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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
PMD PMD '[N-(2,4-DIAMINOPTERIDIN-6-YL)-METHYL' non-polymer 45 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PMD
#
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
PMD "N4'" N NH2 0.000 0.000 0.000 0.000
PMD HN41 H H 0.000 0.993 0.150 -0.143
PMD HN42 H H 0.000 -0.520 -0.549 -0.676
PMD C4B C CR6 0.000 -0.635 0.536 1.099
PMD "N3'" N NRD6 0.000 0.047 1.170 2.042
PMD C2B C CR6 0.000 -0.563 1.688 3.103
PMD "N2'" N NH2 0.000 0.209 2.336 4.049
PMD HN22 H H 0.000 -0.221 2.745 4.873
PMD HN21 H H 0.000 1.215 2.411 3.930
PMD C4 C CR66 0.000 -2.084 0.424 1.265
PMD "N5'" N NRD6 0.000 -2.852 -0.194 0.373
PMD C6B C CR6 0.000 -4.150 -0.266 0.574
PMD C7B C CR16 0.000 -4.725 0.299 1.711
PMD "H7'1" H H 0.000 -5.796 0.231 1.860
PMD "N8'" N NRD6 0.000 -3.983 0.915 2.607
PMD C8 C CR66 0.000 -2.664 1.000 2.423
PMD "N1'" N NRD6 0.000 -1.862 1.611 3.305
PMD C9B C CH2 0.000 -5.024 -0.965 -0.434
PMD "H9'1" H H 0.000 -5.924 -1.337 0.061
PMD "H9'2" H H 0.000 -4.477 -1.804 -0.869
PMD "N0'" N NT 0.000 -5.401 -0.022 -1.494
PMD "C0'" C CR6 0.000 -6.420 -0.621 -2.218
PMD "CC'" C CR6 0.000 -4.281 0.150 -2.291
PMD "CB'" C CR16 0.000 -3.072 -0.644 -1.987
PMD "H11'" H H 0.000 -3.083 -1.347 -1.163
PMD "CA'" C CR16 0.000 -1.985 -0.503 -2.710
PMD "H10'" H H 0.000 -1.103 -1.090 -2.483
PMD "C9'" C CR16 0.000 -1.967 0.453 -3.830
PMD H9B H H 0.000 -1.071 0.575 -4.428
PMD "C8'" C CR16 0.000 -3.041 1.159 -4.102
PMD "H8'1" H H 0.000 -3.031 1.862 -4.925
PMD "C7'" C CR6 0.000 -4.264 0.997 -3.289
PMD C6 C C1 0.000 -5.446 1.800 -3.627
PMD H61 H H 0.000 -5.290 2.822 -3.929
PMD "C6'" C C1 0.000 -6.663 1.361 -3.584
PMD "H6'1" H H 0.000 -7.454 2.041 -3.853
PMD "C5'" C CR6 0.000 -7.035 -0.003 -3.195
PMD "C4'" C CR16 0.000 -8.122 -0.681 -3.931
PMD "H4'1" H H 0.000 -8.633 -0.164 -4.734
PMD "C3'" C CR16 0.000 -8.473 -1.907 -3.617
PMD "H3'1" H H 0.000 -9.270 -2.401 -4.158
PMD "C2'" C CR16 0.000 -7.777 -2.608 -2.524
PMD "H2'1" H H 0.000 -8.059 -3.620 -2.262
PMD "C1'" C CR16 0.000 -6.814 -2.003 -1.868
PMD "H1'1" H H 0.000 -6.304 -2.520 -1.064
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
PMD "N4'" n/a C4B START
PMD HN41 "N4'" . .
PMD HN42 "N4'" . .
PMD C4B "N4'" C4 .
PMD "N3'" C4B C2B .
PMD C2B "N3'" "N2'" .
PMD "N2'" C2B HN21 .
PMD HN22 "N2'" . .
PMD HN21 "N2'" . .
PMD C4 C4B "N5'" .
PMD "N5'" C4 C6B .
PMD C6B "N5'" C9B .
PMD C7B C6B "N8'" .
PMD "H7'1" C7B . .
PMD "N8'" C7B C8 .
PMD C8 "N8'" "N1'" .
PMD "N1'" C8 . .
PMD C9B C6B "N0'" .
PMD "H9'1" C9B . .
PMD "H9'2" C9B . .
PMD "N0'" C9B "CC'" .
PMD "C0'" "N0'" . .
PMD "CC'" "N0'" "C7'" .
PMD "CB'" "CC'" "CA'" .
PMD "H11'" "CB'" . .
PMD "CA'" "CB'" "C9'" .
PMD "H10'" "CA'" . .
PMD "C9'" "CA'" "C8'" .
PMD H9B "C9'" . .
PMD "C8'" "C9'" "H8'1" .
PMD "H8'1" "C8'" . .
PMD "C7'" "CC'" C6 .
PMD C6 "C7'" "C6'" .
PMD H61 C6 . .
PMD "C6'" C6 "C5'" .
PMD "H6'1" "C6'" . .
PMD "C5'" "C6'" "C4'" .
PMD "C4'" "C5'" "C3'" .
PMD "H4'1" "C4'" . .
PMD "C3'" "C4'" "C2'" .
PMD "H3'1" "C3'" . .
PMD "C2'" "C3'" "C1'" .
PMD "H2'1" "C2'" . .
PMD "C1'" "C2'" "H1'1" .
PMD "H1'1" "C1'" . END
PMD C2B "N1'" . ADD
PMD C4 C8 . ADD
PMD "C0'" "C1'" . ADD
PMD "C0'" "C5'" . ADD
PMD "C7'" "C8'" . 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
PMD C2B "N1'" double 1.350 0.020
PMD "N2'" C2B single 1.355 0.020
PMD C2B "N3'" single 1.350 0.020
PMD C4 C4B single 1.490 0.020
PMD "N3'" C4B double 1.350 0.020
PMD C4B "N4'" single 1.355 0.020
PMD C4 C8 double 1.490 0.020
PMD "N5'" C4 single 1.350 0.020
PMD C7B C6B single 1.390 0.020
PMD C9B C6B single 1.511 0.020
PMD C6B "N5'" double 1.350 0.020
PMD "N8'" C7B double 1.337 0.020
PMD "H7'1" C7B single 1.083 0.020
PMD "N1'" C8 single 1.350 0.020
PMD C8 "N8'" single 1.350 0.020
PMD "N0'" C9B single 1.469 0.020
PMD "H9'1" C9B single 1.092 0.020
PMD "H9'2" C9B single 1.092 0.020
PMD "C0'" "C1'" double 1.390 0.020
PMD "C0'" "C5'" single 1.487 0.020
PMD "C0'" "N0'" single 1.405 0.020
PMD "C1'" "C2'" single 1.390 0.020
PMD "H1'1" "C1'" single 1.083 0.020
PMD "C2'" "C3'" double 1.390 0.020
PMD "H2'1" "C2'" single 1.083 0.020
PMD "C3'" "C4'" single 1.390 0.020
PMD "H3'1" "C3'" single 1.083 0.020
PMD "C4'" "C5'" double 1.390 0.020
PMD "H4'1" "C4'" single 1.083 0.020
PMD "C5'" "C6'" single 1.480 0.020
PMD "C6'" C6 double 1.330 0.020
PMD "H6'1" "C6'" single 1.077 0.020
PMD C6 "C7'" single 1.480 0.020
PMD H61 C6 single 1.077 0.020
PMD "C7'" "C8'" double 1.390 0.020
PMD "C7'" "CC'" single 1.487 0.020
PMD "C8'" "C9'" single 1.390 0.020
PMD "H8'1" "C8'" single 1.083 0.020
PMD "C9'" "CA'" double 1.390 0.020
PMD H9B "C9'" single 1.083 0.020
PMD "CA'" "CB'" single 1.390 0.020
PMD "H10'" "CA'" single 1.083 0.020
PMD "CB'" "CC'" double 1.390 0.020
PMD "H11'" "CB'" single 1.083 0.020
PMD "CC'" "N0'" single 1.405 0.020
PMD HN21 "N2'" single 1.010 0.020
PMD HN22 "N2'" single 1.010 0.020
PMD HN41 "N4'" single 1.010 0.020
PMD HN42 "N4'" single 1.010 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
PMD HN41 "N4'" HN42 120.000 3.000
PMD HN41 "N4'" C4B 120.000 3.000
PMD HN42 "N4'" C4B 120.000 3.000
PMD "N4'" C4B "N3'" 120.000 3.000
PMD "N4'" C4B C4 120.000 3.000
PMD "N3'" C4B C4 120.000 3.000
PMD C4B "N3'" C2B 120.000 3.000
PMD "N3'" C2B "N2'" 120.000 3.000
PMD "N3'" C2B "N1'" 120.000 3.000
PMD "N2'" C2B "N1'" 120.000 3.000
PMD C2B "N2'" HN22 120.000 3.000
PMD C2B "N2'" HN21 120.000 3.000
PMD HN22 "N2'" HN21 120.000 3.000
PMD C4B C4 "N5'" 120.000 3.000
PMD C4B C4 C8 120.000 3.000
PMD "N5'" C4 C8 120.000 3.000
PMD C4 "N5'" C6B 120.000 3.000
PMD "N5'" C6B C7B 120.000 3.000
PMD "N5'" C6B C9B 120.000 3.000
PMD C7B C6B C9B 120.000 3.000
PMD C6B C7B "H7'1" 120.000 3.000
PMD C6B C7B "N8'" 120.000 3.000
PMD "H7'1" C7B "N8'" 120.000 3.000
PMD C7B "N8'" C8 120.000 3.000
PMD "N8'" C8 "N1'" 120.000 3.000
PMD "N8'" C8 C4 120.000 3.000
PMD "N1'" C8 C4 120.000 3.000
PMD C8 "N1'" C2B 120.000 3.000
PMD C6B C9B "H9'1" 109.470 3.000
PMD C6B C9B "H9'2" 109.470 3.000
PMD C6B C9B "N0'" 109.500 3.000
PMD "H9'1" C9B "H9'2" 107.900 3.000
PMD "H9'1" C9B "N0'" 109.470 3.000
PMD "H9'2" C9B "N0'" 109.470 3.000
PMD C9B "N0'" "C0'" 109.500 3.000
PMD C9B "N0'" "CC'" 109.500 3.000
PMD "C0'" "N0'" "CC'" 109.500 3.000
PMD "N0'" "C0'" "C1'" 120.000 3.000
PMD "N0'" "C0'" "C5'" 120.000 3.000
PMD "C1'" "C0'" "C5'" 120.000 3.000
PMD "N0'" "CC'" "CB'" 120.000 3.000
PMD "N0'" "CC'" "C7'" 120.000 3.000
PMD "CB'" "CC'" "C7'" 120.000 3.000
PMD "CC'" "CB'" "H11'" 120.000 3.000
PMD "CC'" "CB'" "CA'" 120.000 3.000
PMD "H11'" "CB'" "CA'" 120.000 3.000
PMD "CB'" "CA'" "H10'" 120.000 3.000
PMD "CB'" "CA'" "C9'" 120.000 3.000
PMD "H10'" "CA'" "C9'" 120.000 3.000
PMD "CA'" "C9'" H9B 120.000 3.000
PMD "CA'" "C9'" "C8'" 120.000 3.000
PMD H9B "C9'" "C8'" 120.000 3.000
PMD "C9'" "C8'" "H8'1" 120.000 3.000
PMD "C9'" "C8'" "C7'" 120.000 3.000
PMD "H8'1" "C8'" "C7'" 120.000 3.000
PMD "CC'" "C7'" C6 120.000 3.000
PMD "CC'" "C7'" "C8'" 120.000 3.000
PMD C6 "C7'" "C8'" 120.000 3.000
PMD "C7'" C6 H61 120.000 3.000
PMD "C7'" C6 "C6'" 120.000 3.000
PMD H61 C6 "C6'" 120.000 3.000
PMD C6 "C6'" "H6'1" 120.000 3.000
PMD C6 "C6'" "C5'" 120.000 3.000
PMD "H6'1" "C6'" "C5'" 120.000 3.000
PMD "C6'" "C5'" "C4'" 120.000 3.000
PMD "C6'" "C5'" "C0'" 120.000 3.000
PMD "C4'" "C5'" "C0'" 120.000 3.000
PMD "C5'" "C4'" "H4'1" 120.000 3.000
PMD "C5'" "C4'" "C3'" 120.000 3.000
PMD "H4'1" "C4'" "C3'" 120.000 3.000
PMD "C4'" "C3'" "H3'1" 120.000 3.000
PMD "C4'" "C3'" "C2'" 120.000 3.000
PMD "H3'1" "C3'" "C2'" 120.000 3.000
PMD "C3'" "C2'" "H2'1" 120.000 3.000
PMD "C3'" "C2'" "C1'" 120.000 3.000
PMD "H2'1" "C2'" "C1'" 120.000 3.000
PMD "C2'" "C1'" "H1'1" 120.000 3.000
PMD "C2'" "C1'" "C0'" 120.000 3.000
PMD "H1'1" "C1'" "C0'" 120.000 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
PMD CONST_1 HN42 "N4'" C4B C4 -5.080 0.000 0
PMD CONST_2 "N4'" C4B "N3'" C2B 180.000 0.000 0
PMD CONST_3 C4B "N3'" C2B "N2'" 180.000 0.000 0
PMD CONST_4 "N3'" C2B "N1'" C8 0.000 0.000 0
PMD CONST_5 "N3'" C2B "N2'" HN21 -0.031 0.000 0
PMD CONST_6 "N4'" C4B C4 "N5'" 0.000 0.000 0
PMD CONST_7 C4B C4 C8 "N8'" 180.000 0.000 0
PMD CONST_8 C4B C4 "N5'" C6B 180.000 0.000 0
PMD CONST_9 C4 "N5'" C6B C9B 180.000 0.000 0
PMD CONST_10 "N5'" C6B C7B "N8'" 0.000 0.000 0
PMD CONST_11 C6B C7B "N8'" C8 0.000 0.000 0
PMD CONST_12 C7B "N8'" C8 "N1'" 180.000 0.000 0
PMD CONST_13 "N8'" C8 "N1'" C2B 180.000 0.000 0
PMD var_1 "N5'" C6B C9B "N0'" -85.960 20.000 2
PMD var_2 C6B C9B "N0'" "CC'" 74.743 20.000 1
PMD var_3 C9B "N0'" "C0'" "C1'" -4.123 20.000 1
PMD CONST_14 "N0'" "C0'" "C1'" "C2'" 180.000 0.000 0
PMD CONST_15 "N0'" "C0'" "C5'" "C6'" 0.000 0.000 0
PMD var_4 C9B "N0'" "CC'" "C7'" -176.021 20.000 1
PMD CONST_16 "N0'" "CC'" "CB'" "CA'" 180.000 0.000 0
PMD CONST_17 "CC'" "CB'" "CA'" "C9'" 0.000 0.000 0
PMD CONST_18 "CB'" "CA'" "C9'" "C8'" 0.000 0.000 0
PMD CONST_19 "CA'" "C9'" "C8'" "C7'" 0.000 0.000 0
PMD CONST_20 "N0'" "CC'" "C7'" C6 0.000 0.000 0
PMD CONST_21 "CC'" "C7'" "C8'" "C9'" 0.000 0.000 0
PMD var_5 "CC'" "C7'" C6 "C6'" -38.994 20.000 1
PMD CONST_22 "C7'" C6 "C6'" "C5'" -0.083 0.000 0
PMD var_6 C6 "C6'" "C5'" "C4'" -140.648 20.000 1
PMD CONST_23 "C6'" "C5'" "C4'" "C3'" 180.000 0.000 0
PMD CONST_24 "C5'" "C4'" "C3'" "C2'" 0.000 0.000 0
PMD CONST_25 "C4'" "C3'" "C2'" "C1'" 0.000 0.000 0
PMD CONST_26 "C3'" "C2'" "C1'" "C0'" 0.000 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
PMD chir_01 "N0'" C9B "C0'" "CC'" 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
PMD plan-1 C2B 0.020
PMD plan-1 "N1'" 0.020
PMD plan-1 "N2'" 0.020
PMD plan-1 "N3'" 0.020
PMD plan-1 C4B 0.020
PMD plan-1 C4 0.020
PMD plan-1 "N4'" 0.020
PMD plan-1 C8 0.020
PMD plan-1 "N5'" 0.020
PMD plan-1 C6B 0.020
PMD plan-1 C7B 0.020
PMD plan-1 "N8'" 0.020
PMD plan-1 C9B 0.020
PMD plan-1 "H7'1" 0.020
PMD plan-1 HN22 0.020
PMD plan-1 HN21 0.020
PMD plan-1 HN41 0.020
PMD plan-1 HN42 0.020
PMD plan-2 "C0'" 0.020
PMD plan-2 "C1'" 0.020
PMD plan-2 "C5'" 0.020
PMD plan-2 "N0'" 0.020
PMD plan-2 "C2'" 0.020
PMD plan-2 "C3'" 0.020
PMD plan-2 "C4'" 0.020
PMD plan-2 "H1'1" 0.020
PMD plan-2 "H2'1" 0.020
PMD plan-2 "H3'1" 0.020
PMD plan-2 "H4'1" 0.020
PMD plan-2 "C6'" 0.020
PMD plan-2 "H6'1" 0.020
PMD plan-3 "C6'" 0.020
PMD plan-3 "C5'" 0.020
PMD plan-3 C6 0.020
PMD plan-3 "H6'1" 0.020
PMD plan-3 "C7'" 0.020
PMD plan-3 H61 0.020
PMD plan-4 "C7'" 0.020
PMD plan-4 C6 0.020
PMD plan-4 "C8'" 0.020
PMD plan-4 "CC'" 0.020
PMD plan-4 "C9'" 0.020
PMD plan-4 "CA'" 0.020
PMD plan-4 "CB'" 0.020
PMD plan-4 "H8'1" 0.020
PMD plan-4 H9B 0.020
PMD plan-4 "H10'" 0.020
PMD plan-4 "H11'" 0.020
PMD plan-4 "N0'" 0.020
PMD plan-4 H61 0.020
PMD plan-5 "N2'" 0.020
PMD plan-5 C2B 0.020
PMD plan-5 HN21 0.020
PMD plan-5 HN22 0.020
PMD plan-6 "N4'" 0.020
PMD plan-6 C4B 0.020
PMD plan-6 HN41 0.020
PMD plan-6 HN42 0.020
# ------------------------------------------------------
|
