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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
PYD PYD '2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE ' non-polymer 18 9 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PYD
#
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
PYD "N4'" N NH2 0.000 0.000 0.000 0.000
PYD HN41 H H 0.000 0.158 0.001 -1.003
PYD HN42 H H 0.000 0.802 -0.001 0.623
PYD "C4'" C CR6 0.000 -1.287 0.001 0.510
PYD "C5'" C CR6 0.000 -1.504 0.000 1.888
PYD "C7'" C CH3 0.000 -0.346 -0.001 2.852
PYD HC73 H H 0.000 0.479 0.499 2.414
PYD HC72 H H 0.000 -0.627 0.498 3.743
PYD HC71 H H 0.000 -0.074 -0.999 3.078
PYD "C6'" C CR16 0.000 -2.807 0.001 2.348
PYD "HC6'" H H 0.000 -3.013 0.001 3.411
PYD "N1'" N NRD6 0.000 -3.800 0.001 1.471
PYD "N3'" N NRD6 0.000 -2.337 -0.004 -0.306
PYD "C2'" C CR6 0.000 -3.563 0.001 0.176
PYD CM2 C CH3 0.000 -4.726 0.003 -0.782
PYD HM23 H H 0.000 -4.450 -0.497 -1.674
PYD HM22 H H 0.000 -5.549 -0.496 -0.339
PYD HM21 H H 0.000 -4.998 1.001 -1.006
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
PYD "N4'" n/a "C4'" START
PYD HN41 "N4'" . .
PYD HN42 "N4'" . .
PYD "C4'" "N4'" "N3'" .
PYD "C5'" "C4'" "C6'" .
PYD "C7'" "C5'" HC71 .
PYD HC73 "C7'" . .
PYD HC72 "C7'" . .
PYD HC71 "C7'" . .
PYD "C6'" "C5'" "N1'" .
PYD "HC6'" "C6'" . .
PYD "N1'" "C6'" . .
PYD "N3'" "C4'" "C2'" .
PYD "C2'" "N3'" CM2 .
PYD CM2 "C2'" HM21 .
PYD HM23 CM2 . .
PYD HM22 CM2 . .
PYD HM21 CM2 . END
PYD "N1'" "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
PYD "N1'" "C2'" double 1.350 0.020
PYD "N1'" "C6'" single 1.337 0.020
PYD CM2 "C2'" single 1.506 0.020
PYD "C2'" "N3'" single 1.350 0.020
PYD HM21 CM2 single 1.059 0.020
PYD HM22 CM2 single 1.059 0.020
PYD HM23 CM2 single 1.059 0.020
PYD "N3'" "C4'" double 1.350 0.020
PYD "C4'" "N4'" single 1.355 0.020
PYD "C5'" "C4'" single 1.487 0.020
PYD HN41 "N4'" single 1.010 0.020
PYD HN42 "N4'" single 1.010 0.020
PYD "C6'" "C5'" double 1.390 0.020
PYD "C7'" "C5'" single 1.506 0.020
PYD "HC6'" "C6'" single 1.083 0.020
PYD HC71 "C7'" single 1.059 0.020
PYD HC72 "C7'" single 1.059 0.020
PYD HC73 "C7'" 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
PYD HN41 "N4'" HN42 120.000 3.000
PYD HN41 "N4'" "C4'" 120.000 3.000
PYD HN42 "N4'" "C4'" 120.000 3.000
PYD "N4'" "C4'" "C5'" 120.000 3.000
PYD "N4'" "C4'" "N3'" 120.000 3.000
PYD "C5'" "C4'" "N3'" 120.000 3.000
PYD "C4'" "C5'" "C7'" 120.000 3.000
PYD "C4'" "C5'" "C6'" 120.000 3.000
PYD "C7'" "C5'" "C6'" 120.000 3.000
PYD "C5'" "C7'" HC73 109.470 3.000
PYD "C5'" "C7'" HC72 109.470 3.000
PYD "C5'" "C7'" HC71 109.470 3.000
PYD HC73 "C7'" HC72 109.470 3.000
PYD HC73 "C7'" HC71 109.470 3.000
PYD HC72 "C7'" HC71 109.470 3.000
PYD "C5'" "C6'" "HC6'" 120.000 3.000
PYD "C5'" "C6'" "N1'" 120.000 3.000
PYD "HC6'" "C6'" "N1'" 120.000 3.000
PYD "C6'" "N1'" "C2'" 120.000 3.000
PYD "C4'" "N3'" "C2'" 120.000 3.000
PYD "N3'" "C2'" CM2 120.000 3.000
PYD "N3'" "C2'" "N1'" 120.000 3.000
PYD CM2 "C2'" "N1'" 120.000 3.000
PYD "C2'" CM2 HM23 109.470 3.000
PYD "C2'" CM2 HM22 109.470 3.000
PYD "C2'" CM2 HM21 109.470 3.000
PYD HM23 CM2 HM22 109.470 3.000
PYD HM23 CM2 HM21 109.470 3.000
PYD HM22 CM2 HM21 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
PYD CONST_1 HN42 "N4'" "C4'" "N3'" -179.682 0.000 0
PYD CONST_2 "N4'" "C4'" "C5'" "C6'" 180.000 0.000 0
PYD var_1 "C4'" "C5'" "C7'" HC71 -90.009 20.000 1
PYD CONST_3 "C4'" "C5'" "C6'" "N1'" 0.000 0.000 0
PYD CONST_4 "C5'" "C6'" "N1'" "C2'" 0.000 0.000 0
PYD CONST_5 "C6'" "N1'" "C2'" "N3'" 0.000 0.000 0
PYD CONST_6 "N4'" "C4'" "N3'" "C2'" 180.000 0.000 0
PYD CONST_7 "C4'" "N3'" "C2'" CM2 180.000 0.000 0
PYD var_2 "N3'" "C2'" CM2 HM21 -90.172 20.000 1
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
PYD plan-1 "N1'" 0.020
PYD plan-1 "C2'" 0.020
PYD plan-1 "C6'" 0.020
PYD plan-1 "N3'" 0.020
PYD plan-1 "C4'" 0.020
PYD plan-1 "C5'" 0.020
PYD plan-1 CM2 0.020
PYD plan-1 "N4'" 0.020
PYD plan-1 "C7'" 0.020
PYD plan-1 "HC6'" 0.020
PYD plan-1 HN41 0.020
PYD plan-1 HN42 0.020
PYD plan-2 "N4'" 0.020
PYD plan-2 "C4'" 0.020
PYD plan-2 HN41 0.020
PYD plan-2 HN42 0.020
# ------------------------------------------------------
|
