# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 23:25:06 2022
#   Inital geometry file: a 38 line input string
#   Ligand name: 1,3-dithiolane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1SCCS1
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 UJD  UJD  "1,3-dithiolane-2-carboxylic acid"  ligand  13  8  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UJD
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 UJD  C02  C  C      0   0.458  -38.7098  56.3490  78.3643
 UJD  C04  C  CH1    0  -0.605  -40.0247  55.7283  78.9078
 UJD  C06  C  CH2    0  -0.531  -42.1788  55.7061  77.1772
 UJD  C07  C  CH2    0  -0.547  -41.1023  54.7479  76.7010
 UJD  O01  O  O      0  -0.578  -38.7747  56.9738  77.2938
 UJD  O03  O  OC    -1  -0.599  -37.7047  56.1070  79.0557
 UJD  S05  S  S2     0  -0.004  -41.5242  56.7047  78.5588
 UJD  S08  S  S2     0   0.001  -40.2706  54.0856  78.1655
 UJD  H1   H  HCH1   0   0.298  -39.9622  55.5771  79.9868
 UJD  H2   H  HCH2   0   0.277  -42.4817  56.3748  76.3711
 UJD  H3   H  HCH2   0   0.267  -43.0564  55.1587  77.5191
 UJD  H4   H  HCH2   0   0.286  -41.5376  53.9144  76.1492
 UJD  H5   H  HCH2   0   0.278  -40.3791  55.2498  76.0619

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
_chem_comp_bond.value_dist_neutron
 UJD  C07  C06  single  1.518  0.020  1.518
 UJD  C07  S08  single  1.810  0.020  1.810
 UJD  C06  S05  single  1.826  0.020  1.826
 UJD  O01  C02  deloc   1.241  0.020  1.241
 UJD  S08  C04  single  1.819  0.020  1.819
 UJD  C02  C04  single  1.552  0.020  1.552
 UJD  C02  O03  deloc   1.244  0.020  1.244
 UJD  S05  C04  single  1.823  0.020  1.823
 UJD  C04  H1   single  0.970  0.020  1.090
 UJD  C06  H2   single  0.970  0.020  1.090
 UJD  C06  H3   single  0.970  0.020  1.090
 UJD  C07  H4   single  0.970  0.020  1.090
 UJD  C07  H5   single  0.970  0.020  1.090

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
 UJD  O03  C02  O01  128.29  3.000
 UJD  O03  C02  C04  114.34  3.000
 UJD  O01  C02  C04  117.32  3.000
 UJD  H1   C04  S08  106.62  3.000
 UJD  H1   C04  S05  108.09  3.000
 UJD  S08  C04  S05  107.12  3.000
 UJD  H1   C04  C02  110.68  3.000
 UJD  S05  C04  C02  114.55  3.000
 UJD  S08  C04  C02  109.43  3.000
 UJD  H3   C06  H2   108.44  3.000
 UJD  H3   C06  S05  109.03  3.000
 UJD  H2   C06  S05  108.88  3.000
 UJD  H3   C06  C07  110.65  3.000
 UJD  H2   C06  C07  110.63  3.000
 UJD  S05  C06  C07  109.17  3.000
 UJD  H5   C07  H4   108.71  3.000
 UJD  H5   C07  S08  109.80  3.000
 UJD  H4   C07  S08  108.26  3.000
 UJD  H5   C07  C06  111.38  3.000
 UJD  H4   C07  C06  110.99  3.000
 UJD  S08  C07  C06  107.64  3.000
 UJD  C06  S05  C04   98.44  3.000
 UJD  C07  S08  C04   93.55  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
 UJD  Var_01  C06  C07  S08  C04   -49.25  30.0  1
 UJD  Var_02  C07  C06  S05  C04   -13.21  30.0  1
 UJD  Var_03  S08  C07  C06  S05    41.29  30.0  1
 UJD  Var_04  H4   C07  S08  C04  -169.29  30.0  1
 UJD  Var_05  H5   C07  S08  C04    72.16  30.0  1
 UJD  Var_06  H2   C06  S05  C04  -134.08  30.0  1
 UJD  Var_07  H3   C06  S05  C04   107.78  30.0  1
 UJD  Var_08  H4   C07  C06  S05   159.59  30.0  1
 UJD  Var_09  H5   C07  C06  S05   -79.13  30.0  1
 UJD  Var_10  H2   C06  C07  S08   161.08  30.0  1
 UJD  Var_11  H3   C06  C07  S08   -78.71  30.0  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
 UJD  chir_01  C04  S08  C02  S05  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
 UJD  plan-1  C02  0.020
 UJD  plan-1  C04  0.020
 UJD  plan-1  O01  0.020
 UJD  plan-1  O03  0.020

