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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
JMQ JMQ '(2R,3R,4S)-2-(hydroxymethyl)-1-[(4-h' non-polymer 36 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_JMQ
#
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
JMQ "O5'" O OH1 0.000 0.000 0.000 0.000
JMQ "HO5'" H H 0.000 0.568 -0.779 -0.070
JMQ "C5'" C CH2 0.000 -0.473 0.362 -1.299
JMQ "H5'" H H 0.000 -1.041 -0.469 -1.723
JMQ "H5'A" H H 0.000 0.378 0.587 -1.945
JMQ "C4'" C CH1 0.000 -1.372 1.594 -1.190
JMQ "H4'" H H 0.000 -1.639 1.953 -2.194
JMQ "C3'" C CH1 0.000 -0.644 2.708 -0.409
JMQ "H3'" H H 0.000 0.138 2.284 0.236
JMQ "O3'" O OH1 0.000 -0.091 3.674 -1.305
JMQ "HO3'" H H 0.000 0.292 4.402 -0.797
JMQ "C2'" C CH1 0.000 -1.778 3.336 0.443
JMQ "H2'" H H 0.000 -1.375 3.797 1.356
JMQ "O2'" O OH1 0.000 -2.527 4.284 -0.321
JMQ "HO2'" H H 0.000 -3.285 4.588 0.196
JMQ "C1'" C CH2 0.000 -2.639 2.095 0.784
JMQ "H1'A" H H 0.000 -3.673 2.368 1.001
JMQ "H1'" H H 0.000 -2.226 1.536 1.626
JMQ "N4'" N NT 0.000 -2.594 1.258 -0.434
JMQ C1 C CH2 0.000 -2.626 -0.170 -0.095
JMQ H1 H H 0.000 -1.842 -0.389 0.633
JMQ H1A H H 0.000 -2.459 -0.762 -0.997
JMQ C9 C CR5 0.000 -3.970 -0.516 0.494
JMQ C4 C CR56 0.000 -5.202 -0.766 -0.246
JMQ N3 N NRD6 0.000 -5.541 -0.776 -1.537
JMQ C2 C CR16 0.000 -6.776 -1.045 -1.898
JMQ H2 H H 0.000 -7.024 -1.046 -2.953
JMQ C5 C CR56 0.000 -6.184 -1.048 0.722
JMQ C6 C CR6 0.000 -7.480 -1.327 0.283
JMQ N1 N NRD6 0.000 -7.726 -1.315 -1.021
JMQ O6 O OH1 0.000 -8.466 -1.606 1.170
JMQ H16 H H 0.000 -8.491 -2.558 1.334
JMQ N7 N NR15 0.000 -5.577 -0.971 1.954
JMQ HN7 H H 0.000 -6.052 -1.131 2.865
JMQ C8 C CR15 0.000 -4.259 -0.654 1.801
JMQ H8 H H 0.000 -3.551 -0.532 2.611
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
JMQ "O5'" n/a "C5'" START
JMQ "HO5'" "O5'" . .
JMQ "C5'" "O5'" "C4'" .
JMQ "H5'" "C5'" . .
JMQ "H5'A" "C5'" . .
JMQ "C4'" "C5'" "N4'" .
JMQ "H4'" "C4'" . .
JMQ "C3'" "C4'" "C2'" .
JMQ "H3'" "C3'" . .
JMQ "O3'" "C3'" "HO3'" .
JMQ "HO3'" "O3'" . .
JMQ "C2'" "C3'" "C1'" .
JMQ "H2'" "C2'" . .
JMQ "O2'" "C2'" "HO2'" .
JMQ "HO2'" "O2'" . .
JMQ "C1'" "C2'" "H1'" .
JMQ "H1'A" "C1'" . .
JMQ "H1'" "C1'" . .
JMQ "N4'" "C4'" C1 .
JMQ C1 "N4'" C9 .
JMQ H1 C1 . .
JMQ H1A C1 . .
JMQ C9 C1 C4 .
JMQ C4 C9 C5 .
JMQ N3 C4 C2 .
JMQ C2 N3 H2 .
JMQ H2 C2 . .
JMQ C5 C4 N7 .
JMQ C6 C5 O6 .
JMQ N1 C6 . .
JMQ O6 C6 H16 .
JMQ H16 O6 . .
JMQ N7 C5 C8 .
JMQ HN7 N7 . .
JMQ C8 N7 H8 .
JMQ H8 C8 . END
JMQ C2 N1 . ADD
JMQ C8 C9 . ADD
JMQ "N4'" "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
JMQ C9 C1 single 1.510 0.020
JMQ C1 "N4'" single 1.469 0.020
JMQ H1 C1 single 1.092 0.020
JMQ H1A C1 single 1.092 0.020
JMQ C2 N1 single 1.337 0.020
JMQ C2 N3 double 1.337 0.020
JMQ H2 C2 single 1.083 0.020
JMQ C8 C9 double 1.387 0.020
JMQ C8 N7 single 1.350 0.020
JMQ H8 C8 single 1.083 0.020
JMQ C4 C9 single 1.490 0.020
JMQ O6 C6 single 1.362 0.020
JMQ N1 C6 double 1.350 0.020
JMQ C6 C5 single 1.490 0.020
JMQ N3 C4 single 1.355 0.020
JMQ C5 C4 double 1.490 0.020
JMQ N7 C5 single 1.340 0.020
JMQ HN7 N7 single 1.040 0.020
JMQ "N4'" "C1'" single 1.469 0.020
JMQ "N4'" "C4'" single 1.469 0.020
JMQ "C1'" "C2'" single 1.524 0.020
JMQ "H1'" "C1'" single 1.092 0.020
JMQ "H1'A" "C1'" single 1.092 0.020
JMQ "O2'" "C2'" single 1.432 0.020
JMQ "C2'" "C3'" single 1.524 0.020
JMQ "H2'" "C2'" single 1.099 0.020
JMQ "HO2'" "O2'" single 0.967 0.020
JMQ "O3'" "C3'" single 1.432 0.020
JMQ "C3'" "C4'" single 1.524 0.020
JMQ "H3'" "C3'" single 1.099 0.020
JMQ "HO3'" "O3'" single 0.967 0.020
JMQ "C4'" "C5'" single 1.524 0.020
JMQ "H4'" "C4'" single 1.099 0.020
JMQ "C5'" "O5'" single 1.432 0.020
JMQ "H5'" "C5'" single 1.092 0.020
JMQ "H5'A" "C5'" single 1.092 0.020
JMQ "HO5'" "O5'" single 0.967 0.020
JMQ H16 O6 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
JMQ "HO5'" "O5'" "C5'" 109.470 3.000
JMQ "O5'" "C5'" "H5'" 109.470 3.000
JMQ "O5'" "C5'" "H5'A" 109.470 3.000
JMQ "O5'" "C5'" "C4'" 109.470 3.000
JMQ "H5'" "C5'" "H5'A" 107.900 3.000
JMQ "H5'" "C5'" "C4'" 109.470 3.000
JMQ "H5'A" "C5'" "C4'" 109.470 3.000
JMQ "C5'" "C4'" "H4'" 108.340 3.000
JMQ "C5'" "C4'" "C3'" 111.000 3.000
JMQ "C5'" "C4'" "N4'" 109.500 3.000
JMQ "H4'" "C4'" "C3'" 108.340 3.000
JMQ "H4'" "C4'" "N4'" 109.500 3.000
JMQ "C3'" "C4'" "N4'" 109.500 3.000
JMQ "C4'" "C3'" "H3'" 108.340 3.000
JMQ "C4'" "C3'" "O3'" 109.470 3.000
JMQ "C4'" "C3'" "C2'" 111.000 3.000
JMQ "H3'" "C3'" "O3'" 109.470 3.000
JMQ "H3'" "C3'" "C2'" 108.340 3.000
JMQ "O3'" "C3'" "C2'" 109.470 3.000
JMQ "C3'" "O3'" "HO3'" 109.470 3.000
JMQ "C3'" "C2'" "H2'" 108.340 3.000
JMQ "C3'" "C2'" "O2'" 109.470 3.000
JMQ "C3'" "C2'" "C1'" 111.000 3.000
JMQ "H2'" "C2'" "O2'" 109.470 3.000
JMQ "H2'" "C2'" "C1'" 108.340 3.000
JMQ "O2'" "C2'" "C1'" 109.470 3.000
JMQ "C2'" "O2'" "HO2'" 109.470 3.000
JMQ "C2'" "C1'" "H1'A" 109.470 3.000
JMQ "C2'" "C1'" "H1'" 109.470 3.000
JMQ "C2'" "C1'" "N4'" 109.500 3.000
JMQ "H1'A" "C1'" "H1'" 107.900 3.000
JMQ "H1'A" "C1'" "N4'" 109.470 3.000
JMQ "H1'" "C1'" "N4'" 109.470 3.000
JMQ "C4'" "N4'" C1 109.470 3.000
JMQ "C4'" "N4'" "C1'" 109.470 3.000
JMQ C1 "N4'" "C1'" 109.470 3.000
JMQ "N4'" C1 H1 109.470 3.000
JMQ "N4'" C1 H1A 109.470 3.000
JMQ "N4'" C1 C9 109.500 3.000
JMQ H1 C1 H1A 107.900 3.000
JMQ H1 C1 C9 109.470 3.000
JMQ H1A C1 C9 109.470 3.000
JMQ C1 C9 C4 126.000 3.000
JMQ C1 C9 C8 126.000 3.000
JMQ C4 C9 C8 108.000 3.000
JMQ C9 C4 N3 120.000 3.000
JMQ C9 C4 C5 108.000 3.000
JMQ N3 C4 C5 120.000 3.000
JMQ C4 N3 C2 120.000 3.000
JMQ N3 C2 H2 120.000 3.000
JMQ N3 C2 N1 120.000 3.000
JMQ H2 C2 N1 120.000 3.000
JMQ C4 C5 C6 120.000 3.000
JMQ C4 C5 N7 108.000 3.000
JMQ C6 C5 N7 132.000 3.000
JMQ C5 C6 N1 120.000 3.000
JMQ C5 C6 O6 120.000 3.000
JMQ N1 C6 O6 120.000 3.000
JMQ C6 N1 C2 120.000 3.000
JMQ C6 O6 H16 109.470 3.000
JMQ C5 N7 HN7 126.000 3.000
JMQ C5 N7 C8 108.000 3.000
JMQ HN7 N7 C8 126.000 3.000
JMQ N7 C8 H8 126.000 3.000
JMQ N7 C8 C9 108.000 3.000
JMQ H8 C8 C9 126.000 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
JMQ var_1 "HO5'" "O5'" "C5'" "C4'" 179.992 20.000 1
JMQ var_2 "O5'" "C5'" "C4'" "N4'" -65.839 20.000 3
JMQ var_3 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
JMQ var_4 "C4'" "C3'" "O3'" "HO3'" 175.073 20.000 1
JMQ var_5 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
JMQ var_6 "C3'" "C2'" "O2'" "HO2'" 173.754 20.000 1
JMQ var_7 "C3'" "C2'" "C1'" "N4'" -30.000 20.000 3
JMQ var_8 "C5'" "C4'" "N4'" C1 0.000 20.000 1
JMQ var_9 "C4'" "N4'" "C1'" "C2'" 30.000 20.000 1
JMQ var_10 "C4'" "N4'" C1 C9 -171.778 20.000 1
JMQ var_11 "N4'" C1 C9 C4 80.108 20.000 2
JMQ CONST_1 C1 C9 C4 C5 180.000 0.000 0
JMQ CONST_2 C9 C4 N3 C2 180.000 0.000 0
JMQ CONST_3 C4 N3 C2 N1 0.000 0.000 0
JMQ CONST_4 N3 C2 N1 C6 0.000 0.000 0
JMQ CONST_5 C9 C4 C5 N7 0.000 0.000 0
JMQ CONST_6 C4 C5 C6 O6 180.000 0.000 0
JMQ CONST_7 C5 C6 N1 C2 0.000 0.000 0
JMQ var_12 C5 C6 O6 H16 -89.910 20.000 1
JMQ CONST_8 C4 C5 N7 C8 0.000 0.000 0
JMQ CONST_9 C5 N7 C8 C9 0.000 0.000 0
JMQ CONST_10 N7 C8 C9 C1 180.000 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
JMQ chir_01 "N4'" C1 "C1'" "C4'" negativ
JMQ chir_02 "C2'" "C1'" "O2'" "C3'" positiv
JMQ chir_03 "C3'" "C2'" "O3'" "C4'" positiv
JMQ chir_04 "C4'" "N4'" "C3'" "C5'" 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
JMQ plan-1 C2 0.020
JMQ plan-1 N1 0.020
JMQ plan-1 N3 0.020
JMQ plan-1 H2 0.020
JMQ plan-1 C6 0.020
JMQ plan-1 O6 0.020
JMQ plan-1 C5 0.020
JMQ plan-1 C4 0.020
JMQ plan-1 C9 0.020
JMQ plan-1 N7 0.020
JMQ plan-1 C8 0.020
JMQ plan-1 HN7 0.020
JMQ plan-1 H8 0.020
JMQ plan-1 C1 0.020
# ------------------------------------------------------
|
