# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 13:47:02 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-(thiophen-2-ylsulfanylmethyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(CSc2sccc2)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
 JBB  JBB  '3-(thiophen-2-ylsulfanylmethyl)benzoic acid'  ligand  25  16  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JBB
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
 JBB  C10  C  CR5    0  -0.357   2.8646   0.3985  -0.5768
 JBB  C13  C  CR15   0  -0.190   5.1525   0.0844  -0.3559
 JBB  C15  C  CR16   0  -0.330  -1.9177   0.2245   0.4953
 JBB  O01  O  O      0  -0.593  -3.8386   2.1897   0.9859
 JBB  C03  C  CR6    0  -0.082  -3.2711   0.0200   0.2460
 JBB  C04  C  CR16   0  -0.301  -3.6744  -1.2113  -0.2646
 JBB  C05  C  CR16   0  -0.232  -2.7453  -2.2107  -0.5193
 JBB  C06  C  CR16   0  -0.294  -1.3987  -1.9922  -0.2656
 JBB  C07  C  CR6    0   0.116  -0.9762  -0.7709   0.2532
 JBB  C08  C  CH2    0  -0.615   0.4775  -0.5149   0.5047
 JBB  S09  S  S2     0   0.035   1.1959   0.1768  -1.0379
 JBB  S11  S  S2     0   0.243   3.3743   1.7822   0.3229
 JBB  C12  C  CR15   0  -0.458   5.0032   1.2608   0.3169
 JBB  C14  C  CR15   0  -0.166   3.9254  -0.4122  -0.8669
 JBB  O16  O  OC    -1  -0.593  -5.4778   0.8571   0.2753
 JBB  H1   H  HCR5   0   0.272   6.1039  -0.4126  -0.4808
 JBB  H2   H  HCR6   0   0.242  -1.5929   1.1781   0.8935
 JBB  H3   H  HCR6   0   0.245  -4.7235  -1.3879  -0.4606
 JBB  H4   H  HCR6   0   0.251  -3.0708  -3.1638  -0.9162
 JBB  H5   H  HCR6   0   0.252  -0.6742  -2.7734  -0.4644
 JBB  H6   H  HCH2   0   0.288   0.6209   0.2070   1.3082
 JBB  H7   H  HCH2   0   0.291   1.0126  -1.4308   0.7527
 JBB  H8   H  HCR5   0   0.301   5.7680   1.8461   0.8042
 JBB  H9   H  HCR5   0   0.277   3.8262  -1.3313  -1.4267
 JBB  C02  C  C      0   0.399  -4.2871   1.1212   0.5278

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
 JBB  C13  C12  aromatic  1.363  0.020  1.363
 JBB  C13  C14  aromatic  1.419  0.020  1.419
 JBB  C12  S11  aromatic  1.710  0.020  1.710
 JBB  C14  C10  aromatic  1.366  0.020  1.366
 JBB  S11  C10  aromatic  1.727  0.020  1.727
 JBB  C10  S09  single    1.745  0.020  1.745
 JBB  S09  C08  single    1.837  0.020  1.837
 JBB  C08  C07  single    1.497  0.020  1.497
 JBB  C06  C07  aromatic  1.393  0.020  1.393
 JBB  C06  C05  aromatic  1.388  0.020  1.388
 JBB  C07  C15  aromatic  1.391  0.020  1.391
 JBB  C05  C04  aromatic  1.388  0.020  1.388
 JBB  C15  C03  aromatic  1.391  0.020  1.391
 JBB  C04  C03  aromatic  1.393  0.020  1.393
 JBB  C03  C02  single    1.525  0.020  1.525
 JBB  O01  C02  deloc     1.246  0.020  1.246
 JBB  C02  O16  deloc     1.245  0.020  1.245
 JBB  C13  H1   single    0.930  0.020  1.080
 JBB  C15  H2   single    0.930  0.020  1.080
 JBB  C04  H3   single    0.930  0.020  1.080
 JBB  C05  H4   single    0.930  0.020  1.080
 JBB  C06  H5   single    0.930  0.020  1.080
 JBB  C08  H6   single    0.970  0.020  1.090
 JBB  C08  H7   single    0.970  0.020  1.090
 JBB  C12  H8   single    0.930  0.020  1.080
 JBB  C14  H9   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
 JBB  C14  C10  S11  110.90  3.000
 JBB  S11  C10  S09  121.43  3.000
 JBB  C14  C10  S09  127.65  3.000
 JBB  H1   C13  C14  123.97  3.000
 JBB  H1   C13  C12  123.39  3.000
 JBB  C14  C13  C12  112.64  3.000
 JBB  H2   C15  C07  119.40  3.000
 JBB  H2   C15  C03  119.14  3.000
 JBB  C07  C15  C03  121.46  3.000
 JBB  C04  C03  C02  120.89  3.000
 JBB  C02  C03  C15  120.59  3.000
 JBB  C04  C03  C15  118.52  3.000
 JBB  H3   C04  C05  119.89  3.000
 JBB  H3   C04  C03  119.45  3.000
 JBB  C05  C04  C03  120.66  3.000
 JBB  H4   C05  C06  119.83  3.000
 JBB  H4   C05  C04  120.00  3.000
 JBB  C06  C05  C04  120.18  3.000
 JBB  H5   C06  C07  119.84  3.000
 JBB  H5   C06  C05  120.11  3.000
 JBB  C07  C06  C05  120.04  3.000
 JBB  C08  C07  C06  120.47  3.000
 JBB  C06  C07  C15  119.14  3.000
 JBB  C08  C07  C15  120.36  3.000
 JBB  H7   C08  H6   108.94  3.000
 JBB  H7   C08  S09  108.40  3.000
 JBB  H6   C08  S09  108.56  3.000
 JBB  H7   C08  C07  111.80  3.000
 JBB  H6   C08  C07  111.41  3.000
 JBB  S09  C08  C07  107.64  3.000
 JBB  C08  S09  C10  101.53  3.000
 JBB  C12  S11  C10   92.00  3.000
 JBB  H8   C12  S11  120.53  3.000
 JBB  H8   C12  C13  127.81  3.000
 JBB  S11  C12  C13  111.66  3.000
 JBB  H9   C14  C13  124.30  3.000
 JBB  H9   C14  C10  122.91  3.000
 JBB  C13  C14  C10  112.79  3.000
 JBB  O16  C02  C03  116.52  3.000
 JBB  O16  C02  O01  126.90  3.000
 JBB  C03  C02  O01  116.58  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
 JBB  CONST_01  C12  C13  C14  C10     0.00   0.0  0
 JBB  CONST_02  C13  C12  S11  C10     0.00   0.0  0
 JBB  CONST_03  S11  C10  C14  C13     0.00   0.0  0
 JBB  CONST_04  C05  C06  C07  C15     0.00   0.0  0
 JBB  CONST_05  C05  C04  C03  C15     0.00   0.0  0
 JBB  CONST_06  C06  C07  C15  C03     0.00   0.0  0
 JBB  CONST_07  C06  C05  C04  C03     0.00   0.0  0
 JBB  CONST_08  C07  C06  C05  C04     0.00   0.0  0
 JBB  CONST_09  C07  C15  C03  C04     0.00   0.0  0
 JBB  CONST_10  C14  C13  C12  S11     0.00   0.0  0
 JBB  CONST_11  C14  C10  S11  C12     0.00   0.0  0
 JBB  CONST_12  S09  C10  C14  C13   180.00   0.0  0
 JBB  CONST_13  C07  C15  C03  C02   180.00   0.0  0
 JBB  CONST_14  C05  C04  C03  C02   180.00   0.0  0
 JBB  CONST_15  C08  C07  C15  C03   180.00   0.0  0
 JBB  CONST_16  C08  C07  C06  C05   180.00   0.0  0
 JBB  CONST_17  C12  S11  C10  S09   180.00   0.0  0
 JBB  CONST_18  H1   C13  C14  C10   180.00   0.0  0
 JBB  CONST_19  H8   C12  S11  C10   180.00   0.0  0
 JBB  CONST_20  H5   C06  C07  C15   180.00   0.0  0
 JBB  CONST_21  H3   C04  C03  C15   180.00   0.0  0
 JBB  CONST_22  H4   C05  C04  C03   180.00   0.0  0
 JBB  CONST_23  H2   C15  C03  C04   180.00   0.0  0
 JBB  CONST_24  H9   C14  C10  S11   180.00   0.0  0
 JBB  Var_01    C07  C08  S09  C10  -179.57  30.0  3
 JBB  Var_02    S09  C08  C07  C15   -89.18  30.0  2
 JBB  Var_03    O01  C02  C03  C15    -0.06  30.0  2
 JBB  Var_04    C14  C10  S09  C08   100.13  30.0  1

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
 JBB  plan-1  C10  0.020
 JBB  plan-1  C13  0.020
 JBB  plan-1  S09  0.020
 JBB  plan-1  S11  0.020
 JBB  plan-1  C12  0.020
 JBB  plan-1  C14  0.020
 JBB  plan-1  H1   0.020
 JBB  plan-1  H8   0.020
 JBB  plan-1  H9   0.020
 JBB  plan-2  C15  0.020
 JBB  plan-2  C03  0.020
 JBB  plan-2  C04  0.020
 JBB  plan-2  C05  0.020
 JBB  plan-2  C06  0.020
 JBB  plan-2  C07  0.020
 JBB  plan-2  C08  0.020
 JBB  plan-2  H2   0.020
 JBB  plan-2  H3   0.020
 JBB  plan-2  H4   0.020
 JBB  plan-2  H5   0.020
 JBB  plan-2  C02  0.020
 JBB  plan-3  O01  0.020
 JBB  plan-3  C03  0.020
 JBB  plan-3  O16  0.020
 JBB  plan-3  C02  0.020

