# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 03:16:13 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-(5-bromo-1H-indol-3-yl)-2-thioxopropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=S)Cc1c[nH]c2ccc(Br)cc12
#
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
 2UD  2UD  '3-(5-bromo-1H-indol-3-yl)-2-thioxopropanoic acid'  ligand  24  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2UD
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
 2UD  OAN  O   O     0  -0.412   4.0180   1.8067  -1.4689
 2UD  CAM  C   C     0   0.559   3.8358   1.5402  -0.3080
 2UD  OAO  O   OH1   0  -0.567   4.4517   2.1249   0.6968
 2UD  CAK  C   C     0  -0.168   2.8510   0.4744   0.1236
 2UD  SAL  S   S1    0  -0.017   2.4063   0.3236   1.6624
 2UD  CAJ  C   CH2   0  -0.598   2.3493  -0.3779  -1.0061
 2UD  CAI  C   CR5   0   0.037   1.3127  -1.3747  -0.6371
 2UD  CAE  C   CR56  0   0.054  -0.0589  -1.1127  -0.3292
 2UD  CAF  C   CR16  0  -0.348  -0.8220   0.0571  -0.2723
 2UD  CAA  C   CR6   0  -0.121  -2.1548  -0.0594   0.0622
 2UD  BR   BR  BR    0  -0.071  -3.2238   1.5036   0.1494
 2UD  CAB  C   CR16  0  -0.259  -2.7560  -1.2949   0.3469
 2UD  CAC  C   CR16  0  -0.295  -2.0113  -2.4568   0.2965
 2UD  CAD  C   CR56  0   0.359  -0.6642  -2.3547  -0.0400
 2UD  NAG  N   NR15  0  -0.686   0.2965  -3.3129  -0.1649
 2UD  CAH  C   CR15  0  -0.067   1.4746  -2.7259  -0.5242
 2UD  H1   H   HOH1  0   0.492   5.0603   2.8000   0.3594
 2UD  H2   H   HCH2  0   0.294   1.9815   0.2907  -1.7922
 2UD  H3   H   HCH2  0   0.306   3.2176  -0.8753  -1.4524
 2UD  H4   H   HCR6  0   0.263  -0.3768   1.0204  -0.4873
 2UD  H5   H   HCR6  0   0.273  -3.8046  -1.3475   0.6064
 2UD  H6   H   HCR6  0   0.272  -2.4707  -3.4118   0.5159
 2UD  H7   H   HNR5  0   0.414   0.1596  -4.3020  -0.0425
 2UD  H8   H   HCR5  0   0.289   2.3602  -3.3224  -0.6786

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
 2UD  BR   CAA  single    1.896  0.020  1.896
 2UD  CAA  CAF  aromatic  1.379  0.020  1.379
 2UD  CAA  CAB  aromatic  1.403  0.020  1.403
 2UD  CAF  CAE  aromatic  1.398  0.020  1.398
 2UD  CAB  CAC  aromatic  1.381  0.020  1.381
 2UD  CAE  CAD  aromatic  1.412  0.020  1.412
 2UD  CAE  CAI  aromatic  1.430  0.020  1.430
 2UD  CAC  CAD  aromatic  1.392  0.020  1.392
 2UD  CAJ  CAI  single    1.485  0.020  1.485
 2UD  CAJ  CAK  single    1.501  0.020  1.501
 2UD  CAD  NAG  aromatic  1.363  0.020  1.363
 2UD  CAI  CAH  aromatic  1.366  0.020  1.366
 2UD  SAL  CAK  double    1.609  0.020  1.609
 2UD  CAK  CAM  single    1.514  0.020  1.514
 2UD  NAG  CAH  aromatic  1.364  0.020  1.364
 2UD  CAM  OAN  double    1.205  0.020  1.205
 2UD  CAM  OAO  single    1.316  0.020  1.316
 2UD  OAO  H1   single    0.850  0.020  0.980
 2UD  CAJ  H2   single    0.970  0.020  1.090
 2UD  CAJ  H3   single    0.970  0.020  1.090
 2UD  CAF  H4   single    0.930  0.020  1.080
 2UD  CAB  H5   single    0.930  0.020  1.080
 2UD  CAC  H6   single    0.930  0.020  1.080
 2UD  NAG  H7   single    0.860  0.020  1.020
 2UD  CAH  H8   single    0.930  0.020  1.080

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
 2UD  CAK  CAM  OAO  113.56  3.000
 2UD  OAO  CAM  OAN  124.52  3.000
 2UD  CAK  CAM  OAN  121.92  3.000
 2UD  H1   OAO  CAM  109.73  3.000
 2UD  CAJ  CAK  SAL  125.04  3.000
 2UD  SAL  CAK  CAM  121.23  3.000
 2UD  CAJ  CAK  CAM  113.73  3.000
 2UD  H3   CAJ  H2   104.52  3.000
 2UD  H3   CAJ  CAI  110.47  3.000
 2UD  H2   CAJ  CAI  110.71  3.000
 2UD  H3   CAJ  CAK  107.42  3.000
 2UD  H2   CAJ  CAK  107.80  3.000
 2UD  CAI  CAJ  CAK  115.30  3.000
 2UD  CAH  CAI  CAE  106.10  3.000
 2UD  CAH  CAI  CAJ  127.02  3.000
 2UD  CAE  CAI  CAJ  126.88  3.000
 2UD  CAD  CAE  CAF  119.60  3.000
 2UD  CAD  CAE  CAI  107.11  3.000
 2UD  CAF  CAE  CAI  133.29  3.000
 2UD  H4   CAF  CAA  121.38  3.000
 2UD  H4   CAF  CAE  120.80  3.000
 2UD  CAA  CAF  CAE  117.82  3.000
 2UD  CAB  CAA  BR   118.36  3.000
 2UD  CAB  CAA  CAF  122.53  3.000
 2UD  BR   CAA  CAF  119.11  3.000
 2UD  H5   CAB  CAC  119.38  3.000
 2UD  H5   CAB  CAA  120.46  3.000
 2UD  CAC  CAB  CAA  120.16  3.000
 2UD  H6   CAC  CAD  121.63  3.000
 2UD  H6   CAC  CAB  120.41  3.000
 2UD  CAD  CAC  CAB  117.96  3.000
 2UD  NAG  CAD  CAC  130.75  3.000
 2UD  NAG  CAD  CAE  107.31  3.000
 2UD  CAC  CAD  CAE  121.93  3.000
 2UD  H7   NAG  CAH  124.93  3.000
 2UD  H7   NAG  CAD  125.75  3.000
 2UD  CAH  NAG  CAD  109.29  3.000
 2UD  H8   CAH  NAG  120.57  3.000
 2UD  H8   CAH  CAI  129.24  3.000
 2UD  NAG  CAH  CAI  110.19  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
 2UD  CONST_01  CAA  CAF  CAE  CAI   180.00   0.0  0
 2UD  CONST_02  CAC  CAD  CAE  CAI   180.00   0.0  0
 2UD  CONST_03  NAG  CAD  CAE  CAI     0.00   0.0  0
 2UD  CONST_04  CAD  NAG  CAH  CAI     0.00   0.0  0
 2UD  CONST_05  CAB  CAA  CAF  CAE     0.00   0.0  0
 2UD  CONST_06  CAB  CAC  CAD  CAE     0.00   0.0  0
 2UD  CONST_07  CAH  NAG  CAD  CAE     0.00   0.0  0
 2UD  CONST_08  NAG  CAH  CAI  CAE     0.00   0.0  0
 2UD  CONST_09  CAC  CAB  CAA  CAF     0.00   0.0  0
 2UD  CONST_10  CAC  CAD  CAE  CAF     0.00   0.0  0
 2UD  CONST_11  NAG  CAD  CAE  CAF   180.00   0.0  0
 2UD  CONST_12  CAH  CAI  CAE  CAF   180.00   0.0  0
 2UD  CONST_13  CAD  CAE  CAF  CAA     0.00   0.0  0
 2UD  CONST_14  CAD  CAC  CAB  CAA     0.00   0.0  0
 2UD  CONST_15  NAG  CAD  CAC  CAB   180.00   0.0  0
 2UD  CONST_16  CAH  NAG  CAD  CAC   180.00   0.0  0
 2UD  CONST_17  CAH  CAI  CAE  CAD     0.00   0.0  0
 2UD  CONST_18  CAF  CAE  CAI  CAJ     0.00   0.0  0
 2UD  CONST_19  CAD  CAE  CAI  CAJ   180.00   0.0  0
 2UD  CONST_20  NAG  CAH  CAI  CAJ   180.00   0.0  0
 2UD  CONST_21  BR   CAA  CAF  CAE   180.00   0.0  0
 2UD  CONST_22  CAC  CAB  CAA  BR    180.00   0.0  0
 2UD  CONST_23  H4   CAF  CAE  CAI     0.00   0.0  0
 2UD  CONST_24  H7   NAG  CAH  CAI   180.00   0.0  0
 2UD  CONST_25  H6   CAC  CAD  CAE   180.00   0.0  0
 2UD  CONST_26  H8   CAH  CAI  CAE   180.00   0.0  0
 2UD  CONST_27  H5   CAB  CAA  CAF   180.00   0.0  0
 2UD  CONST_28  H1   OAO  CAM  OAN     0.00   0.0  0
 2UD  Var_01    CAE  CAI  CAJ  CAK    73.77  30.0  2
 2UD  Var_02    CAI  CAJ  CAK  CAM  -176.05  30.0  1
 2UD  Var_03    CAJ  CAK  CAM  OAN    11.42  30.0  3

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
 2UD  plan-1  CAJ  0.020
 2UD  plan-1  CAI  0.020
 2UD  plan-1  CAE  0.020
 2UD  plan-1  CAF  0.020
 2UD  plan-1  CAA  0.020
 2UD  plan-1  BR   0.020
 2UD  plan-1  CAB  0.020
 2UD  plan-1  CAC  0.020
 2UD  plan-1  CAD  0.020
 2UD  plan-1  NAG  0.020
 2UD  plan-1  CAH  0.020
 2UD  plan-1  H4   0.020
 2UD  plan-1  H5   0.020
 2UD  plan-1  H6   0.020
 2UD  plan-1  H7   0.020
 2UD  plan-1  H8   0.020
 2UD  plan-2  OAN  0.020
 2UD  plan-2  CAM  0.020
 2UD  plan-2  OAO  0.020
 2UD  plan-2  CAK  0.020
 2UD  plan-2  H1   0.020
 2UD  plan-3  CAM  0.020
 2UD  plan-3  CAK  0.020
 2UD  plan-3  SAL  0.020
 2UD  plan-3  CAJ  0.020

