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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
PMT PMT '"PHOSPHORIC ACID MONO-[3-(3-{[5-(4-A' non-polymer 66 39 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PMT
#
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
PMT O2 O O 0.000 0.000 0.000 0.000
PMT C2 C CR6 0.000 0.715 -0.361 0.920
PMT N3 N NRD6 0.000 1.437 -1.473 0.792
PMT C4 C CR6 0.000 2.223 -1.888 1.776
PMT N4 N NH2 0.000 2.961 -3.040 1.633
PMT HN42 H H 0.000 2.910 -3.579 0.776
PMT HN41 H H 0.000 3.562 -3.360 2.384
PMT C5 C CR16 0.000 2.297 -1.142 2.970
PMT H5 H H 0.000 2.934 -1.467 3.783
PMT C6 C CR16 0.000 1.560 -0.012 3.085
PMT H6 H H 0.000 1.599 0.578 3.992
PMT N1 N NR6 0.000 0.768 0.375 2.045
PMT C1B C CH1 0.000 -0.034 1.596 2.156
PMT "H1'" H H 0.000 0.072 2.039 3.156
PMT O4B O O2 0.000 -1.421 1.321 1.866
PMT C2B C CH1 0.000 0.368 2.618 1.062
PMT "H2'" H H 0.000 0.600 2.108 0.116
PMT "O2'" O OH1 0.000 1.469 3.420 1.493
PMT H2 H H 0.000 1.702 4.048 0.796
PMT C3B C CH1 0.000 -0.919 3.474 0.928
PMT H3B H H 0.000 -1.118 3.706 -0.128
PMT "O3'" O OH1 0.000 -0.801 4.677 1.690
PMT H3 H H 0.000 -0.061 5.200 1.352
PMT C4B C CH1 0.000 -2.029 2.571 1.498
PMT "H4'" H H 0.000 -2.476 3.043 2.384
PMT C5B C CH2 0.000 -3.105 2.334 0.436
PMT "H5'1" H H 0.000 -2.675 1.775 -0.398
PMT "H5''" H H 0.000 -3.477 3.295 0.076
PMT O5B O O2 0.000 -4.182 1.588 1.007
PMT P P P 0.000 -5.271 1.377 -0.160
PMT OP3 O OP -0.500 -5.831 2.691 -0.557
PMT OP1 O OP -0.500 -4.622 0.741 -1.332
PMT OP2 O O2 -0.500 -6.522 0.401 0.322
PMT "C1'" C C 0.000 -7.429 0.031 -0.456
PMT "O1'" O O -0.500 -7.415 0.398 -1.652
PMT "C2'" C CH2 0.000 -8.538 -0.855 0.047
PMT "H2'1" H H 0.000 -9.071 -0.348 0.854
PMT "H2'2" H H 0.000 -8.114 -1.789 0.424
PMT "C3'" C CH2 0.000 -9.508 -1.158 -1.096
PMT "H3'1" H H 0.000 -8.972 -1.665 -1.902
PMT "H3'2" H H 0.000 -9.929 -0.224 -1.472
PMT "N3'" N NH1 0.000 -10.586 -2.020 -0.607
PMT "H3'" H H 0.000 -10.598 -2.315 0.359
PMT "C4'" C C 0.000 -11.563 -2.420 -1.446
PMT "O4'" O O 0.000 -11.563 -2.046 -2.600
PMT "C5'" C CH1 0.000 -12.658 -3.329 -0.949
PMT H1 H H 0.000 -12.216 -4.149 -0.366
PMT "O5'" O OH1 0.000 -13.371 -3.868 -2.064
PMT "H5'" H H 0.000 -13.759 -3.146 -2.577
PMT "C6'" C CT 0.000 -13.620 -2.533 -0.064
PMT "C8'" C CH3 0.000 -14.803 -3.421 0.328
PMT "H8'3" H H 0.000 -15.273 -3.792 -0.546
PMT "H8'2" H H 0.000 -14.458 -4.233 0.914
PMT "H8'1" H H 0.000 -15.501 -2.854 0.889
PMT "C9'" C CH3 0.000 -12.889 -2.072 1.197
PMT "H9'3" H H 0.000 -12.149 -1.359 0.936
PMT "H9'2" H H 0.000 -13.581 -1.632 1.867
PMT "H9'1" H H 0.000 -12.427 -2.903 1.663
PMT "C7'" C CH2 0.000 -14.130 -1.313 -0.835
PMT "H7'1" H H 0.000 -14.652 -1.644 -1.736
PMT "H7'2" H H 0.000 -13.286 -0.681 -1.116
PMT "O7'" O O2 0.000 -15.029 -0.571 -0.008
PMT "P'" P P 0.000 -15.524 0.692 -0.877
PMT O12 O OP -0.666 -16.576 1.455 -0.102
PMT O13 O OP -0.666 -14.348 1.601 -1.161
PMT O11 O OP -0.666 -16.113 0.205 -2.183
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
PMT O2 n/a C2 START
PMT C2 O2 N1 .
PMT N3 C2 C4 .
PMT C4 N3 C5 .
PMT N4 C4 HN41 .
PMT HN42 N4 . .
PMT HN41 N4 . .
PMT C5 C4 C6 .
PMT H5 C5 . .
PMT C6 C5 H6 .
PMT H6 C6 . .
PMT N1 C2 C1B .
PMT C1B N1 C2B .
PMT "H1'" C1B . .
PMT O4B C1B . .
PMT C2B C1B C3B .
PMT "H2'" C2B . .
PMT "O2'" C2B H2 .
PMT H2 "O2'" . .
PMT C3B C2B C4B .
PMT H3B C3B . .
PMT "O3'" C3B H3 .
PMT H3 "O3'" . .
PMT C4B C3B C5B .
PMT "H4'" C4B . .
PMT C5B C4B O5B .
PMT "H5'1" C5B . .
PMT "H5''" C5B . .
PMT O5B C5B P .
PMT P O5B OP2 .
PMT OP3 P . .
PMT OP1 P . .
PMT OP2 P "C1'" .
PMT "C1'" OP2 "C2'" .
PMT "O1'" "C1'" . .
PMT "C2'" "C1'" "C3'" .
PMT "H2'1" "C2'" . .
PMT "H2'2" "C2'" . .
PMT "C3'" "C2'" "N3'" .
PMT "H3'1" "C3'" . .
PMT "H3'2" "C3'" . .
PMT "N3'" "C3'" "C4'" .
PMT "H3'" "N3'" . .
PMT "C4'" "N3'" "C5'" .
PMT "O4'" "C4'" . .
PMT "C5'" "C4'" "C6'" .
PMT H1 "C5'" . .
PMT "O5'" "C5'" "H5'" .
PMT "H5'" "O5'" . .
PMT "C6'" "C5'" "C7'" .
PMT "C8'" "C6'" "H8'1" .
PMT "H8'3" "C8'" . .
PMT "H8'2" "C8'" . .
PMT "H8'1" "C8'" . .
PMT "C9'" "C6'" "H9'1" .
PMT "H9'3" "C9'" . .
PMT "H9'2" "C9'" . .
PMT "H9'1" "C9'" . .
PMT "C7'" "C6'" "O7'" .
PMT "H7'1" "C7'" . .
PMT "H7'2" "C7'" . .
PMT "O7'" "C7'" "P'" .
PMT "P'" "O7'" O11 .
PMT O12 "P'" . .
PMT O13 "P'" . .
PMT O11 "P'" . END
PMT C4B O4B . ADD
PMT N1 C6 . 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
PMT O11 "P'" deloc 1.510 0.020
PMT O12 "P'" deloc 1.510 0.020
PMT O13 "P'" deloc 1.510 0.020
PMT "P'" "O7'" single 1.610 0.020
PMT "O7'" "C7'" single 1.426 0.020
PMT "C7'" "C6'" single 1.524 0.020
PMT "H7'1" "C7'" single 1.092 0.020
PMT "H7'2" "C7'" single 1.092 0.020
PMT "C9'" "C6'" single 1.524 0.020
PMT "C8'" "C6'" single 1.524 0.020
PMT "C6'" "C5'" single 1.524 0.020
PMT "H9'1" "C9'" single 1.059 0.020
PMT "H9'2" "C9'" single 1.059 0.020
PMT "H9'3" "C9'" single 1.059 0.020
PMT "H8'1" "C8'" single 1.059 0.020
PMT "H8'2" "C8'" single 1.059 0.020
PMT "H8'3" "C8'" single 1.059 0.020
PMT "O5'" "C5'" single 1.432 0.020
PMT "C5'" "C4'" single 1.500 0.020
PMT H1 "C5'" single 1.099 0.020
PMT "H5'" "O5'" single 0.967 0.020
PMT "O4'" "C4'" double 1.220 0.020
PMT "C4'" "N3'" single 1.330 0.020
PMT "N3'" "C3'" single 1.450 0.020
PMT "H3'" "N3'" single 1.010 0.020
PMT "C3'" "C2'" single 1.524 0.020
PMT "H3'1" "C3'" single 1.092 0.020
PMT "H3'2" "C3'" single 1.092 0.020
PMT "C2'" "C1'" single 1.510 0.020
PMT "H2'1" "C2'" single 1.092 0.020
PMT "H2'2" "C2'" single 1.092 0.020
PMT "O1'" "C1'" deloc 1.220 0.020
PMT "C1'" OP2 deloc 1.454 0.020
PMT OP2 P single 1.610 0.020
PMT OP1 P deloc 1.510 0.020
PMT OP3 P deloc 1.510 0.020
PMT P O5B single 1.610 0.020
PMT O5B C5B single 1.426 0.020
PMT C5B C4B single 1.524 0.020
PMT "H5'1" C5B single 1.092 0.020
PMT "H5''" C5B single 1.092 0.020
PMT C4B O4B single 1.426 0.020
PMT C4B C3B single 1.524 0.020
PMT "H4'" C4B single 1.099 0.020
PMT O4B C1B single 1.426 0.020
PMT "O3'" C3B single 1.432 0.020
PMT C3B C2B single 1.524 0.020
PMT H3B C3B single 1.099 0.020
PMT H3 "O3'" single 0.967 0.020
PMT "O2'" C2B single 1.432 0.020
PMT C2B C1B single 1.524 0.020
PMT "H2'" C2B single 1.099 0.020
PMT H2 "O2'" single 0.967 0.020
PMT C1B N1 single 1.465 0.020
PMT "H1'" C1B single 1.099 0.020
PMT N1 C6 single 1.337 0.020
PMT N1 C2 single 1.410 0.020
PMT C6 C5 double 1.390 0.020
PMT H6 C6 single 1.083 0.020
PMT C5 C4 single 1.390 0.020
PMT H5 C5 single 1.083 0.020
PMT N4 C4 single 1.355 0.020
PMT C4 N3 double 1.350 0.020
PMT HN41 N4 single 1.010 0.020
PMT HN42 N4 single 1.010 0.020
PMT N3 C2 single 1.350 0.020
PMT C2 O2 double 1.250 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
PMT O2 C2 N3 120.000 3.000
PMT O2 C2 N1 120.000 3.000
PMT N3 C2 N1 120.000 3.000
PMT C2 N3 C4 120.000 3.000
PMT N3 C4 N4 120.000 3.000
PMT N3 C4 C5 120.000 3.000
PMT N4 C4 C5 120.000 3.000
PMT C4 N4 HN42 120.000 3.000
PMT C4 N4 HN41 120.000 3.000
PMT HN42 N4 HN41 120.000 3.000
PMT C4 C5 H5 120.000 3.000
PMT C4 C5 C6 120.000 3.000
PMT H5 C5 C6 120.000 3.000
PMT C5 C6 H6 120.000 3.000
PMT C5 C6 N1 120.000 3.000
PMT H6 C6 N1 120.000 3.000
PMT C2 N1 C1B 120.000 3.000
PMT C2 N1 C6 120.000 3.000
PMT C1B N1 C6 120.000 3.000
PMT N1 C1B "H1'" 109.470 3.000
PMT N1 C1B O4B 109.470 3.000
PMT N1 C1B C2B 109.470 3.000
PMT "H1'" C1B O4B 109.470 3.000
PMT "H1'" C1B C2B 108.340 3.000
PMT O4B C1B C2B 109.470 3.000
PMT C1B O4B C4B 111.800 3.000
PMT C1B C2B "H2'" 108.340 3.000
PMT C1B C2B "O2'" 109.470 3.000
PMT C1B C2B C3B 111.000 3.000
PMT "H2'" C2B "O2'" 109.470 3.000
PMT "H2'" C2B C3B 108.340 3.000
PMT "O2'" C2B C3B 109.470 3.000
PMT C2B "O2'" H2 109.470 3.000
PMT C2B C3B H3B 108.340 3.000
PMT C2B C3B "O3'" 109.470 3.000
PMT C2B C3B C4B 111.000 3.000
PMT H3B C3B "O3'" 109.470 3.000
PMT H3B C3B C4B 108.340 3.000
PMT "O3'" C3B C4B 109.470 3.000
PMT C3B "O3'" H3 109.470 3.000
PMT C3B C4B "H4'" 108.340 3.000
PMT C3B C4B C5B 111.000 3.000
PMT C3B C4B O4B 109.470 3.000
PMT "H4'" C4B C5B 108.340 3.000
PMT "H4'" C4B O4B 109.470 3.000
PMT C5B C4B O4B 109.470 3.000
PMT C4B C5B "H5'1" 109.470 3.000
PMT C4B C5B "H5''" 109.470 3.000
PMT C4B C5B O5B 109.470 3.000
PMT "H5'1" C5B "H5''" 107.900 3.000
PMT "H5'1" C5B O5B 109.470 3.000
PMT "H5''" C5B O5B 109.470 3.000
PMT C5B O5B P 120.500 3.000
PMT O5B P OP3 108.200 3.000
PMT O5B P OP1 108.200 3.000
PMT O5B P OP2 102.600 3.000
PMT OP3 P OP1 119.900 3.000
PMT OP3 P OP2 108.200 3.000
PMT OP1 P OP2 108.200 3.000
PMT P OP2 "C1'" 120.000 3.000
PMT OP2 "C1'" "O1'" 119.000 3.000
PMT OP2 "C1'" "C2'" 120.000 3.000
PMT "O1'" "C1'" "C2'" 120.500 3.000
PMT "C1'" "C2'" "H2'1" 109.470 3.000
PMT "C1'" "C2'" "H2'2" 109.470 3.000
PMT "C1'" "C2'" "C3'" 109.470 3.000
PMT "H2'1" "C2'" "H2'2" 107.900 3.000
PMT "H2'1" "C2'" "C3'" 109.470 3.000
PMT "H2'2" "C2'" "C3'" 109.470 3.000
PMT "C2'" "C3'" "H3'1" 109.470 3.000
PMT "C2'" "C3'" "H3'2" 109.470 3.000
PMT "C2'" "C3'" "N3'" 112.000 3.000
PMT "H3'1" "C3'" "H3'2" 107.900 3.000
PMT "H3'1" "C3'" "N3'" 109.470 3.000
PMT "H3'2" "C3'" "N3'" 109.470 3.000
PMT "C3'" "N3'" "H3'" 118.500 3.000
PMT "C3'" "N3'" "C4'" 121.500 3.000
PMT "H3'" "N3'" "C4'" 120.000 3.000
PMT "N3'" "C4'" "O4'" 123.000 3.000
PMT "N3'" "C4'" "C5'" 116.500 3.000
PMT "O4'" "C4'" "C5'" 120.500 3.000
PMT "C4'" "C5'" H1 108.810 3.000
PMT "C4'" "C5'" "O5'" 109.470 3.000
PMT "C4'" "C5'" "C6'" 109.470 3.000
PMT H1 "C5'" "O5'" 109.470 3.000
PMT H1 "C5'" "C6'" 108.340 3.000
PMT "O5'" "C5'" "C6'" 109.470 3.000
PMT "C5'" "O5'" "H5'" 109.470 3.000
PMT "C5'" "C6'" "C8'" 111.000 3.000
PMT "C5'" "C6'" "C9'" 111.000 3.000
PMT "C5'" "C6'" "C7'" 111.000 3.000
PMT "C8'" "C6'" "C9'" 111.000 3.000
PMT "C8'" "C6'" "C7'" 111.000 3.000
PMT "C9'" "C6'" "C7'" 111.000 3.000
PMT "C6'" "C8'" "H8'3" 109.470 3.000
PMT "C6'" "C8'" "H8'2" 109.470 3.000
PMT "C6'" "C8'" "H8'1" 109.470 3.000
PMT "H8'3" "C8'" "H8'2" 109.470 3.000
PMT "H8'3" "C8'" "H8'1" 109.470 3.000
PMT "H8'2" "C8'" "H8'1" 109.470 3.000
PMT "C6'" "C9'" "H9'3" 109.470 3.000
PMT "C6'" "C9'" "H9'2" 109.470 3.000
PMT "C6'" "C9'" "H9'1" 109.470 3.000
PMT "H9'3" "C9'" "H9'2" 109.470 3.000
PMT "H9'3" "C9'" "H9'1" 109.470 3.000
PMT "H9'2" "C9'" "H9'1" 109.470 3.000
PMT "C6'" "C7'" "H7'1" 109.470 3.000
PMT "C6'" "C7'" "H7'2" 109.470 3.000
PMT "C6'" "C7'" "O7'" 109.500 3.000
PMT "H7'1" "C7'" "H7'2" 107.900 3.000
PMT "H7'1" "C7'" "O7'" 109.470 3.000
PMT "H7'2" "C7'" "O7'" 109.470 3.000
PMT "C7'" "O7'" "P'" 120.500 3.000
PMT "O7'" "P'" O12 108.200 3.000
PMT "O7'" "P'" O13 108.200 3.000
PMT "O7'" "P'" O11 108.200 3.000
PMT O12 "P'" O13 119.900 3.000
PMT O12 "P'" O11 119.900 3.000
PMT O13 "P'" O11 119.900 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
PMT CONST_1 O2 C2 N3 C4 180.000 0.000 0
PMT CONST_2 C2 N3 C4 C5 0.000 0.000 0
PMT CONST_3 N3 C4 N4 HN41 -179.984 0.000 0
PMT CONST_4 N3 C4 C5 C6 0.000 0.000 0
PMT CONST_5 C4 C5 C6 N1 0.000 0.000 0
PMT CONST_6 O2 C2 N1 C1B 0.000 0.000 0
PMT CONST_7 C2 N1 C6 C5 0.000 0.000 0
PMT var_1 C2 N1 C1B C2B -60.814 20.000 1
PMT var_2 N1 C1B O4B C4B -150.000 20.000 1
PMT var_3 N1 C1B C2B C3B 150.000 20.000 3
PMT var_4 C1B C2B "O2'" H2 179.992 20.000 1
PMT var_5 C1B C2B C3B C4B -30.000 20.000 3
PMT var_6 C2B C3B "O3'" H3 61.433 20.000 1
PMT var_7 C2B C3B C4B C5B -120.000 20.000 3
PMT var_8 C3B C4B O4B C1B 30.000 20.000 1
PMT var_9 C3B C4B C5B O5B -175.285 20.000 3
PMT var_10 C4B C5B O5B P -179.994 20.000 1
PMT var_11 C5B O5B P OP2 174.744 20.000 1
PMT var_12 O5B P OP2 "C1'" -174.909 20.000 1
PMT var_13 P OP2 "C1'" "C2'" -179.980 20.000 1
PMT var_14 OP2 "C1'" "C2'" "C3'" -179.998 20.000 3
PMT var_15 "C1'" "C2'" "C3'" "N3'" -179.993 20.000 3
PMT var_16 "C2'" "C3'" "N3'" "C4'" -179.966 20.000 3
PMT CONST_8 "C3'" "N3'" "C4'" "C5'" 180.000 0.000 0
PMT var_17 "N3'" "C4'" "C5'" "C6'" 74.018 20.000 3
PMT var_18 "C4'" "C5'" "O5'" "H5'" -60.027 20.000 1
PMT var_19 "C4'" "C5'" "C6'" "C7'" 54.543 20.000 1
PMT var_20 "C5'" "C6'" "C8'" "H8'1" -176.423 20.000 1
PMT var_21 "C5'" "C6'" "C9'" "H9'1" -52.660 20.000 1
PMT var_22 "C5'" "C6'" "C7'" "O7'" 179.981 20.000 1
PMT var_23 "C6'" "C7'" "O7'" "P'" 179.959 20.000 1
PMT var_24 "C7'" "O7'" "P'" O11 55.006 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
PMT chir_01 "C6'" "C7'" "C9'" "C8'" negativ
PMT chir_02 "C5'" "C6'" "O5'" "C4'" negativ
PMT chir_03 C4B C5B O4B C3B negativ
PMT chir_04 C3B C4B "O3'" C2B negativ
PMT chir_05 C2B C3B "O2'" C1B negativ
PMT chir_06 C1B O4B C2B N1 positiv
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
PMT plan-1 "C4'" 0.020
PMT plan-1 "C5'" 0.020
PMT plan-1 "O4'" 0.020
PMT plan-1 "N3'" 0.020
PMT plan-1 "H3'" 0.020
PMT plan-2 "N3'" 0.020
PMT plan-2 "C4'" 0.020
PMT plan-2 "C3'" 0.020
PMT plan-2 "H3'" 0.020
PMT plan-3 "C1'" 0.020
PMT plan-3 "C2'" 0.020
PMT plan-3 "O1'" 0.020
PMT plan-3 OP2 0.020
PMT plan-4 N1 0.020
PMT plan-4 C1B 0.020
PMT plan-4 C6 0.020
PMT plan-4 C2 0.020
PMT plan-4 C5 0.020
PMT plan-4 C4 0.020
PMT plan-4 N3 0.020
PMT plan-4 H6 0.020
PMT plan-4 H5 0.020
PMT plan-4 N4 0.020
PMT plan-4 O2 0.020
PMT plan-4 HN42 0.020
PMT plan-4 HN41 0.020
PMT plan-5 N4 0.020
PMT plan-5 C4 0.020
PMT plan-5 HN41 0.020
PMT plan-5 HN42 0.020
# ------------------------------------------------------
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