# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 14:46:20 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (5-chloro-3-methyl-1-benzothiophen-2-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(CC(O)=O)sc2ccc(Cl)cc12
#
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
 3N1  3N1  '(5-chloro-3-methyl-1-benzothiophen-2-yl)acetic acid'  ligand  23  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3N1
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
 3N1  CL1   CL  CL     0  -0.136  -4.5328   0.9495   0.2639
 3N1  C2    C   CR6    0  -0.034  -3.0014   0.1425   0.1191
 3N1  C3    C   CR16   0  -0.300  -1.8769   0.8842  -0.1753
 3N1  C5    C   CR56   0   0.191  -0.6494   0.2240  -0.2890
 3N1  C6    C   CR56   0  -0.218  -0.6017  -1.1669  -0.0964
 3N1  S7    S   S2     0   0.192   1.0141  -1.7527  -0.2824
 3N1  C8    C   CR5    0  -0.173   1.6166  -0.1532  -0.6193
 3N1  C9    C   CR5    0   0.149   0.6396   0.7895  -0.5883
 3N1  C10   C   CH3    0  -0.748   0.8331   2.2546  -0.8045
 3N1  C14   C   CH2    0  -0.706   3.0719   0.0231  -0.8587
 3N1  C17   C   C      0   0.432   3.9196   0.1947   0.4331
 3N1  O18   O   OC    -1  -0.619   5.1213   0.4573   0.2385
 3N1  O19   O   O      0  -0.587   3.3415   0.0477   1.5209
 3N1  C21   C   CR16   0  -0.289  -1.7442  -1.9018   0.1985
 3N1  C23   C   CR16   0  -0.237  -2.9535  -1.2408   0.3071
 3N1  H3    H   HCR6   0   0.272  -1.9441   1.9553  -0.3143
 3N1  H10   H   HCH3   0   0.246   0.5823   2.8190   0.0961
 3N1  H10A  H   HCH3   0   0.253   1.8613   2.4969  -1.0651
 3N1  H10B  H   HCH3   0   0.243   0.1929   2.6286  -1.6060
 3N1  H14   H   HCH2   0   0.260   3.4727  -0.8322  -1.4121
 3N1  H14A  H   HCH2   0   0.258   3.2363   0.8859  -1.5079
 3N1  H21   H   HCR6   0   0.274  -1.6985  -2.9735   0.3429
 3N1  H23   H   HCR6   0   0.279  -3.8548  -1.7922   0.5363

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
 3N1  C2   CL1   single    1.737  0.020  1.737
 3N1  C23  C2    aromatic  1.397  0.020  1.397
 3N1  C2   C3    aromatic  1.379  0.020  1.379
 3N1  C5   C3    aromatic  1.398  0.020  1.398
 3N1  C3   H3    single    0.930  0.020  1.080
 3N1  C6   C5    aromatic  1.405  0.020  1.405
 3N1  C5   C9    aromatic  1.439  0.020  1.439
 3N1  S7   C6    aromatic  1.729  0.020  1.729
 3N1  C21  C6    aromatic  1.390  0.020  1.390
 3N1  S7   C8    aromatic  1.742  0.020  1.742
 3N1  C14  C8    single    1.485  0.020  1.485
 3N1  C8   C9    aromatic  1.358  0.020  1.358
 3N1  C9   C10   single    1.494  0.020  1.494
 3N1  C10  H10   single    0.970  0.020  1.090
 3N1  C10  H10A  single    0.970  0.020  1.090
 3N1  C10  H10B  single    0.970  0.020  1.090
 3N1  C17  C14   single    1.555  0.020  1.555
 3N1  C14  H14   single    0.970  0.020  1.090
 3N1  C14  H14A  single    0.970  0.020  1.090
 3N1  O19  C17   deloc     1.241  0.020  1.241
 3N1  O18  C17   deloc     1.245  0.020  1.245
 3N1  C21  C23   aromatic  1.382  0.020  1.382
 3N1  C21  H21   single    0.930  0.020  1.080
 3N1  C23  H23   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
 3N1  C23   C2   C3    122.24  3.000
 3N1  C3    C2   CL1   119.14  3.000
 3N1  C23   C2   CL1   118.62  3.000
 3N1  H3    C3   C5    120.75  3.000
 3N1  H3    C3   C2    120.61  3.000
 3N1  C5    C3   C2    118.64  3.000
 3N1  C9    C5   C6    112.78  3.000
 3N1  C9    C5   C3    128.14  3.000
 3N1  C6    C5   C3    119.08  3.000
 3N1  C21   C6   S7    127.72  3.000
 3N1  C21   C6   C5    121.64  3.000
 3N1  S7    C6   C5    110.64  3.000
 3N1  C8    S7   C6     91.88  3.000
 3N1  C14   C8   C9    128.77  3.000
 3N1  C9    C8   S7    112.59  3.000
 3N1  C14   C8   S7    118.62  3.000
 3N1  C10   C9   C8    125.76  3.000
 3N1  C10   C9   C5    122.12  3.000
 3N1  C8    C9   C5    112.11  3.000
 3N1  H10B  C10  H10A  107.58  3.000
 3N1  H10B  C10  H10   107.09  3.000
 3N1  H10A  C10  H10   107.43  3.000
 3N1  H10B  C10  C9    111.48  3.000
 3N1  H10A  C10  C9    112.06  3.000
 3N1  H10   C10  C9    110.97  3.000
 3N1  H14A  C14  H14   105.17  3.000
 3N1  H14A  C14  C17   108.94  3.000
 3N1  H14   C14  C17   107.86  3.000
 3N1  H14A  C14  C8    109.69  3.000
 3N1  H14   C14  C8    110.33  3.000
 3N1  C17   C14  C8    114.42  3.000
 3N1  O19   C17  O18   127.70  3.000
 3N1  O18   C17  C14   114.81  3.000
 3N1  O19   C17  C14   117.48  3.000
 3N1  H21   C21  C23   119.99  3.000
 3N1  H21   C21  C6    121.14  3.000
 3N1  C23   C21  C6    118.87  3.000
 3N1  H23   C23  C21   120.14  3.000
 3N1  H23   C23  C2    120.33  3.000
 3N1  C21   C23  C2    119.53  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
 3N1  CONST_01  C6   C21  C23  C2     0.00   0.0  0
 3N1  CONST_02  C6   C5   C3   C2     0.00   0.0  0
 3N1  CONST_03  C9   C5   C3   C2   180.00   0.0  0
 3N1  CONST_04  C21  C23  C2   C3     0.00   0.0  0
 3N1  CONST_05  S7   C6   C5   C3   180.00   0.0  0
 3N1  CONST_06  C21  C6   C5   C3     0.00   0.0  0
 3N1  CONST_07  C8   C9   C5   C3   180.00   0.0  0
 3N1  CONST_08  C23  C2   C3   C5     0.00   0.0  0
 3N1  CONST_09  C8   S7   C6   C5     0.00   0.0  0
 3N1  CONST_10  C23  C21  C6   C5     0.00   0.0  0
 3N1  CONST_11  S7   C8   C9   C5     0.00   0.0  0
 3N1  CONST_12  C8   C9   C5   C6     0.00   0.0  0
 3N1  CONST_13  C9   C8   S7   C6     0.00   0.0  0
 3N1  CONST_14  C9   C5   C6   S7     0.00   0.0  0
 3N1  CONST_15  C23  C21  C6   S7   180.00   0.0  0
 3N1  CONST_16  C21  C6   S7   C8   180.00   0.0  0
 3N1  CONST_17  C21  C6   C5   C9   180.00   0.0  0
 3N1  CONST_18  C21  C23  C2   CL1  180.00   0.0  0
 3N1  CONST_19  C5   C3   C2   CL1  180.00   0.0  0
 3N1  CONST_20  C10  C9   C5   C3     0.00   0.0  0
 3N1  CONST_21  C14  C8   C9   C5   180.00   0.0  0
 3N1  CONST_22  C10  C9   C5   C6   180.00   0.0  0
 3N1  CONST_23  C14  C8   S7   C6   180.00   0.0  0
 3N1  CONST_24  C10  C9   C8   S7   180.00   0.0  0
 3N1  CONST_25  H21  C21  C23  C2   180.00   0.0  0
 3N1  CONST_26  H23  C23  C2   C3   180.00   0.0  0
 3N1  CONST_27  H3   C3   C5   C6   180.00   0.0  0
 3N1  Var_01    C17  C14  C8   S7   -85.07  30.0  3
 3N1  Var_02    H10  C10  C9   C5    62.57  30.0  2
 3N1  Var_03    O19  C17  C14  C8     6.45  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
 3N1  plan-1  CL1  0.020
 3N1  plan-1  C2   0.020
 3N1  plan-1  C3   0.020
 3N1  plan-1  C5   0.020
 3N1  plan-1  C6   0.020
 3N1  plan-1  S7   0.020
 3N1  plan-1  C8   0.020
 3N1  plan-1  C9   0.020
 3N1  plan-1  C10  0.020
 3N1  plan-1  C14  0.020
 3N1  plan-1  C21  0.020
 3N1  plan-1  C23  0.020
 3N1  plan-1  H3   0.020
 3N1  plan-1  H21  0.020
 3N1  plan-1  H23  0.020
 3N1  plan-2  C14  0.020
 3N1  plan-2  C17  0.020
 3N1  plan-2  O18  0.020
 3N1  plan-2  O19  0.020

