# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 17:39:01 2021
#   Inital geometry file: a 52 line input string
#   Ligand name: 1-benzothiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sc2ccccc2c1
#
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
 ND8  ND8  '1-benzothiophene-2-carboxylic acid'  ligand  18  12  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ND8
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
 ND8  C01  C  CR16  0  -0.255  19.7366  10.3506  28.1868
 ND8  C02  C  CR16  0  -0.259  19.2850   9.2458  27.4490
 ND8  C03  C  CR16  0  -0.277  18.5175   9.4090  26.3134
 ND8  C04  C  CR56  0  -0.213  18.2000  10.7074  25.9178
 ND8  C05  C  CR56  0   0.216  18.6444  11.8272  26.6462
 ND8  C06  C  CR16  0  -0.305  19.4234  11.6334  27.7954
 ND8  C07  C  CR15  0  -0.205  18.2031  13.0514  26.0599
 ND8  C08  C  CR5   0  -0.313  17.4608  12.8490  24.9423
 ND8  C09  C  C     0   0.528  16.8304  13.8318  24.0583
 ND8  O10  O  O     0  -0.440  16.1767  13.5147  23.0929
 ND8  O11  O  OH1   0  -0.586  17.0588  15.0795  24.4335
 ND8  S12  S  S2    0   0.260  17.2579  11.1718  24.5443
 ND8  H1   H  HCR6  0   0.265  20.3368  10.1888  29.0721
 ND8  H2   H  HCR6  0   0.268  19.5408   8.2469  27.7766
 ND8  H3   H  HCR6  0   0.274  18.1743   8.5527  25.7480
 ND8  H4   H  HCR6  0   0.265  19.7701  12.4869  28.3641
 ND8  H5   H  HCR5  0   0.284  18.4347  14.0259  26.4663
 ND8  H6   H  HOH1  0   0.493  16.6288  15.6964  23.8222

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
 ND8  O10  C09  double    1.208  0.020  1.208
 ND8  O11  C09  single    1.323  0.020  1.323
 ND8  C09  C08  single    1.464  0.020  1.464
 ND8  S12  C08  aromatic  1.736  0.020  1.736
 ND8  S12  C04  aromatic  1.729  0.020  1.729
 ND8  C08  C07  aromatic  1.357  0.020  1.357
 ND8  C04  C03  aromatic  1.394  0.020  1.394
 ND8  C04  C05  aromatic  1.408  0.020  1.408
 ND8  C07  C05  aromatic  1.427  0.020  1.427
 ND8  C03  C02  aromatic  1.380  0.020  1.380
 ND8  C05  C06  aromatic  1.402  0.020  1.402
 ND8  C02  C01  aromatic  1.403  0.020  1.403
 ND8  C06  C01  aromatic  1.377  0.020  1.377
 ND8  C01  H1   single    0.930  0.020  1.080
 ND8  C02  H2   single    0.930  0.020  1.080
 ND8  C03  H3   single    0.930  0.020  1.080
 ND8  C06  H4   single    0.930  0.020  1.080
 ND8  C07  H5   single    0.930  0.020  1.080
 ND8  O11  H6   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
 ND8  H1   C01  C06  119.87  3.000
 ND8  H1   C01  C02  119.41  3.000
 ND8  C06  C01  C02  120.71  3.000
 ND8  H2   C02  C03  119.33  3.000
 ND8  H2   C02  C01  119.45  3.000
 ND8  C03  C02  C01  121.23  3.000
 ND8  H3   C03  C04  121.11  3.000
 ND8  H3   C03  C02  120.84  3.000
 ND8  C04  C03  C02  118.05  3.000
 ND8  S12  C04  C05  111.68  3.000
 ND8  C05  C04  C03  121.48  3.000
 ND8  S12  C04  C03  126.85  3.000
 ND8  C07  C05  C06  128.84  3.000
 ND8  C06  C05  C04  119.32  3.000
 ND8  C07  C05  C04  111.84  3.000
 ND8  H4   C06  C05  119.98  3.000
 ND8  H4   C06  C01  120.81  3.000
 ND8  C05  C06  C01  119.22  3.000
 ND8  H5   C07  C08  124.15  3.000
 ND8  H5   C07  C05  123.54  3.000
 ND8  C08  C07  C05  112.31  3.000
 ND8  S12  C08  C09  117.37  3.000
 ND8  S12  C08  C07  113.39  3.000
 ND8  C09  C08  C07  129.24  3.000
 ND8  O11  C09  O10  124.58  3.000
 ND8  O11  C09  C08  112.79  3.000
 ND8  O10  C09  C08  122.62  3.000
 ND8  H6   O11  C09  110.18  3.000
 ND8  C08  S12  C04   90.78  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
 ND8  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 ND8  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 ND8  CONST_03  C07  C05  C06  C01   180.00   0.0  0
 ND8  CONST_04  S12  C04  C03  C02   180.00   0.0  0
 ND8  CONST_05  C05  C04  C03  C02     0.00   0.0  0
 ND8  CONST_06  C05  C06  C01  C02     0.00   0.0  0
 ND8  CONST_07  C08  S12  C04  C03   180.00   0.0  0
 ND8  CONST_08  C07  C05  C04  C03   180.00   0.0  0
 ND8  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 ND8  CONST_10  C06  C01  C02  C03     0.00   0.0  0
 ND8  CONST_11  C07  C08  S12  C04     0.00   0.0  0
 ND8  CONST_12  C08  C07  C05  C04     0.00   0.0  0
 ND8  CONST_13  C08  S12  C04  C05     0.00   0.0  0
 ND8  CONST_14  S12  C08  C07  C05     0.00   0.0  0
 ND8  CONST_15  S12  C04  C05  C06   180.00   0.0  0
 ND8  CONST_16  C08  C07  C05  C06   180.00   0.0  0
 ND8  CONST_17  S12  C04  C05  C07     0.00   0.0  0
 ND8  CONST_18  C09  C08  S12  C04   180.00   0.0  0
 ND8  CONST_19  C09  C08  C07  C05   180.00   0.0  0
 ND8  CONST_20  H3   C03  C02  C01   180.00   0.0  0
 ND8  CONST_21  H4   C06  C01  C02   180.00   0.0  0
 ND8  CONST_22  H1   C01  C02  C03   180.00   0.0  0
 ND8  CONST_23  H2   C02  C03  C04   180.00   0.0  0
 ND8  CONST_24  H5   C07  C05  C04   180.00   0.0  0
 ND8  CONST_25  H6   O11  C09  C08   180.00   0.0  0
 ND8  Var_01    O10  C09  C08  C07  -179.16  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
 ND8  plan-1  C01  0.020
 ND8  plan-1  C02  0.020
 ND8  plan-1  C03  0.020
 ND8  plan-1  C04  0.020
 ND8  plan-1  C05  0.020
 ND8  plan-1  C06  0.020
 ND8  plan-1  C07  0.020
 ND8  plan-1  C08  0.020
 ND8  plan-1  C09  0.020
 ND8  plan-1  S12  0.020
 ND8  plan-1  H1   0.020
 ND8  plan-1  H2   0.020
 ND8  plan-1  H3   0.020
 ND8  plan-1  H4   0.020
 ND8  plan-1  H5   0.020
 ND8  plan-2  C08  0.020
 ND8  plan-2  C09  0.020
 ND8  plan-2  O10  0.020
 ND8  plan-2  O11  0.020
 ND8  plan-2  H6   0.020

