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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
XGA XGA '"6-AMINO-3-(2-DEOXY-5-O-PHOSPHONO-BE' DNA 41 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XGA
#
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
XGA OP3 O OP -0.666 0.000 0.000 0.000
XGA P P P 0.000 -0.446 1.293 0.646
XGA OP1 O OP -0.666 -1.312 1.933 -0.417
XGA OP2 O OP -0.666 0.674 2.162 1.177
XGA "O5'" O O2 0.000 -1.511 0.795 1.759
XGA "C5'" C CH2 0.000 -2.590 -0.023 1.343
XGA "H5'1" H H 0.000 -2.207 -0.945 0.900
XGA "H5'2" H H 0.000 -3.196 0.509 0.607
XGA "C4'" C CH1 0.000 -3.444 -0.359 2.558
XGA "H4'" H H 0.000 -2.828 -0.861 3.318
XGA "C3'" C CH1 0.000 -4.645 -1.232 2.211
XGA "H3'" H H 0.000 -4.453 -1.854 1.325
XGA "C2'" C CH2 0.000 -5.743 -0.224 1.961
XGA "H2'1" H H 0.000 -6.741 -0.615 2.169
XGA "H2'2" H H 0.000 -5.721 0.196 0.953
XGA "C1'" C CH1 0.000 -5.400 0.861 2.971
XGA "H1'" H H 0.000 -5.830 0.582 3.944
XGA "O4'" O O2 0.000 -3.966 0.876 3.092
XGA N9 N NR5 0.000 -5.883 2.190 2.614
XGA C10 C CR56 0.000 -7.068 2.761 3.002
XGA CD C CR16 0.000 -8.116 2.298 3.800
XGA HD H H 0.000 -8.087 1.312 4.248
XGA C4 C CR66 0.000 -9.208 3.157 4.000
XGA C11 C CR56 0.000 -7.057 4.017 2.405
XGA N7 N NRD5 0.000 -5.904 4.204 1.678
XGA C8 C CR15 0.000 -5.224 3.090 1.826
XGA H8 H H 0.000 -4.255 2.907 1.376
XGA CP C CR16 0.000 -8.148 4.880 2.603
XGA HP H H 0.000 -8.170 5.864 2.152
XGA C5 C CR66 0.000 -9.210 4.428 3.405
XGA C6 C CR6 0.000 -10.376 5.307 3.636
XGA N1 N NR16 0.000 -11.358 4.752 4.440
XGA HN1 H H 0.000 -12.203 5.325 4.638
XGA C2 C CR6 0.000 -11.292 3.483 5.001
XGA N2 N NH2 0.000 -12.364 3.115 5.768
XGA HN22 H H 0.000 -12.794 2.206 5.643
XGA HN21 H H 0.000 -12.734 3.748 6.466
XGA N3 N NRD6 0.000 -10.270 2.700 4.803
XGA O6 O O 0.000 -10.444 6.427 3.144
XGA "O3'" O OH1 0.000 -5.006 -2.020 3.342
XGA "HO3'" H H 0.000 -5.734 -2.594 3.057
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
XGA OP3 n/a P START
XGA P OP3 "O5'" .
XGA OP1 P . .
XGA OP2 P . .
XGA "O5'" P "C5'" .
XGA "C5'" "O5'" "C4'" .
XGA "H5'1" "C5'" . .
XGA "H5'2" "C5'" . .
XGA "C4'" "C5'" "C3'" .
XGA "H4'" "C4'" . .
XGA "C3'" "C4'" "O3'" .
XGA "H3'" "C3'" . .
XGA "C2'" "C3'" "C1'" .
XGA "H2'1" "C2'" . .
XGA "H2'2" "C2'" . .
XGA "C1'" "C2'" N9 .
XGA "H1'" "C1'" . .
XGA "O4'" "C1'" . .
XGA N9 "C1'" C10 .
XGA C10 N9 C11 .
XGA CD C10 C4 .
XGA HD CD . .
XGA C4 CD . .
XGA C11 C10 CP .
XGA N7 C11 C8 .
XGA C8 N7 H8 .
XGA H8 C8 . .
XGA CP C11 C5 .
XGA HP CP . .
XGA C5 CP C6 .
XGA C6 C5 O6 .
XGA N1 C6 C2 .
XGA HN1 N1 . .
XGA C2 N1 N3 .
XGA N2 C2 HN21 .
XGA HN22 N2 . .
XGA HN21 N2 . .
XGA N3 C2 . .
XGA O6 C6 . .
XGA "O3'" "C3'" . END
XGA "HO3'" "O3'" . .
XGA "C4'" "O4'" . ADD
XGA N9 C8 . ADD
XGA C4 C5 . ADD
XGA C4 N3 . 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
XGA P OP3 deloc 1.510 0.020
XGA "O5'" P single 1.610 0.020
XGA OP1 P deloc 1.510 0.020
XGA OP2 P deloc 1.510 0.020
XGA "C4'" "C5'" single 1.524 0.020
XGA "C5'" "O5'" single 1.426 0.020
XGA "H5'1" "C5'" single 1.092 0.020
XGA "H5'2" "C5'" single 1.092 0.020
XGA "C4'" "O4'" single 1.426 0.020
XGA "C3'" "C4'" single 1.524 0.020
XGA "H4'" "C4'" single 1.099 0.020
XGA "O4'" "C1'" single 1.426 0.020
XGA "O3'" "C3'" single 1.432 0.020
XGA "C2'" "C3'" single 1.524 0.020
XGA "H3'" "C3'" single 1.099 0.020
XGA "C1'" "C2'" single 1.524 0.020
XGA "H2'1" "C2'" single 1.092 0.020
XGA "H2'2" "C2'" single 1.092 0.020
XGA N9 "C1'" single 1.485 0.020
XGA "H1'" "C1'" single 1.099 0.020
XGA C10 N9 single 1.337 0.020
XGA N9 C8 single 1.337 0.020
XGA C8 N7 double 1.350 0.020
XGA H8 C8 single 1.083 0.020
XGA N7 C11 single 1.350 0.020
XGA C4 N3 single 1.350 0.020
XGA C4 C5 double 1.490 0.020
XGA C4 CD single 1.390 0.020
XGA C6 C5 single 1.490 0.020
XGA C5 CP single 1.390 0.020
XGA N3 C2 double 1.350 0.020
XGA N2 C2 single 1.355 0.020
XGA C2 N1 single 1.337 0.020
XGA HN21 N2 single 1.010 0.020
XGA HN22 N2 single 1.010 0.020
XGA N1 C6 single 1.337 0.020
XGA HN1 N1 single 1.040 0.020
XGA O6 C6 double 1.250 0.020
XGA CD C10 double 1.390 0.020
XGA C11 C10 single 1.490 0.020
XGA CP C11 double 1.390 0.020
XGA HP CP single 1.083 0.020
XGA HD CD single 1.083 0.020
XGA "HO3'" "O3'" 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
XGA OP3 P OP1 119.900 3.000
XGA OP3 P OP2 119.900 3.000
XGA OP3 P "O5'" 108.200 3.000
XGA OP1 P OP2 119.900 3.000
XGA OP1 P "O5'" 108.200 3.000
XGA OP2 P "O5'" 108.200 3.000
XGA P "O5'" "C5'" 120.500 3.000
XGA "O5'" "C5'" "H5'1" 109.470 3.000
XGA "O5'" "C5'" "H5'2" 109.470 3.000
XGA "O5'" "C5'" "C4'" 109.470 3.000
XGA "H5'1" "C5'" "H5'2" 107.900 3.000
XGA "H5'1" "C5'" "C4'" 109.470 3.000
XGA "H5'2" "C5'" "C4'" 109.470 3.000
XGA "C5'" "C4'" "H4'" 108.340 3.000
XGA "C5'" "C4'" "C3'" 111.000 3.000
XGA "C5'" "C4'" "O4'" 109.470 3.000
XGA "H4'" "C4'" "C3'" 108.340 3.000
XGA "H4'" "C4'" "O4'" 109.470 3.000
XGA "C3'" "C4'" "O4'" 109.470 3.000
XGA "C4'" "C3'" "H3'" 108.340 3.000
XGA "C4'" "C3'" "C2'" 111.000 3.000
XGA "C4'" "C3'" "O3'" 109.470 3.000
XGA "H3'" "C3'" "C2'" 108.340 3.000
XGA "H3'" "C3'" "O3'" 109.470 3.000
XGA "C2'" "C3'" "O3'" 109.470 3.000
XGA "C3'" "C2'" "H2'1" 109.470 3.000
XGA "C3'" "C2'" "H2'2" 109.470 3.000
XGA "C3'" "C2'" "C1'" 111.000 3.000
XGA "H2'1" "C2'" "H2'2" 107.900 3.000
XGA "H2'1" "C2'" "C1'" 109.470 3.000
XGA "H2'2" "C2'" "C1'" 109.470 3.000
XGA "C2'" "C1'" "H1'" 108.340 3.000
XGA "C2'" "C1'" "O4'" 109.470 3.000
XGA "C2'" "C1'" N9 109.470 3.000
XGA "H1'" "C1'" "O4'" 109.470 3.000
XGA "H1'" "C1'" N9 109.470 3.000
XGA "O4'" "C1'" N9 109.470 3.000
XGA "C1'" "O4'" "C4'" 111.800 3.000
XGA "C1'" N9 C10 126.000 3.000
XGA "C1'" N9 C8 126.000 3.000
XGA C10 N9 C8 108.000 3.000
XGA N9 C10 CD 132.000 3.000
XGA N9 C10 C11 108.000 3.000
XGA CD C10 C11 120.000 3.000
XGA C10 CD HD 120.000 3.000
XGA C10 CD C4 120.000 3.000
XGA HD CD C4 120.000 3.000
XGA CD C4 C5 120.000 3.000
XGA CD C4 N3 120.000 3.000
XGA C5 C4 N3 120.000 3.000
XGA C10 C11 N7 108.000 3.000
XGA C10 C11 CP 120.000 3.000
XGA N7 C11 CP 132.000 3.000
XGA C11 N7 C8 108.000 3.000
XGA N7 C8 H8 126.000 3.000
XGA N7 C8 N9 108.000 3.000
XGA H8 C8 N9 126.000 3.000
XGA C11 CP HP 120.000 3.000
XGA C11 CP C5 120.000 3.000
XGA HP CP C5 120.000 3.000
XGA CP C5 C6 120.000 3.000
XGA CP C5 C4 120.000 3.000
XGA C6 C5 C4 120.000 3.000
XGA C5 C6 N1 120.000 3.000
XGA C5 C6 O6 120.000 3.000
XGA N1 C6 O6 120.000 3.000
XGA C6 N1 HN1 120.000 3.000
XGA C6 N1 C2 120.000 3.000
XGA HN1 N1 C2 120.000 3.000
XGA N1 C2 N2 120.000 3.000
XGA N1 C2 N3 120.000 3.000
XGA N2 C2 N3 120.000 3.000
XGA C2 N2 HN22 120.000 3.000
XGA C2 N2 HN21 120.000 3.000
XGA HN22 N2 HN21 120.000 3.000
XGA C2 N3 C4 120.000 3.000
XGA "C3'" "O3'" "HO3'" 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
XGA var_1 OP3 P "O5'" "C5'" -54.180 20.000 1
XGA var_2 P "O5'" "C5'" "C4'" 179.954 20.000 1
XGA var_3 "O5'" "C5'" "C4'" "C3'" 179.546 20.000 3
XGA var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
XGA var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
XGA var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
XGA var_7 "C3'" "C2'" "C1'" N9 150.000 20.000 3
XGA var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
XGA var_9 "C2'" "C1'" N9 C10 93.448 20.000 1
XGA CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
XGA CONST_2 "C1'" N9 C10 C11 180.000 0.000 0
XGA CONST_3 N9 C10 CD C4 180.000 0.000 0
XGA CONST_4 C10 CD C4 C5 0.000 0.000 0
XGA CONST_5 CD C4 C5 CP 0.000 0.000 0
XGA CONST_6 CD C4 N3 C2 180.000 0.000 0
XGA CONST_7 N9 C10 C11 CP 180.000 0.000 0
XGA CONST_8 C10 C11 N7 C8 0.000 0.000 0
XGA CONST_9 C11 N7 C8 N9 0.000 0.000 0
XGA CONST_10 C10 C11 CP C5 0.000 0.000 0
XGA CONST_11 C11 CP C5 C6 180.000 0.000 0
XGA CONST_12 CP C5 C6 O6 0.000 0.000 0
XGA CONST_13 C5 C6 N1 C2 0.000 0.000 0
XGA CONST_14 C6 N1 C2 N3 0.000 0.000 0
XGA CONST_15 N1 C2 N2 HN21 -47.034 0.000 0
XGA CONST_16 N1 C2 N3 C4 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
XGA chir_01 "C4'" "C5'" "O4'" "C3'" negativ
XGA chir_02 "C3'" "C4'" "C2'" "O3'" positiv
XGA chir_03 "C1'" "O4'" "C2'" N9 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
XGA plan-1 N9 0.020
XGA plan-1 "C1'" 0.020
XGA plan-1 C8 0.020
XGA plan-1 C10 0.020
XGA plan-1 N7 0.020
XGA plan-1 H8 0.020
XGA plan-1 C11 0.020
XGA plan-1 C4 0.020
XGA plan-1 C5 0.020
XGA plan-1 N3 0.020
XGA plan-1 CD 0.020
XGA plan-1 CP 0.020
XGA plan-1 C6 0.020
XGA plan-1 C2 0.020
XGA plan-1 N1 0.020
XGA plan-1 N2 0.020
XGA plan-1 HN1 0.020
XGA plan-1 O6 0.020
XGA plan-1 HP 0.020
XGA plan-1 HD 0.020
XGA plan-1 HN22 0.020
XGA plan-1 HN21 0.020
XGA plan-2 N2 0.020
XGA plan-2 C2 0.020
XGA plan-2 HN21 0.020
XGA plan-2 HN22 0.020
# ------------------------------------------------------
|
