# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:39:36 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 4-[(6-chloronaphthalen-2-yl)sulfonyl]-1-[(1-pyridin-4-ylpiperidin-4-yl)methyl]piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2cc(ccc2c1)[S](=O)(=O)N3CCN(CC4CCN(CC4)c5ccncc5)C(=O)C3
#
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
 XMI  XMI  4-[(6-chloronaphthalen-2-yl)sulfonyl]-1-[(1-pyridin-4-ylpiperidin-4-yl)methyl]piperazin-2-one  ligand  61  34  .  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_XMI
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
 XMI  S1    S   S      0   1.381   2.0303   0.0457  -1.9981
 XMI  O2    O   OS     0  -0.641   3.0309  -0.9895  -1.8125
 XMI  C3    C   C      0   0.549  -1.0628   0.6293   0.4800
 XMI  O4    O   O      0  -0.502  -1.8316   1.5360   0.7676
 XMI  C5    C   CH2    0  -0.405  -0.1717   0.8115  -0.7368
 XMI  N6    N   N     -1  -0.575   0.8881  -0.1800  -0.8183
 XMI  C7    C   CH2    0  -0.256  -0.1022  -1.6158   0.8164
 XMI  C8    C   CH2    0  -0.355   0.3708  -1.5263  -0.6136
 XMI  N9    N   NT     0  -0.469  -0.9963  -0.5226   1.1653
 XMI  O10   O   OS     0  -0.642   2.4114   1.4454  -1.9427
 XMI  C11   C   CH2    0  -0.286  -1.8140  -0.6779   2.3608
 XMI  C12   C   CR16   0  -0.077   1.8348   0.2685   9.3329
 XMI  N13   N   NT     0  -0.512  -0.3423   0.0811   6.3660
 XMI  C14   C   CR6    0   0.479   0.0941   0.1322   7.6617
 XMI  C15   C   CR16   0  -0.429   1.4533   0.2720   8.0048
 XMI  C16   C   CH2    0  -0.305  -1.6987   0.4942   6.0314
 XMI  C17   C   CR16   0  -0.417  -0.7816   0.0216   8.7610
 XMI  C18   C   CH2    0  -0.298   0.6034   0.2468   5.2747
 XMI  C19   C   CH1    0  -0.256  -1.2735   0.0370   3.5963
 XMI  C20   C   CH2    0  -0.427  -2.2084  -0.1925   4.7762
 XMI  N21   N   N      0  -0.434   1.0058   0.1499  10.3645
 XMI  C22   C   CR16   0  -0.077  -0.2814   0.0310  10.0465
 XMI  C23   C   CH2    0  -0.433   0.1211  -0.4212   3.9944
 XMI  C24   C   CR16   0  -0.291   0.6617   0.7969  -4.2232
 XMI  C25   C   CR6    0  -0.207   1.2091  -0.2535  -3.5366
 XMI  C26   C   CR66   0   0.127  -0.1634  -0.7727  -5.9014
 XMI  C27   C   CR16   0  -0.303   0.4231  -1.8283  -5.1642
 XMI  C28   C   CR16   0  -0.234   1.0997  -1.5813  -4.0048
 XMI  C29   C   CR66   0   0.139  -0.0397   0.5562  -5.4237
 XMI  C31   C   CR16   0  -0.308  -0.6187   1.6115  -6.1652
 XMI  C32   C   CR16   0  -0.266  -0.8633  -1.0146  -7.1038
 XMI  C33   C   CR16   0  -0.209  -1.2927   1.3628  -7.3265
 XMI  C34   C   CR6    0  -0.037  -1.4084   0.0354  -7.7866
 XMI  H51   H   HCH2   0   0.308   0.2532   1.8112  -0.6707
 XMI  H52   H   HCH2   0   0.279  -0.8304   0.7829  -1.6162
 XMI  H71   H   HCH2   0   0.268  -0.6378  -2.5571   0.9448
 XMI  H72   H   HCH2   0   0.257   0.7599  -1.6319   1.4878
 XMI  H81   H   HCH2   0   0.260  -0.4461  -1.7452  -1.3117
 XMI  H82   H   HCH2   0   0.296   1.1526  -2.2679  -0.7598
 XMI  H111  H   HCH2   0   0.261  -2.8252  -0.3247   2.1515
 XMI  H112  H   HCH2   0   0.247  -1.8890  -1.7488   2.5624
 XMI  H15   H   HCR6   0   0.271   2.2264   0.3981   7.2627
 XMI  H161  H   HCH2   0   0.228  -1.7283   1.5836   5.8888
 XMI  H162  H   HCH2   0   0.264  -2.3757   0.2659   6.8488
 XMI  H17   H   HCR6   0   0.271  -1.8485  -0.0895   8.6401
 XMI  H181  H   HCH2   0   0.226   0.7945   1.3131   5.0903
 XMI  H182  H   HCH2   0   0.259   1.5537  -0.2079   5.5427
 XMI  H19   H   HCH1   0   0.235  -1.2421   1.1125   3.3891
 XMI  H201  H   HCH2   0   0.245  -3.2091   0.1886   4.5581
 XMI  H202  H   HCH2   0   0.226  -2.3082  -1.2663   4.9663
 XMI  H22   H   HCR6   0   0.255  -0.9766  -0.0665  10.8740
 XMI  H231  H   HCH2   0   0.225   0.1279  -1.5076   4.1339
 XMI  H232  H   HCH2   0   0.246   0.8503  -0.1934   3.2136
 XMI  H24   H   HCR6   0   0.293   0.7637   1.8155  -3.8710
 XMI  H27   H   HCR6   0   0.275   0.3371  -2.8423  -5.5328
 XMI  H28   H   HCR6   0   0.290   1.5571  -2.3977  -3.4631
 XMI  H31   H   HCR6   0   0.277  -0.5244   2.6274  -5.8036
 XMI  H32   H   HCR6   0   0.286  -0.9610  -2.0282  -7.4701
 XMI  H33   H   HCR6   0   0.289  -1.7345   2.1721  -7.8912
 XMI  CL30  CL  CL     0  -0.111  -2.2690  -0.2514  -9.2588
 XMI  H12   H   HCR6   0   0.255   2.8884   0.3791   9.5692

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
 XMI  S1    O2    double    1.452  0.020  1.452
 XMI  S1    N6    single    1.658  0.020  1.658
 XMI  S1    O10   double    1.452  0.020  1.452
 XMI  S1    C25   single    1.769  0.020  1.769
 XMI  C3    O4    double    1.223  0.020  1.223
 XMI  C3    C5    single    1.519  0.020  1.519
 XMI  C3    N9    single    1.342  0.020  1.342
 XMI  C5    N6    single    1.454  0.020  1.454
 XMI  C5    H51   single    0.970  0.020  1.090
 XMI  C5    H52   single    0.970  0.020  1.090
 XMI  N6    C8    single    1.457  0.020  1.457
 XMI  C7    C8    single    1.509  0.020  1.509
 XMI  C7    N9    single    1.455  0.020  1.455
 XMI  C7    H71   single    0.970  0.020  1.090
 XMI  C7    H72   single    0.970  0.020  1.090
 XMI  C8    H81   single    0.970  0.020  1.090
 XMI  C8    H82   single    0.970  0.020  1.090
 XMI  N9    C11   single    1.457  0.020  1.457
 XMI  C11   C19   single    1.526  0.020  1.526
 XMI  C11   H111  single    0.970  0.020  1.090
 XMI  C11   H112  single    0.970  0.020  1.090
 XMI  C12   C15   aromatic  1.382  0.020  1.382
 XMI  C12   N21   aromatic  1.329  0.020  1.329
 XMI  C12   H12   single    0.930  0.020  1.080
 XMI  N13   C14   single    1.368  0.020  1.368
 XMI  N13   C16   single    1.457  0.020  1.457
 XMI  N13   C18   single    1.454  0.020  1.454
 XMI  C14   C15   aromatic  1.409  0.020  1.409
 XMI  C14   C17   aromatic  1.410  0.020  1.410
 XMI  C15   H15   single    0.930  0.020  1.080
 XMI  C16   C20   single    1.519  0.020  1.519
 XMI  C16   H161  single    0.970  0.020  1.090
 XMI  C16   H162  single    0.970  0.020  1.090
 XMI  C17   C22   aromatic  1.379  0.020  1.379
 XMI  C17   H17   single    0.930  0.020  1.080
 XMI  C18   C23   single    1.522  0.020  1.522
 XMI  C18   H181  single    0.970  0.020  1.090
 XMI  C18   H182  single    0.970  0.020  1.090
 XMI  C19   C20   single    1.523  0.020  1.523
 XMI  C19   C23   single    1.521  0.020  1.521
 XMI  C19   H19   single    0.970  0.020  1.090
 XMI  C20   H201  single    0.970  0.020  1.090
 XMI  C20   H202  single    0.970  0.020  1.090
 XMI  N21   C22   aromatic  1.331  0.020  1.331
 XMI  C22   H22   single    0.930  0.020  1.080
 XMI  C23   H231  single    0.970  0.020  1.090
 XMI  C23   H232  single    0.970  0.020  1.090
 XMI  C24   C25   aromatic  1.369  0.020  1.369
 XMI  C24   C29   aromatic  1.411  0.020  1.411
 XMI  C24   H24   single    0.930  0.020  1.080
 XMI  C25   C28   aromatic  1.412  0.020  1.412
 XMI  C26   C27   aromatic  1.415  0.020  1.415
 XMI  C26   C29   aromatic  1.418  0.020  1.418
 XMI  C26   C32   aromatic  1.412  0.020  1.412
 XMI  C27   C28   aromatic  1.365  0.020  1.365
 XMI  C27   H27   single    0.930  0.020  1.080
 XMI  C28   H28   single    0.930  0.020  1.080
 XMI  C29   C31   aromatic  1.414  0.020  1.414
 XMI  CL30  C34   single    1.729  0.020  1.729
 XMI  C31   C33   aromatic  1.366  0.020  1.366
 XMI  C31   H31   single    0.930  0.020  1.080
 XMI  C32   C34   aromatic  1.366  0.020  1.366
 XMI  C32   H32   single    0.930  0.020  1.080
 XMI  C33   C34   aromatic  1.410  0.020  1.410
 XMI  C33   H33   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
 XMI  C25   S1   O10   108.54  3.000
 XMI  C25   S1   N6    106.02  3.000
 XMI  O10   S1   N6    106.56  3.000
 XMI  C25   S1   O2    108.09  3.000
 XMI  O10   S1   O2    120.12  3.000
 XMI  N6    S1   O2    106.67  3.000
 XMI  N9    C3   C5    118.87  3.000
 XMI  N9    C3   O4    123.19  3.000
 XMI  C5    C3   O4    117.91  3.000
 XMI  H52   C5   H51   107.84  3.000
 XMI  H52   C5   N6    111.98  3.000
 XMI  H51   C5   N6    110.20  3.000
 XMI  H52   C5   C3    106.63  3.000
 XMI  H51   C5   C3    106.89  3.000
 XMI  N6    C5   C3    113.00  3.000
 XMI  C8    N6   C5    111.33  3.000
 XMI  C8    N6   S1    118.07  3.000
 XMI  C5    N6   S1    116.71  3.000
 XMI  H72   C7   H71   107.60  3.000
 XMI  H72   C7   N9    110.40  3.000
 XMI  H71   C7   N9    108.57  3.000
 XMI  H72   C7   C8    109.63  3.000
 XMI  H71   C7   C8    108.47  3.000
 XMI  N9    C7   C8    112.04  3.000
 XMI  H82   C8   H81   108.29  3.000
 XMI  H82   C8   C7    108.20  3.000
 XMI  H81   C8   C7    110.97  3.000
 XMI  H82   C8   N6    110.87  3.000
 XMI  H81   C8   N6    111.07  3.000
 XMI  C7    C8   N6    107.42  3.000
 XMI  C11   N9   C7    117.49  3.000
 XMI  C11   N9   C3    118.87  3.000
 XMI  C7    N9   C3    123.58  3.000
 XMI  H112  C11  H111  106.80  3.000
 XMI  H112  C11  C19   109.52  3.000
 XMI  H111  C11  C19   109.37  3.000
 XMI  H112  C11  N9    107.13  3.000
 XMI  H111  C11  N9    109.16  3.000
 XMI  C19   C11  N9    114.56  3.000
 XMI  H12   C12  N21   116.48  3.000
 XMI  H12   C12  C15   118.49  3.000
 XMI  N21   C12  C15   125.03  3.000
 XMI  C18   N13  C16   113.64  3.000
 XMI  C18   N13  C14   119.95  3.000
 XMI  C16   N13  C14   120.26  3.000
 XMI  C17   C14  C15   114.65  3.000
 XMI  C17   C14  N13   122.50  3.000
 XMI  C15   C14  N13   122.83  3.000
 XMI  H15   C15  C14   122.37  3.000
 XMI  H15   C15  C12   117.61  3.000
 XMI  C14   C15  C12   120.02  3.000
 XMI  H162  C16  H161  106.81  3.000
 XMI  H162  C16  C20   108.53  3.000
 XMI  H161  C16  C20   109.39  3.000
 XMI  H162  C16  N13   110.37  3.000
 XMI  H161  C16  N13   109.63  3.000
 XMI  C20   C16  N13   111.97  3.000
 XMI  H17   C17  C22   117.62  3.000
 XMI  H17   C17  C14   122.32  3.000
 XMI  C22   C17  C14   120.06  3.000
 XMI  H182  C18  H181  107.18  3.000
 XMI  H182  C18  C23   107.50  3.000
 XMI  H181  C18  C23   109.86  3.000
 XMI  H182  C18  N13   109.63  3.000
 XMI  H181  C18  N13   110.47  3.000
 XMI  C23   C18  N13   112.04  3.000
 XMI  H19   C19  C23   108.59  3.000
 XMI  H19   C19  C20   108.19  3.000
 XMI  C23   C19  C20   108.34  3.000
 XMI  H19   C19  C11   108.47  3.000
 XMI  C23   C19  C11   113.29  3.000
 XMI  C20   C19  C11   109.83  3.000
 XMI  H202  C20  H201  107.04  3.000
 XMI  H202  C20  C19   109.77  3.000
 XMI  H201  C20  C19   110.79  3.000
 XMI  H202  C20  C16   109.30  3.000
 XMI  H201  C20  C16   108.34  3.000
 XMI  C19   C20  C16   111.48  3.000
 XMI  C22   N21  C12   115.21  3.000
 XMI  H22   C22  N21   116.45  3.000
 XMI  H22   C22  C17   118.53  3.000
 XMI  N21   C22  C17   125.02  3.000
 XMI  H232  C23  H231  107.08  3.000
 XMI  H232  C23  C19   111.23  3.000
 XMI  H231  C23  C19   109.74  3.000
 XMI  H232  C23  C18   107.35  3.000
 XMI  H231  C23  C18   109.03  3.000
 XMI  C19   C23  C18   112.23  3.000
 XMI  H24   C24  C29   118.96  3.000
 XMI  H24   C24  C25   121.40  3.000
 XMI  C29   C24  C25   119.64  3.000
 XMI  C28   C25  C24   121.62  3.000
 XMI  C28   C25  S1    118.89  3.000
 XMI  C24   C25  S1    119.46  3.000
 XMI  C32   C26  C29   119.39  3.000
 XMI  C32   C26  C27   121.42  3.000
 XMI  C29   C26  C27   119.19  3.000
 XMI  H27   C27  C28   119.88  3.000
 XMI  H27   C27  C26   119.25  3.000
 XMI  C28   C27  C26   120.87  3.000
 XMI  H28   C28  C27   119.91  3.000
 XMI  H28   C28  C25   120.74  3.000
 XMI  C27   C28  C25   119.35  3.000
 XMI  C31   C29  C26   119.17  3.000
 XMI  C31   C29  C24   121.50  3.000
 XMI  C26   C29  C24   119.34  3.000
 XMI  H31   C31  C33   119.87  3.000
 XMI  H31   C31  C29   119.32  3.000
 XMI  C33   C31  C29   120.81  3.000
 XMI  H32   C32  C34   120.98  3.000
 XMI  H32   C32  C26   119.56  3.000
 XMI  C34   C32  C26   119.46  3.000
 XMI  H33   C33  C34   120.05  3.000
 XMI  H33   C33  C31   120.63  3.000
 XMI  C34   C33  C31   119.31  3.000
 XMI  C33   C34  C32   121.87  3.000
 XMI  C33   C34  CL30  118.35  3.000
 XMI  C32   C34  CL30  119.78  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
 XMI  CONST_01  C17   C14  C15  C12      0.00   0.0  0
 XMI  CONST_02  C17   C22  N21  C12      0.00   0.0  0
 XMI  CONST_03  N21   C12  C15  C14      0.00   0.0  0
 XMI  CONST_04  N21   C22  C17  C14      0.00   0.0  0
 XMI  CONST_05  C22   N21  C12  C15      0.00   0.0  0
 XMI  CONST_06  C22   C17  C14  C15      0.00   0.0  0
 XMI  CONST_07  C27   C28  C25  C24      0.00   0.0  0
 XMI  CONST_08  C27   C26  C29  C24      0.00   0.0  0
 XMI  CONST_09  C32   C26  C29  C24    180.00   0.0  0
 XMI  CONST_10  C33   C31  C29  C24    180.00   0.0  0
 XMI  CONST_11  C26   C29  C24  C25      0.00   0.0  0
 XMI  CONST_12  C31   C29  C24  C25    180.00   0.0  0
 XMI  CONST_13  C26   C27  C28  C25      0.00   0.0  0
 XMI  CONST_14  C33   C31  C29  C26      0.00   0.0  0
 XMI  CONST_15  C33   C34  C32  C26      0.00   0.0  0
 XMI  CONST_16  C31   C29  C26  C27    180.00   0.0  0
 XMI  CONST_17  C34   C32  C26  C27    180.00   0.0  0
 XMI  CONST_18  C29   C24  C25  C28      0.00   0.0  0
 XMI  CONST_19  C29   C26  C27  C28      0.00   0.0  0
 XMI  CONST_20  C32   C26  C27  C28    180.00   0.0  0
 XMI  CONST_21  C34   C32  C26  C29      0.00   0.0  0
 XMI  CONST_22  C34   C33  C31  C29      0.00   0.0  0
 XMI  CONST_23  C32   C26  C29  C31      0.00   0.0  0
 XMI  CONST_24  C32   C34  C33  C31      0.00   0.0  0
 XMI  CONST_25  N13   C14  C15  C12    180.00   0.0  0
 XMI  CONST_26  C22   C17  C14  N13    180.00   0.0  0
 XMI  CONST_27  C7    N9   C3   C5       0.00   0.0  0
 XMI  CONST_28  C29   C24  C25  S1     180.00   0.0  0
 XMI  CONST_29  C27   C28  C25  S1     180.00   0.0  0
 XMI  CONST_30  CL30  C34  C32  C26    180.00   0.0  0
 XMI  CONST_31  C31   C33  C34  CL30   180.00   0.0  0
 XMI  CONST_32  C7    N9   C3   O4     180.00   0.0  0
 XMI  CONST_33  C11   N9   C3   C5     180.00   0.0  0
 XMI  CONST_34  H22   C22  N21  C12    180.00   0.0  0
 XMI  CONST_35  H15   C15  C14  N13      0.00   0.0  0
 XMI  CONST_36  H17   C17  C14  N13      0.00   0.0  0
 XMI  CONST_37  H12   C12  C15  C14    180.00   0.0  0
 XMI  CONST_38  H28   C28  C25  C24    180.00   0.0  0
 XMI  CONST_39  H31   C31  C29  C24      0.00   0.0  0
 XMI  CONST_40  H27   C27  C28  C25    180.00   0.0  0
 XMI  CONST_41  H24   C24  C29  C26    180.00   0.0  0
 XMI  CONST_42  H32   C32  C26  C27      0.00   0.0  0
 XMI  CONST_43  H33   C33  C31  C29    180.00   0.0  0
 XMI  CONST_44  C11   N9   C3   O4       0.00   0.0  0
 XMI  Var_01    C8    C7   N9   C3     -19.72  30.0  1
 XMI  Var_02    N9    C3   C5   N6     -14.12  30.0  1
 XMI  Var_03    N9    C7   C8   N6      51.13  30.0  1
 XMI  Var_04    C19   C20  C16  N13    -55.58  30.0  1
 XMI  Var_05    C19   C23  C18  N13     53.72  30.0  1
 XMI  Var_06    C20   C16  N13  C14   -153.69  30.0  1
 XMI  Var_07    C23   C18  N13  C14    154.76  30.0  1
 XMI  Var_08    C16   N13  C14  C15   -154.09  30.0  2
 XMI  Var_09    C19   C11  N9   C3     -77.54  30.0  3
 XMI  Var_10    C24   C25  S1   N6      93.43  30.0  2

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
 XMI  chir_01  N6   S1   C5   C8   negativ
 XMI  chir_02  C19  C11  C20  C23  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
 XMI  plan-1  C12   0.020
 XMI  plan-1  N13   0.020
 XMI  plan-1  C14   0.020
 XMI  plan-1  C15   0.020
 XMI  plan-1  C17   0.020
 XMI  plan-1  N21   0.020
 XMI  plan-1  C22   0.020
 XMI  plan-1  H15   0.020
 XMI  plan-1  H17   0.020
 XMI  plan-1  H22   0.020
 XMI  plan-1  H12   0.020
 XMI  plan-2  C3    0.020
 XMI  plan-2  O4    0.020
 XMI  plan-2  C5    0.020
 XMI  plan-2  C7    0.020
 XMI  plan-2  N9    0.020
 XMI  plan-2  C11   0.020
 XMI  plan-3  S1    0.020
 XMI  plan-3  C24   0.020
 XMI  plan-3  C25   0.020
 XMI  plan-3  C26   0.020
 XMI  plan-3  C27   0.020
 XMI  plan-3  C28   0.020
 XMI  plan-3  C29   0.020
 XMI  plan-3  C31   0.020
 XMI  plan-3  C32   0.020
 XMI  plan-3  C33   0.020
 XMI  plan-3  C34   0.020
 XMI  plan-3  H24   0.020
 XMI  plan-3  H27   0.020
 XMI  plan-3  H28   0.020
 XMI  plan-3  H31   0.020
 XMI  plan-3  H32   0.020
 XMI  plan-3  H33   0.020
 XMI  plan-3  CL30  0.020

