# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:08:29 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 1-{[(E)-2-(4-chlorophenyl)ethenyl]sulfonyl}-4-[(1-pyridin-4-ylpiperidin-4-yl)methyl]piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)\C=C\[S](=O)(=O)N2CCN(CC2)CC3CCN(CC3)c4ccncc4
#
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
 XMK  XMK  1-{[(E)-2-(4-chlorophenyl)ethenyl]sulfonyl}-4-[(1-pyridin-4-ylpiperidin-4-yl)methyl]piperazine  ligand  60  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XMK
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
 XMK  C1    C   CH2   0  -0.246   2.4699  -0.3939   2.7699
 XMK  C2    C   CR16  0  -0.078  -2.6682  -0.2237   8.6634
 XMK  N3    N   NR6   0  -0.511  -0.8817   0.0464   5.4600
 XMK  C4    C   CR6   0   0.478  -1.8814  -0.0613   6.3854
 XMK  C5    C   CR16  0  -0.415  -1.6274  -0.0667   7.7724
 XMK  C6    C   C     0  -0.306  -1.1816   0.0083   4.0378
 XMK  C7    C   CR16  0  -0.430  -3.2371  -0.2068   6.0331
 XMK  C8    C   C     0  -0.306   0.3444   0.7694   5.7708
 XMK  C9    C   CR16  0  -0.281   1.2866   0.2100   3.5170
 XMK  C10   C   C     0  -0.409  -0.0082  -0.5380   3.2361
 XMK  N11   N   N     0  -0.435  -3.9476  -0.3705   8.3246
 XMK  C12   C   CR16  0  -0.077  -4.1938  -0.3572   7.0189
 XMK  C13   C   C     0  -0.417   1.5367   0.2029   5.0191
 XMK  C14   C   C1    0  -0.187   0.7239   0.4907  -4.1493
 XMK  C15   C   C1    0  -0.511   1.5721  -0.4240  -3.6780
 XMK  C16   C   CR16  0  -0.304  -1.3799   1.3252  -5.0894
 XMK  C18   C   CR6   0   0.152  -0.6083   0.2344  -4.6869
 XMK  O20   O   OS    0  -0.663   4.1005  -0.9690  -3.4614
 XMK  C21   C   CH2   0  -0.279   3.2129  -1.3190   0.6775
 XMK  C22   C   CH2   0  -0.314   2.9172  -1.4082  -0.8075
 XMK  N23   N   N     0  -0.573   3.0246  -0.0694  -1.3907
 XMK  C24   C   CR16  0  -0.313  -1.1469  -1.0485  -4.8183
 XMK  C25   C   CH2   0  -0.287   2.4330   0.9173   0.7459
 XMK  C26   C   CH2   0  -0.309   2.1309   0.8886  -0.7394
 XMK  C27   C   CR16  0  -0.196  -2.6546   1.1537  -5.6039
 XMK  N28   N   NT    0  -0.422   2.3014  -0.4017   1.3292
 XMK  C29   C   CR16  0  -0.184  -2.4162  -1.2358  -5.3313
 XMK  C30   C   CR6   0  -0.049  -3.1623  -0.1299  -5.7203
 XMK  O31   O   OS    0  -0.655   3.3858   1.4351  -3.3532
 XMK  H11   H   HCH2  0   0.226   2.5860  -1.4319   3.0986
 XMK  H12A  H   HCH2  0   0.205   3.3958   0.1294   3.0672
 XMK  H2    H   HCR6  0   0.254  -2.4462  -0.2345   9.7255
 XMK  H5    H   HCR6  0   0.270  -0.6289   0.0261   8.1732
 XMK  H61   H   H     0   0.223  -1.4507   1.0106   3.6754
 XMK  H62   H   H     0   0.256  -2.0370  -0.6399   3.8608
 XMK  H7    H   HCR6  0   0.269  -3.5692  -0.1885   5.0059
 XMK  H81   H   H     0   0.227   0.2171   1.8287   5.5064
 XMK  H82   H   H     0   0.262   0.5458   0.7358   6.8370
 XMK  H9    H   HCR6  0   0.226   1.1563   1.2567   3.2135
 XMK  H101  H   H     0   0.243  -0.2580  -0.4893   2.1751
 XMK  H102  H   H     0   0.217   0.1307  -1.5964   3.4833
 XMK  H12   H   HCR6  0   0.254  -5.2323  -0.4633   6.7219
 XMK  H131  H   H     0   0.223   1.7263  -0.8202   5.3610
 XMK  H132  H   H     0   0.239   2.4194   0.7969   5.2691
 XMK  H14   H   H     0   0.293   1.0271   1.5326  -4.1479
 XMK  H15   H   H     0   0.324   1.3657  -1.4868  -3.6299
 XMK  H16   H   HCR6  0   0.276  -0.9815   2.3278  -4.9965
 XMK  H211  H   HCH2  0   0.250   3.0900  -2.3156   1.1060
 XMK  H212  H   HCH2  0   0.203   4.2679  -1.0282   0.8157
 XMK  H221  H   HCH2  0   0.237   1.9119  -1.8207  -0.9552
 XMK  H222  H   HCH2  0   0.275   3.6375  -2.0754  -1.2756
 XMK  H24   H   HCR6  0   0.271  -0.5781  -1.9201  -4.5234
 XMK  H251  H   HCH2  0   0.254   1.7257   1.6057   1.2100
 XMK  H252  H   HCH2  0   0.206   3.4427   1.3328   0.9054
 XMK  H261  H   HCH2  0   0.272   2.2917   1.8840  -1.1483
 XMK  H262  H   HCH2  0   0.237   1.0805   0.6126  -0.8949
 XMK  H27   H   HCR6  0   0.287  -3.2406   2.0101  -5.9083
 XMK  H29   H   HCR6  0   0.289  -2.8210  -2.2335  -5.4299
 XMK  S17   S   S     0   1.372   3.1397   0.0368  -3.0371
 XMK  CL19  CL  CL    0  -0.113  -4.7507  -0.3630  -6.3611

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
 XMK  C1    C9    single    1.524  0.020  1.524
 XMK  C1    N28   single    1.451  0.020  1.451
 XMK  C1    H11   single    0.970  0.020  1.090
 XMK  C1    H12A  single    0.970  0.020  1.090
 XMK  C2    C5    aromatic  1.379  0.020  1.379
 XMK  C2    N11   aromatic  1.332  0.020  1.332
 XMK  C2    H2    single    0.930  0.020  1.080
 XMK  N3    C4    single    1.366  0.020  1.366
 XMK  N3    C6    single    1.454  0.020  1.454
 XMK  N3    C8    single    1.457  0.020  1.457
 XMK  C4    C5    aromatic  1.410  0.020  1.410
 XMK  C4    C7    aromatic  1.408  0.020  1.408
 XMK  C5    H5    single    0.930  0.020  1.080
 XMK  C6    C10   single    1.523  0.020  1.523
 XMK  C6    H61   single    0.970  0.020  1.090
 XMK  C6    H62   single    0.970  0.020  1.090
 XMK  C7    C12   aromatic  1.382  0.020  1.382
 XMK  C7    H7    single    0.930  0.020  1.080
 XMK  C8    C13   single    1.519  0.020  1.519
 XMK  C8    H81   single    0.970  0.020  1.090
 XMK  C8    H82   single    0.970  0.020  1.090
 XMK  C9    C10   single    1.521  0.020  1.521
 XMK  C9    C13   single    1.523  0.020  1.523
 XMK  C9    H9    single    0.970  0.020  1.090
 XMK  C10   H101  single    0.970  0.020  1.090
 XMK  C10   H102  single    0.970  0.020  1.090
 XMK  N11   C12   aromatic  1.329  0.020  1.329
 XMK  C12   H12   single    0.930  0.020  1.080
 XMK  C13   H131  single    0.970  0.020  1.090
 XMK  C13   H132  single    0.970  0.020  1.090
 XMK  C14   C15   double    1.334  0.020  1.334
 XMK  C14   C18   single    1.459  0.020  1.459
 XMK  C14   H14   single    0.930  0.020  1.080
 XMK  C15   S17   single    1.755  0.020  1.755
 XMK  C15   H15   single    0.930  0.020  1.080
 XMK  C16   C18   aromatic  1.395  0.020  1.395
 XMK  C16   C27   aromatic  1.385  0.020  1.385
 XMK  C16   H16   single    0.930  0.020  1.080
 XMK  S17   O20   double    1.454  0.020  1.454
 XMK  S17   N23   single    1.654  0.020  1.654
 XMK  S17   O31   double    1.455  0.020  1.455
 XMK  C18   C24   aromatic  1.398  0.020  1.398
 XMK  CL19  C30   single    1.729  0.020  1.729
 XMK  C21   C22   single    1.517  0.020  1.517
 XMK  C21   N28   single    1.448  0.020  1.448
 XMK  C21   H211  single    0.970  0.020  1.090
 XMK  C21   H212  single    0.970  0.020  1.090
 XMK  C22   N23   single    1.464  0.020  1.464
 XMK  C22   H221  single    0.970  0.020  1.090
 XMK  C22   H222  single    0.970  0.020  1.090
 XMK  N23   C26   single    1.463  0.020  1.463
 XMK  C24   C29   aromatic  1.382  0.020  1.382
 XMK  C24   H24   single    0.930  0.020  1.080
 XMK  C25   C26   single    1.516  0.020  1.516
 XMK  C25   N28   single    1.448  0.020  1.448
 XMK  C25   H251  single    0.970  0.020  1.090
 XMK  C25   H252  single    0.970  0.020  1.090
 XMK  C26   H261  single    0.970  0.020  1.090
 XMK  C26   H262  single    0.970  0.020  1.090
 XMK  C27   C30   aromatic  1.385  0.020  1.385
 XMK  C27   H27   single    0.930  0.020  1.080
 XMK  C29   C30   aromatic  1.390  0.020  1.390
 XMK  C29   H29   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
 XMK  H12A  C1   H11   106.23  3.000
 XMK  H12A  C1   N28   111.55  3.000
 XMK  H11   C1   N28   107.78  3.000
 XMK  H12A  C1   C9    109.34  3.000
 XMK  H11   C1   C9    108.11  3.000
 XMK  N28   C1   C9    113.50  3.000
 XMK  H2    C2   N11   116.40  3.000
 XMK  H2    C2   C5    118.62  3.000
 XMK  N11   C2   C5    124.98  3.000
 XMK  C8    N3   C6    113.28  3.000
 XMK  C8    N3   C4    120.68  3.000
 XMK  C6    N3   C4    120.63  3.000
 XMK  C7    C4   C5    114.77  3.000
 XMK  C7    C4   N3    122.89  3.000
 XMK  C5    C4   N3    122.33  3.000
 XMK  H5    C5   C4    122.08  3.000
 XMK  H5    C5   C2    117.90  3.000
 XMK  C4    C5   C2    120.00  3.000
 XMK  H62   C6   H61   107.29  3.000
 XMK  H62   C6   C10   107.85  3.000
 XMK  H61   C6   C10   110.01  3.000
 XMK  H62   C6   N3    109.69  3.000
 XMK  H61   C6   N3    110.43  3.000
 XMK  C10   C6   N3    111.44  3.000
 XMK  H7    C7   C12   117.87  3.000
 XMK  H7    C7   C4    122.17  3.000
 XMK  C12   C7   C4    119.95  3.000
 XMK  H82   C8   H81   106.72  3.000
 XMK  H82   C8   C13   109.20  3.000
 XMK  H81   C8   C13   109.35  3.000
 XMK  H82   C8   N3    110.50  3.000
 XMK  H81   C8   N3    109.24  3.000
 XMK  C13   C8   N3    111.71  3.000
 XMK  H9    C9   C13   107.26  3.000
 XMK  H9    C9   C10   108.47  3.000
 XMK  C13   C9   C10   108.64  3.000
 XMK  H9    C9   C1    109.54  3.000
 XMK  C13   C9   C1    110.74  3.000
 XMK  C10   C9   C1    112.05  3.000
 XMK  H102  C10  H101  106.95  3.000
 XMK  H102  C10  C9    108.99  3.000
 XMK  H101  C10  C9    110.63  3.000
 XMK  H102  C10  C6    109.00  3.000
 XMK  H101  C10  C6    108.63  3.000
 XMK  C9    C10  C6    112.48  3.000
 XMK  C12   N11  C2    115.28  3.000
 XMK  H12   C12  N11   116.43  3.000
 XMK  H12   C12  C7    118.55  3.000
 XMK  N11   C12  C7    125.01  3.000
 XMK  H132  C13  H131  107.25  3.000
 XMK  H132  C13  C9    110.83  3.000
 XMK  H131  C13  C9    109.92  3.000
 XMK  H132  C13  C8    108.54  3.000
 XMK  H131  C13  C8    109.26  3.000
 XMK  C9    C13  C8    110.94  3.000
 XMK  H14   C14  C18   115.11  3.000
 XMK  H14   C14  C15   118.71  3.000
 XMK  C18   C14  C15   126.18  3.000
 XMK  H15   C15  S17   114.29  3.000
 XMK  H15   C15  C14   124.56  3.000
 XMK  S17   C15  C14   121.14  3.000
 XMK  H16   C16  C27   119.01  3.000
 XMK  H16   C16  C18   119.71  3.000
 XMK  C27   C16  C18   121.28  3.000
 XMK  C24   C18  C16   118.51  3.000
 XMK  C24   C18  C14   123.21  3.000
 XMK  C16   C18  C14   118.28  3.000
 XMK  H212  C21  H211  107.41  3.000
 XMK  H212  C21  N28   112.25  3.000
 XMK  H211  C21  N28   109.31  3.000
 XMK  H212  C21  C22   108.94  3.000
 XMK  H211  C21  C22   107.98  3.000
 XMK  N28   C21  C22   110.80  3.000
 XMK  H222  C22  H221  108.56  3.000
 XMK  H222  C22  N23   109.93  3.000
 XMK  H221  C22  N23   110.95  3.000
 XMK  H222  C22  C21   109.16  3.000
 XMK  H221  C22  C21   109.43  3.000
 XMK  N23   C22  C21   108.78  3.000
 XMK  C26   N23  C22   112.12  3.000
 XMK  C26   N23  S17   116.33  3.000
 XMK  C22   N23  S17   117.41  3.000
 XMK  H24   C24  C29   118.36  3.000
 XMK  H24   C24  C18   120.75  3.000
 XMK  C29   C24  C18   120.89  3.000
 XMK  H252  C25  H251  107.12  3.000
 XMK  H252  C25  N28   111.58  3.000
 XMK  H251  C25  N28   110.15  3.000
 XMK  H252  C25  C26   109.34  3.000
 XMK  H251  C25  C26   107.44  3.000
 XMK  N28   C25  C26   111.06  3.000
 XMK  H262  C26  H261  108.57  3.000
 XMK  H262  C26  C25   109.53  3.000
 XMK  H261  C26  C25   108.75  3.000
 XMK  H262  C26  N23   110.92  3.000
 XMK  H261  C26  N23   109.97  3.000
 XMK  C25   C26  N23   109.08  3.000
 XMK  H27   C27  C30   120.77  3.000
 XMK  H27   C27  C16   120.34  3.000
 XMK  C30   C27  C16   118.89  3.000
 XMK  C25   N28  C21   109.78  3.000
 XMK  C25   N28  C1    112.62  3.000
 XMK  C21   N28  C1    112.16  3.000
 XMK  H29   C29  C30   120.52  3.000
 XMK  H29   C29  C24   120.19  3.000
 XMK  C30   C29  C24   119.29  3.000
 XMK  C29   C30  C27   121.14  3.000
 XMK  C29   C30  CL19  119.33  3.000
 XMK  C27   C30  CL19  119.53  3.000
 XMK  O31   S17  N23   106.85  3.000
 XMK  O31   S17  O20   119.32  3.000
 XMK  N23   S17  O20   106.98  3.000
 XMK  O31   S17  C15   108.92  3.000
 XMK  N23   S17  C15   106.53  3.000
 XMK  O20   S17  C15   107.58  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
 XMK  CONST_01  C7    C4   C5   C2       0.00   0.0  0
 XMK  CONST_02  C7    C12  N11  C2       0.00   0.0  0
 XMK  CONST_03  N11   C2   C5   C4       0.00   0.0  0
 XMK  CONST_04  N11   C12  C7   C4       0.00   0.0  0
 XMK  CONST_05  C12   N11  C2   C5       0.00   0.0  0
 XMK  CONST_06  C12   C7   C4   C5       0.00   0.0  0
 XMK  CONST_07  C29   C24  C18  C16      0.00   0.0  0
 XMK  CONST_08  C29   C30  C27  C16      0.00   0.0  0
 XMK  CONST_09  C30   C27  C16  C18      0.00   0.0  0
 XMK  CONST_10  C30   C29  C24  C18      0.00   0.0  0
 XMK  CONST_11  C27   C16  C18  C24      0.00   0.0  0
 XMK  CONST_12  C27   C30  C29  C24      0.00   0.0  0
 XMK  CONST_13  N3    C4   C5   C2     180.00   0.0  0
 XMK  CONST_14  C12   C7   C4   N3     180.00   0.0  0
 XMK  CONST_15  C27   C16  C18  C14    180.00   0.0  0
 XMK  CONST_16  C29   C24  C18  C14    180.00   0.0  0
 XMK  CONST_17  CL19  C30  C27  C16    180.00   0.0  0
 XMK  CONST_18  C24   C29  C30  CL19   180.00   0.0  0
 XMK  CONST_19  H12   C12  N11  C2     180.00   0.0  0
 XMK  CONST_20  H5    C5   C4   N3       0.00   0.0  0
 XMK  CONST_21  H7    C7   C4   N3       0.00   0.0  0
 XMK  CONST_22  H2    C2   C5   C4     180.00   0.0  0
 XMK  CONST_23  H24   C24  C18  C16    180.00   0.0  0
 XMK  CONST_24  H27   C27  C16  C18    180.00   0.0  0
 XMK  CONST_25  H29   C29  C24  C18    180.00   0.0  0
 XMK  CONST_26  H16   C16  C18  C24    180.00   0.0  0
 XMK  Var_01    C9    C10  C6   N3     -53.74  30.0  1
 XMK  Var_02    C9    C13  C8   N3      56.53  30.0  1
 XMK  Var_03    C10   C6   N3   C4    -151.81  30.0  1
 XMK  Var_04    C13   C8   N3   C4     149.88  30.0  1
 XMK  Var_05    C6    N3   C4   C5     178.17  30.0  3
 XMK  Var_06    C26   N23  C22  C21    -57.10  30.0  1
 XMK  Var_07    C26   C25  N28  C21     59.24  30.0  1
 XMK  Var_08    C25   N28  C21  C22    -59.74  30.0  1
 XMK  Var_09    C25   C26  N23  C22     56.64  30.0  1
 XMK  Var_10    N28   C21  C22  N23     58.07  30.0  1
 XMK  Var_11    N28   C25  C26  N23    -57.11  30.0  1
 XMK  Var_12    C21   N28  C1   C9    -162.46  30.0  3
 XMK  Var_13    C16   C18  C14  C15    177.57  30.0  2
 XMK  Var_14    C22   N23  S17  C15     70.00  30.0  3
 XMK  Var_15    C18   C14  C15  S17   -179.05   0.0  2
 XMK  Var_16    N23   S17  C15  C14    104.43  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XMK  chir_01  C9  C1  C10  C13  negativ

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
 XMK  plan-1  C2    0.020
 XMK  plan-1  N3    0.020
 XMK  plan-1  C4    0.020
 XMK  plan-1  C5    0.020
 XMK  plan-1  C7    0.020
 XMK  plan-1  N11   0.020
 XMK  plan-1  C12   0.020
 XMK  plan-1  H2    0.020
 XMK  plan-1  H5    0.020
 XMK  plan-1  H7    0.020
 XMK  plan-1  H12   0.020
 XMK  plan-2  C14   0.020
 XMK  plan-2  C15   0.020
 XMK  plan-2  C18   0.020
 XMK  plan-2  H14   0.020
 XMK  plan-2  H15   0.020
 XMK  plan-2  S17   0.020
 XMK  plan-3  C14   0.020
 XMK  plan-3  C16   0.020
 XMK  plan-3  C18   0.020
 XMK  plan-3  C24   0.020
 XMK  plan-3  C27   0.020
 XMK  plan-3  C29   0.020
 XMK  plan-3  C30   0.020
 XMK  plan-3  H16   0.020
 XMK  plan-3  H24   0.020
 XMK  plan-3  H27   0.020
 XMK  plan-3  H29   0.020
 XMK  plan-3  CL19  0.020

