.470 3.000
AMP "C3'" "O3'" "HO3'" 109.470 3.000
AMP "C3'" "C2'" "H2'" 108.340 3.000
AMP "C3'" "C2'" "O2'" 109.470 3.000
AMP "C3'" "C2'" "C1'" 111.000 3.000
AMP "H2'" "C2'" "O2'" 109.470 3.000
AMP "H2'" "C2'" "C1'" 108.340 3.000
AMP "O2'" "C2'" "C1'" 109.470 3.000
AMP "C2'" "O2'" "HO2'" 109.470 3.000
AMP "C2'" "C1'" "H1'" 108.340 3.000
AMP "C2'" "C1'" "O4'" 109.470 3.000
AMP "C2'" "C1'" N9 109.470 3.000
AMP "H1'" "C1'" "O4'" 109.470 3.000
AMP "H1'" "C1'" N9 109.470 3.000
AMP "O4'" "C1'" N9 109.470 3.000
AMP "C1'" "O4'" "C4'" 111.800 3.000
AMP "C1'" N9 C4 126.000 3.000
AMP "C1'" N9 C8 126.000 3.000
AMP C4 N9 C8 108.000 3.000
AMP N9 C4 C5 108.000 3.000
AMP N9 C4 N3 132.000 3.000
AMP C5 C4 N3 120.000 3.000
AMP C4 C5 N7 108.000 3.000
AMP C4 C5 C6 120.000 3.000
AMP N7 C5 C6 132.000 3.000
AMP C5 N7 C8 108.000 3.000
AMP N7 C8 H8 126.000 3.000
AMP N7 C8 N9 108.000 3.000
AMP H8 C8 N9 126.000 3.000
AMP C4 N3 C2 120.000 3.000
AMP N3 C2 H2 120.000 3.000
AMP N3 C2 N1 120.000 3.000
AMP H2 C2 N1 120.000 3.000
AMP C2 N1 C6 120.000 3.000
AMP N1 C6 N6 120.000 3.000
AMP N1 C6 C5 120.000 3.000
AMP N6 C6 C5 120.000 3.000
AMP C6 N6 HN62 120.000 3.000
AMP C6 N6 HN61 120.000 3.000
AMP 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
AMP var_1 O3P P "O5'" "C5'" -175.001 20.000 1
AMP var_2 P "O5'" "C5'" "C4'" -179.958 20.000 1
AMP var_3 "O5'" "C5'" "C4'" "C3'" -178.105 20.000 3
AMP var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
AMP var_5 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
AMP var_6 "C4'" "C3'" "O3'" "HO3'" -179.951 20.000 1
AMP var_7 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
AMP var_8 "C3'" "C2'" "O2'" "HO2'" -61.481 20.000 1
AMP var_9 "C3'" "C2'" "C1'" N9 150.000 20.000 3
AMP var_10 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
AMP var_11 "C2'" "C1'" N9 C4 86.574 20.000 1
AMP CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
AMP CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
AMP CONST_3 N9 C4 C5 N7 0.000 0.000 0
AMP CONST_4 C4 C5 C6 N1 0.000 0.000 0
AMP CONST_5 C4 C5 N7 C8 0.000 0.000 0
AMP CONST_6 C5 N7 C8 N9 0.000 0.000 0
AMP CONST_7 N9 C4 N3 C2 180.000 0.000 0
AMP CONST_8 C4 N3 C2 N1 0.000 0.000 0
AMP CONST_9 N3 C2 N1 C6 0.000 0.000 0
AMP CONST_10 C2 N1 C6 N6 180.000 0.000 0
AMP CONST_11 N1 C6 N6 HN61 0.041 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
AMP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
AMP chir_02 "C3'" "C4'" "O3'" "C2'" negativ
AMP chir_03 "C2'" "C3'" "O2'" "C1'" negativ
AMP 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
AMP plan-1 N9 0.020
AMP plan-1 "C1'" 0.020
AMP plan-1 C8 0.020
AMP plan-1 C4 0.020
AMP plan-1 N7 0.020
AMP plan-1 H8 0.020
AMP plan-1 C5 0.020
AMP plan-1 C6 0.020
AMP plan-1 N1 0.020
AMP plan-1 C2 0.020
AMP plan-1 N3 0.020
AMP plan-1 N6 0.020
AMP plan-1 H2 0.020
AMP plan-1 HN62 0.020
AMP plan-1 HN61 0.020
AMP plan-2 N6 0.020
AMP plan-2 C6 0.020
AMP plan-2 HN61 0.020
AMP plan-2 HN62 0.020
# ------------------------------------------------------
|
