# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 08:27:51 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N-[2-(4-chloro-2-methylphenoxy)ethyl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Cl)ccc1OCCNC(=O)c2sccc2
#
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
 Q5F  Q5F  N-[2-(4-chloro-2-methylphenoxy)ethyl]thiophene-2-carboxamide  ligand  33  19  .  2021-08-20  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q5F
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
 Q5F  C06  C   CH2   0  -0.335   1.0871  -2.7349  -0.6514
 Q5F  C07  C   CH2   0  -0.191  -0.2125  -2.3701   0.0395
 Q5F  C08  C   CR6   0   0.370  -1.8513  -0.6508  -0.1783
 Q5F  C09  C   CR6   0  -0.005  -2.1642   0.5754  -0.7869
 Q5F  C10  C   CR16  0  -0.381  -2.6280  -1.1361   0.8673
 Q5F  C11  C   CR16  0  -0.245  -3.2674   1.2783  -0.3289
 Q5F  C12  C   CH3   0  -0.709  -1.3082   1.1131  -1.8941
 Q5F  C13  C   C     0   0.553   2.7787  -1.1960   0.2309
 Q5F  C14  C   CR16  0  -0.218  -3.7293  -0.4167   1.3172
 Q5F  C15  C   CR6   0  -0.053  -4.0412   0.7846   0.7136
 Q5F  C16  C   CR5   0  -0.313   3.5295   0.0576   0.0003
 Q5F  C17  C   CR15  0  -0.187   4.5970   0.4811   0.7411
 Q5F  C18  C   CR15  0  -0.175   5.1085   1.7281   0.3070
 Q5F  C19  C   CR15  0  -0.449   4.4142   2.2369  -0.7505
 Q5F  N05  N   NH1   0  -0.648   1.9872  -1.6124  -0.7722
 Q5F  O03  O   O2    0  -0.463  -0.7811  -1.2926  -0.6800
 Q5F  O04  O   O     0  -0.482   2.8960  -1.8036   1.2862
 Q5F  S02  S   S2    0   0.233   3.1386   1.2062  -1.2257
 Q5F  CL1  CL  CL    0  -0.143  -5.4140   1.6975   1.2609
 Q5F  H1   H   HCH2  0   0.266   1.5613  -3.5444  -0.0966
 Q5F  H2   H   HCH2  0   0.270   0.8870  -3.1071  -1.6557
 Q5F  H3   H   HCH2  0   0.241  -0.8744  -3.2428   0.0449
 Q5F  H4   H   HCH2  0   0.234  -0.0278  -2.0802   1.0791
 Q5F  H5   H   HCR6  0   0.285  -2.3994  -2.0795   1.3445
 Q5F  H6   H   HCR6  0   0.271  -3.5190   2.2266  -0.7868
 Q5F  H7   H   HCH3  0   0.247  -1.2425   0.4179  -2.7317
 Q5F  H8   H   HCH3  0   0.246  -1.7058   2.0546  -2.2686
 Q5F  H9   H   HCH3  0   0.240  -0.2878   1.2964  -1.5518
 Q5F  H10  H   HCR6  0   0.279  -4.3291  -0.8043   2.1294
 Q5F  H11  H   HCR5  0   0.274   5.0043  -0.0874   1.5645
 Q5F  H12  H   HCR5  0   0.276   5.9511   2.2284   0.7611
 Q5F  H13  H   HCR5  0   0.308   4.5785   3.1694  -1.2685
 Q5F  H14  H   HNH1  0   0.405   1.9671  -1.1081  -1.6431

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
 Q5F  C17  C18  aromatic  1.416  0.020  1.416
 Q5F  C17  C16  aromatic  1.367  0.020  1.367
 Q5F  C18  C19  aromatic  1.364  0.020  1.364
 Q5F  O04  C13  double    1.223  0.020  1.223
 Q5F  C16  C13  single    1.479  0.020  1.479
 Q5F  C16  S02  aromatic  1.725  0.020  1.725
 Q5F  C19  S02  aromatic  1.707  0.020  1.707
 Q5F  C13  N05  single    1.344  0.020  1.344
 Q5F  N05  C06  single    1.444  0.020  1.444
 Q5F  C14  C10  aromatic  1.390  0.020  1.390
 Q5F  C14  C15  aromatic  1.380  0.020  1.380
 Q5F  C10  C08  aromatic  1.390  0.020  1.390
 Q5F  CL1  C15  single    1.737  0.020  1.737
 Q5F  C06  C07  single    1.516  0.020  1.516
 Q5F  C15  C11  aromatic  1.389  0.020  1.389
 Q5F  C07  O03  single    1.415  0.020  1.415
 Q5F  C08  O03  single    1.345  0.020  1.345
 Q5F  C08  C09  aromatic  1.404  0.020  1.404
 Q5F  C11  C09  aromatic  1.386  0.020  1.386
 Q5F  C09  C12  single    1.499  0.020  1.499
 Q5F  C06  H1   single    0.970  0.020  1.090
 Q5F  C06  H2   single    0.970  0.020  1.090
 Q5F  C07  H3   single    0.970  0.020  1.090
 Q5F  C07  H4   single    0.970  0.020  1.090
 Q5F  C10  H5   single    0.930  0.020  1.080
 Q5F  C11  H6   single    0.930  0.020  1.080
 Q5F  C12  H7   single    0.970  0.020  1.090
 Q5F  C12  H8   single    0.970  0.020  1.090
 Q5F  C12  H9   single    0.970  0.020  1.090
 Q5F  C14  H10  single    0.930  0.020  1.080
 Q5F  C17  H11  single    0.930  0.020  1.080
 Q5F  C18  H12  single    0.930  0.020  1.080
 Q5F  C19  H13  single    0.930  0.020  1.080
 Q5F  N05  H14  single    0.860  0.020  1.020

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
 Q5F  H2   C06  H1   107.18  3.000
 Q5F  H2   C06  N05  107.63  3.000
 Q5F  H1   C06  N05  110.41  3.000
 Q5F  H2   C06  C07  110.17  3.000
 Q5F  H1   C06  C07  108.64  3.000
 Q5F  N05  C06  C07  112.67  3.000
 Q5F  H4   C07  H3   107.96  3.000
 Q5F  H4   C07  O03  110.43  3.000
 Q5F  H3   C07  O03  111.50  3.000
 Q5F  H4   C07  C06  110.59  3.000
 Q5F  H3   C07  C06  109.17  3.000
 Q5F  O03  C07  C06  107.21  3.000
 Q5F  O03  C08  C10  123.96  3.000
 Q5F  O03  C08  C09  115.61  3.000
 Q5F  C10  C08  C09  120.42  3.000
 Q5F  C12  C09  C11  121.10  3.000
 Q5F  C12  C09  C08  120.40  3.000
 Q5F  C11  C09  C08  118.49  3.000
 Q5F  H5   C10  C14  118.43  3.000
 Q5F  H5   C10  C08  121.21  3.000
 Q5F  C14  C10  C08  120.36  3.000
 Q5F  H6   C11  C15  119.95  3.000
 Q5F  H6   C11  C09  119.30  3.000
 Q5F  C15  C11  C09  120.74  3.000
 Q5F  H9   C12  H8   107.70  3.000
 Q5F  H9   C12  H7   106.95  3.000
 Q5F  H8   C12  H7   108.01  3.000
 Q5F  H9   C12  C09  111.24  3.000
 Q5F  H8   C12  C09  110.84  3.000
 Q5F  H7   C12  C09  111.90  3.000
 Q5F  O04  C13  N05  123.12  3.000
 Q5F  N05  C13  C16  116.43  3.000
 Q5F  O04  C13  C16  120.44  3.000
 Q5F  H10  C14  C15  121.00  3.000
 Q5F  H10  C14  C10  119.80  3.000
 Q5F  C15  C14  C10  119.20  3.000
 Q5F  CL1  C15  C14  119.88  3.000
 Q5F  CL1  C15  C11  119.34  3.000
 Q5F  C14  C15  C11  120.78  3.000
 Q5F  S02  C16  C17  110.85  3.000
 Q5F  S02  C16  C13  124.06  3.000
 Q5F  C17  C16  C13  125.07  3.000
 Q5F  H11  C17  C18  124.12  3.000
 Q5F  H11  C17  C16  123.00  3.000
 Q5F  C18  C17  C16  112.88  3.000
 Q5F  H12  C18  C19  123.40  3.000
 Q5F  H12  C18  C17  124.11  3.000
 Q5F  C19  C18  C17  112.49  3.000
 Q5F  H13  C19  S02  120.11  3.000
 Q5F  H13  C19  C18  128.11  3.000
 Q5F  S02  C19  C18  111.77  3.000
 Q5F  H14  N05  C13  120.16  3.000
 Q5F  H14  N05  C06  116.70  3.000
 Q5F  C13  N05  C06  123.07  3.000
 Q5F  C08  O03  C07  119.57  3.000
 Q5F  C19  S02  C16   92.00  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
 Q5F  CONST_01  C15  C14  C10  C08    0.00   0.0  0
 Q5F  CONST_02  C15  C11  C09  C08    0.00   0.0  0
 Q5F  CONST_03  C14  C10  C08  C09    0.00   0.0  0
 Q5F  CONST_04  C14  C15  C11  C09    0.00   0.0  0
 Q5F  CONST_05  C11  C15  C14  C10    0.00   0.0  0
 Q5F  CONST_06  C11  C09  C08  C10    0.00   0.0  0
 Q5F  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 Q5F  CONST_08  C18  C19  S02  C16    0.00   0.0  0
 Q5F  CONST_09  S02  C19  C18  C17    0.00   0.0  0
 Q5F  CONST_10  C19  S02  C16  C17    0.00   0.0  0
 Q5F  CONST_11  S02  C16  C17  C18    0.00   0.0  0
 Q5F  CONST_12  CL1  C15  C11  C09  180.00   0.0  0
 Q5F  CONST_13  CL1  C15  C14  C10  180.00   0.0  0
 Q5F  CONST_14  C12  C09  C08  C10  180.00   0.0  0
 Q5F  CONST_15  O03  C08  C09  C11  180.00   0.0  0
 Q5F  CONST_16  C15  C11  C09  C12  180.00   0.0  0
 Q5F  CONST_17  C18  C17  C16  C13  180.00   0.0  0
 Q5F  CONST_18  C19  S02  C16  C13  180.00   0.0  0
 Q5F  CONST_19  O03  C08  C10  C14  180.00   0.0  0
 Q5F  CONST_20  H10  C14  C10  C08  180.00   0.0  0
 Q5F  CONST_21  H6   C11  C09  C08  180.00   0.0  0
 Q5F  CONST_22  H5   C10  C08  C09  180.00   0.0  0
 Q5F  CONST_23  H12  C18  C17  C16  180.00   0.0  0
 Q5F  CONST_24  H13  C19  S02  C16  180.00   0.0  0
 Q5F  CONST_25  H11  C17  C18  C19  180.00   0.0  0
 Q5F  CONST_26  C16  C13  N05  C06  180.00   0.0  0
 Q5F  CONST_27  H14  N05  C13  C16    0.00   0.0  0
 Q5F  CONST_28  O04  C13  N05  C06    0.00   0.0  0
 Q5F  Var_01    C10  C08  O03  C07  -14.15  30.0  3
 Q5F  Var_02    O04  C13  C16  C17   15.58  30.0  2
 Q5F  Var_03    H7   C12  C09  C08   57.84  30.0  2
 Q5F  Var_04    H3   C07  O03  C08   69.51  30.0  2
 Q5F  Var_05    C13  N05  C06  C07   81.06  30.0  1
 Q5F  Var_06    O03  C07  C06  N05   55.59  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
 Q5F  plan-1  C13  0.020
 Q5F  plan-1  C16  0.020
 Q5F  plan-1  C17  0.020
 Q5F  plan-1  C18  0.020
 Q5F  plan-1  C19  0.020
 Q5F  plan-1  S02  0.020
 Q5F  plan-1  H11  0.020
 Q5F  plan-1  H12  0.020
 Q5F  plan-1  H13  0.020
 Q5F  plan-2  C08  0.020
 Q5F  plan-2  C09  0.020
 Q5F  plan-2  C10  0.020
 Q5F  plan-2  C11  0.020
 Q5F  plan-2  C12  0.020
 Q5F  plan-2  C14  0.020
 Q5F  plan-2  C15  0.020
 Q5F  plan-2  O03  0.020
 Q5F  plan-2  CL1  0.020
 Q5F  plan-2  H5   0.020
 Q5F  plan-2  H6   0.020
 Q5F  plan-2  H10  0.020
 Q5F  plan-3  C06  0.020
 Q5F  plan-3  C13  0.020
 Q5F  plan-3  C16  0.020
 Q5F  plan-3  N05  0.020
 Q5F  plan-3  O04  0.020
 Q5F  plan-3  H14  0.020

