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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
C5G C5G '. ' non-polymer 59 36 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_C5G
#
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
C5G O2B O OP -0.500 0.000 0.000 0.000
C5G PB P P 0.000 -0.957 1.132 -0.055
C5G O1B O OP -0.500 -1.237 1.475 -1.470
C5G "O1'" O O2 0.000 -0.321 2.410 0.691
C5G "C1'" C CH1 0.000 0.822 2.806 -0.071
C5G "H1'" H H 0.000 1.258 1.923 -0.559
C5G "O5'" O O2 0.000 0.426 3.750 -1.063
C5G "C5'" C CH1 0.000 -0.292 4.792 -0.405
C5G "H5'" H H 0.000 -1.096 4.354 0.203
C5G "C6'" C CH2 0.000 -0.900 5.729 -1.450
C5G "H6'1" H H 0.000 -0.111 6.096 -2.111
C5G "H6'2" H H 0.000 -1.373 6.575 -0.947
C5G "O6'" O OH1 0.000 -1.876 5.021 -2.217
C5G "HO'6" H H 0.000 -2.259 5.614 -2.877
C5G "C4'" C CH1 0.000 0.655 5.584 0.499
C5G "H4'" H H 0.000 1.472 6.005 -0.104
C5G "O4'" O OH1 0.000 -0.064 6.644 1.133
C5G "HO'4" H H 0.000 0.536 7.143 1.703
C5G "C3'" C CH1 0.000 1.233 4.644 1.563
C5G "H3'" H H 0.000 0.430 4.305 2.232
C5G "O3'" O OH1 0.000 2.230 5.333 2.320
C5G "HO'3" H H 0.000 2.592 4.739 2.991
C5G "C2'" C CH1 0.000 1.860 3.437 0.860
C5G "H2'" H H 0.000 2.729 3.763 0.273
C5G "O2'" O OH1 0.000 2.273 2.477 1.835
C5G HOD H H 0.000 2.668 1.716 1.390
C5G O3A O O2 0.000 -2.328 0.711 0.677
C5G PA P P 0.000 -3.104 -0.283 -0.325
C5G O1A O OP -0.500 -2.149 -1.275 -0.873
C5G O2A O OP -0.500 -3.698 0.499 -1.436
C5G O5D O O2 0.000 -4.271 -1.047 0.478
C5G C5D C CH2 0.000 -4.842 -1.995 -0.427
C5G "H5'1" H H 0.000 -4.071 -2.695 -0.754
C5G "H5'2" H H 0.000 -5.247 -1.470 -1.295
C5G C4D C CH1 0.000 -5.964 -2.761 0.276
C5G H4D H H 0.000 -5.588 -3.233 1.194
C5G C3D C CH1 0.000 -6.566 -3.825 -0.669
C5G H3D H H 0.000 -6.399 -3.547 -1.719
C5G O3D O OH1 0.000 -6.005 -5.111 -0.396
C5G H3T H H 0.000 -6.393 -5.764 -0.995
C5G C2D C CH1 0.000 -8.078 -3.810 -0.337
C5G H2D H H 0.000 -8.662 -3.525 -1.223
C5G O2D O OH1 0.000 -8.496 -5.088 0.147
C5G "HO'2" H H 0.000 -8.350 -5.755 -0.537
C5G O4D O O2 0.000 -7.063 -1.874 0.581
C5G C1D C CH1 0.000 -8.208 -2.736 0.765
C5G H1D H H 0.000 -8.178 -3.203 1.760
C5G N1 N NR6 0.000 -9.449 -1.978 0.595
C5G C6 C CR16 0.000 -10.413 -2.031 1.557
C5G H6 H H 0.000 -10.267 -2.633 2.445
C5G C5 C CR16 0.000 -11.554 -1.322 1.391
C5G H5 H H 0.000 -12.329 -1.342 2.147
C5G C4 C CR6 0.000 -11.718 -0.556 0.219
C5G N4 N NH2 0.000 -12.869 0.171 0.021
C5G H42 H H 0.000 -13.609 0.158 0.715
C5G H41 H H 0.000 -12.988 0.725 -0.819
C5G N3 N NRD6 0.000 -10.752 -0.535 -0.691
C5G C2 C CR6 0.000 -9.633 -1.234 -0.510
C5G O2 O O 0.000 -8.759 -1.198 -1.362
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
C5G O2B n/a PB START
C5G PB O2B O3A .
C5G O1B PB . .
C5G "O1'" PB "C1'" .
C5G "C1'" "O1'" "O5'" .
C5G "H1'" "C1'" . .
C5G "O5'" "C1'" "C5'" .
C5G "C5'" "O5'" "C4'" .
C5G "H5'" "C5'" . .
C5G "C6'" "C5'" "O6'" .
C5G "H6'1" "C6'" . .
C5G "H6'2" "C6'" . .
C5G "O6'" "C6'" "HO'6" .
C5G "HO'6" "O6'" . .
C5G "C4'" "C5'" "C3'" .
C5G "H4'" "C4'" . .
C5G "O4'" "C4'" "HO'4" .
C5G "HO'4" "O4'" . .
C5G "C3'" "C4'" "C2'" .
C5G "H3'" "C3'" . .
C5G "O3'" "C3'" "HO'3" .
C5G "HO'3" "O3'" . .
C5G "C2'" "C3'" "O2'" .
C5G "H2'" "C2'" . .
C5G "O2'" "C2'" HOD .
C5G HOD "O2'" . .
C5G O3A PB PA .
C5G PA O3A O5D .
C5G O1A PA . .
C5G O2A PA . .
C5G O5D PA C5D .
C5G C5D O5D C4D .
C5G "H5'1" C5D . .
C5G "H5'2" C5D . .
C5G C4D C5D O4D .
C5G H4D C4D . .
C5G C3D C4D C2D .
C5G H3D C3D . .
C5G O3D C3D H3T .
C5G H3T O3D . .
C5G C2D C3D O2D .
C5G H2D C2D . .
C5G O2D C2D "HO'2" .
C5G "HO'2" O2D . .
C5G O4D C4D C1D .
C5G C1D O4D N1 .
C5G H1D C1D . .
C5G N1 C1D C6 .
C5G C6 N1 C5 .
C5G H6 C6 . .
C5G C5 C6 C4 .
C5G H5 C5 . .
C5G C4 C5 N3 .
C5G N4 C4 H41 .
C5G H42 N4 . .
C5G H41 N4 . .
C5G N3 C4 C2 .
C5G C2 N3 O2 .
C5G O2 C2 . END
C5G N1 C2 . ADD
C5G C1D C2D . ADD
C5G "C1'" "C2'" . 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
C5G N1 C2 single 1.410 0.020
C5G C6 N1 single 1.337 0.020
C5G N1 C1D single 1.465 0.020
C5G C2 N3 single 1.350 0.020
C5G O2 C2 double 1.250 0.020
C5G N3 C4 double 1.350 0.020
C5G C4 C5 single 1.390 0.020
C5G N4 C4 single 1.355 0.020
C5G C5 C6 double 1.390 0.020
C5G H5 C5 single 1.083 0.020
C5G H6 C6 single 1.083 0.020
C5G H41 N4 single 1.010 0.020
C5G H42 N4 single 1.010 0.020
C5G C1D C2D single 1.524 0.020
C5G C1D O4D single 1.426 0.020
C5G H1D C1D single 1.099 0.020
C5G O2D C2D single 1.432 0.020
C5G C2D C3D single 1.524 0.020
C5G H2D C2D single 1.099 0.020
C5G "HO'2" O2D single 0.967 0.020
C5G C3D C4D single 1.524 0.020
C5G O3D C3D single 1.432 0.020
C5G H3D C3D single 1.099 0.020
C5G O4D C4D single 1.426 0.020
C5G C4D C5D single 1.524 0.020
C5G H4D C4D single 1.099 0.020
C5G H3T O3D single 0.967 0.020
C5G C5D O5D single 1.426 0.020
C5G "H5'1" C5D single 1.092 0.020
C5G "H5'2" C5D single 1.092 0.020
C5G O5D PA single 1.610 0.020
C5G O1A PA deloc 1.510 0.020
C5G O2A PA deloc 1.510 0.020
C5G PA O3A single 1.610 0.020
C5G O3A PB single 1.610 0.020
C5G O1B PB deloc 1.510 0.020
C5G PB O2B deloc 1.510 0.020
C5G "O1'" PB single 1.610 0.020
C5G "C1'" "O1'" single 1.426 0.020
C5G "C1'" "C2'" single 1.524 0.020
C5G "O5'" "C1'" single 1.426 0.020
C5G "H1'" "C1'" single 1.099 0.020
C5G "O2'" "C2'" single 1.432 0.020
C5G "C2'" "C3'" single 1.524 0.020
C5G "H2'" "C2'" single 1.099 0.020
C5G HOD "O2'" single 0.967 0.020
C5G "O3'" "C3'" single 1.432 0.020
C5G "C3'" "C4'" single 1.524 0.020
C5G "H3'" "C3'" single 1.099 0.020
C5G "HO'3" "O3'" single 0.967 0.020
C5G "O4'" "C4'" single 1.432 0.020
C5G "C4'" "C5'" single 1.524 0.020
C5G "H4'" "C4'" single 1.099 0.020
C5G "HO'4" "O4'" single 0.967 0.020
C5G "C6'" "C5'" single 1.524 0.020
C5G "C5'" "O5'" single 1.426 0.020
C5G "H5'" "C5'" single 1.099 0.020
C5G "O6'" "C6'" single 1.432 0.020
C5G "H6'1" "C6'" single 1.092 0.020
C5G "H6'2" "C6'" single 1.092 0.020
C5G "HO'6" "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
C5G O2B PB O1B 119.900 3.000
C5G O2B PB "O1'" 108.200 3.000
C5G O2B PB O3A 108.200 3.000
C5G O1B PB "O1'" 108.200 3.000
C5G O1B PB O3A 108.200 3.000
C5G "O1'" PB O3A 102.600 3.000
C5G PB "O1'" "C1'" 120.500 3.000
C5G "O1'" "C1'" "H1'" 109.470 3.000
C5G "O1'" "C1'" "O5'" 109.470 3.000
C5G "O1'" "C1'" "C2'" 109.470 3.000
C5G "H1'" "C1'" "O5'" 109.470 3.000
C5G "H1'" "C1'" "C2'" 108.340 3.000
C5G "O5'" "C1'" "C2'" 109.470 3.000
C5G "C1'" "O5'" "C5'" 111.800 3.000
C5G "O5'" "C5'" "H5'" 109.470 3.000
C5G "O5'" "C5'" "C6'" 109.470 3.000
C5G "O5'" "C5'" "C4'" 109.470 3.000
C5G "H5'" "C5'" "C6'" 108.340 3.000
C5G "H5'" "C5'" "C4'" 108.340 3.000
C5G "C6'" "C5'" "C4'" 111.000 3.000
C5G "C5'" "C6'" "H6'1" 109.470 3.000
C5G "C5'" "C6'" "H6'2" 109.470 3.000
C5G "C5'" "C6'" "O6'" 109.470 3.000
C5G "H6'1" "C6'" "H6'2" 107.900 3.000
C5G "H6'1" "C6'" "O6'" 109.470 3.000
C5G "H6'2" "C6'" "O6'" 109.470 3.000
C5G "C6'" "O6'" "HO'6" 109.470 3.000
C5G "C5'" "C4'" "H4'" 108.340 3.000
C5G "C5'" "C4'" "O4'" 109.470 3.000
C5G "C5'" "C4'" "C3'" 111.000 3.000
C5G "H4'" "C4'" "O4'" 109.470 3.000
C5G "H4'" "C4'" "C3'" 108.340 3.000
C5G "O4'" "C4'" "C3'" 109.470 3.000
C5G "C4'" "O4'" "HO'4" 109.470 3.000
C5G "C4'" "C3'" "H3'" 108.340 3.000
C5G "C4'" "C3'" "O3'" 109.470 3.000
C5G "C4'" "C3'" "C2'" 111.000 3.000
C5G "H3'" "C3'" "O3'" 109.470 3.000
C5G "H3'" "C3'" "C2'" 108.340 3.000
C5G "O3'" "C3'" "C2'" 109.470 3.000
C5G "C3'" "O3'" "HO'3" 109.470 3.000
C5G "C3'" "C2'" "H2'" 108.340 3.000
C5G "C3'" "C2'" "O2'" 109.470 3.000
C5G "C3'" "C2'" "C1'" 111.000 3.000
C5G "H2'" "C2'" "O2'" 109.470 3.000
C5G "H2'" "C2'" "C1'" 108.340 3.000
C5G "O2'" "C2'" "C1'" 109.470 3.000
C5G "C2'" "O2'" HOD 109.470 3.000
C5G PB O3A PA 120.500 3.000
C5G O3A PA O1A 108.200 3.000
C5G O3A PA O2A 108.200 3.000
C5G O3A PA O5D 102.600 3.000
C5G O1A PA O2A 119.900 3.000
C5G O1A PA O5D 108.200 3.000
C5G O2A PA O5D 108.200 3.000
C5G PA O5D C5D 120.500 3.000
C5G O5D C5D "H5'1" 109.470 3.000
C5G O5D C5D "H5'2" 109.470 3.000
C5G O5D C5D C4D 109.470 3.000
C5G "H5'1" C5D "H5'2" 107.900 3.000
C5G "H5'1" C5D C4D 109.470 3.000
C5G "H5'2" C5D C4D 109.470 3.000
C5G C5D C4D H4D 108.340 3.000
C5G C5D C4D C3D 111.000 3.000
C5G C5D C4D O4D 109.470 3.000
C5G H4D C4D C3D 108.340 3.000
C5G H4D C4D O4D 109.470 3.000
C5G C3D C4D O4D 109.470 3.000
C5G C4D C3D H3D 108.340 3.000
C5G C4D C3D O3D 109.470 3.000
C5G C4D C3D C2D 111.000 3.000
C5G H3D C3D O3D 109.470 3.000
C5G H3D C3D C2D 108.340 3.000
C5G O3D C3D C2D 109.470 3.000
C5G C3D O3D H3T 109.470 3.000
C5G C3D C2D H2D 108.340 3.000
C5G C3D C2D O2D 109.470 3.000
C5G C3D C2D C1D 111.000 3.000
C5G H2D C2D O2D 109.470 3.000
C5G H2D C2D C1D 108.340 3.000
C5G O2D C2D C1D 109.470 3.000
C5G C2D O2D "HO'2" 109.470 3.000
C5G C4D O4D C1D 111.800 3.000
C5G O4D C1D H1D 109.470 3.000
C5G O4D C1D N1 109.470 3.000
C5G O4D C1D C2D 109.470 3.000
C5G H1D C1D N1 109.470 3.000
C5G H1D C1D C2D 108.340 3.000
C5G N1 C1D C2D 109.470 3.000
C5G C1D N1 C6 120.000 3.000
C5G C1D N1 C2 120.000 3.000
C5G C6 N1 C2 120.000 3.000
C5G N1 C6 H6 120.000 3.000
C5G N1 C6 C5 120.000 3.000
C5G H6 C6 C5 120.000 3.000
C5G C6 C5 H5 120.000 3.000
C5G C6 C5 C4 120.000 3.000
C5G H5 C5 C4 120.000 3.000
C5G C5 C4 N4 120.000 3.000
C5G C5 C4 N3 120.000 3.000
C5G N4 C4 N3 120.000 3.000
C5G C4 N4 H42 120.000 3.000
C5G C4 N4 H41 120.000 3.000
C5G H42 N4 H41 120.000 3.000
C5G C4 N3 C2 120.000 3.000
C5G N3 C2 O2 120.000 3.000
C5G N3 C2 N1 120.000 3.000
C5G O2 C2 N1 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
C5G var_1 O2B PB "O1'" "C1'" 65.011 20.000 1
C5G var_2 PB "O1'" "C1'" "O5'" 89.854 20.000 1
C5G var_3 "O1'" "C1'" "C2'" "C3'" -60.000 20.000 3
C5G var_4 "O1'" "C1'" "O5'" "C5'" 60.000 20.000 1
C5G var_5 "C1'" "O5'" "C5'" "C4'" 60.000 20.000 1
C5G var_6 "O5'" "C5'" "C6'" "O6'" 64.925 20.000 3
C5G var_7 "C5'" "C6'" "O6'" "HO'6" 179.991 20.000 1
C5G var_8 "O5'" "C5'" "C4'" "C3'" -60.000 20.000 3
C5G var_9 "C5'" "C4'" "O4'" "HO'4" -179.982 20.000 1
C5G var_10 "C5'" "C4'" "C3'" "C2'" 60.000 20.000 3
C5G var_11 "C4'" "C3'" "O3'" "HO'3" 179.935 20.000 1
C5G var_12 "C4'" "C3'" "C2'" "O2'" 180.000 20.000 3
C5G var_13 "C3'" "C2'" "O2'" HOD -179.994 20.000 1
C5G var_14 O2B PB O3A PA -74.998 20.000 1
C5G var_15 PB O3A PA O5D 164.990 20.000 1
C5G var_16 O3A PA O5D C5D -174.984 20.000 1
C5G var_17 PA O5D C5D C4D 179.973 20.000 1
C5G var_18 O5D C5D C4D O4D 66.488 20.000 3
C5G var_19 C5D C4D C3D C2D -150.000 20.000 3
C5G var_20 C4D C3D O3D H3T 179.965 20.000 1
C5G var_21 C4D C3D C2D O2D -120.000 20.000 3
C5G var_22 C3D C2D O2D "HO'2" -61.445 20.000 1
C5G var_23 C5D C4D O4D C1D 150.000 20.000 1
C5G var_24 C4D O4D C1D N1 -150.000 20.000 1
C5G var_25 O4D C1D C2D C3D 30.000 20.000 3
C5G var_26 O4D C1D N1 C6 -127.936 20.000 1
C5G CONST_1 C1D N1 C2 N3 180.000 0.000 0
C5G CONST_2 C1D N1 C6 C5 180.000 0.000 0
C5G CONST_3 N1 C6 C5 C4 0.000 0.000 0
C5G CONST_4 C6 C5 C4 N3 0.000 0.000 0
C5G CONST_5 C5 C4 N4 H41 179.722 0.000 0
C5G CONST_6 C5 C4 N3 C2 0.000 0.000 0
C5G CONST_7 C4 N3 C2 O2 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
C5G chir_01 C1D N1 C2D O4D negativ
C5G chir_02 C2D C1D O2D C3D positiv
C5G chir_03 C3D C2D C4D O3D negativ
C5G chir_04 C4D C3D O4D C5D positiv
C5G chir_05 "C1'" "O1'" "C2'" "O5'" positiv
C5G chir_06 "C2'" "C1'" "O2'" "C3'" positiv
C5G chir_07 "C3'" "C2'" "O3'" "C4'" negativ
C5G chir_08 "C4'" "C3'" "O4'" "C5'" positiv
C5G chir_09 "C5'" "C4'" "C6'" "O5'" 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
C5G plan-1 N1 0.020
C5G plan-1 C2 0.020
C5G plan-1 C6 0.020
C5G plan-1 C1D 0.020
C5G plan-1 N3 0.020
C5G plan-1 C4 0.020
C5G plan-1 C5 0.020
C5G plan-1 O2 0.020
C5G plan-1 N4 0.020
C5G plan-1 H5 0.020
C5G plan-1 H6 0.020
C5G plan-1 H42 0.020
C5G plan-1 H41 0.020
C5G plan-2 N4 0.020
C5G plan-2 C4 0.020
C5G plan-2 H41 0.020
C5G plan-2 H42 0.020
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