# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:03:15 2020
#   Inital geometry file: a 38 line input string
#   Ligand name: 5-chloranylthiophene-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1csc(Cl)c1
#
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
 9E6  9E6  '5-chloranylthiophene-3-carboxylic acid'  ligand  12  9  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9E6
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
 9E6  C1   C   C     0   0.522  -2.3939  -0.5212  -0.0413
 9E6  S1   S   S2    0   0.324   0.9941   1.5689   0.0084
 9E6  C2   C   CR5   0   0.012  -1.0211   0.0104  -0.0228
 9E6  C4   C   CR15  0  -0.131   0.1180  -0.8455  -0.0129
 9E6  C5   C   CR5   0  -0.251   1.2697  -0.1324   0.0039
 9E6  C7   C   CR15  0  -0.490  -0.6930   1.3368  -0.0127
 9E6  O8   O   O     0  -0.435  -2.6465  -1.7016  -0.0503
 9E6  O9   O   OH1   0  -0.593  -3.3126   0.4329  -0.0466
 9E6  CL1  CL  CL    0  -0.067   2.8615  -0.7453   0.0204
 9E6  H1   H   HCR5  0   0.296   0.0737  -1.9242  -0.0178
 9E6  H2   H   HCR5  0   0.320  -1.3525   2.1908  -0.0164
 9E6  H3   H   HOH1  0   0.491  -4.1997   0.0432  -0.0568

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
 9E6  CL1  C5  single    1.706  0.020  1.706
 9E6  C5   C4  aromatic  1.355  0.020  1.355
 9E6  C5   S1  aromatic  1.724  0.020  1.724
 9E6  C4   C2  aromatic  1.425  0.020  1.425
 9E6  S1   C7  aromatic  1.703  0.020  1.703
 9E6  C2   C7  aromatic  1.366  0.020  1.366
 9E6  C2   C1  single    1.472  0.020  1.472
 9E6  O8   C1  double    1.207  0.020  1.207
 9E6  C1   O9  single    1.325  0.020  1.325
 9E6  C4   H1  single    0.930  0.020  1.080
 9E6  C7   H2  single    0.930  0.020  1.080
 9E6  O9   H3  single    0.850  0.020  0.980

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
 9E6  O9   C1  O8  124.00  3.000
 9E6  O9   C1  C2  112.75  3.000
 9E6  O8   C1  C2  123.25  3.000
 9E6  C7   S1  C5   91.36  3.000
 9E6  C7   C2  C4  113.02  3.000
 9E6  C7   C2  C1  125.07  3.000
 9E6  C4   C2  C1  121.91  3.000
 9E6  H1   C4  C5  124.11  3.000
 9E6  H1   C4  C2  124.57  3.000
 9E6  C5   C4  C2  111.32  3.000
 9E6  CL1  C5  C4  127.18  3.000
 9E6  C4   C5  S1  112.56  3.000
 9E6  CL1  C5  S1  120.25  3.000
 9E6  H2   C7  C2  128.42  3.000
 9E6  H2   C7  S1  119.85  3.000
 9E6  C2   C7  S1  111.73  3.000
 9E6  H3   O9  C1  110.20  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
 9E6  CONST_01  C2   C4  C5  S1    0.00   0.0  0
 9E6  CONST_02  C4   C2  C7  S1    0.00   0.0  0
 9E6  CONST_03  C5   S1  C7  C2    0.00   0.0  0
 9E6  CONST_04  C7   S1  C5  C4    0.00   0.0  0
 9E6  CONST_05  C7   C2  C4  C5    0.00   0.0  0
 9E6  CONST_06  C5   C4  C2  C1  180.00   0.0  0
 9E6  CONST_07  S1   C7  C2  C1  180.00   0.0  0
 9E6  CONST_08  CL1  C5  C4  C2  180.00   0.0  0
 9E6  CONST_09  CL1  C5  S1  C7  180.00   0.0  0
 9E6  CONST_10  H1   C4  C5  S1  180.00   0.0  0
 9E6  CONST_11  H2   C7  C2  C4  180.00   0.0  0
 9E6  CONST_12  H3   O9  C1  C2  180.00   0.0  0
 9E6  Var_01    O8   C1  C2  C4   -0.05  30.0  2

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
 9E6  plan-1  C1   0.020
 9E6  plan-1  S1   0.020
 9E6  plan-1  C2   0.020
 9E6  plan-1  C4   0.020
 9E6  plan-1  C5   0.020
 9E6  plan-1  C7   0.020
 9E6  plan-1  CL1  0.020
 9E6  plan-1  H1   0.020
 9E6  plan-1  H2   0.020
 9E6  plan-2  C1   0.020
 9E6  plan-2  C2   0.020
 9E6  plan-2  O8   0.020
 9E6  plan-2  O9   0.020
 9E6  plan-2  H3   0.020

