# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:18:31 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  24  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  -0.129  -4.5589   0.8965   0.2324
 3N1  C2    C   CR6   0  -0.033  -3.0162   0.1108   0.1142
 3N1  C3    C   CR16  0  -0.294  -1.8978   0.8647  -0.1680
 3N1  C5    C   CR56  0   0.192  -0.6617   0.2176  -0.2592
 3N1  C6    C   CR56  0  -0.216  -0.5978  -1.1700  -0.0586
 3N1  S7    S   S2    0   0.217   1.0254  -1.7423  -0.2172
 3N1  C8    C   CR5   0  -0.215   1.6061  -0.1359  -0.5520
 3N1  C9    C   CR5   0   0.174   0.6248   0.7998  -0.5408
 3N1  C10   C   CH3   0  -0.749   0.8064   2.2646  -0.7619
 3N1  C14   C   CH2   0  -0.699   3.0633   0.0665  -0.7816
 3N1  C17   C   C     0   0.566   3.8256   0.3189   0.4990
 3N1  O18   O   OH1   0  -0.590   5.1118   0.5307   0.2554
 3N1  O19   O   O     0  -0.429   3.3402   0.3287   1.5995
 3N1  C21   C   CR16  0  -0.284  -1.7351  -1.9195   0.2239
 3N1  C23   C   CR16  0  -0.231  -2.9517  -1.2716   0.3105
 3N1  H3    H   HCR6  0   0.277  -1.9747   1.9341  -0.3144
 3N1  H10   H   HCH3  0   0.255   0.5484   2.8270   0.1374
 3N1  H10A  H   HCH3  0   0.256   1.8316   2.5183  -1.0230
 3N1  H10B  H   HCH3  0   0.252   0.1619   2.6260  -1.5650
 3N1  H14   H   HCH2  0   0.318   3.5110  -0.7963  -1.2838
 3N1  H14A  H   HCH2  0   0.317   3.2299   0.9082  -1.4582
 3N1  HO18  H   HOH1  0   0.484   5.5864   0.6929   1.0845
 3N1  H21   H   HCR6  0   0.279  -1.6783  -2.9894   0.3738
 3N1  H23   H   HCR6  0   0.283  -3.8497  -1.8325   0.5299

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    1.735  0.020  1.735
 3N1  C23  C2    aromatic  1.398  0.020  1.398
 3N1  C2   C3    aromatic  1.378  0.020  1.378
 3N1  C5   C3    aromatic  1.398  0.020  1.398
 3N1  C3   H3    single    0.930  0.020  1.080
 3N1  C6   C5    aromatic  1.403  0.020  1.403
 3N1  C5   C9    aromatic  1.440  0.020  1.440
 3N1  S7   C6    aromatic  1.728  0.020  1.728
 3N1  C21  C6    aromatic  1.391  0.020  1.391
 3N1  S7   C8    aromatic  1.741  0.020  1.741
 3N1  C14  C8    single    1.489  0.020  1.489
 3N1  C8   C9    aromatic  1.356  0.020  1.356
 3N1  C9   C10   single    1.492  0.020  1.492
 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    1.512  0.020  1.512
 3N1  C14  H14   single    0.970  0.020  1.090
 3N1  C14  H14A  single    0.970  0.020  1.090
 3N1  O19  C17   double    1.203  0.020  1.203
 3N1  O18  C17   single    1.326  0.020  1.326
 3N1  O18  HO18  single    0.850  0.020  0.980
 3N1  C21  C23   aromatic  1.381  0.020  1.381
 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    122.17  3.000
 3N1  C3    C2   CL1   119.20  3.000
 3N1  C23   C2   CL1   118.63  3.000
 3N1  H3    C3   C5    120.76  3.000
 3N1  H3    C3   C2    120.71  3.000
 3N1  C5    C3   C2    118.53  3.000
 3N1  C9    C5   C6    112.77  3.000
 3N1  C9    C5   C3    127.99  3.000
 3N1  C6    C5   C3    119.24  3.000
 3N1  C21   C6   S7    127.45  3.000
 3N1  C21   C6   C5    121.64  3.000
 3N1  S7    C6   C5    110.92  3.000
 3N1  C8    S7   C6     91.45  3.000
 3N1  C14   C8   C9    128.00  3.000
 3N1  C9    C8   S7    113.19  3.000
 3N1  C14   C8   S7    118.79  3.000
 3N1  C10   C9   C8    126.02  3.000
 3N1  C10   C9   C5    122.31  3.000
 3N1  C8    C9   C5    111.66  3.000
 3N1  H10B  C10  H10A  107.62  3.000
 3N1  H10B  C10  H10   107.21  3.000
 3N1  H10A  C10  H10   107.48  3.000
 3N1  H10B  C10  C9    111.23  3.000
 3N1  H10A  C10  C9    112.28  3.000
 3N1  H10   C10  C9    110.78  3.000
 3N1  H14A  C14  H14   105.12  3.000
 3N1  H14A  C14  C17   108.61  3.000
 3N1  H14   C14  C17   108.31  3.000
 3N1  H14A  C14  C8    110.45  3.000
 3N1  H14   C14  C8    111.35  3.000
 3N1  C17   C14  C8    112.68  3.000
 3N1  O19   C17  O18   123.93  3.000
 3N1  O18   C17  C14   111.11  3.000
 3N1  O19   C17  C14   124.96  3.000
 3N1  HO18  O18  C17   110.16  3.000
 3N1  H21   C21  C23   120.09  3.000
 3N1  H21   C21  C6    121.21  3.000
 3N1  C23   C21  C6    118.70  3.000
 3N1  H23   C23  C21   120.07  3.000
 3N1  H23   C23  C2    120.21  3.000
 3N1  C21   C23  C2    119.72  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  CONST_28  HO18  O18  C17  C14  180.00   0.0  0
 3N1  Var_01    C17   C14  C8   S7   -88.14  30.0  3
 3N1  Var_02    H10   C10  C9   C5    63.41  30.0  2
 3N1  Var_03    O19   C17  C14  C8     1.71  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
 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
 3N1  plan-2  HO18  0.020

