# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 22:22:29 2022
#   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  17  12  .  2022-03-23  2022-03-23
;
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  -0.257  19.7248  10.3142  28.2120
 ND8  C02  C  CR16   0  -0.269  19.3056   9.2261  27.4344
 ND8  C03  C  CR16   0  -0.283  18.5534   9.4195  26.2913
 ND8  C04  C  CR56   0  -0.217  18.2211  10.7232  25.9286
 ND8  C05  C  CR56   0   0.213  18.6343  11.8282  26.6987
 ND8  C06  C  CR16   0  -0.319  19.3950  11.6049  27.8534
 ND8  C07  C  CR15   0  -0.254  18.1820  13.0659  26.1370
 ND8  C08  C  CR5    0  -0.317  17.4646  12.9029  25.0007
 ND8  C09  C  C      0   0.400  16.8190  13.9386  24.1127
 ND8  O10  O  O      0  -0.589  16.2170  13.4774  23.1248
 ND8  O11  O  OC    -1  -0.573  16.9565  15.1241  24.4572
 ND8  S12  S  S2     0   0.191  17.2989  11.2318  24.5519
 ND8  H1   H  HCR6   0   0.253  20.3133  10.1369  29.1027
 ND8  H2   H  HCR6   0   0.255  19.5734   8.2205  27.7324
 ND8  H3   H  HCR6   0   0.261  18.2305   8.5763  25.6940
 ND8  H4   H  HCR6   0   0.252  19.7209  12.4437  28.4561
 ND8  H5   H  HCR5   0   0.254  18.3917  14.0337  26.5715

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  deloc     1.245  0.020  1.245
 ND8  O11  C09  deloc     1.242  0.020  1.242
 ND8  C09  C08  single    1.509  0.020  1.509
 ND8  S12  C08  aromatic  1.738  0.020  1.738
 ND8  S12  C04  aromatic  1.733  0.020  1.733
 ND8  C08  C07  aromatic  1.354  0.020  1.354
 ND8  C04  C03  aromatic  1.393  0.020  1.393
 ND8  C04  C05  aromatic  1.409  0.020  1.409
 ND8  C07  C05  aromatic  1.432  0.020  1.432
 ND8  C03  C02  aromatic  1.382  0.020  1.382
 ND8  C05  C06  aromatic  1.401  0.020  1.401
 ND8  C02  C01  aromatic  1.402  0.020  1.402
 ND8  C06  C01  aromatic  1.380  0.020  1.380
 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

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  119.81  3.000
 ND8  H1   C01  C02  119.48  3.000
 ND8  C06  C01  C02  120.71  3.000
 ND8  H2   C02  C03  119.50  3.000
 ND8  H2   C02  C01  119.63  3.000
 ND8  C03  C02  C01  120.87  3.000
 ND8  H3   C03  C04  120.93  3.000
 ND8  H3   C03  C02  120.64  3.000
 ND8  C04  C03  C02  118.43  3.000
 ND8  S12  C04  C05  111.11  3.000
 ND8  C05  C04  C03  121.44  3.000
 ND8  S12  C04  C03  127.46  3.000
 ND8  C07  C05  C06  129.23  3.000
 ND8  C06  C05  C04  119.01  3.000
 ND8  C07  C05  C04  111.76  3.000
 ND8  H4   C06  C05  119.91  3.000
 ND8  H4   C06  C01  120.53  3.000
 ND8  C05  C06  C01  119.55  3.000
 ND8  H5   C07  C08  123.21  3.000
 ND8  H5   C07  C05  123.68  3.000
 ND8  C08  C07  C05  113.11  3.000
 ND8  S12  C08  C09  117.84  3.000
 ND8  S12  C08  C07  112.52  3.000
 ND8  C09  C08  C07  129.64  3.000
 ND8  O11  C09  O10  128.82  3.000
 ND8  O11  C09  C08  116.39  3.000
 ND8  O10  C09  C08  114.79  3.000
 ND8  C08  S12  C04   91.51  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  Var_01    O10  C09  C08  C07  -179.93  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

