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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
MRG MRG 'N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUANOS' DNA 45 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MRG
#
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
MRG OP3 O OP -0.666 0.000 0.000 0.000
MRG P P P 0.000 -1.032 0.952 0.565
MRG OP1 O OP -0.666 -0.849 1.298 2.026
MRG OP2 O OP -0.666 -0.983 2.125 -0.390
MRG "O5'" O O2 0.000 -2.432 0.222 0.204
MRG "C5'" C CH2 0.000 -2.681 -0.136 -1.143
MRG "H5'" H H 0.000 -1.914 -0.833 -1.488
MRG "H5''" H H 0.000 -2.669 0.756 -1.772
MRG "C4'" C CH1 0.000 -4.048 -0.800 -1.227
MRG "H4'" H H 0.000 -4.075 -1.678 -0.566
MRG "O4'" O O2 0.000 -5.039 0.160 -0.805
MRG "C1'" C CH1 0.000 -5.903 0.451 -1.916
MRG "H1'" H H 0.000 -6.826 -0.135 -1.804
MRG N9 N NR5 0.000 -6.250 1.868 -1.920
MRG C8 C CR15 0.000 -5.441 2.902 -1.509
MRG H8 H H 0.000 -4.435 2.765 -1.131
MRG N7 N NRD5 0.000 -6.026 4.078 -1.628
MRG C5 C CR56 0.000 -7.256 3.782 -2.134
MRG C4 C CR56 0.000 -7.426 2.432 -2.325
MRG C6 C CR6 0.000 -8.329 4.678 -2.468
MRG N1 N NR16 0.000 -9.433 3.970 -2.963
MRG H1 H H 0.000 -10.271 4.521 -3.238
MRG C2 C CR6 0.000 -9.500 2.565 -3.120
MRG N2 N NH1 0.000 -10.680 2.086 -3.623
MRG H21 H H 0.000 -11.425 2.729 -3.853
MRG C21 C CH2 0.000 -10.867 0.679 -3.827
MRG H211 H H 0.000 -10.797 0.191 -2.852
MRG H212 H H 0.000 -10.057 0.326 -4.468
MRG C22 C CH2 0.000 -12.211 0.346 -4.471
MRG H221 H H 0.000 -12.250 -0.734 -4.627
MRG H222 H H 0.000 -12.256 0.854 -5.436
MRG C23 C CH2 0.000 -13.394 0.781 -3.608
MRG H231 H H 0.000 -13.340 1.861 -3.453
MRG H232 H H 0.000 -13.334 0.273 -2.644
MRG S24 S SH1 0.000 -14.966 0.362 -4.419
MRG H24 H H 0.000 -14.518 -0.730 -5.034
MRG N3 N NRD6 0.000 -8.501 1.768 -2.805
MRG O6 O O 0.000 -8.269 5.893 -2.330
MRG "C3'" C CH1 0.000 -4.414 -1.215 -2.649
MRG "H3'" H H 0.000 -3.522 -1.423 -3.256
MRG "C2'" C CH2 0.000 -5.178 -0.020 -3.169
MRG "H2''" H H 0.000 -5.909 -0.279 -3.938
MRG "H2'" H H 0.000 -4.531 0.778 -3.539
MRG "O3'" O OH1 0.000 -5.298 -2.333 -2.608
MRG "HO3'" H H 0.000 -5.976 -2.123 -1.947
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
MRG OP3 n/a P START
MRG P OP3 "O5'" .
MRG OP1 P . .
MRG OP2 P . .
MRG "O5'" P "C5'" .
MRG "C5'" "O5'" "C4'" .
MRG "H5'" "C5'" . .
MRG "H5''" "C5'" . .
MRG "C4'" "C5'" "C3'" .
MRG "H4'" "C4'" . .
MRG "O4'" "C4'" "C1'" .
MRG "C1'" "O4'" N9 .
MRG "H1'" "C1'" . .
MRG N9 "C1'" C8 .
MRG C8 N9 N7 .
MRG H8 C8 . .
MRG N7 C8 C5 .
MRG C5 N7 C6 .
MRG C4 C5 . .
MRG C6 C5 O6 .
MRG N1 C6 C2 .
MRG H1 N1 . .
MRG C2 N1 N3 .
MRG N2 C2 C21 .
MRG H21 N2 . .
MRG C21 N2 C22 .
MRG H211 C21 . .
MRG H212 C21 . .
MRG C22 C21 C23 .
MRG H221 C22 . .
MRG H222 C22 . .
MRG C23 C22 S24 .
MRG H231 C23 . .
MRG H232 C23 . .
MRG S24 C23 H24 .
MRG H24 S24 . .
MRG N3 C2 . .
MRG O6 C6 . .
MRG "C3'" "C4'" "O3'" .
MRG "H3'" "C3'" . .
MRG "C2'" "C3'" "H2'" .
MRG "H2''" "C2'" . .
MRG "H2'" "C2'" . .
MRG "O3'" "C3'" . END
MRG "HO3'" "O3'" . .
MRG N9 C4 . ADD
MRG C4 N3 . ADD
MRG "C2'" "C1'" . 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
MRG OP1 P deloc 1.510 0.020
MRG OP2 P deloc 1.510 0.020
MRG "O5'" P single 1.610 0.020
MRG P OP3 deloc 1.510 0.020
MRG "C5'" "O5'" single 1.426 0.020
MRG N9 C4 single 1.337 0.020
MRG C8 N9 single 1.337 0.020
MRG N9 "C1'" single 1.485 0.020
MRG C4 N3 single 1.355 0.020
MRG C4 C5 double 1.490 0.020
MRG N3 C2 double 1.350 0.020
MRG C2 N1 single 1.337 0.020
MRG N2 C2 single 1.350 0.020
MRG N1 C6 single 1.337 0.020
MRG H1 N1 single 1.040 0.020
MRG O6 C6 double 1.250 0.020
MRG C6 C5 single 1.490 0.020
MRG C5 N7 single 1.350 0.020
MRG N7 C8 double 1.350 0.020
MRG H8 C8 single 1.083 0.020
MRG C21 N2 single 1.450 0.020
MRG H21 N2 single 1.010 0.020
MRG C22 C21 single 1.524 0.020
MRG H211 C21 single 1.092 0.020
MRG H212 C21 single 1.092 0.020
MRG C23 C22 single 1.524 0.020
MRG H221 C22 single 1.092 0.020
MRG H222 C22 single 1.092 0.020
MRG S24 C23 single 1.810 0.020
MRG H231 C23 single 1.092 0.020
MRG H232 C23 single 1.092 0.020
MRG H24 S24 single 1.330 0.020
MRG "C2'" "C1'" single 1.524 0.020
MRG "C2'" "C3'" single 1.524 0.020
MRG "H2'" "C2'" single 1.092 0.020
MRG "H2''" "C2'" single 1.092 0.020
MRG "C4'" "C5'" single 1.524 0.020
MRG "H5'" "C5'" single 1.092 0.020
MRG "H5''" "C5'" single 1.092 0.020
MRG "O4'" "C4'" single 1.426 0.020
MRG "C3'" "C4'" single 1.524 0.020
MRG "H4'" "C4'" single 1.099 0.020
MRG "C1'" "O4'" single 1.426 0.020
MRG "H1'" "C1'" single 1.099 0.020
MRG "O3'" "C3'" single 1.432 0.020
MRG "H3'" "C3'" single 1.099 0.020
MRG "HO3'" "O3'" 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
MRG OP3 P OP1 119.900 3.000
MRG OP3 P OP2 119.900 3.000
MRG OP3 P "O5'" 108.200 3.000
MRG OP1 P OP2 119.900 3.000
MRG OP1 P "O5'" 108.200 3.000
MRG OP2 P "O5'" 108.200 3.000
MRG P "O5'" "C5'" 120.500 3.000
MRG "O5'" "C5'" "H5'" 109.470 3.000
MRG "O5'" "C5'" "H5''" 109.470 3.000
MRG "O5'" "C5'" "C4'" 109.470 3.000
MRG "H5'" "C5'" "H5''" 107.900 3.000
MRG "H5'" "C5'" "C4'" 109.470 3.000
MRG "H5''" "C5'" "C4'" 109.470 3.000
MRG "C5'" "C4'" "H4'" 108.340 3.000
MRG "C5'" "C4'" "O4'" 109.470 3.000
MRG "C5'" "C4'" "C3'" 111.000 3.000
MRG "H4'" "C4'" "O4'" 109.470 3.000
MRG "H4'" "C4'" "C3'" 108.340 3.000
MRG "O4'" "C4'" "C3'" 109.470 3.000
MRG "C4'" "O4'" "C1'" 111.800 3.000
MRG "O4'" "C1'" "H1'" 109.470 3.000
MRG "O4'" "C1'" N9 109.470 3.000
MRG "O4'" "C1'" "C2'" 109.470 3.000
MRG "H1'" "C1'" N9 109.470 3.000
MRG "H1'" "C1'" "C2'" 108.340 3.000
MRG N9 "C1'" "C2'" 109.470 3.000
MRG "C1'" N9 C8 126.000 3.000
MRG "C1'" N9 C4 126.000 3.000
MRG C8 N9 C4 108.000 3.000
MRG N9 C8 H8 126.000 3.000
MRG N9 C8 N7 108.000 3.000
MRG H8 C8 N7 126.000 3.000
MRG C8 N7 C5 108.000 3.000
MRG N7 C5 C4 108.000 3.000
MRG N7 C5 C6 132.000 3.000
MRG C4 C5 C6 120.000 3.000
MRG C5 C4 N9 108.000 3.000
MRG C5 C4 N3 120.000 3.000
MRG N9 C4 N3 132.000 3.000
MRG C5 C6 N1 120.000 3.000
MRG C5 C6 O6 120.000 3.000
MRG N1 C6 O6 120.000 3.000
MRG C6 N1 H1 120.000 3.000
MRG C6 N1 C2 120.000 3.000
MRG H1 N1 C2 120.000 3.000
MRG N1 C2 N2 120.000 3.000
MRG N1 C2 N3 120.000 3.000
MRG N2 C2 N3 120.000 3.000
MRG C2 N2 H21 120.000 3.000
MRG C2 N2 C21 120.000 3.000
MRG H21 N2 C21 118.500 3.000
MRG N2 C21 H211 109.470 3.000
MRG N2 C21 H212 109.470 3.000
MRG N2 C21 C22 112.000 3.000
MRG H211 C21 H212 107.900 3.000
MRG H211 C21 C22 109.470 3.000
MRG H212 C21 C22 109.470 3.000
MRG C21 C22 H221 109.470 3.000
MRG C21 C22 H222 109.470 3.000
MRG C21 C22 C23 111.000 3.000
MRG H221 C22 H222 107.900 3.000
MRG H221 C22 C23 109.470 3.000
MRG H222 C22 C23 109.470 3.000
MRG C22 C23 H231 109.470 3.000
MRG C22 C23 H232 109.470 3.000
MRG C22 C23 S24 109.470 3.000
MRG H231 C23 H232 107.900 3.000
MRG H231 C23 S24 109.470 3.000
MRG H232 C23 S24 109.470 3.000
MRG C23 S24 H24 96.000 3.000
MRG C2 N3 C4 120.000 3.000
MRG "C4'" "C3'" "H3'" 108.340 3.000
MRG "C4'" "C3'" "C2'" 111.000 3.000
MRG "C4'" "C3'" "O3'" 109.470 3.000
MRG "H3'" "C3'" "C2'" 108.340 3.000
MRG "H3'" "C3'" "O3'" 109.470 3.000
MRG "C2'" "C3'" "O3'" 109.470 3.000
MRG "C3'" "C2'" "H2''" 109.470 3.000
MRG "C3'" "C2'" "H2'" 109.470 3.000
MRG "C3'" "C2'" "C1'" 111.000 3.000
MRG "H2''" "C2'" "H2'" 107.900 3.000
MRG "H2''" "C2'" "C1'" 109.470 3.000
MRG "H2'" "C2'" "C1'" 109.470 3.000
MRG "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
MRG var_1 OP3 P "O5'" "C5'" -54.168 20.000 1
MRG var_2 P "O5'" "C5'" "C4'" 179.992 20.000 1
MRG var_3 "O5'" "C5'" "C4'" "C3'" 179.515 20.000 3
MRG var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
MRG var_5 "C4'" "O4'" "C1'" N9 -150.000 20.000 1
MRG var_6 "O4'" "C1'" N9 C8 33.412 20.000 1
MRG CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
MRG CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
MRG CONST_3 N9 C8 N7 C5 0.000 0.000 0
MRG CONST_4 C8 N7 C5 C6 180.000 0.000 0
MRG CONST_5 N7 C5 C4 N9 0.000 0.000 0
MRG CONST_6 C5 C4 N3 C2 0.000 0.000 0
MRG CONST_7 N7 C5 C6 O6 0.000 0.000 0
MRG CONST_8 C5 C6 N1 C2 0.000 0.000 0
MRG CONST_9 C6 N1 C2 N3 0.000 0.000 0
MRG var_7 N1 C2 N2 C21 -179.997 20.000 1
MRG var_8 C2 N2 C21 C22 -176.563 20.000 3
MRG var_9 N2 C21 C22 C23 -61.437 20.000 3
MRG var_10 C21 C22 C23 S24 179.997 20.000 3
MRG var_11 C22 C23 S24 H24 31.702 20.000 1
MRG CONST_10 N1 C2 N3 C4 0.000 0.000 0
MRG var_12 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
MRG var_13 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
MRG var_14 "C3'" "C2'" "C1'" "O4'" 30.000 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
MRG chir_01 "C4'" "C5'" "O4'" "C3'" negativ
MRG chir_02 "C1'" N9 "C2'" "O4'" negativ
MRG chir_03 "C3'" "C2'" "C4'" "O3'" 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
MRG plan-1 N9 0.020
MRG plan-1 C4 0.020
MRG plan-1 C8 0.020
MRG plan-1 "C1'" 0.020
MRG plan-1 N7 0.020
MRG plan-1 N3 0.020
MRG plan-1 C5 0.020
MRG plan-1 C2 0.020
MRG plan-1 N1 0.020
MRG plan-1 C6 0.020
MRG plan-1 N2 0.020
MRG plan-1 H1 0.020
MRG plan-1 O6 0.020
MRG plan-1 H8 0.020
MRG plan-1 H21 0.020
MRG plan-2 N2 0.020
MRG plan-2 C2 0.020
MRG plan-2 C21 0.020
MRG plan-2 H21 0.020
# ------------------------------------------------------
|
