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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
DAD DAD '2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHA' non-polymer 41 29 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DAD
#
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
DAD O2A O OP -0.500 0.000 0.000 0.000
DAD PA P P 0.000 -1.164 0.061 0.917
DAD O1A O OP -0.500 -1.440 -1.293 1.456
DAD O3A O O2 0.000 -0.839 1.066 2.130
DAD PB P P 0.000 0.455 0.478 2.888
DAD O1B O OP -0.500 0.154 -0.882 3.397
DAD O2B O OP -0.500 1.594 0.411 1.941
DAD O3B O O2 0.000 0.838 1.440 4.120
DAD PG P P 0.000 2.132 0.795 4.828
DAD O3G O OP -0.666 1.799 -0.598 5.317
DAD O2G O OP -0.666 2.546 1.656 6.002
DAD O1G O OP -0.666 3.268 0.722 3.832
DAD "O5'" O O2 0.000 -2.454 0.590 0.112
DAD "C5'" C CH2 0.000 -2.689 -0.339 -0.947
DAD "H5'1" H H 0.000 -2.873 -1.330 -0.526
DAD "H5'2" H H 0.000 -1.814 -0.378 -1.598
DAD "C4'" C CH1 0.000 -3.910 0.107 -1.756
DAD "H4'" H H 0.000 -3.754 1.120 -2.153
DAD "C3'" C CH2 0.000 -4.183 -0.883 -2.908
DAD "H3'1" H H 0.000 -3.787 -1.878 -2.697
DAD "H3'2" H H 0.000 -3.783 -0.527 -3.859
DAD "C2'" C CH2 0.000 -5.725 -0.948 -2.987
DAD "H2'1" H H 0.000 -6.104 -1.953 -2.790
DAD "H2'2" H H 0.000 -6.101 -0.601 -3.952
DAD "C1'" C CH1 0.000 -6.200 0.011 -1.874
DAD "H1'" H H 0.000 -6.400 1.009 -2.289
DAD "O4'" O O2 0.000 -5.100 0.067 -0.939
DAD N9 N NR5 0.000 -7.399 -0.518 -1.220
DAD C4 C CR56 0.000 -8.699 -0.254 -1.572
DAD C5 C CR56 0.000 -9.497 -0.971 -0.666
DAD N7 N NRD5 0.000 -8.660 -1.631 0.169
DAD C8 C CR15 0.000 -7.427 -1.365 -0.153
DAD H8 H H 0.000 -6.554 -1.757 0.353
DAD N3 N NRD6 0.000 -9.287 0.482 -2.509
DAD C2 C CR16 0.000 -10.598 0.536 -2.594
DAD H2 H H 0.000 -11.045 1.146 -3.370
DAD N1 N NRD6 0.000 -11.390 -0.125 -1.770
DAD C6 C CR6 0.000 -10.894 -0.886 -0.802
DAD N6 N NH2 0.000 -11.732 -1.576 0.057
DAD HN62 H H 0.000 -11.348 -2.158 0.796
DAD HN61 H H 0.000 -12.740 -1.509 -0.041
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
DAD O2A n/a PA START
DAD PA O2A "O5'" .
DAD O1A PA . .
DAD O3A PA PB .
DAD PB O3A O3B .
DAD O1B PB . .
DAD O2B PB . .
DAD O3B PB PG .
DAD PG O3B O1G .
DAD O3G PG . .
DAD O2G PG . .
DAD O1G PG . .
DAD "O5'" PA "C5'" .
DAD "C5'" "O5'" "C4'" .
DAD "H5'1" "C5'" . .
DAD "H5'2" "C5'" . .
DAD "C4'" "C5'" "C3'" .
DAD "H4'" "C4'" . .
DAD "C3'" "C4'" "C2'" .
DAD "H3'1" "C3'" . .
DAD "H3'2" "C3'" . .
DAD "C2'" "C3'" "C1'" .
DAD "H2'1" "C2'" . .
DAD "H2'2" "C2'" . .
DAD "C1'" "C2'" N9 .
DAD "H1'" "C1'" . .
DAD "O4'" "C1'" . .
DAD N9 "C1'" C4 .
DAD C4 N9 N3 .
DAD C5 C4 N7 .
DAD N7 C5 C8 .
DAD C8 N7 H8 .
DAD H8 C8 . .
DAD N3 C4 C2 .
DAD C2 N3 N1 .
DAD H2 C2 . .
DAD N1 C2 C6 .
DAD C6 N1 N6 .
DAD N6 C6 HN61 .
DAD HN62 N6 . .
DAD HN61 N6 . END
DAD "C4'" "O4'" . ADD
DAD N9 C8 . ADD
DAD C5 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
DAD O1G PG deloc 1.510 0.020
DAD O2G PG deloc 1.510 0.020
DAD O3G PG deloc 1.510 0.020
DAD PG O3B single 1.610 0.020
DAD O1B PB deloc 1.510 0.020
DAD O2B PB deloc 1.510 0.020
DAD O3B PB single 1.610 0.020
DAD PB O3A single 1.610 0.020
DAD O1A PA deloc 1.510 0.020
DAD PA O2A deloc 1.510 0.020
DAD O3A PA single 1.610 0.020
DAD "O5'" PA single 1.610 0.020
DAD "C5'" "O5'" single 1.426 0.020
DAD "C4'" "C5'" single 1.524 0.020
DAD "H5'1" "C5'" single 1.092 0.020
DAD "H5'2" "C5'" single 1.092 0.020
DAD "C4'" "O4'" single 1.426 0.020
DAD "C3'" "C4'" single 1.524 0.020
DAD "H4'" "C4'" single 1.099 0.020
DAD "O4'" "C1'" single 1.426 0.020
DAD "C2'" "C3'" single 1.524 0.020
DAD "H3'1" "C3'" single 1.092 0.020
DAD "H3'2" "C3'" single 1.092 0.020
DAD "C1'" "C2'" single 1.524 0.020
DAD "H2'1" "C2'" single 1.092 0.020
DAD "H2'2" "C2'" single 1.092 0.020
DAD N9 "C1'" single 1.485 0.020
DAD "H1'" "C1'" single 1.099 0.020
DAD N9 C8 single 1.337 0.020
DAD C4 N9 single 1.337 0.020
DAD C8 N7 double 1.350 0.020
DAD H8 C8 single 1.083 0.020
DAD N7 C5 single 1.350 0.020
DAD C5 C6 single 1.490 0.020
DAD C5 C4 double 1.490 0.020
DAD N6 C6 single 1.355 0.020
DAD C6 N1 double 1.350 0.020
DAD HN61 N6 single 1.010 0.020
DAD HN62 N6 single 1.010 0.020
DAD N1 C2 single 1.337 0.020
DAD C2 N3 double 1.337 0.020
DAD H2 C2 single 1.083 0.020
DAD N3 C4 single 1.355 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
DAD O2A PA O1A 119.900 3.000
DAD O2A PA O3A 108.200 3.000
DAD O2A PA "O5'" 108.200 3.000
DAD O1A PA O3A 108.200 3.000
DAD O1A PA "O5'" 108.200 3.000
DAD O3A PA "O5'" 102.600 3.000
DAD PA O3A PB 120.500 3.000
DAD O3A PB O1B 108.200 3.000
DAD O3A PB O2B 108.200 3.000
DAD O3A PB O3B 102.600 3.000
DAD O1B PB O2B 119.900 3.000
DAD O1B PB O3B 108.200 3.000
DAD O2B PB O3B 108.200 3.000
DAD PB O3B PG 120.500 3.000
DAD O3B PG O3G 108.200 3.000
DAD O3B PG O2G 108.200 3.000
DAD O3B PG O1G 108.200 3.000
DAD O3G PG O2G 119.900 3.000
DAD O3G PG O1G 119.900 3.000
DAD O2G PG O1G 119.900 3.000
DAD PA "O5'" "C5'" 120.500 3.000
DAD "O5'" "C5'" "H5'1" 109.470 3.000
DAD "O5'" "C5'" "H5'2" 109.470 3.000
DAD "O5'" "C5'" "C4'" 109.470 3.000
DAD "H5'1" "C5'" "H5'2" 107.900 3.000
DAD "H5'1" "C5'" "C4'" 109.470 3.000
DAD "H5'2" "C5'" "C4'" 109.470 3.000
DAD "C5'" "C4'" "H4'" 108.340 3.000
DAD "C5'" "C4'" "C3'" 109.470 3.000
DAD "C5'" "C4'" "O4'" 109.470 3.000
DAD "H4'" "C4'" "C3'" 108.340 3.000
DAD "H4'" "C4'" "O4'" 109.470 3.000
DAD "C3'" "C4'" "O4'" 109.470 3.000
DAD "C4'" "C3'" "H3'1" 109.470 3.000
DAD "C4'" "C3'" "H3'2" 109.470 3.000
DAD "C4'" "C3'" "C2'" 111.000 3.000
DAD "H3'1" "C3'" "H3'2" 107.900 3.000
DAD "H3'1" "C3'" "C2'" 109.470 3.000
DAD "H3'2" "C3'" "C2'" 109.470 3.000
DAD "C3'" "C2'" "H2'1" 109.470 3.000
DAD "C3'" "C2'" "H2'2" 109.470 3.000
DAD "C3'" "C2'" "C1'" 111.000 3.000
DAD "H2'1" "C2'" "H2'2" 107.900 3.000
DAD "H2'1" "C2'" "C1'" 109.470 3.000
DAD "H2'2" "C2'" "C1'" 109.470 3.000
DAD "C2'" "C1'" "H1'" 108.340 3.000
DAD "C2'" "C1'" "O4'" 109.470 3.000
DAD "C2'" "C1'" N9 109.470 3.000
DAD "H1'" "C1'" "O4'" 109.470 3.000
DAD "H1'" "C1'" N9 109.470 3.000
DAD "O4'" "C1'" N9 109.470 3.000
DAD "C1'" "O4'" "C4'" 111.800 3.000
DAD "C1'" N9 C4 126.000 3.000
DAD "C1'" N9 C8 126.000 3.000
DAD C4 N9 C8 108.000 3.000
DAD N9 C4 C5 108.000 3.000
DAD N9 C4 N3 132.000 3.000
DAD C5 C4 N3 120.000 3.000
DAD C4 C5 N7 108.000 3.000
DAD C4 C5 C6 120.000 3.000
DAD N7 C5 C6 132.000 3.000
DAD C5 N7 C8 108.000 3.000
DAD N7 C8 H8 126.000 3.000
DAD N7 C8 N9 108.000 3.000
DAD H8 C8 N9 126.000 3.000
DAD C4 N3 C2 120.000 3.000
DAD N3 C2 H2 120.000 3.000
DAD N3 C2 N1 120.000 3.000
DAD H2 C2 N1 120.000 3.000
DAD C2 N1 C6 120.000 3.000
DAD N1 C6 N6 120.000 3.000
DAD N1 C6 C5 120.000 3.000
DAD N6 C6 C5 120.000 3.000
DAD C6 N6 HN62 120.000 3.000
DAD C6 N6 HN61 120.000 3.000
DAD HN62 N6 HN61 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
DAD var_1 O2A PA O3A PB -60.016 20.000 1
DAD var_2 PA O3A PB O3B 179.999 20.000 1
DAD var_3 O3A PB O3B PG 179.973 20.000 1
DAD var_4 PB O3B PG O1G 60.049 20.000 1
DAD var_5 O2A PA "O5'" "C5'" 60.001 20.000 1
DAD var_6 PA "O5'" "C5'" "C4'" 179.971 20.000 1
DAD var_7 "O5'" "C5'" "C4'" "C3'" 179.956 20.000 3
DAD var_8 "C5'" "C4'" "O4'" "C1'" -150.000 20.000 1
DAD var_9 "C5'" "C4'" "C3'" "C2'" 150.000 20.000 3
DAD var_10 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
DAD var_11 "C3'" "C2'" "C1'" N9 -150.000 20.000 3
DAD var_12 "C2'" "C1'" "O4'" "C4'" 30.000 20.000 1
DAD var_13 "C2'" "C1'" N9 C4 -91.484 20.000 1
DAD CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
DAD CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
DAD CONST_3 N9 C4 C5 N7 0.000 0.000 0
DAD CONST_4 C4 C5 C6 N1 0.000 0.000 0
DAD CONST_5 C4 C5 N7 C8 0.000 0.000 0
DAD CONST_6 C5 N7 C8 N9 0.000 0.000 0
DAD CONST_7 N9 C4 N3 C2 180.000 0.000 0
DAD CONST_8 C4 N3 C2 N1 0.000 0.000 0
DAD CONST_9 N3 C2 N1 C6 0.000 0.000 0
DAD CONST_10 C2 N1 C6 N6 180.000 0.000 0
DAD CONST_11 N1 C6 N6 HN61 -0.076 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
DAD chir_01 "C4'" "C5'" "O4'" "C3'" positiv
DAD chir_02 "C1'" "O4'" "C2'" N9 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
DAD plan-1 N9 0.020
DAD plan-1 "C1'" 0.020
DAD plan-1 C8 0.020
DAD plan-1 C4 0.020
DAD plan-1 N7 0.020
DAD plan-1 H8 0.020
DAD plan-1 C5 0.020
DAD plan-1 C6 0.020
DAD plan-1 N1 0.020
DAD plan-1 C2 0.020
DAD plan-1 N3 0.020
DAD plan-1 N6 0.020
DAD plan-1 H2 0.020
DAD plan-1 HN62 0.020
DAD plan-1 HN61 0.020
DAD plan-2 N6 0.020
DAD plan-2 C6 0.020
DAD plan-2 HN61 0.020
DAD plan-2 HN62 0.020
# ------------------------------------------------------
|
