# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:40:23 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-[4-(3-chlorophenyl)piperazin-1-yl]-4-sulfanylbutan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCCC(=O)N1CCN(CC1)c2cccc(Cl)c2
#
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
 2A2  2A2  1-[4-(3-chlorophenyl)piperazin-1-yl]-4-sulfanylbutan-1-one  ligand  38  19  .  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_2A2
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
 2A2  C1    C   CH2   0  -0.554  -5.6964   0.5933  -0.9635
 2A2  SD    S   S2    0  -0.257  -7.2526  -0.2994  -1.2941
 2A2  C15   C   CH2   0  -0.407  -4.7773  -0.2989  -0.1435
 2A2  C16   C   CH2   0  -0.602  -3.4678   0.4192   0.1502
 2A2  C17   C   C     0   0.574  -2.4917  -0.4328   0.9405
 2A2  O18   O   O     0  -0.500  -2.7744  -1.5780   1.2665
 2A2  N19   N   NT    0  -0.463  -1.3088   0.1331   1.2712
 2A2  C20   C   CH2   0  -0.314  -0.2708  -0.6159   1.9485
 2A2  C21   C   CH2   0  -0.311   0.9610  -0.7538   1.0668
 2A2  N22   N   NT    0  -0.525   1.4172   0.5492   0.6230
 2A2  C23   C   CH2   0  -0.295   0.3678   1.3163  -0.0355
 2A2  C24   C   CH2   0  -0.326  -0.8497   1.4441   0.8631
 2A2  C25   C   CR6   0   0.378   2.7091   0.6633   0.1218
 2A2  C26   C   CR16  0  -0.324   3.2509   1.9277  -0.1622
 2A2  C27   C   CR16  0  -0.249   4.5458   2.0562  -0.6257
 2A2  C28   C   CR16  0  -0.260   5.3617   0.9471  -0.8208
 2A2  C29   C   CR6   0  -0.022   4.8235  -0.2938  -0.5384
 2A2  C30   C   CR16  0  -0.316   3.5232  -0.4571  -0.0851
 2A2  CL99  CL  CL    0  -0.135   5.7961  -1.7139  -0.7775
 2A2  H1    H   HCH2  0   0.265  -5.2259   0.8581  -1.9108
 2A2  H1A   H   HCH2  0   0.264  -5.9189   1.5156  -0.4260
 2A2  HSD   H   HSH1  0   0.222  -7.8645   0.6577  -1.9997
 2A2  H15   H   HCH2  0   0.241  -5.2708  -0.5773   0.7898
 2A2  H15A  H   HCH2  0   0.240  -4.5829  -1.2238  -0.6897
 2A2  H16   H   HCH2  0   0.269  -2.9997   0.7263  -0.7907
 2A2  H16A  H   HCH2  0   0.273  -3.6715   1.3463   0.6946
 2A2  H20   H   HCH2  0   0.249   0.0005  -0.0921   2.8700
 2A2  H20A  H   HCH2  0   0.271  -0.6385  -1.6015   2.2187
 2A2  H21   H   HCH2  0   0.262   1.7404  -1.2292   1.6633
 2A2  H21A  H   HCH2  0   0.226   0.7366  -1.4229   0.2227
 2A2  H23   H   HCH2  0   0.265   0.7218   2.3164  -0.2730
 2A2  H23A  H   HCH2  0   0.229   0.0738   0.8390  -0.9813
 2A2  H24   H   HCH2  0   0.281  -1.6250   1.9935   0.3384
 2A2  H24A  H   HCH2  0   0.255  -0.5859   2.0207   1.7546
 2A2  H26   H   HCR6  0   0.268   2.6674   2.8231   0.0037
 2A2  H27   H   HCR6  0   0.265   4.9385   3.0441  -0.8272
 2A2  H28   H   HCR6  0   0.273   6.3776   1.0538  -1.1739
 2A2  H30   H   HCR6  0   0.289   3.1557  -1.4576   0.0901

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
 2A2  SD    C1    single    1.824  0.020  1.824
 2A2  C15   C1    single    1.521  0.020  1.521
 2A2  C1    H1    single    0.970  0.020  1.090
 2A2  C1    H1A   single    0.970  0.020  1.090
 2A2  SD    HSD   single    1.200  0.020  1.300
 2A2  C15   C16   single    1.522  0.020  1.522
 2A2  C15   H15   single    0.970  0.020  1.090
 2A2  C15   H15A  single    0.970  0.020  1.090
 2A2  C17   C16   single    1.518  0.020  1.518
 2A2  C16   H16   single    0.970  0.020  1.090
 2A2  C16   H16A  single    0.970  0.020  1.090
 2A2  N19   C17   single    1.352  0.020  1.352
 2A2  C17   O18   double    1.224  0.020  1.224
 2A2  C24   N19   single    1.448  0.020  1.448
 2A2  C20   N19   single    1.448  0.020  1.448
 2A2  C21   C20   single    1.521  0.020  1.521
 2A2  C20   H20   single    0.970  0.020  1.090
 2A2  C20   H20A  single    0.970  0.020  1.090
 2A2  N22   C21   single    1.450  0.020  1.450
 2A2  C21   H21   single    0.970  0.020  1.090
 2A2  C21   H21A  single    0.970  0.020  1.090
 2A2  C25   N22   single    1.390  0.020  1.390
 2A2  C23   N22   single    1.457  0.020  1.457
 2A2  C23   C24   single    1.519  0.020  1.519
 2A2  C23   H23   single    0.970  0.020  1.090
 2A2  C23   H23A  single    0.970  0.020  1.090
 2A2  C24   H24   single    0.970  0.020  1.090
 2A2  C24   H24A  single    0.970  0.020  1.090
 2A2  C30   C25   aromatic  1.400  0.020  1.400
 2A2  C25   C26   aromatic  1.405  0.020  1.405
 2A2  C27   C26   aromatic  1.381  0.020  1.381
 2A2  C26   H26   single    0.930  0.020  1.080
 2A2  C28   C27   aromatic  1.391  0.020  1.391
 2A2  C27   H27   single    0.930  0.020  1.080
 2A2  C29   C28   aromatic  1.382  0.020  1.382
 2A2  C28   H28   single    0.930  0.020  1.080
 2A2  CL99  C29   single    1.738  0.020  1.738
 2A2  C29   C30   aromatic  1.387  0.020  1.387
 2A2  C30   H30   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
 2A2  H1A   C1   H1   108.12  3.000
 2A2  H1A   C1   C15  110.71  3.000
 2A2  H1    C1   C15  110.49  3.000
 2A2  H1A   C1   SD   109.22  3.000
 2A2  H1    C1   SD   109.24  3.000
 2A2  C15   C1   SD   109.04  3.000
 2A2  HSD   SD   C1    97.80  3.000
 2A2  H15A  C15  H15  106.99  3.000
 2A2  H15A  C15  C16  110.07  3.000
 2A2  H15   C15  C16  110.14  3.000
 2A2  H15A  C15  C1   109.56  3.000
 2A2  H15   C15  C1   109.71  3.000
 2A2  C16   C15  C1   110.31  3.000
 2A2  H16A  C16  H16  105.64  3.000
 2A2  H16A  C16  C17  109.65  3.000
 2A2  H16   C16  C17  109.27  3.000
 2A2  H16A  C16  C15  109.61  3.000
 2A2  H16   C16  C15  109.53  3.000
 2A2  C17   C16  C15  112.89  3.000
 2A2  N19   C17  O18  121.90  3.000
 2A2  O18   C17  C16  121.03  3.000
 2A2  N19   C17  C16  117.07  3.000
 2A2  C24   N19  C20  111.89  3.000
 2A2  C20   N19  C17  121.66  3.000
 2A2  C24   N19  C17  125.97  3.000
 2A2  H20A  C20  H20  107.99  3.000
 2A2  H20A  C20  C21  109.64  3.000
 2A2  H20   C20  C21  109.32  3.000
 2A2  H20A  C20  N19  110.06  3.000
 2A2  H20   C20  N19  108.90  3.000
 2A2  C21   C20  N19  110.87  3.000
 2A2  H21A  C21  H21  107.47  3.000
 2A2  H21A  C21  N22  112.07  3.000
 2A2  H21   C21  N22  109.53  3.000
 2A2  H21A  C21  C20  109.55  3.000
 2A2  H21   C21  C20  107.53  3.000
 2A2  N22   C21  C20  110.53  3.000
 2A2  C25   N22  C23  117.58  3.000
 2A2  C23   N22  C21  112.63  3.000
 2A2  C25   N22  C21  118.45  3.000
 2A2  H23A  C23  H23  107.36  3.000
 2A2  H23A  C23  C24  109.34  3.000
 2A2  H23   C23  C24  108.23  3.000
 2A2  H23A  C23  N22  110.66  3.000
 2A2  H23   C23  N22  110.40  3.000
 2A2  C24   C23  N22  110.75  3.000
 2A2  H24A  C24  H24  107.42  3.000
 2A2  H24A  C24  C23  109.46  3.000
 2A2  H24   C24  C23  109.22  3.000
 2A2  H24A  C24  N19  108.90  3.000
 2A2  H24   C24  N19  111.60  3.000
 2A2  C23   C24  N19  110.17  3.000
 2A2  C30   C25  C26  117.78  3.000
 2A2  C26   C25  N22  120.34  3.000
 2A2  C30   C25  N22  121.86  3.000
 2A2  H26   C26  C27  118.70  3.000
 2A2  H26   C26  C25  120.40  3.000
 2A2  C27   C26  C25  120.88  3.000
 2A2  H27   C27  C28  119.28  3.000
 2A2  H27   C27  C26  119.19  3.000
 2A2  C28   C27  C26  121.52  3.000
 2A2  H28   C28  C29  121.43  3.000
 2A2  H28   C28  C27  121.24  3.000
 2A2  C29   C28  C27  117.33  3.000
 2A2  CL99  C29  C30  118.26  3.000
 2A2  C30   C29  C28  122.53  3.000
 2A2  CL99  C29  C28  119.20  3.000
 2A2  H30   C30  C29  118.76  3.000
 2A2  H30   C30  C25  121.29  3.000
 2A2  C29   C30  C25  119.95  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
 2A2  CONST_01  C28   C29  C30  C25     0.00   0.0  0
 2A2  CONST_02  C28   C27  C26  C25     0.00   0.0  0
 2A2  CONST_03  C29   C30  C25  C26     0.00   0.0  0
 2A2  CONST_04  C29   C28  C27  C26     0.00   0.0  0
 2A2  CONST_05  C30   C25  C26  C27     0.00   0.0  0
 2A2  CONST_06  C30   C29  C28  C27     0.00   0.0  0
 2A2  CONST_07  C29   C30  C25  N22   180.00   0.0  0
 2A2  CONST_08  C27   C26  C25  N22   180.00   0.0  0
 2A2  CONST_09  CL99  C29  C30  C25   180.00   0.0  0
 2A2  CONST_10  CL99  C29  C28  C27   180.00   0.0  0
 2A2  CONST_11  H30   C30  C25  N22     0.00   0.0  0
 2A2  CONST_12  H26   C26  C25  N22     0.00   0.0  0
 2A2  CONST_13  H27   C27  C26  C25   180.00   0.0  0
 2A2  CONST_14  H28   C28  C27  C26   180.00   0.0  0
 2A2  CONST_15  C24   N19  C17  C16     0.00   0.0  0
 2A2  CONST_16  C20   N19  C17  C16   180.00   0.0  0
 2A2  CONST_17  C24   N19  C17  O18   180.00   0.0  0
 2A2  CONST_18  C20   N19  C17  O18     0.00   0.0  0
 2A2  Var_01    N22   C23  C24  N19   -55.44  30.0  1
 2A2  Var_02    N22   C21  C20  N19    54.57  30.0  1
 2A2  Var_03    C23   C24  N19  C20    57.34  30.0  1
 2A2  Var_04    C25   N22  C21  C20   162.87  30.0  1
 2A2  Var_05    C24   N19  C20  C21   -57.10  30.0  1
 2A2  Var_06    C30   C25  N22  C21     6.35  30.0  2
 2A2  Var_07    C24   C23  N22  C21    55.08  30.0  1
 2A2  Var_08    N19   C17  C16  C15  -178.73  30.0  1
 2A2  Var_09    C17   C16  C15  C1   -178.67  30.0  3
 2A2  Var_10    C16   C15  C1   SD   -179.97  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
 2A2  plan-1  N22   0.020
 2A2  plan-1  C25   0.020
 2A2  plan-1  C26   0.020
 2A2  plan-1  C27   0.020
 2A2  plan-1  C28   0.020
 2A2  plan-1  C29   0.020
 2A2  plan-1  C30   0.020
 2A2  plan-1  CL99  0.020
 2A2  plan-1  H26   0.020
 2A2  plan-1  H27   0.020
 2A2  plan-1  H28   0.020
 2A2  plan-1  H30   0.020
 2A2  plan-2  C16   0.020
 2A2  plan-2  C17   0.020
 2A2  plan-2  O18   0.020
 2A2  plan-2  N19   0.020
 2A2  plan-2  C20   0.020
 2A2  plan-2  C24   0.020

