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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
GMS GMS '2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSP' non-polymer 37 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GMS
#
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
GMS O6 O O 0.000 0.000 0.000 0.000
GMS C6 C CR6 0.000 -0.962 0.677 0.321
GMS N1 N NR16 0.000 -0.798 1.845 0.981
GMS H1 H H 0.000 0.160 2.174 1.220
GMS C2 C CR6 0.000 -1.880 2.593 1.335
GMS N2 N NH2 0.000 -1.682 3.775 2.005
GMS H22 H H 0.000 -0.744 4.084 2.230
GMS H21 H H 0.000 -2.473 4.346 2.278
GMS N3 N NRD6 0.000 -3.107 2.215 1.056
GMS C5 C CR56 0.000 -2.278 0.258 0.014
GMS C4 C CR56 0.000 -3.348 1.071 0.405
GMS N7 N NRD5 0.000 -2.802 -0.822 -0.615
GMS C8 C CR15 0.000 -4.099 -0.722 -0.634
GMS H8 H H 0.000 -4.773 -1.445 -1.076
GMS N9 N NR5 0.000 -4.483 0.432 -0.014
GMS "C1'" C CH1 0.000 -5.859 0.899 0.173
GMS "H1'" H H 0.000 -5.969 1.381 1.154
GMS "O4'" O O2 0.000 -6.784 -0.203 0.047
GMS "C4'" C CH1 0.000 -8.062 0.404 -0.249
GMS "H4'" H H 0.000 -8.514 0.810 0.667
GMS "C3'" C CH1 0.000 -7.736 1.545 -1.239
GMS "H3'" H H 0.000 -7.862 1.202 -2.276
GMS "O3'" O OH1 0.000 -8.562 2.682 -0.983
GMS "HO3'" H H 0.000 -8.304 3.406 -1.569
GMS "C2'" C CH2 0.000 -6.254 1.877 -0.956
GMS "H2''" H H 0.000 -6.123 2.905 -0.611
GMS "H2'" H H 0.000 -5.621 1.703 -1.828
GMS "C5'" C CH2 0.000 -8.999 -0.615 -0.899
GMS "H5'" H H 0.000 -8.506 -1.061 -1.765
GMS "H5''" H H 0.000 -9.914 -0.114 -1.220
GMS "O5'" O O2 0.000 -9.320 -1.637 0.046
GMS P P P 0.000 -10.289 -2.876 -0.298
GMS OP1 O O 0.000 -9.925 -3.434 -1.620
GMS OP2 O OH1 0.000 -10.123 -4.016 0.827
GMS HOP2 H H 0.000 -10.637 -4.832 0.768
GMS SE SE SE 0.000 -12.443 -2.165 -0.343
GMS HS H H 0.000 -12.542 -1.758 0.796
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
GMS O6 n/a C6 START
GMS C6 O6 C5 .
GMS N1 C6 C2 .
GMS H1 N1 . .
GMS C2 N1 N3 .
GMS N2 C2 H21 .
GMS H22 N2 . .
GMS H21 N2 . .
GMS N3 C2 . .
GMS C5 C6 N7 .
GMS C4 C5 . .
GMS N7 C5 C8 .
GMS C8 N7 N9 .
GMS H8 C8 . .
GMS N9 C8 "C1'" .
GMS "C1'" N9 "O4'" .
GMS "H1'" "C1'" . .
GMS "O4'" "C1'" "C4'" .
GMS "C4'" "O4'" "C5'" .
GMS "H4'" "C4'" . .
GMS "C3'" "C4'" "C2'" .
GMS "H3'" "C3'" . .
GMS "O3'" "C3'" "HO3'" .
GMS "HO3'" "O3'" . .
GMS "C2'" "C3'" "H2'" .
GMS "H2''" "C2'" . .
GMS "H2'" "C2'" . .
GMS "C5'" "C4'" "O5'" .
GMS "H5'" "C5'" . .
GMS "H5''" "C5'" . .
GMS "O5'" "C5'" P .
GMS P "O5'" SE .
GMS OP1 P . .
GMS OP2 P HOP2 .
GMS HOP2 OP2 . .
GMS SE P HS .
GMS HS SE . END
GMS N9 C4 . ADD
GMS C4 N3 . ADD
GMS "C2'" "C1'" . 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
GMS OP1 P double 1.480 0.020
GMS SE P single 1.925 0.020
GMS P "O5'" single 1.610 0.020
GMS OP2 P single 1.610 0.020
GMS HS SE single 1.209 0.020
GMS "O5'" "C5'" single 1.426 0.020
GMS N9 C4 single 1.337 0.020
GMS N9 C8 single 1.337 0.020
GMS "C1'" N9 single 1.485 0.020
GMS C4 N3 single 1.355 0.020
GMS C4 C5 double 1.490 0.020
GMS N3 C2 double 1.350 0.020
GMS N2 C2 single 1.355 0.020
GMS C2 N1 single 1.337 0.020
GMS H21 N2 single 1.010 0.020
GMS H22 N2 single 1.010 0.020
GMS N1 C6 single 1.337 0.020
GMS H1 N1 single 1.040 0.020
GMS C6 O6 double 1.250 0.020
GMS C5 C6 single 1.490 0.020
GMS N7 C5 single 1.350 0.020
GMS C8 N7 double 1.350 0.020
GMS H8 C8 single 1.083 0.020
GMS "C2'" "C1'" single 1.524 0.020
GMS "C2'" "C3'" single 1.524 0.020
GMS "H2'" "C2'" single 1.092 0.020
GMS "H2''" "C2'" single 1.092 0.020
GMS "C5'" "C4'" single 1.524 0.020
GMS "H5'" "C5'" single 1.092 0.020
GMS "H5''" "C5'" single 1.092 0.020
GMS "C4'" "O4'" single 1.426 0.020
GMS "C3'" "C4'" single 1.524 0.020
GMS "H4'" "C4'" single 1.099 0.020
GMS "O4'" "C1'" single 1.426 0.020
GMS "H1'" "C1'" single 1.099 0.020
GMS "O3'" "C3'" single 1.432 0.020
GMS "H3'" "C3'" single 1.099 0.020
GMS "HO3'" "O3'" single 0.967 0.020
GMS HOP2 OP2 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
GMS O6 C6 N1 120.000 3.000
GMS O6 C6 C5 120.000 3.000
GMS N1 C6 C5 120.000 3.000
GMS C6 N1 H1 120.000 3.000
GMS C6 N1 C2 120.000 3.000
GMS H1 N1 C2 120.000 3.000
GMS N1 C2 N2 120.000 3.000
GMS N1 C2 N3 120.000 3.000
GMS N2 C2 N3 120.000 3.000
GMS C2 N2 H22 120.000 3.000
GMS C2 N2 H21 120.000 3.000
GMS H22 N2 H21 120.000 3.000
GMS C2 N3 C4 120.000 3.000
GMS C6 C5 C4 120.000 3.000
GMS C6 C5 N7 132.000 3.000
GMS C4 C5 N7 108.000 3.000
GMS C5 C4 N9 108.000 3.000
GMS C5 C4 N3 120.000 3.000
GMS N9 C4 N3 132.000 3.000
GMS C5 N7 C8 108.000 3.000
GMS N7 C8 H8 126.000 3.000
GMS N7 C8 N9 108.000 3.000
GMS H8 C8 N9 126.000 3.000
GMS C8 N9 "C1'" 126.000 3.000
GMS C8 N9 C4 108.000 3.000
GMS "C1'" N9 C4 126.000 3.000
GMS N9 "C1'" "H1'" 109.470 3.000
GMS N9 "C1'" "O4'" 109.470 3.000
GMS N9 "C1'" "C2'" 109.470 3.000
GMS "H1'" "C1'" "O4'" 109.470 3.000
GMS "H1'" "C1'" "C2'" 108.340 3.000
GMS "O4'" "C1'" "C2'" 109.470 3.000
GMS "C1'" "O4'" "C4'" 111.800 3.000
GMS "O4'" "C4'" "H4'" 109.470 3.000
GMS "O4'" "C4'" "C3'" 109.470 3.000
GMS "O4'" "C4'" "C5'" 109.470 3.000
GMS "H4'" "C4'" "C3'" 108.340 3.000
GMS "H4'" "C4'" "C5'" 108.340 3.000
GMS "C3'" "C4'" "C5'" 111.000 3.000
GMS "C4'" "C3'" "H3'" 108.340 3.000
GMS "C4'" "C3'" "O3'" 109.470 3.000
GMS "C4'" "C3'" "C2'" 111.000 3.000
GMS "H3'" "C3'" "O3'" 109.470 3.000
GMS "H3'" "C3'" "C2'" 108.340 3.000
GMS "O3'" "C3'" "C2'" 109.470 3.000
GMS "C3'" "O3'" "HO3'" 109.470 3.000
GMS "C3'" "C2'" "H2''" 109.470 3.000
GMS "C3'" "C2'" "H2'" 109.470 3.000
GMS "C3'" "C2'" "C1'" 111.000 3.000
GMS "H2''" "C2'" "H2'" 107.900 3.000
GMS "H2''" "C2'" "C1'" 109.470 3.000
GMS "H2'" "C2'" "C1'" 109.470 3.000
GMS "C4'" "C5'" "H5'" 109.470 3.000
GMS "C4'" "C5'" "H5''" 109.470 3.000
GMS "C4'" "C5'" "O5'" 109.470 3.000
GMS "H5'" "C5'" "H5''" 107.900 3.000
GMS "H5'" "C5'" "O5'" 109.470 3.000
GMS "H5''" "C5'" "O5'" 109.470 3.000
GMS "C5'" "O5'" P 120.500 3.000
GMS "O5'" P OP1 109.500 3.000
GMS "O5'" P OP2 109.500 3.000
GMS "O5'" P SE 109.500 3.000
GMS OP1 P OP2 109.500 3.000
GMS OP1 P SE 109.500 3.000
GMS OP2 P SE 109.500 3.000
GMS P OP2 HOP2 120.000 3.000
GMS P SE HS 98.000 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
GMS CONST_1 O6 C6 N1 C2 180.000 0.000 0
GMS CONST_2 C6 N1 C2 N3 0.000 0.000 0
GMS CONST_3 N1 C2 N2 H21 -179.940 0.000 0
GMS CONST_4 N1 C2 N3 C4 0.000 0.000 0
GMS CONST_5 O6 C6 C5 N7 0.000 0.000 0
GMS CONST_6 C6 C5 C4 N9 180.000 0.000 0
GMS CONST_7 C5 C4 N3 C2 0.000 0.000 0
GMS CONST_8 C6 C5 N7 C8 180.000 0.000 0
GMS CONST_9 C5 N7 C8 N9 0.000 0.000 0
GMS CONST_10 N7 C8 N9 "C1'" 180.000 0.000 0
GMS CONST_11 C8 N9 C4 C5 0.000 0.000 0
GMS var_1 C8 N9 "C1'" "O4'" 20.178 20.000 1
GMS var_2 N9 "C1'" "O4'" "C4'" -150.000 20.000 1
GMS var_3 "C1'" "O4'" "C4'" "C5'" 150.000 20.000 1
GMS var_4 "O4'" "C4'" "C3'" "C2'" -30.000 20.000 3
GMS var_5 "C4'" "C3'" "O3'" "HO3'" 176.097 20.000 1
GMS var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
GMS var_7 "C3'" "C2'" "C1'" N9 150.000 20.000 3
GMS var_8 "O4'" "C4'" "C5'" "O5'" 66.414 20.000 3
GMS var_9 "C4'" "C5'" "O5'" P 179.923 20.000 1
GMS var_10 "C5'" "O5'" P SE -74.902 20.000 1
GMS var_11 "O5'" P OP2 HOP2 -179.927 20.000 1
GMS var_12 "O5'" P SE HS -60.042 20.000 1
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
GMS chir_01 "C4'" "C5'" "O4'" "C3'" negativ
GMS chir_02 "C1'" N9 "C2'" "O4'" negativ
GMS chir_03 "C3'" "C2'" "C4'" "O3'" 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
GMS plan-1 N9 0.020
GMS plan-1 C4 0.020
GMS plan-1 C8 0.020
GMS plan-1 "C1'" 0.020
GMS plan-1 N7 0.020
GMS plan-1 N3 0.020
GMS plan-1 C5 0.020
GMS plan-1 C2 0.020
GMS plan-1 N1 0.020
GMS plan-1 C6 0.020
GMS plan-1 N2 0.020
GMS plan-1 H1 0.020
GMS plan-1 O6 0.020
GMS plan-1 H8 0.020
GMS plan-1 H22 0.020
GMS plan-1 H21 0.020
GMS plan-2 N2 0.020
GMS plan-2 C2 0.020
GMS plan-2 H21 0.020
GMS plan-2 H22 0.020
# ------------------------------------------------------
|
