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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
SMP SMP '2'-DEOXY-ADENOSINE-5'-SP-MONOMETHYLP' non-polymer 38 22 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SMP
#
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
SMP OP1 O O 0.000 0.000 0.000 0.000
SMP P P P 0.000 -1.342 -0.588 -0.327
SMP OP3 O OH1 0.000 -2.180 0.252 -1.425
SMP HOP3 H H 0.000 -2.312 1.204 -1.311
SMP CMP C CH3 0.000 -1.255 -2.226 -1.023
SMP HMP3 H H 0.000 -2.173 -2.451 -1.497
SMP HMP2 H H 0.000 -0.470 -2.262 -1.730
SMP HMP1 H H 0.000 -1.073 -2.923 -0.250
SMP "O5'" O O2 0.000 -2.343 -0.704 0.937
SMP "C5'" C CH2 0.000 -3.685 -1.126 0.768
SMP "H5'" H H 0.000 -3.707 -2.131 0.342
SMP "H5''" H H 0.000 -4.208 -0.437 0.101
SMP "C4'" C CH1 0.000 -4.368 -1.134 2.129
SMP "H4'" H H 0.000 -3.822 -1.797 2.814
SMP "C3'" C CH1 0.000 -5.829 -1.566 2.051
SMP "H3'" H H 0.000 -6.011 -2.234 1.198
SMP "O3'" O OH1 0.000 -6.216 -2.166 3.284
SMP "HO3'" H H 0.000 -5.914 -1.614 4.018
SMP "C2'" C CH2 0.000 -6.569 -0.256 1.904
SMP "H2'" H H 0.000 -7.585 -0.288 2.302
SMP "H2''" H H 0.000 -6.593 0.112 0.877
SMP "C1'" C CH1 0.000 -5.718 0.674 2.758
SMP "H1'" H H 0.000 -6.033 0.573 3.806
SMP "O4'" O O2 0.000 -4.359 0.214 2.642
SMP N9 N NR5 0.000 -5.801 2.080 2.381
SMP C4 C CR56 0.000 -6.642 3.023 2.905
SMP C5 C CR56 0.000 -6.345 4.196 2.228
SMP N7 N NRD5 0.000 -5.346 3.985 1.310
SMP C8 C CR15 0.000 -5.043 2.709 1.427
SMP H8 H H 0.000 -4.282 2.213 0.837
SMP N3 N NRD6 0.000 -7.561 2.853 3.868
SMP C2 C CR16 0.000 -8.200 4.015 4.121
SMP H2 H H 0.000 -8.963 3.972 4.889
SMP N1 N NRD6 0.000 -8.018 5.228 3.544
SMP C6 C CR6 0.000 -7.073 5.327 2.579
SMP N6 N NH2 0.000 -6.837 6.558 1.944
SMP H62 H H 0.000 -6.201 7.244 2.351
SMP H61 H H 0.000 -7.296 6.790 1.063
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
SMP OP1 n/a P START
SMP P OP1 "O5'" .
SMP OP3 P HOP3 .
SMP HOP3 OP3 . .
SMP CMP P HMP1 .
SMP HMP3 CMP . .
SMP HMP2 CMP . .
SMP HMP1 CMP . .
SMP "O5'" P "C5'" .
SMP "C5'" "O5'" "C4'" .
SMP "H5'" "C5'" . .
SMP "H5''" "C5'" . .
SMP "C4'" "C5'" "C3'" .
SMP "H4'" "C4'" . .
SMP "C3'" "C4'" "C2'" .
SMP "H3'" "C3'" . .
SMP "O3'" "C3'" "HO3'" .
SMP "HO3'" "O3'" . .
SMP "C2'" "C3'" "C1'" .
SMP "H2'" "C2'" . .
SMP "H2''" "C2'" . .
SMP "C1'" "C2'" N9 .
SMP "H1'" "C1'" . .
SMP "O4'" "C1'" . .
SMP N9 "C1'" C4 .
SMP C4 N9 N3 .
SMP C5 C4 N7 .
SMP N7 C5 C8 .
SMP C8 N7 H8 .
SMP H8 C8 . .
SMP N3 C4 C2 .
SMP C2 N3 N1 .
SMP H2 C2 . .
SMP N1 C2 C6 .
SMP C6 N1 N6 .
SMP N6 C6 H61 .
SMP H62 N6 . .
SMP H61 N6 . END
SMP "C4'" "O4'" . ADD
SMP N9 C8 . ADD
SMP 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
SMP CMP P single 1.812 0.020
SMP P OP1 double 1.480 0.020
SMP "O5'" P single 1.610 0.020
SMP OP3 P single 1.610 0.020
SMP HMP1 CMP single 1.059 0.020
SMP HMP2 CMP single 1.059 0.020
SMP HMP3 CMP single 1.059 0.020
SMP "C5'" "O5'" single 1.426 0.020
SMP "C4'" "C5'" single 1.524 0.020
SMP "H5'" "C5'" single 1.092 0.020
SMP "H5''" "C5'" single 1.092 0.020
SMP "C4'" "O4'" single 1.426 0.020
SMP "C3'" "C4'" single 1.524 0.020
SMP "H4'" "C4'" single 1.099 0.020
SMP "O4'" "C1'" single 1.426 0.020
SMP N9 "C1'" single 1.485 0.020
SMP "C1'" "C2'" single 1.524 0.020
SMP "H1'" "C1'" single 1.099 0.020
SMP N9 C8 single 1.337 0.020
SMP C4 N9 single 1.337 0.020
SMP C8 N7 double 1.350 0.020
SMP H8 C8 single 1.083 0.020
SMP N7 C5 single 1.350 0.020
SMP C5 C6 double 1.490 0.020
SMP C5 C4 single 1.490 0.020
SMP N6 C6 single 1.355 0.020
SMP C6 N1 single 1.350 0.020
SMP H61 N6 single 1.010 0.020
SMP H62 N6 single 1.010 0.020
SMP N1 C2 double 1.337 0.020
SMP C2 N3 single 1.337 0.020
SMP H2 C2 single 1.083 0.020
SMP N3 C4 double 1.355 0.020
SMP "C2'" "C3'" single 1.524 0.020
SMP "O3'" "C3'" single 1.432 0.020
SMP "H3'" "C3'" single 1.099 0.020
SMP "H2'" "C2'" single 1.092 0.020
SMP "H2''" "C2'" single 1.092 0.020
SMP "HO3'" "O3'" single 0.967 0.020
SMP HOP3 OP3 single 0.967 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
SMP OP1 P OP3 109.500 3.000
SMP OP1 P CMP 109.500 3.000
SMP OP1 P "O5'" 109.500 3.000
SMP OP3 P CMP 109.500 3.000
SMP OP3 P "O5'" 109.500 3.000
SMP CMP P "O5'" 109.500 3.000
SMP P OP3 HOP3 120.000 3.000
SMP P CMP HMP3 109.500 3.000
SMP P CMP HMP2 109.500 3.000
SMP P CMP HMP1 109.500 3.000
SMP HMP3 CMP HMP2 109.470 3.000
SMP HMP3 CMP HMP1 109.470 3.000
SMP HMP2 CMP HMP1 109.470 3.000
SMP P "O5'" "C5'" 120.500 3.000
SMP "O5'" "C5'" "H5'" 109.470 3.000
SMP "O5'" "C5'" "H5''" 109.470 3.000
SMP "O5'" "C5'" "C4'" 109.470 3.000
SMP "H5'" "C5'" "H5''" 107.900 3.000
SMP "H5'" "C5'" "C4'" 109.470 3.000
SMP "H5''" "C5'" "C4'" 109.470 3.000
SMP "C5'" "C4'" "H4'" 108.340 3.000
SMP "C5'" "C4'" "C3'" 111.000 3.000
SMP "C5'" "C4'" "O4'" 109.470 3.000
SMP "H4'" "C4'" "C3'" 108.340 3.000
SMP "H4'" "C4'" "O4'" 109.470 3.000
SMP "C3'" "C4'" "O4'" 109.470 3.000
SMP "C4'" "C3'" "H3'" 108.340 3.000
SMP "C4'" "C3'" "O3'" 109.470 3.000
SMP "C4'" "C3'" "C2'" 111.000 3.000
SMP "H3'" "C3'" "O3'" 109.470 3.000
SMP "H3'" "C3'" "C2'" 108.340 3.000
SMP "O3'" "C3'" "C2'" 109.470 3.000
SMP "C3'" "O3'" "HO3'" 109.470 3.000
SMP "C3'" "C2'" "H2'" 109.470 3.000
SMP "C3'" "C2'" "H2''" 109.470 3.000
SMP "C3'" "C2'" "C1'" 111.000 3.000
SMP "H2'" "C2'" "H2''" 107.900 3.000
SMP "H2'" "C2'" "C1'" 109.470 3.000
SMP "H2''" "C2'" "C1'" 109.470 3.000
SMP "C2'" "C1'" "H1'" 108.340 3.000
SMP "C2'" "C1'" "O4'" 109.470 3.000
SMP "C2'" "C1'" N9 109.470 3.000
SMP "H1'" "C1'" "O4'" 109.470 3.000
SMP "H1'" "C1'" N9 109.470 3.000
SMP "O4'" "C1'" N9 109.470 3.000
SMP "C1'" "O4'" "C4'" 111.800 3.000
SMP "C1'" N9 C4 126.000 3.000
SMP "C1'" N9 C8 126.000 3.000
SMP C4 N9 C8 108.000 3.000
SMP N9 C4 C5 108.000 3.000
SMP N9 C4 N3 132.000 3.000
SMP C5 C4 N3 120.000 3.000
SMP C4 C5 N7 108.000 3.000
SMP C4 C5 C6 120.000 3.000
SMP N7 C5 C6 132.000 3.000
SMP C5 N7 C8 108.000 3.000
SMP N7 C8 H8 126.000 3.000
SMP N7 C8 N9 108.000 3.000
SMP H8 C8 N9 126.000 3.000
SMP C4 N3 C2 120.000 3.000
SMP N3 C2 H2 120.000 3.000
SMP N3 C2 N1 120.000 3.000
SMP H2 C2 N1 120.000 3.000
SMP C2 N1 C6 120.000 3.000
SMP N1 C6 N6 120.000 3.000
SMP N1 C6 C5 120.000 3.000
SMP N6 C6 C5 120.000 3.000
SMP C6 N6 H62 120.000 3.000
SMP C6 N6 H61 120.000 3.000
SMP H62 N6 H61 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
SMP var_1 OP1 P OP3 HOP3 -51.291 20.000 1
SMP var_2 OP1 P CMP HMP1 77.470 20.000 1
SMP var_3 OP1 P "O5'" "C5'" 174.246 20.000 1
SMP var_4 P "O5'" "C5'" "C4'" 179.985 20.000 1
SMP var_5 "O5'" "C5'" "C4'" "C3'" 179.546 20.000 3
SMP var_6 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
SMP var_7 "C5'" "C4'" "C3'" "C2'" -90.000 20.000 3
SMP var_8 "C4'" "C3'" "O3'" "HO3'" 46.621 20.000 1
SMP var_9 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
SMP var_10 "C3'" "C2'" "C1'" N9 150.000 20.000 3
SMP var_11 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
SMP var_12 "C2'" "C1'" N9 C4 93.514 20.000 1
SMP CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
SMP CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
SMP CONST_3 N9 C4 C5 N7 0.000 0.000 0
SMP CONST_4 C4 C5 C6 N1 0.000 0.000 0
SMP CONST_5 C4 C5 N7 C8 0.000 0.000 0
SMP CONST_6 C5 N7 C8 N9 0.000 0.000 0
SMP CONST_7 N9 C4 N3 C2 180.000 0.000 0
SMP CONST_8 C4 N3 C2 N1 0.000 0.000 0
SMP CONST_9 N3 C2 N1 C6 0.000 0.000 0
SMP CONST_10 C2 N1 C6 N6 180.000 0.000 0
SMP CONST_11 N1 C6 N6 H61 -94.601 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
SMP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
SMP chir_02 "C1'" "O4'" N9 "C2'" negativ
SMP chir_03 "C3'" "C4'" "C2'" "O3'" 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
SMP plan-1 N9 0.020
SMP plan-1 "C1'" 0.020
SMP plan-1 C8 0.020
SMP plan-1 C4 0.020
SMP plan-1 N7 0.020
SMP plan-1 H8 0.020
SMP plan-1 C5 0.020
SMP plan-1 C6 0.020
SMP plan-1 N1 0.020
SMP plan-1 C2 0.020
SMP plan-1 N3 0.020
SMP plan-1 N6 0.020
SMP plan-1 H2 0.020
SMP plan-1 H62 0.020
SMP plan-1 H61 0.020
SMP plan-2 N6 0.020
SMP plan-2 C6 0.020
SMP plan-2 H61 0.020
SMP plan-2 H62 0.020
# ------------------------------------------------------
|
