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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
MDR MDR '9-(2-DEOXY-BETA-D-RIBOFURANOSYL)-6-M' non-polymer 32 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MDR
#
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
MDR "O5'" O OH1 0.000 0.000 0.000 0.000
MDR "H5'" H H 0.000 0.842 0.409 0.240
MDR "C5'" C CH2 0.000 -0.896 1.004 -0.482
MDR "H5'1" H H 0.000 -0.462 1.487 -1.359
MDR "H5'2" H H 0.000 -1.060 1.749 0.299
MDR "C4'" C CH1 0.000 -2.229 0.357 -0.861
MDR "H4'" H H 0.000 -2.076 -0.431 -1.611
MDR "C3'" C CH1 0.000 -3.222 1.423 -1.387
MDR "H3'" H H 0.000 -3.122 2.363 -0.826
MDR "O3'" O OH1 0.000 -3.040 1.644 -2.787
MDR H1 H H 0.000 -3.727 2.242 -3.111
MDR "C2'" C CH2 0.000 -4.592 0.757 -1.106
MDR "H2'2" H H 0.000 -4.992 0.257 -1.990
MDR "H2'1" H H 0.000 -5.326 1.472 -0.730
MDR "O4'" O O2 0.000 -2.892 -0.176 0.308
MDR "C1'" C CH1 0.000 -4.287 -0.289 -0.018
MDR "H1'" H H 0.000 -4.501 -1.297 -0.397
MDR N9 N NR5 0.000 -5.099 -0.021 1.171
MDR C4 C CR56 0.000 -6.347 -0.527 1.433
MDR N3 N NRD6 0.000 -7.181 -1.339 0.798
MDR C2 C CR16 0.000 -8.348 -1.645 1.328
MDR H2 H H 0.000 -9.009 -2.310 0.786
MDR N1 N NRD6 0.000 -8.740 -1.170 2.496
MDR C8 C CR15 0.000 -4.753 0.775 2.221
MDR H8 H H 0.000 -3.820 1.317 2.307
MDR N7 N NRD5 0.000 -5.708 0.789 3.105
MDR C5 C CR56 0.000 -6.730 0.006 2.679
MDR C6 C CR6 0.000 -7.973 -0.354 3.198
MDR "C6'" C CH3 0.000 -8.436 0.180 4.529
MDR "H6'3" H H 0.000 -8.010 1.136 4.693
MDR "H6'2" H H 0.000 -9.492 0.259 4.530
MDR "H6'1" H H 0.000 -8.130 -0.479 5.300
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
MDR "O5'" n/a "C5'" START
MDR "H5'" "O5'" . .
MDR "C5'" "O5'" "C4'" .
MDR "H5'1" "C5'" . .
MDR "H5'2" "C5'" . .
MDR "C4'" "C5'" "O4'" .
MDR "H4'" "C4'" . .
MDR "C3'" "C4'" "C2'" .
MDR "H3'" "C3'" . .
MDR "O3'" "C3'" H1 .
MDR H1 "O3'" . .
MDR "C2'" "C3'" "H2'1" .
MDR "H2'2" "C2'" . .
MDR "H2'1" "C2'" . .
MDR "O4'" "C4'" "C1'" .
MDR "C1'" "O4'" N9 .
MDR "H1'" "C1'" . .
MDR N9 "C1'" C8 .
MDR C4 N9 N3 .
MDR N3 C4 C2 .
MDR C2 N3 N1 .
MDR H2 C2 . .
MDR N1 C2 . .
MDR C8 N9 N7 .
MDR H8 C8 . .
MDR N7 C8 C5 .
MDR C5 N7 C6 .
MDR C6 C5 "C6'" .
MDR "C6'" C6 "H6'1" .
MDR "H6'3" "C6'" . .
MDR "H6'2" "C6'" . .
MDR "H6'1" "C6'" . END
MDR C6 N1 . ADD
MDR C4 C5 . ADD
MDR "C1'" "C2'" . 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
MDR "C6'" C6 single 1.506 0.020
MDR "H6'1" "C6'" single 1.059 0.020
MDR "H6'2" "C6'" single 1.059 0.020
MDR "H6'3" "C6'" single 1.059 0.020
MDR C6 N1 double 1.350 0.020
MDR C6 C5 single 1.490 0.020
MDR N1 C2 single 1.337 0.020
MDR C2 N3 double 1.337 0.020
MDR H2 C2 single 1.083 0.020
MDR N3 C4 single 1.355 0.020
MDR C4 C5 double 1.490 0.020
MDR C4 N9 single 1.337 0.020
MDR C5 N7 single 1.350 0.020
MDR N7 C8 double 1.350 0.020
MDR C8 N9 single 1.337 0.020
MDR H8 C8 single 1.083 0.020
MDR N9 "C1'" single 1.485 0.020
MDR "C1'" "C2'" single 1.524 0.020
MDR "C1'" "O4'" single 1.426 0.020
MDR "H1'" "C1'" single 1.099 0.020
MDR "C2'" "C3'" single 1.524 0.020
MDR "H2'1" "C2'" single 1.092 0.020
MDR "H2'2" "C2'" single 1.092 0.020
MDR "O3'" "C3'" single 1.432 0.020
MDR "C3'" "C4'" single 1.524 0.020
MDR "H3'" "C3'" single 1.099 0.020
MDR H1 "O3'" single 0.967 0.020
MDR "C4'" "C5'" single 1.524 0.020
MDR "O4'" "C4'" single 1.426 0.020
MDR "H4'" "C4'" single 1.099 0.020
MDR "C5'" "O5'" single 1.432 0.020
MDR "H5'1" "C5'" single 1.092 0.020
MDR "H5'2" "C5'" single 1.092 0.020
MDR "H5'" "O5'" 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
MDR "H5'" "O5'" "C5'" 109.470 3.000
MDR "O5'" "C5'" "H5'1" 109.470 3.000
MDR "O5'" "C5'" "H5'2" 109.470 3.000
MDR "O5'" "C5'" "C4'" 109.470 3.000
MDR "H5'1" "C5'" "H5'2" 107.900 3.000
MDR "H5'1" "C5'" "C4'" 109.470 3.000
MDR "H5'2" "C5'" "C4'" 109.470 3.000
MDR "C5'" "C4'" "H4'" 108.340 3.000
MDR "C5'" "C4'" "C3'" 111.000 3.000
MDR "C5'" "C4'" "O4'" 109.470 3.000
MDR "H4'" "C4'" "C3'" 108.340 3.000
MDR "H4'" "C4'" "O4'" 109.470 3.000
MDR "C3'" "C4'" "O4'" 109.470 3.000
MDR "C4'" "C3'" "H3'" 108.340 3.000
MDR "C4'" "C3'" "O3'" 109.470 3.000
MDR "C4'" "C3'" "C2'" 111.000 3.000
MDR "H3'" "C3'" "O3'" 109.470 3.000
MDR "H3'" "C3'" "C2'" 108.340 3.000
MDR "O3'" "C3'" "C2'" 109.470 3.000
MDR "C3'" "O3'" H1 109.470 3.000
MDR "C3'" "C2'" "H2'2" 109.470 3.000
MDR "C3'" "C2'" "H2'1" 109.470 3.000
MDR "C3'" "C2'" "C1'" 111.000 3.000
MDR "H2'2" "C2'" "H2'1" 107.900 3.000
MDR "H2'2" "C2'" "C1'" 109.470 3.000
MDR "H2'1" "C2'" "C1'" 109.470 3.000
MDR "C4'" "O4'" "C1'" 111.800 3.000
MDR "O4'" "C1'" "H1'" 109.470 3.000
MDR "O4'" "C1'" N9 109.470 3.000
MDR "O4'" "C1'" "C2'" 109.470 3.000
MDR "H1'" "C1'" N9 109.470 3.000
MDR "H1'" "C1'" "C2'" 108.340 3.000
MDR N9 "C1'" "C2'" 109.470 3.000
MDR "C1'" N9 C4 126.000 3.000
MDR "C1'" N9 C8 126.000 3.000
MDR C4 N9 C8 108.000 3.000
MDR N9 C4 N3 132.000 3.000
MDR N9 C4 C5 108.000 3.000
MDR N3 C4 C5 120.000 3.000
MDR C4 N3 C2 120.000 3.000
MDR N3 C2 H2 120.000 3.000
MDR N3 C2 N1 120.000 3.000
MDR H2 C2 N1 120.000 3.000
MDR C2 N1 C6 120.000 3.000
MDR N9 C8 H8 126.000 3.000
MDR N9 C8 N7 108.000 3.000
MDR H8 C8 N7 126.000 3.000
MDR C8 N7 C5 108.000 3.000
MDR N7 C5 C6 132.000 3.000
MDR N7 C5 C4 108.000 3.000
MDR C6 C5 C4 120.000 3.000
MDR C5 C6 "C6'" 120.000 3.000
MDR C5 C6 N1 120.000 3.000
MDR "C6'" C6 N1 120.000 3.000
MDR C6 "C6'" "H6'3" 109.470 3.000
MDR C6 "C6'" "H6'2" 109.470 3.000
MDR C6 "C6'" "H6'1" 109.470 3.000
MDR "H6'3" "C6'" "H6'2" 109.470 3.000
MDR "H6'3" "C6'" "H6'1" 109.470 3.000
MDR "H6'2" "C6'" "H6'1" 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
MDR var_1 "H5'" "O5'" "C5'" "C4'" -179.934 20.000 1
MDR var_2 "O5'" "C5'" "C4'" "O4'" 65.726 20.000 3
MDR var_3 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
MDR var_4 "C4'" "C3'" "O3'" H1 174.155 20.000 1
MDR var_5 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
MDR var_6 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
MDR var_7 "C4'" "O4'" "C1'" N9 -150.000 20.000 1
MDR var_8 "O4'" "C1'" "C2'" "C3'" 0.000 20.000 3
MDR var_9 "O4'" "C1'" N9 C8 28.178 20.000 1
MDR CONST_1 "C1'" N9 C4 N3 0.000 0.000 0
MDR CONST_2 N9 C4 C5 N7 0.000 0.000 0
MDR CONST_3 N9 C4 N3 C2 180.000 0.000 0
MDR CONST_4 C4 N3 C2 N1 0.000 0.000 0
MDR CONST_5 N3 C2 N1 C6 0.000 0.000 0
MDR CONST_6 "C1'" N9 C8 N7 180.000 0.000 0
MDR CONST_7 N9 C8 N7 C5 0.000 0.000 0
MDR CONST_8 C8 N7 C5 C6 180.000 0.000 0
MDR CONST_9 N7 C5 C6 "C6'" 0.000 0.000 0
MDR CONST_10 C5 C6 N1 C2 0.000 0.000 0
MDR var_10 C5 C6 "C6'" "H6'1" -90.284 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
MDR chir_01 "C1'" N9 "C2'" "O4'" negativ
MDR chir_02 "C3'" "C2'" "O3'" "C4'" positiv
MDR chir_03 "C4'" "C3'" "C5'" "O4'" 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
MDR plan-1 C6 0.020
MDR plan-1 "C6'" 0.020
MDR plan-1 N1 0.020
MDR plan-1 C5 0.020
MDR plan-1 C2 0.020
MDR plan-1 N3 0.020
MDR plan-1 H2 0.020
MDR plan-1 C4 0.020
MDR plan-1 N9 0.020
MDR plan-1 N7 0.020
MDR plan-1 C8 0.020
MDR plan-1 H8 0.020
MDR plan-1 "C1'" 0.020
# ------------------------------------------------------
|
