# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:58:36 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (2~{S})-2-chloranyl-3-(1~{H}-imidazol-5-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cl)Cc1[nH]cnc1
#
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
 DYT  DYT  '(2~{S})-2-chloranyl-3-(1~{H}-imidazol-5-yl)propanoic acid'  ligand  17  11  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DYT
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
 DYT  OAA  O   O      0  -0.590   2.7708   0.3451   1.2941
 DYT  CAI  C   C      0   0.444   2.4814   0.4239   0.0891
 DYT  OAB  O   OC    -1  -0.593   3.2249   0.7202  -0.8614
 DYT  CAK  C   CH1    0  -0.367   1.0085   0.1152  -0.2788
 DYT  CL1  CL  CL     0  -0.192   0.8148  -1.6948  -0.2168
 DYT  CAF  C   CH2    0  -0.522   0.0086   0.7631   0.6639
 DYT  CAJ  C   CR5    0   0.309  -1.4181   0.5705   0.2898
 DYT  CAE  C   CR15   0  -0.267  -2.3005   1.3932  -0.3571
 DYT  NAG  N   N      0  -0.444  -3.5199   0.7903  -0.4912
 DYT  CAD  C   CR15   0   0.075  -3.3850  -0.3850   0.0678
 DYT  NAH  N   NR15   0  -0.600  -2.1396  -0.5612   0.5523
 DYT  HAK  H   HCH1   0   0.282   0.7969   0.3863  -1.3121
 DYT  HAG  H   HCH2   0   0.265   0.2010   0.4211   1.6822
 DYT  HAF  H   HCH2   0   0.270   0.2130   1.8375   0.6564
 DYT  HAE  H   HCR5   0   0.248  -2.1094   2.3896  -0.7283
 DYT  HAD  H   HCR5   0   0.273  -4.1494  -1.1418   0.1532
 DYT  HAH  H   HNR5   0   0.410  -1.7973  -1.3893   1.0132

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
 DYT  OAA  CAI  deloc     1.242  0.020  1.242
 DYT  CAI  OAB  deloc     1.243  0.020  1.243
 DYT  CAI  CAK  single    1.549  0.020  1.549
 DYT  NAG  CAE  aromatic  1.367  0.020  1.367
 DYT  NAG  CAD  aromatic  1.308  0.020  1.308
 DYT  CAE  CAJ  aromatic  1.369  0.020  1.369
 DYT  CAD  NAH  aromatic  1.348  0.020  1.348
 DYT  CAK  CL1  single    1.821  0.020  1.821
 DYT  CAK  CAF  single    1.519  0.020  1.519
 DYT  CAJ  NAH  aromatic  1.368  0.020  1.368
 DYT  CAJ  CAF  single    1.487  0.020  1.487
 DYT  CAK  HAK  single    0.970  0.020  1.090
 DYT  CAF  HAG  single    0.970  0.020  1.090
 DYT  CAF  HAF  single    0.970  0.020  1.090
 DYT  CAE  HAE  single    0.930  0.020  1.080
 DYT  CAD  HAD  single    0.930  0.020  1.080
 DYT  NAH  HAH  single    0.860  0.020  1.020

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
 DYT  CAK  CAI  OAB  115.77  3.000
 DYT  CAK  CAI  OAA  116.06  3.000
 DYT  OAB  CAI  OAA  128.17  3.000
 DYT  HAK  CAK  CAF  110.77  3.000
 DYT  HAK  CAK  CL1  105.01  3.000
 DYT  CAF  CAK  CL1  109.43  3.000
 DYT  HAK  CAK  CAI  111.13  3.000
 DYT  CAF  CAK  CAI  113.16  3.000
 DYT  CL1  CAK  CAI  106.92  3.000
 DYT  HAF  CAF  HAG  106.34  3.000
 DYT  HAF  CAF  CAJ  107.74  3.000
 DYT  HAG  CAF  CAJ  111.29  3.000
 DYT  HAF  CAF  CAK  106.96  3.000
 DYT  HAG  CAF  CAK  109.22  3.000
 DYT  CAJ  CAF  CAK  114.84  3.000
 DYT  NAH  CAJ  CAE  104.36  3.000
 DYT  NAH  CAJ  CAF  124.40  3.000
 DYT  CAE  CAJ  CAF  131.25  3.000
 DYT  HAE  CAE  NAG  122.07  3.000
 DYT  HAE  CAE  CAJ  127.06  3.000
 DYT  NAG  CAE  CAJ  110.87  3.000
 DYT  CAD  NAG  CAE  105.21  3.000
 DYT  HAD  CAD  NAH  122.30  3.000
 DYT  HAD  CAD  NAG  126.21  3.000
 DYT  NAH  CAD  NAG  111.48  3.000
 DYT  HAH  NAH  CAD  125.86  3.000
 DYT  HAH  NAH  CAJ  126.06  3.000
 DYT  CAD  NAH  CAJ  108.08  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
 DYT  CONST_01  CAD  NAG  CAE  CAJ    0.00   0.0  0
 DYT  CONST_02  NAG  CAD  NAH  CAJ    0.00   0.0  0
 DYT  CONST_03  NAH  CAD  NAG  CAE    0.00   0.0  0
 DYT  CONST_04  CAD  NAH  CAJ  CAE    0.00   0.0  0
 DYT  CONST_05  NAH  CAJ  CAE  NAG    0.00   0.0  0
 DYT  CONST_06  NAG  CAE  CAJ  CAF  180.00   0.0  0
 DYT  CONST_07  CAD  NAH  CAJ  CAF  180.00   0.0  0
 DYT  CONST_08  HAD  CAD  NAH  CAJ  180.00   0.0  0
 DYT  CONST_09  HAH  NAH  CAJ  CAE  180.00   0.0  0
 DYT  CONST_10  HAE  CAE  NAG  CAD  180.00   0.0  0
 DYT  Var_01    CAE  CAJ  CAF  CAK  -99.31  30.0  2

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
 DYT  chir_01  CAK  CAI  CL1  CAF  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
 DYT  plan-1  CAF  0.020
 DYT  plan-1  CAJ  0.020
 DYT  plan-1  CAE  0.020
 DYT  plan-1  NAG  0.020
 DYT  plan-1  CAD  0.020
 DYT  plan-1  NAH  0.020
 DYT  plan-1  HAE  0.020
 DYT  plan-1  HAD  0.020
 DYT  plan-1  HAH  0.020
 DYT  plan-2  OAA  0.020
 DYT  plan-2  CAI  0.020
 DYT  plan-2  OAB  0.020
 DYT  plan-2  CAK  0.020

