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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
NMS NMS '"1-(O2-(2-METHYLAMINO-2-OXO-ETHYL)-O' DNA 45 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_NMS
#
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
NMS OP3 O OP -0.666 0.000 0.000 0.000
NMS P P P 0.000 -0.530 1.416 0.049
NMS OP2 O OP -0.666 -1.420 1.497 -1.172
NMS OP1 O OP -0.666 0.531 2.491 0.149
NMS "O5'" O O2 0.000 -1.575 1.370 1.285
NMS "C5'" C CH2 0.000 -2.598 0.391 1.268
NMS "H5'" H H 0.000 -2.156 -0.607 1.248
NMS "H5''" H H 0.000 -3.226 0.527 0.385
NMS "C4'" C CH1 0.000 -3.444 0.549 2.524
NMS "H4'" H H 0.000 -2.807 0.459 3.415
NMS "O4'" O O2 0.000 -4.059 1.855 2.492
NMS "C1'" C CH1 0.000 -5.468 1.707 2.248
NMS "H1'" H H 0.000 -6.026 1.920 3.171
NMS N1 N NR6 0.000 -5.864 2.630 1.223
NMS C2 C CR6 0.000 -7.152 3.209 1.216
NMS O2 O O 0.000 -8.013 2.975 2.065
NMS N3 N NR16 0.000 -7.401 4.090 0.157
NMS HN3 H H 0.000 -8.344 4.528 0.129
NMS C4 C CR6 0.000 -6.526 4.441 -0.860
NMS O4 O O 0.000 -6.811 5.225 -1.761
NMS C5 C CR6 0.000 -5.190 3.791 -0.785
NMS C5M C CH3 0.000 -4.190 4.118 -1.847
NMS H73 H H 0.000 -4.589 4.859 -2.488
NMS H72 H H 0.000 -3.304 4.480 -1.394
NMS H71 H H 0.000 -3.972 3.246 -2.404
NMS C6 C CR16 0.000 -4.948 2.948 0.226
NMS H6 H H 0.000 -3.972 2.481 0.271
NMS "C3'" C CH1 0.000 -4.591 -0.451 2.607
NMS "H3'" H H 0.000 -4.330 -1.416 2.151
NMS "C2'" C CH1 0.000 -5.687 0.260 1.843
NMS "H2'" H H 0.000 -5.523 0.146 0.762
NMS "O6'" O O2 0.000 -6.974 -0.213 2.186
NMS "C7'" C CH2 0.000 -7.118 -1.603 1.913
NMS "H7'1" H H 0.000 -6.372 -2.155 2.490
NMS "H7'2" H H 0.000 -6.951 -1.773 0.847
NMS "C8'" C C 0.000 -8.503 -2.081 2.291
NMS "N9'" N NH1 0.000 -8.662 -3.436 2.045
NMS "H9'" H H 0.000 -7.882 -3.950 1.659
NMS C10 C CH3 0.000 -9.890 -4.148 2.316
NMS H103 H H 0.000 -9.869 -4.522 3.307
NMS H102 H H 0.000 -10.711 -3.489 2.204
NMS H101 H H 0.000 -9.987 -4.953 1.636
NMS "O8'" O O 0.000 -9.360 -1.334 2.755
NMS "O3'" O OH1 0.000 -4.954 -0.589 3.981
NMS "HO3'" H H 0.000 -4.548 0.157 4.448
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
NMS OP3 n/a P START
NMS P OP3 "O5'" .
NMS OP2 P . .
NMS OP1 P . .
NMS "O5'" P "C5'" .
NMS "C5'" "O5'" "C4'" .
NMS "H5'" "C5'" . .
NMS "H5''" "C5'" . .
NMS "C4'" "C5'" "C3'" .
NMS "H4'" "C4'" . .
NMS "O4'" "C4'" "C1'" .
NMS "C1'" "O4'" N1 .
NMS "H1'" "C1'" . .
NMS N1 "C1'" C2 .
NMS C2 N1 N3 .
NMS O2 C2 . .
NMS N3 C2 C4 .
NMS HN3 N3 . .
NMS C4 N3 C5 .
NMS O4 C4 . .
NMS C5 C4 C6 .
NMS C5M C5 H71 .
NMS H73 C5M . .
NMS H72 C5M . .
NMS H71 C5M . .
NMS C6 C5 H6 .
NMS H6 C6 . .
NMS "C3'" "C4'" "O3'" .
NMS "H3'" "C3'" . .
NMS "C2'" "C3'" "O6'" .
NMS "H2'" "C2'" . .
NMS "O6'" "C2'" "C7'" .
NMS "C7'" "O6'" "C8'" .
NMS "H7'1" "C7'" . .
NMS "H7'2" "C7'" . .
NMS "C8'" "C7'" "O8'" .
NMS "N9'" "C8'" C10 .
NMS "H9'" "N9'" . .
NMS C10 "N9'" H101 .
NMS H103 C10 . .
NMS H102 C10 . .
NMS H101 C10 . .
NMS "O8'" "C8'" . .
NMS "O3'" "C3'" . END
NMS "HO3'" "O3'" . .
NMS N1 C6 . ADD
NMS "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
NMS OP2 P deloc 1.510 0.020
NMS OP1 P deloc 1.510 0.020
NMS "O5'" P single 1.610 0.020
NMS P OP3 deloc 1.510 0.020
NMS "C5'" "O5'" single 1.426 0.020
NMS N1 C6 single 1.337 0.020
NMS C2 N1 single 1.410 0.020
NMS N1 "C1'" single 1.465 0.020
NMS C6 C5 double 1.390 0.020
NMS H6 C6 single 1.083 0.020
NMS O2 C2 double 1.250 0.020
NMS N3 C2 single 1.337 0.020
NMS C4 N3 single 1.337 0.020
NMS HN3 N3 single 1.040 0.020
NMS O4 C4 double 1.250 0.020
NMS C5 C4 single 1.487 0.020
NMS C5M C5 single 1.506 0.020
NMS H71 C5M single 1.059 0.020
NMS H72 C5M single 1.059 0.020
NMS H73 C5M single 1.059 0.020
NMS "C2'" "C1'" single 1.524 0.020
NMS "C2'" "C3'" single 1.524 0.020
NMS "O6'" "C2'" single 1.426 0.020
NMS "H2'" "C2'" single 1.099 0.020
NMS "C4'" "C5'" single 1.524 0.020
NMS "H5'" "C5'" single 1.092 0.020
NMS "H5''" "C5'" single 1.092 0.020
NMS "O4'" "C4'" single 1.426 0.020
NMS "C3'" "C4'" single 1.524 0.020
NMS "H4'" "C4'" single 1.099 0.020
NMS "C1'" "O4'" single 1.426 0.020
NMS "H1'" "C1'" single 1.099 0.020
NMS "O3'" "C3'" single 1.432 0.020
NMS "H3'" "C3'" single 1.099 0.020
NMS "HO3'" "O3'" single 0.967 0.020
NMS "C7'" "O6'" single 1.426 0.020
NMS "C8'" "C7'" single 1.510 0.020
NMS "H7'1" "C7'" single 1.092 0.020
NMS "H7'2" "C7'" single 1.092 0.020
NMS "O8'" "C8'" double 1.220 0.020
NMS "N9'" "C8'" single 1.330 0.020
NMS C10 "N9'" single 1.450 0.020
NMS "H9'" "N9'" single 1.010 0.020
NMS H101 C10 single 1.059 0.020
NMS H102 C10 single 1.059 0.020
NMS H103 C10 single 1.059 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
NMS OP3 P OP2 119.900 3.000
NMS OP3 P OP1 119.900 3.000
NMS OP3 P "O5'" 108.200 3.000
NMS OP2 P OP1 119.900 3.000
NMS OP2 P "O5'" 108.200 3.000
NMS OP1 P "O5'" 108.200 3.000
NMS P "O5'" "C5'" 120.500 3.000
NMS "O5'" "C5'" "H5'" 109.470 3.000
NMS "O5'" "C5'" "H5''" 109.470 3.000
NMS "O5'" "C5'" "C4'" 109.470 3.000
NMS "H5'" "C5'" "H5''" 107.900 3.000
NMS "H5'" "C5'" "C4'" 109.470 3.000
NMS "H5''" "C5'" "C4'" 109.470 3.000
NMS "C5'" "C4'" "H4'" 108.340 3.000
NMS "C5'" "C4'" "O4'" 109.470 3.000
NMS "C5'" "C4'" "C3'" 111.000 3.000
NMS "H4'" "C4'" "O4'" 109.470 3.000
NMS "H4'" "C4'" "C3'" 108.340 3.000
NMS "O4'" "C4'" "C3'" 109.470 3.000
NMS "C4'" "O4'" "C1'" 111.800 3.000
NMS "O4'" "C1'" "H1'" 109.470 3.000
NMS "O4'" "C1'" N1 109.470 3.000
NMS "O4'" "C1'" "C2'" 109.470 3.000
NMS "H1'" "C1'" N1 109.470 3.000
NMS "H1'" "C1'" "C2'" 108.340 3.000
NMS N1 "C1'" "C2'" 109.470 3.000
NMS "C1'" N1 C2 120.000 3.000
NMS "C1'" N1 C6 120.000 3.000
NMS C2 N1 C6 120.000 3.000
NMS N1 C2 O2 120.000 3.000
NMS N1 C2 N3 120.000 3.000
NMS O2 C2 N3 120.000 3.000
NMS C2 N3 HN3 120.000 3.000
NMS C2 N3 C4 120.000 3.000
NMS HN3 N3 C4 120.000 3.000
NMS N3 C4 O4 120.000 3.000
NMS N3 C4 C5 120.000 3.000
NMS O4 C4 C5 120.000 3.000
NMS C4 C5 C5M 120.000 3.000
NMS C4 C5 C6 120.000 3.000
NMS C5M C5 C6 120.000 3.000
NMS C5 C5M H73 109.470 3.000
NMS C5 C5M H72 109.470 3.000
NMS C5 C5M H71 109.470 3.000
NMS H73 C5M H72 109.470 3.000
NMS H73 C5M H71 109.470 3.000
NMS H72 C5M H71 109.470 3.000
NMS C5 C6 H6 120.000 3.000
NMS C5 C6 N1 120.000 3.000
NMS H6 C6 N1 120.000 3.000
NMS "C4'" "C3'" "H3'" 108.340 3.000
NMS "C4'" "C3'" "C2'" 111.000 3.000
NMS "C4'" "C3'" "O3'" 109.470 3.000
NMS "H3'" "C3'" "C2'" 108.340 3.000
NMS "H3'" "C3'" "O3'" 109.470 3.000
NMS "C2'" "C3'" "O3'" 109.470 3.000
NMS "C3'" "C2'" "H2'" 108.340 3.000
NMS "C3'" "C2'" "O6'" 109.470 3.000
NMS "C3'" "C2'" "C1'" 111.000 3.000
NMS "H2'" "C2'" "O6'" 109.470 3.000
NMS "H2'" "C2'" "C1'" 108.340 3.000
NMS "O6'" "C2'" "C1'" 109.470 3.000
NMS "C2'" "O6'" "C7'" 111.800 3.000
NMS "O6'" "C7'" "H7'1" 109.470 3.000
NMS "O6'" "C7'" "H7'2" 109.470 3.000
NMS "O6'" "C7'" "C8'" 109.470 3.000
NMS "H7'1" "C7'" "H7'2" 107.900 3.000
NMS "H7'1" "C7'" "C8'" 109.470 3.000
NMS "H7'2" "C7'" "C8'" 109.470 3.000
NMS "C7'" "C8'" "N9'" 116.500 3.000
NMS "C7'" "C8'" "O8'" 120.500 3.000
NMS "N9'" "C8'" "O8'" 123.000 3.000
NMS "C8'" "N9'" "H9'" 120.000 3.000
NMS "C8'" "N9'" C10 121.500 3.000
NMS "H9'" "N9'" C10 118.500 3.000
NMS "N9'" C10 H103 109.470 3.000
NMS "N9'" C10 H102 109.470 3.000
NMS "N9'" C10 H101 109.470 3.000
NMS H103 C10 H102 109.470 3.000
NMS H103 C10 H101 109.470 3.000
NMS H102 C10 H101 109.470 3.000
NMS "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
NMS var_1 OP3 P "O5'" "C5'" -54.172 20.000 1
NMS var_2 P "O5'" "C5'" "C4'" -179.986 20.000 1
NMS var_3 "O5'" "C5'" "C4'" "C3'" 179.497 20.000 3
NMS var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
NMS var_5 "C4'" "O4'" "C1'" N1 -120.000 20.000 1
NMS var_6 "O4'" "C1'" N1 C2 -147.813 20.000 1
NMS CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
NMS CONST_2 "C1'" N1 C2 N3 180.000 0.000 0
NMS CONST_3 N1 C2 N3 C4 0.000 0.000 0
NMS CONST_4 C2 N3 C4 C5 0.000 0.000 0
NMS CONST_5 N3 C4 C5 C6 0.000 0.000 0
NMS var_7 C4 C5 C5M H71 -115.793 20.000 1
NMS CONST_6 C4 C5 C6 N1 0.000 0.000 0
NMS var_8 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
NMS var_9 "C4'" "C3'" "C2'" "O6'" -150.000 20.000 3
NMS var_10 "C3'" "C2'" "C1'" "O4'" 30.000 20.000 3
NMS var_11 "C3'" "C2'" "O6'" "C7'" -59.966 20.000 1
NMS var_12 "C2'" "O6'" "C7'" "C8'" 179.976 20.000 1
NMS var_13 "O6'" "C7'" "C8'" "O8'" 0.579 20.000 3
NMS CONST_7 "C7'" "C8'" "N9'" C10 180.000 0.000 0
NMS var_14 "C8'" "N9'" C10 H101 150.294 20.000 1
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
NMS chir_01 "C2'" "C1'" "C3'" "O6'" negativ
NMS chir_02 "C4'" "C5'" "O4'" "C3'" negativ
NMS chir_03 "C1'" N1 "C2'" "O4'" negativ
NMS chir_04 "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
NMS plan-1 N1 0.020
NMS plan-1 C6 0.020
NMS plan-1 C2 0.020
NMS plan-1 "C1'" 0.020
NMS plan-1 N3 0.020
NMS plan-1 C4 0.020
NMS plan-1 C5 0.020
NMS plan-1 H6 0.020
NMS plan-1 O2 0.020
NMS plan-1 HN3 0.020
NMS plan-1 O4 0.020
NMS plan-1 C5M 0.020
NMS plan-2 "C8'" 0.020
NMS plan-2 "C7'" 0.020
NMS plan-2 "O8'" 0.020
NMS plan-2 "N9'" 0.020
NMS plan-2 "H9'" 0.020
NMS plan-3 "N9'" 0.020
NMS plan-3 "C8'" 0.020
NMS plan-3 C10 0.020
NMS plan-3 "H9'" 0.020
# ------------------------------------------------------
|
