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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
GEO GEO 'GEMCITABINE ' non-polymer 29 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GEO
#
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
GEO F2 F F 0.000 0.000 0.000 0.000
GEO "C2'" C CT 0.000 -1.349 -0.363 0.065
GEO F1 F F 0.000 -1.506 -1.539 0.807
GEO "C3'" C CH1 0.000 -1.932 -0.537 -1.358
GEO "H3'" H H 0.000 -2.346 -1.548 -1.483
GEO "O3'" O OH1 0.000 -0.932 -0.281 -2.345
GEO H1 H H 0.000 -0.238 -0.951 -2.281
GEO "C4'" C CH1 0.000 -3.055 0.520 -1.436
GEO "H4'" H H 0.000 -2.678 1.445 -1.895
GEO "C5'" C CH2 0.000 -4.245 -0.021 -2.230
GEO "H5'1" H H 0.000 -4.654 -0.897 -1.721
GEO "H5'2" H H 0.000 -3.915 -0.306 -3.231
GEO "O5'" O OH1 0.000 -5.252 0.989 -2.327
GEO "H5'" H H 0.000 -6.004 0.646 -2.829
GEO "C1'" C CH1 0.000 -2.192 0.778 0.676
GEO "H1'" H H 0.000 -1.683 1.743 0.545
GEO "O4'" O O2 0.000 -3.433 0.759 -0.062
GEO N1 N NR6 0.000 -2.442 0.523 2.097
GEO C2 C CR6 0.000 -3.159 -0.553 2.468
GEO O2 O O 0.000 -3.595 -1.307 1.615
GEO N3 N NRD6 0.000 -3.399 -0.809 3.754
GEO C4 C CR6 0.000 -2.936 -0.006 4.703
GEO N4 N NH2 0.000 -3.193 -0.280 6.026
GEO HN42 H H 0.000 -2.841 0.333 6.753
GEO HN41 H H 0.000 -3.736 -1.095 6.285
GEO C5 C CR16 0.000 -2.186 1.133 4.346
GEO H5 H H 0.000 -1.809 1.803 5.108
GEO C6 C CR16 0.000 -1.945 1.376 3.036
GEO H6 H H 0.000 -1.363 2.240 2.737
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
GEO F2 n/a "C2'" START
GEO "C2'" F2 "C1'" .
GEO F1 "C2'" . .
GEO "C3'" "C2'" "C4'" .
GEO "H3'" "C3'" . .
GEO "O3'" "C3'" H1 .
GEO H1 "O3'" . .
GEO "C4'" "C3'" "C5'" .
GEO "H4'" "C4'" . .
GEO "C5'" "C4'" "O5'" .
GEO "H5'1" "C5'" . .
GEO "H5'2" "C5'" . .
GEO "O5'" "C5'" "H5'" .
GEO "H5'" "O5'" . .
GEO "C1'" "C2'" N1 .
GEO "H1'" "C1'" . .
GEO "O4'" "C1'" . .
GEO N1 "C1'" C2 .
GEO C2 N1 N3 .
GEO O2 C2 . .
GEO N3 C2 C4 .
GEO C4 N3 C5 .
GEO N4 C4 HN41 .
GEO HN42 N4 . .
GEO HN41 N4 . .
GEO C5 C4 C6 .
GEO H5 C5 . .
GEO C6 C5 H6 .
GEO H6 C6 . END
GEO "C4'" "O4'" . ADD
GEO N1 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
GEO "O5'" "C5'" single 1.432 0.020
GEO "H5'" "O5'" single 0.967 0.020
GEO "C5'" "C4'" single 1.524 0.020
GEO "H5'1" "C5'" single 1.092 0.020
GEO "H5'2" "C5'" single 1.092 0.020
GEO "C4'" "O4'" single 1.426 0.020
GEO "C4'" "C3'" single 1.524 0.020
GEO "H4'" "C4'" single 1.099 0.020
GEO "O4'" "C1'" single 1.426 0.020
GEO N1 "C1'" single 1.465 0.020
GEO "C1'" "C2'" single 1.524 0.020
GEO "H1'" "C1'" single 1.099 0.020
GEO N1 C6 single 1.337 0.020
GEO C2 N1 single 1.410 0.020
GEO C6 C5 double 1.390 0.020
GEO H6 C6 single 1.083 0.020
GEO C5 C4 single 1.390 0.020
GEO H5 C5 single 1.083 0.020
GEO C4 N3 double 1.350 0.020
GEO N4 C4 single 1.355 0.020
GEO N3 C2 single 1.350 0.020
GEO O2 C2 double 1.250 0.020
GEO HN41 N4 single 1.010 0.020
GEO HN42 N4 single 1.010 0.020
GEO F1 "C2'" single 1.320 0.020
GEO "C2'" F2 single 1.320 0.020
GEO "C3'" "C2'" single 1.524 0.020
GEO "O3'" "C3'" single 1.432 0.020
GEO "H3'" "C3'" single 1.099 0.020
GEO H1 "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
GEO F2 "C2'" F1 109.470 3.000
GEO F2 "C2'" "C3'" 109.470 3.000
GEO F2 "C2'" "C1'" 109.470 3.000
GEO F1 "C2'" "C3'" 109.470 3.000
GEO F1 "C2'" "C1'" 109.470 3.000
GEO "C3'" "C2'" "C1'" 111.000 3.000
GEO "C2'" "C3'" "H3'" 108.340 3.000
GEO "C2'" "C3'" "O3'" 109.470 3.000
GEO "C2'" "C3'" "C4'" 111.000 3.000
GEO "H3'" "C3'" "O3'" 109.470 3.000
GEO "H3'" "C3'" "C4'" 108.340 3.000
GEO "O3'" "C3'" "C4'" 109.470 3.000
GEO "C3'" "O3'" H1 109.470 3.000
GEO "C3'" "C4'" "H4'" 108.340 3.000
GEO "C3'" "C4'" "C5'" 111.000 3.000
GEO "C3'" "C4'" "O4'" 109.470 3.000
GEO "H4'" "C4'" "C5'" 108.340 3.000
GEO "H4'" "C4'" "O4'" 109.470 3.000
GEO "C5'" "C4'" "O4'" 109.470 3.000
GEO "C4'" "C5'" "H5'1" 109.470 3.000
GEO "C4'" "C5'" "H5'2" 109.470 3.000
GEO "C4'" "C5'" "O5'" 109.470 3.000
GEO "H5'1" "C5'" "H5'2" 107.900 3.000
GEO "H5'1" "C5'" "O5'" 109.470 3.000
GEO "H5'2" "C5'" "O5'" 109.470 3.000
GEO "C5'" "O5'" "H5'" 109.470 3.000
GEO "C2'" "C1'" "H1'" 108.340 3.000
GEO "C2'" "C1'" "O4'" 109.470 3.000
GEO "C2'" "C1'" N1 109.500 3.000
GEO "H1'" "C1'" "O4'" 109.470 3.000
GEO "H1'" "C1'" N1 109.470 3.000
GEO "O4'" "C1'" N1 109.470 3.000
GEO "C1'" "O4'" "C4'" 111.800 3.000
GEO "C1'" N1 C2 120.000 3.000
GEO "C1'" N1 C6 120.000 3.000
GEO C2 N1 C6 120.000 3.000
GEO N1 C2 O2 120.000 3.000
GEO N1 C2 N3 120.000 3.000
GEO O2 C2 N3 120.000 3.000
GEO C2 N3 C4 120.000 3.000
GEO N3 C4 N4 120.000 3.000
GEO N3 C4 C5 120.000 3.000
GEO N4 C4 C5 120.000 3.000
GEO C4 N4 HN42 120.000 3.000
GEO C4 N4 HN41 120.000 3.000
GEO HN42 N4 HN41 120.000 3.000
GEO C4 C5 H5 120.000 3.000
GEO C4 C5 C6 120.000 3.000
GEO H5 C5 C6 120.000 3.000
GEO C5 C6 H6 120.000 3.000
GEO C5 C6 N1 120.000 3.000
GEO H6 C6 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
GEO var_1 F2 "C2'" "C3'" "C4'" -120.000 20.000 1
GEO var_2 "C2'" "C3'" "O3'" H1 65.244 20.000 1
GEO var_3 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
GEO var_4 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
GEO var_5 "C3'" "C4'" "C5'" "O5'" -178.065 20.000 3
GEO var_6 "C4'" "C5'" "O5'" "H5'" -179.997 20.000 1
GEO var_7 F2 "C2'" "C1'" N1 -90.000 20.000 1
GEO var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
GEO var_9 "C2'" "C1'" N1 C2 -63.386 20.000 1
GEO CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
GEO CONST_2 "C1'" N1 C2 N3 180.000 0.000 0
GEO CONST_3 N1 C2 N3 C4 0.000 0.000 0
GEO CONST_4 C2 N3 C4 C5 0.000 0.000 0
GEO CONST_5 N3 C4 N4 HN41 0.022 0.000 0
GEO CONST_6 N3 C4 C5 C6 0.000 0.000 0
GEO CONST_7 C4 C5 C6 N1 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
GEO chir_01 "C4'" "C5'" "O4'" "C3'" negativ
GEO chir_02 "C1'" "O4'" N1 "C2'" negativ
GEO chir_03 "C2'" "C1'" F1 F2 positiv
GEO chir_04 "C3'" "C4'" "C2'" "O3'" 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
GEO plan-1 N1 0.020
GEO plan-1 "C1'" 0.020
GEO plan-1 C6 0.020
GEO plan-1 C2 0.020
GEO plan-1 C5 0.020
GEO plan-1 C4 0.020
GEO plan-1 N3 0.020
GEO plan-1 H6 0.020
GEO plan-1 H5 0.020
GEO plan-1 N4 0.020
GEO plan-1 O2 0.020
GEO plan-1 HN42 0.020
GEO plan-1 HN41 0.020
GEO plan-2 N4 0.020
GEO plan-2 C4 0.020
GEO plan-2 HN41 0.020
GEO plan-2 HN42 0.020
# ------------------------------------------------------
|
