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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
G3D G3D 'GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOS' non-polymer 43 32 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_G3D
#
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
G3D O6P O OP -0.666 0.000 0.000 0.000
G3D P1 P P 0.000 -0.017 -0.329 -1.477
G3D O4P O OP -0.666 1.167 -1.210 -1.811
G3D O5P O OP -0.666 0.065 0.952 -2.279
G3D "O3'" O O2 0.000 -1.381 -1.101 -1.838
G3D "C3'" C CH1 0.000 -2.457 -0.223 -1.501
G3D "H3'" H H 0.000 -2.069 0.740 -1.140
G3D "C4'" C CH1 0.000 -3.373 -0.869 -0.441
G3D "H4'" H H 0.000 -3.286 -1.964 -0.475
G3D "C5'" C CH2 0.000 -3.022 -0.351 0.956
G3D "H5'1" H H 0.000 -3.100 0.738 0.970
G3D "H5'2" H H 0.000 -2.001 -0.645 1.207
G3D "O5'" O O2 0.000 -3.927 -0.906 1.911
G3D PA P P 0.000 -3.501 -0.323 3.351
G3D O1A O OP -0.500 -3.597 1.157 3.332
G3D O2A O OP -0.500 -2.105 -0.723 3.653
G3D O3A O O2 0.000 -4.485 -0.911 4.480
G3D PB P P 0.000 -4.004 -0.289 5.886
G3D O3B O OP -0.666 -2.573 -0.698 6.154
G3D O2B O OP -0.666 -4.893 -0.805 6.996
G3D O1B O OP -0.666 -4.095 1.220 5.827
G3D "C2'" C CH1 0.000 -3.385 -0.010 -2.720
G3D "H2'" H H 0.000 -3.458 1.059 -2.965
G3D "O2'" O OH1 0.000 -2.910 -0.749 -3.847
G3D "HO2'" H H 0.000 -3.501 -0.605 -4.599
G3D "C1'" C CH1 0.000 -4.751 -0.550 -2.247
G3D "H1'" H H 0.000 -4.878 -1.596 -2.561
G3D "O4'" O O2 0.000 -4.707 -0.459 -0.806
G3D N9 N NR5 0.000 -5.838 0.276 -2.777
G3D C4 C CR56 0.000 -6.513 0.072 -3.949
G3D C5 C CR56 0.000 -7.456 1.101 -4.040
G3D N7 N NRD5 0.000 -7.314 1.875 -2.936
G3D C8 C CR15 0.000 -6.363 1.392 -2.191
G3D H8 H H 0.000 -6.038 1.811 -1.247
G3D N3 N NRD6 0.000 -6.437 -0.844 -4.922
G3D C2 C CR6 0.000 -7.236 -0.796 -5.964
G3D N2 N NH2 0.000 -7.121 -1.757 -6.937
G3D HN22 H H 0.000 -7.726 -1.737 -7.750
G3D HN21 H H 0.000 -6.432 -2.494 -6.848
G3D N1 N NR16 0.000 -8.169 0.186 -6.113
G3D HN1 H H 0.000 -8.777 0.200 -6.956
G3D C6 C CR6 0.000 -8.308 1.142 -5.168
G3D O6 O O 0.000 -9.144 2.022 -5.289
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
G3D O6P n/a P1 START
G3D P1 O6P "O3'" .
G3D O4P P1 . .
G3D O5P P1 . .
G3D "O3'" P1 "C3'" .
G3D "C3'" "O3'" "C2'" .
G3D "H3'" "C3'" . .
G3D "C4'" "C3'" "C5'" .
G3D "H4'" "C4'" . .
G3D "C5'" "C4'" "O5'" .
G3D "H5'1" "C5'" . .
G3D "H5'2" "C5'" . .
G3D "O5'" "C5'" PA .
G3D PA "O5'" O3A .
G3D O1A PA . .
G3D O2A PA . .
G3D O3A PA PB .
G3D PB O3A O1B .
G3D O3B PB . .
G3D O2B PB . .
G3D O1B PB . .
G3D "C2'" "C3'" "C1'" .
G3D "H2'" "C2'" . .
G3D "O2'" "C2'" "HO2'" .
G3D "HO2'" "O2'" . .
G3D "C1'" "C2'" N9 .
G3D "H1'" "C1'" . .
G3D "O4'" "C1'" . .
G3D N9 "C1'" C4 .
G3D C4 N9 N3 .
G3D C5 C4 N7 .
G3D N7 C5 C8 .
G3D C8 N7 H8 .
G3D H8 C8 . .
G3D N3 C4 C2 .
G3D C2 N3 N1 .
G3D N2 C2 HN21 .
G3D HN22 N2 . .
G3D HN21 N2 . .
G3D N1 C2 C6 .
G3D HN1 N1 . .
G3D C6 N1 O6 .
G3D O6 C6 . END
G3D "C4'" "O4'" . ADD
G3D N9 C8 . ADD
G3D 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
G3D O1B PB deloc 1.510 0.020
G3D O2B PB deloc 1.510 0.020
G3D O3B PB deloc 1.510 0.020
G3D PB O3A single 1.610 0.020
G3D O3A PA single 1.610 0.020
G3D O1A PA deloc 1.510 0.020
G3D O2A PA deloc 1.510 0.020
G3D PA "O5'" single 1.610 0.020
G3D "O5'" "C5'" single 1.426 0.020
G3D "C5'" "C4'" single 1.524 0.020
G3D "H5'1" "C5'" single 1.092 0.020
G3D "H5'2" "C5'" single 1.092 0.020
G3D "C4'" "O4'" single 1.426 0.020
G3D "C4'" "C3'" single 1.524 0.020
G3D "H4'" "C4'" single 1.099 0.020
G3D "O4'" "C1'" single 1.426 0.020
G3D "C3'" "O3'" single 1.426 0.020
G3D "C2'" "C3'" single 1.524 0.020
G3D "H3'" "C3'" single 1.099 0.020
G3D "O3'" P1 single 1.610 0.020
G3D "O2'" "C2'" single 1.432 0.020
G3D "C1'" "C2'" single 1.524 0.020
G3D "H2'" "C2'" single 1.099 0.020
G3D "HO2'" "O2'" single 0.967 0.020
G3D N9 "C1'" single 1.485 0.020
G3D "H1'" "C1'" single 1.099 0.020
G3D N9 C8 single 1.337 0.020
G3D C4 N9 single 1.337 0.020
G3D C8 N7 double 1.350 0.020
G3D H8 C8 single 1.083 0.020
G3D N7 C5 single 1.350 0.020
G3D C5 C6 single 1.490 0.020
G3D C5 C4 double 1.490 0.020
G3D O6 C6 double 1.250 0.020
G3D C6 N1 single 1.337 0.020
G3D N1 C2 single 1.337 0.020
G3D HN1 N1 single 1.040 0.020
G3D N2 C2 single 1.355 0.020
G3D C2 N3 double 1.350 0.020
G3D HN21 N2 single 1.010 0.020
G3D HN22 N2 single 1.010 0.020
G3D N3 C4 single 1.355 0.020
G3D O4P P1 deloc 1.510 0.020
G3D O5P P1 deloc 1.510 0.020
G3D P1 O6P deloc 1.510 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
G3D O6P P1 O4P 119.900 3.000
G3D O6P P1 O5P 119.900 3.000
G3D O6P P1 "O3'" 108.200 3.000
G3D O4P P1 O5P 119.900 3.000
G3D O4P P1 "O3'" 108.200 3.000
G3D O5P P1 "O3'" 108.200 3.000
G3D P1 "O3'" "C3'" 120.500 3.000
G3D "O3'" "C3'" "H3'" 109.470 3.000
G3D "O3'" "C3'" "C4'" 109.470 3.000
G3D "O3'" "C3'" "C2'" 109.470 3.000
G3D "H3'" "C3'" "C4'" 108.340 3.000
G3D "H3'" "C3'" "C2'" 108.340 3.000
G3D "C4'" "C3'" "C2'" 111.000 3.000
G3D "C3'" "C4'" "H4'" 108.340 3.000
G3D "C3'" "C4'" "C5'" 111.000 3.000
G3D "C3'" "C4'" "O4'" 109.470 3.000
G3D "H4'" "C4'" "C5'" 108.340 3.000
G3D "H4'" "C4'" "O4'" 109.470 3.000
G3D "C5'" "C4'" "O4'" 109.470 3.000
G3D "C4'" "C5'" "H5'1" 109.470 3.000
G3D "C4'" "C5'" "H5'2" 109.470 3.000
G3D "C4'" "C5'" "O5'" 109.470 3.000
G3D "H5'1" "C5'" "H5'2" 107.900 3.000
G3D "H5'1" "C5'" "O5'" 109.470 3.000
G3D "H5'2" "C5'" "O5'" 109.470 3.000
G3D "C5'" "O5'" PA 120.500 3.000
G3D "O5'" PA O1A 108.200 3.000
G3D "O5'" PA O2A 108.200 3.000
G3D "O5'" PA O3A 102.600 3.000
G3D O1A PA O2A 119.900 3.000
G3D O1A PA O3A 108.200 3.000
G3D O2A PA O3A 108.200 3.000
G3D PA O3A PB 120.500 3.000
G3D O3A PB O3B 108.200 3.000
G3D O3A PB O2B 108.200 3.000
G3D O3A PB O1B 108.200 3.000
G3D O3B PB O2B 119.900 3.000
G3D O3B PB O1B 119.900 3.000
G3D O2B PB O1B 119.900 3.000
G3D "C3'" "C2'" "H2'" 108.340 3.000
G3D "C3'" "C2'" "O2'" 109.470 3.000
G3D "C3'" "C2'" "C1'" 111.000 3.000
G3D "H2'" "C2'" "O2'" 109.470 3.000
G3D "H2'" "C2'" "C1'" 108.340 3.000
G3D "O2'" "C2'" "C1'" 109.470 3.000
G3D "C2'" "O2'" "HO2'" 109.470 3.000
G3D "C2'" "C1'" "H1'" 108.340 3.000
G3D "C2'" "C1'" "O4'" 109.470 3.000
G3D "C2'" "C1'" N9 109.470 3.000
G3D "H1'" "C1'" "O4'" 109.470 3.000
G3D "H1'" "C1'" N9 109.470 3.000
G3D "O4'" "C1'" N9 109.470 3.000
G3D "C1'" "O4'" "C4'" 111.800 3.000
G3D "C1'" N9 C4 126.000 3.000
G3D "C1'" N9 C8 126.000 3.000
G3D C4 N9 C8 108.000 3.000
G3D N9 C4 C5 108.000 3.000
G3D N9 C4 N3 132.000 3.000
G3D C5 C4 N3 120.000 3.000
G3D C4 C5 N7 108.000 3.000
G3D C4 C5 C6 120.000 3.000
G3D N7 C5 C6 132.000 3.000
G3D C5 N7 C8 108.000 3.000
G3D N7 C8 H8 126.000 3.000
G3D N7 C8 N9 108.000 3.000
G3D H8 C8 N9 126.000 3.000
G3D C4 N3 C2 120.000 3.000
G3D N3 C2 N2 120.000 3.000
G3D N3 C2 N1 120.000 3.000
G3D N2 C2 N1 120.000 3.000
G3D C2 N2 HN22 120.000 3.000
G3D C2 N2 HN21 120.000 3.000
G3D HN22 N2 HN21 120.000 3.000
G3D C2 N1 HN1 120.000 3.000
G3D C2 N1 C6 120.000 3.000
G3D HN1 N1 C6 120.000 3.000
G3D N1 C6 O6 120.000 3.000
G3D N1 C6 C5 120.000 3.000
G3D O6 C6 C5 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
G3D var_1 O6P P1 "O3'" "C3'" 59.954 20.000 1
G3D var_2 P1 "O3'" "C3'" "C2'" 125.305 20.000 1
G3D var_3 "O3'" "C3'" "C4'" "C5'" 90.000 20.000 3
G3D var_4 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
G3D var_5 "C3'" "C4'" "C5'" "O5'" 176.938 20.000 3
G3D var_6 "C4'" "C5'" "O5'" PA 179.941 20.000 1
G3D var_7 "C5'" "O5'" PA O3A 179.982 20.000 1
G3D var_8 "O5'" PA O3A PB -179.950 20.000 1
G3D var_9 PA O3A PB O1B 59.997 20.000 1
G3D var_10 "O3'" "C3'" "C2'" "C1'" 120.000 20.000 3
G3D var_11 "C3'" "C2'" "O2'" "HO2'" 179.992 20.000 1
G3D var_12 "C3'" "C2'" "C1'" N9 150.000 20.000 3
G3D var_13 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
G3D var_14 "C2'" "C1'" N9 C4 91.537 20.000 1
G3D CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
G3D CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
G3D CONST_3 N9 C4 C5 N7 0.000 0.000 0
G3D CONST_4 C4 C5 C6 N1 0.000 0.000 0
G3D CONST_5 C4 C5 N7 C8 0.000 0.000 0
G3D CONST_6 C5 N7 C8 N9 0.000 0.000 0
G3D CONST_7 N9 C4 N3 C2 180.000 0.000 0
G3D CONST_8 C4 N3 C2 N1 0.000 0.000 0
G3D CONST_9 N3 C2 N2 HN21 0.113 0.000 0
G3D CONST_10 N3 C2 N1 C6 0.000 0.000 0
G3D CONST_11 C2 N1 C6 O6 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
G3D chir_01 "C4'" "C5'" "O4'" "C3'" negativ
G3D chir_02 "C3'" "C4'" "O3'" "C2'" negativ
G3D chir_03 "C2'" "C3'" "O2'" "C1'" negativ
G3D chir_04 "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
G3D plan-1 N9 0.020
G3D plan-1 "C1'" 0.020
G3D plan-1 C8 0.020
G3D plan-1 C4 0.020
G3D plan-1 N7 0.020
G3D plan-1 H8 0.020
G3D plan-1 C5 0.020
G3D plan-1 C6 0.020
G3D plan-1 N1 0.020
G3D plan-1 C2 0.020
G3D plan-1 N3 0.020
G3D plan-1 O6 0.020
G3D plan-1 HN1 0.020
G3D plan-1 N2 0.020
G3D plan-1 HN22 0.020
G3D plan-1 HN21 0.020
G3D plan-2 N2 0.020
G3D plan-2 C2 0.020
G3D plan-2 HN21 0.020
G3D plan-2 HN22 0.020
# ------------------------------------------------------
|
