# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:14:46 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-{4-[(5-chlorothiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)Cc2sc(Cl)cc2
#
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
 T6Y  T6Y  1-{4-[(5-chlorothiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one  ligand  31  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T6Y
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
 T6Y  N1   N   NT    0  -0.407  -0.8876  -1.0798  -0.0767
 T6Y  C4   C   CH2   0  -0.307   0.2176  -1.6450  -0.8269
 T6Y  C5   C   CR5   0  -0.193   1.5362  -1.1540  -0.3170
 T6Y  C6   C   CR15  0  -0.178   2.0485  -1.2899   0.9370
 T6Y  C7   C   CR15  0  -0.110   3.3185  -0.6773   1.0993
 T6Y  C8   C   CR5   0  -0.253   3.7390  -0.0812  -0.0471
 T6Y  C10  C   CH2   0  -0.293  -2.0904   0.9100   0.6628
 T6Y  N    N   NT    0  -0.446  -3.3489   0.2261   0.4209
 T6Y  C    C   CH3   0  -0.787  -5.7390   0.0984  -0.0861
 T6Y  O    O   O     0  -0.509  -4.4951   2.1203  -0.0179
 T6Y  C1   C   C     0   0.516  -4.4729   0.9018   0.1036
 T6Y  C2   C   CH2   0  -0.303  -3.2389  -1.2145   0.5321
 T6Y  C3   C   CH2   0  -0.258  -2.1407  -1.7309  -0.3837
 T6Y  C9   C   CH2   0  -0.275  -0.9985   0.3558  -0.2334
 T6Y  S    S   S2    0   0.276   2.6060  -0.2573  -1.3266
 T6Y  CL   CL  CL    0  -0.073   5.2041   0.7577  -0.2964
 T6Y  H8   H   HCH2  0   0.257   0.1806  -2.7315  -0.7154
 T6Y  H7   H   HCH2  0   0.209   0.1320  -1.4508  -1.9090
 T6Y  H9   H   HCR5  0   0.244   1.5318  -1.8114   1.7295
 T6Y  H10  H   HCR5  0   0.262   3.8870  -0.6816   2.0168
 T6Y  H13  H   HCH2  0   0.256  -2.2151   1.9741   0.4872
 T6Y  H14  H   HCH2  0   0.244  -1.8089   0.7760   1.7117
 T6Y  H    H   HCH3  0   0.258  -6.0109  -0.4533   0.8145
 T6Y  H2   H   HCH3  0   0.263  -6.5549   0.7747  -0.3258
 T6Y  H1   H   HCH3  0   0.247  -5.6498  -0.6259  -0.8962
 T6Y  H3   H   HCH2  0   0.236  -2.9999  -1.4830   1.5661
 T6Y  H4   H   HCH2  0   0.252  -4.1791  -1.6981   0.2810
 T6Y  H5   H   HCH2  0   0.190  -2.4474  -1.5830  -1.4348
 T6Y  H6   H   HCH2  0   0.233  -2.0321  -2.8071  -0.2297
 T6Y  H11  H   HCH2  0   0.256  -0.0527   0.8223   0.0471
 T6Y  H12  H   HCH2  0   0.192  -1.2042   0.6408  -1.2803

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
 T6Y  C1   C    single    1.511  0.020  1.511
 T6Y  C1   O    double    1.225  0.020  1.225
 T6Y  N    C1   single    1.349  0.020  1.349
 T6Y  C2   N    single    1.449  0.020  1.449
 T6Y  C3   C2   single    1.520  0.020  1.520
 T6Y  N1   C3   single    1.445  0.020  1.445
 T6Y  C4   N1   single    1.450  0.020  1.450
 T6Y  C5   C4   single    1.497  0.020  1.497
 T6Y  C6   C5   aromatic  1.361  0.020  1.361
 T6Y  C7   C6   aromatic  1.419  0.020  1.419
 T6Y  C8   C7   aromatic  1.359  0.020  1.359
 T6Y  CL   C8   single    1.707  0.020  1.707
 T6Y  C8   S    aromatic  1.718  0.020  1.718
 T6Y  S    C5   aromatic  1.723  0.020  1.723
 T6Y  N1   C9   single    1.448  0.020  1.448
 T6Y  C9   C10  single    1.517  0.020  1.517
 T6Y  C10  N    single    1.453  0.020  1.453
 T6Y  C4   H8   single    0.970  0.020  1.090
 T6Y  C4   H7   single    0.970  0.020  1.090
 T6Y  C6   H9   single    0.930  0.020  1.080
 T6Y  C7   H10  single    0.930  0.020  1.080
 T6Y  C10  H13  single    0.970  0.020  1.090
 T6Y  C10  H14  single    0.970  0.020  1.090
 T6Y  C    H    single    0.970  0.020  1.090
 T6Y  C    H2   single    0.970  0.020  1.090
 T6Y  C    H1   single    0.970  0.020  1.090
 T6Y  C2   H3   single    0.970  0.020  1.090
 T6Y  C2   H4   single    0.970  0.020  1.090
 T6Y  C3   H5   single    0.970  0.020  1.090
 T6Y  C3   H6   single    0.970  0.020  1.090
 T6Y  C9   H11  single    0.970  0.020  1.090
 T6Y  C9   H12  single    0.970  0.020  1.090

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
 T6Y  C9   N1   C3   110.93  3.000
 T6Y  C9   N1   C4   112.87  3.000
 T6Y  C3   N1   C4   112.04  3.000
 T6Y  H7   C4   H8   105.82  3.000
 T6Y  H7   C4   C5   110.18  3.000
 T6Y  H8   C4   C5   108.74  3.000
 T6Y  H7   C4   N1   112.32  3.000
 T6Y  H8   C4   N1   107.99  3.000
 T6Y  C5   C4   N1   111.55  3.000
 T6Y  S    C5   C6   110.98  3.000
 T6Y  S    C5   C4   121.21  3.000
 T6Y  C6   C5   C4   127.78  3.000
 T6Y  H9   C6   C7   123.53  3.000
 T6Y  H9   C6   C5   122.95  3.000
 T6Y  C7   C6   C5   113.52  3.000
 T6Y  H10  C7   C8   123.77  3.000
 T6Y  H10  C7   C6   124.53  3.000
 T6Y  C8   C7   C6   111.70  3.000
 T6Y  CL   C8   S    120.52  3.000
 T6Y  S    C8   C7   112.29  3.000
 T6Y  CL   C8   C7   127.19  3.000
 T6Y  H14  C10  H13  107.74  3.000
 T6Y  H14  C10  C9   109.65  3.000
 T6Y  H13  C10  C9   110.18  3.000
 T6Y  H14  C10  N    108.96  3.000
 T6Y  H13  C10  N    109.57  3.000
 T6Y  C9   C10  N    110.68  3.000
 T6Y  C2   N    C1   125.39  3.000
 T6Y  C2   N    C10  112.92  3.000
 T6Y  C1   N    C10  121.68  3.000
 T6Y  H1   C    H2   108.12  3.000
 T6Y  H1   C    H    107.33  3.000
 T6Y  H2   C    H    108.05  3.000
 T6Y  H1   C    C1   112.20  3.000
 T6Y  H2   C    C1   109.02  3.000
 T6Y  H    C    C1   111.97  3.000
 T6Y  O    C1   C    120.08  3.000
 T6Y  O    C1   N    122.45  3.000
 T6Y  C    C1   N    117.46  3.000
 T6Y  H4   C2   H3   107.34  3.000
 T6Y  H4   C2   C3   109.55  3.000
 T6Y  H3   C2   C3   109.15  3.000
 T6Y  H4   C2   N    111.04  3.000
 T6Y  H3   C2   N    109.44  3.000
 T6Y  C3   C2   N    110.27  3.000
 T6Y  H6   C3   H5   107.07  3.000
 T6Y  H6   C3   C2   108.75  3.000
 T6Y  H5   C3   C2   109.09  3.000
 T6Y  H6   C3   N1   109.13  3.000
 T6Y  H5   C3   N1   112.48  3.000
 T6Y  C2   C3   N1   110.20  3.000
 T6Y  H12  C9   H11  107.14  3.000
 T6Y  H12  C9   C10  109.37  3.000
 T6Y  H11  C9   C10  108.40  3.000
 T6Y  H12  C9   N1   111.88  3.000
 T6Y  H11  C9   N1   109.24  3.000
 T6Y  C10  C9   N1   110.68  3.000
 T6Y  C8   S    C5    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
 T6Y  CONST_01  C8   C7   C6  C5     0.00   0.0  0
 T6Y  CONST_02  C7   C8   S   C5     0.00   0.0  0
 T6Y  CONST_03  C8   S    C5  C6     0.00   0.0  0
 T6Y  CONST_04  S    C8   C7  C6     0.00   0.0  0
 T6Y  CONST_05  S    C5   C6  C7     0.00   0.0  0
 T6Y  CONST_06  C7   C6   C5  C4   180.00   0.0  0
 T6Y  CONST_07  C8   S    C5  C4   180.00   0.0  0
 T6Y  CONST_08  CL   C8   S   C5   180.00   0.0  0
 T6Y  CONST_09  CL   C8   C7  C6   180.00   0.0  0
 T6Y  CONST_10  H10  C7   C6  C5   180.00   0.0  0
 T6Y  CONST_11  H9   C6   C7  C8   180.00   0.0  0
 T6Y  CONST_12  C    C1   N   C10  180.00   0.0  0
 T6Y  CONST_13  O    C1   N   C10    0.00   0.0  0
 T6Y  CONST_14  C2   N    C1  C      0.00   0.0  0
 T6Y  CONST_15  C2   N    C1  O    180.00   0.0  0
 T6Y  Var_01    N    C2   C3  N1    56.54  30.0  1
 T6Y  Var_02    N    C10  C9  N1   -54.60  30.0  1
 T6Y  Var_03    C3   N1   C9  C10   58.23  30.0  1
 T6Y  Var_04    C3   C2   N   C10  -54.60  30.0  1
 T6Y  Var_05    C9   C10  N   C2    53.71  30.0  1
 T6Y  Var_06    C9   N1   C3  C2   -59.10  30.0  1
 T6Y  Var_07    C6   C5   C4  N1    59.25  30.0  1
 T6Y  Var_08    H    C    C1  N     59.93  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
 T6Y  plan-1  C4   0.020
 T6Y  plan-1  C5   0.020
 T6Y  plan-1  C6   0.020
 T6Y  plan-1  C7   0.020
 T6Y  plan-1  C8   0.020
 T6Y  plan-1  S    0.020
 T6Y  plan-1  CL   0.020
 T6Y  plan-1  H9   0.020
 T6Y  plan-1  H10  0.020
 T6Y  plan-2  C10  0.020
 T6Y  plan-2  N    0.020
 T6Y  plan-2  C    0.020
 T6Y  plan-2  O    0.020
 T6Y  plan-2  C1   0.020
 T6Y  plan-2  C2   0.020

