# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 07:33:16 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-chloro-6-(4-{4-[4-(methylsulfonyl)benzyl]piperazin-1-yl}-1H-pyrazol-5-yl)benzene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc(CN2CCN(CC2)c3cn[nH]c3c4cc(Cl)c(O)cc4O)cc1
#
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
 2D9  2D9  4-chloro-6-(4-{4-[4-(methylsulfonyl)benzyl]piperazin-1-yl}-1H-pyrazol-5-yl)benzene-1,3-diol  ligand  54  31  .  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_2D9
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
 2D9  C31   C   CH3   0  -0.789   8.5524   1.2220  -0.5622
 2D9  S28   S   S     0   1.215   7.7437  -0.1051   0.3030
 2D9  O29   O   OS    0  -0.671   8.2877  -0.1669   1.6586
 2D9  O30   O   OS    0  -0.671   7.8089  -1.3012  -0.5346
 2D9  C25   C   CR6   0  -0.220   6.0538   0.4179   0.4033
 2D9  C26   C   CR16  0  -0.215   5.1796   0.0992  -0.6284
 2D9  C27   C   CR16  0  -0.267   3.8622   0.5154  -0.5486
 2D9  C24   C   CR16  0  -0.215   5.6247   1.1348   1.5106
 2D9  C23   C   CR16  0  -0.298   4.3002   1.5391   1.5770
 2D9  C19   C   CR6   0   0.092   3.4090   1.2413   0.5513
 2D9  C18   C   CH2   0  -0.314   1.9849   1.7307   0.6083
 2D9  N15   N   NT    0  -0.421   1.0572   0.7820   0.0384
 2D9  C16   C   CH2   0  -0.297  -0.2259   1.3699  -0.2848
 2D9  C17   C   CH2   0  -0.306  -1.0893   0.3632  -1.0183
 2D9  C14   C   CH2   0  -0.299   0.8811  -0.3923   0.8692
 2D9  C13   C   CH2   0  -0.302   0.0282  -1.4222   0.1568
 2D9  N12   N   NT    0  -0.612  -1.2664  -0.8427  -0.1981
 2D9  C3    C   CR5   0   0.025  -2.1735  -1.7690  -0.7576
 2D9  C2    C   CR15  0  -0.093  -1.9211  -2.9325  -1.5058
 2D9  N1    N   N     0  -0.258  -3.0481  -3.5203  -1.8589
 2D9  N5    N   NR15  0  -0.510  -4.0089  -2.7535  -1.3650
 2D9  C4    C   CR5   0   0.427  -3.5554  -1.6827  -0.6777
 2D9  C6    C   CR6   0  -0.099  -4.4497  -0.7141  -0.0501
 2D9  C7    C   CR16  0  -0.258  -5.7101  -0.4819  -0.6010
 2D9  C8    C   CR6   0  -0.184  -6.6189   0.3573   0.0065
 2D9  CL20  CL  CL    0  -0.119  -8.1785   0.6232  -0.7075
 2D9  C9    C   CR6   0   0.432  -6.2949   1.0128   1.1976
 2D9  O21   O   OH1   0  -0.609  -7.1341   1.8338   1.8382
 2D9  C10   C   CR16  0  -0.442  -5.0335   0.8124   1.7384
 2D9  C11   C   CR6   0   0.324  -4.1070  -0.0366   1.1385
 2D9  O22   O   OH1   0  -0.654  -2.9341  -0.1929   1.7531
 2D9  H311  H   HCH3  0   0.295   8.0809   1.3638  -1.5319
 2D9  H312  H   HCH3  0   0.295   8.4867   2.1332   0.0277
 2D9  H313  H   HCH3  0   0.309   9.5959   0.9364  -0.6926
 2D9  H26   H   HCR6  0   0.281   5.5147  -0.4686  -1.4863
 2D9  H27   H   HCR6  0   0.263   3.1689   0.2641  -1.3402
 2D9  H24   H   HCR6  0   0.282   6.3029   1.3701   2.3198
 2D9  H23   H   HCR6  0   0.265   3.9571   2.0868   2.4464
 2D9  H181  H   HCH2  0   0.224   1.7308   2.0036   1.6452
 2D9  H182  H   HCH2  0   0.267   1.9236   2.6560   0.0268
 2D9  H161  H   HCH2  0   0.203  -0.7597   1.7248   0.6129
 2D9  H162  H   HCH2  0   0.254  -0.0748   2.2353  -0.9331
 2D9  H171  H   HCH2  0   0.261  -2.0670   0.8001  -1.2251
 2D9  H172  H   HCH2  0   0.239  -0.6282   0.1050  -1.9796
 2D9  H141  H   HCH2  0   0.255   1.8528  -0.8421   1.0822
 2D9  H142  H   HCH2  0   0.210   0.4235  -0.1379   1.8407
 2D9  H131  H   HCH2  0   0.262  -0.1368  -2.2779   0.8120
 2D9  H132  H   HCH2  0   0.234   0.5596  -1.7736  -0.7368
 2D9  H2    H   HCR5  0   0.272  -0.9688  -3.3573  -1.7849
 2D9  H5    H   HNR5  0   0.423  -4.9701  -3.0376  -1.4721
 2D9  H7    H   HCR6  0   0.283  -5.9878  -0.9597  -1.5319
 2D9  H21   H   HOH1  0   0.471  -7.9818   1.8930   1.3789
 2D9  H10   H   HCR6  0   0.280  -4.7656   1.3217   2.6560
 2D9  H22   H   HOH1  0   0.483  -2.2077  -0.4454   1.1044

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
 2D9  C31  S28   single    1.779  0.020  1.779
 2D9  C31  H311  single    0.970  0.020  1.090
 2D9  C31  H312  single    0.970  0.020  1.090
 2D9  C31  H313  single    0.970  0.020  1.090
 2D9  S28  O29   double    1.462  0.020  1.462
 2D9  S28  O30   double    1.462  0.020  1.462
 2D9  S28  C25   single    1.772  0.020  1.772
 2D9  C25  C26   aromatic  1.389  0.020  1.389
 2D9  C25  C24   aromatic  1.387  0.020  1.387
 2D9  C26  C27   aromatic  1.384  0.020  1.384
 2D9  C26  H26   single    0.930  0.020  1.080
 2D9  C27  C19   aromatic  1.394  0.020  1.394
 2D9  C27  H27   single    0.930  0.020  1.080
 2D9  C24  C23   aromatic  1.386  0.020  1.386
 2D9  C24  H24   single    0.930  0.020  1.080
 2D9  C23  C19   aromatic  1.391  0.020  1.391
 2D9  C23  H23   single    0.930  0.020  1.080
 2D9  C19  C18   single    1.507  0.020  1.507
 2D9  C18  N15   single    1.444  0.020  1.444
 2D9  C18  H181  single    0.970  0.020  1.090
 2D9  C18  H182  single    0.970  0.020  1.090
 2D9  N15  C16   single    1.448  0.020  1.448
 2D9  N15  C14   single    1.449  0.020  1.449
 2D9  C16  C17   single    1.516  0.020  1.516
 2D9  C16  H161  single    0.970  0.020  1.090
 2D9  C16  H162  single    0.970  0.020  1.090
 2D9  C17  N12   single    1.469  0.020  1.469
 2D9  C17  H171  single    0.970  0.020  1.090
 2D9  C17  H172  single    0.970  0.020  1.090
 2D9  C14  C13   single    1.515  0.020  1.515
 2D9  C14  H141  single    0.970  0.020  1.090
 2D9  C14  H142  single    0.970  0.020  1.090
 2D9  C13  N12   single    1.462  0.020  1.462
 2D9  C13  H131  single    0.970  0.020  1.090
 2D9  C13  H132  single    0.970  0.020  1.090
 2D9  N12  C3    single    1.412  0.020  1.412
 2D9  C3   C2    aromatic  1.406  0.020  1.406
 2D9  C3   C4    aromatic  1.387  0.020  1.387
 2D9  C2   N1    aromatic  1.319  0.020  1.319
 2D9  C2   H2    single    0.930  0.020  1.080
 2D9  N1   N5    aromatic  1.325  0.020  1.325
 2D9  N5   C4    aromatic  1.351  0.020  1.351
 2D9  N5   H5    single    0.860  0.020  1.020
 2D9  C4   C6    single    1.460  0.020  1.460
 2D9  C6   C7    aromatic  1.395  0.020  1.395
 2D9  C6   C11   aromatic  1.410  0.020  1.410
 2D9  C7   C8    aromatic  1.378  0.020  1.378
 2D9  C7   H7    single    0.930  0.020  1.080
 2D9  C8   CL20  single    1.736  0.020  1.736
 2D9  C8   C9    aromatic  1.398  0.020  1.398
 2D9  C9   O21   single    1.337  0.020  1.337
 2D9  C9   C10   aromatic  1.387  0.020  1.387
 2D9  O21  H21   single    0.850  0.020  0.980
 2D9  C10  C11   aromatic  1.392  0.020  1.392
 2D9  C10  H10   single    0.930  0.020  1.080
 2D9  C11  O22   single    1.333  0.020  1.333
 2D9  O22  H22   single    0.850  0.020  0.980

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
 2D9  H313  C31  H312  110.02  3.000
 2D9  H313  C31  H311  110.03  3.000
 2D9  H312  C31  H311  110.38  3.000
 2D9  H313  C31  S28   107.34  3.000
 2D9  H312  C31  S28   109.51  3.000
 2D9  H311  C31  S28   109.50  3.000
 2D9  C25   S28  O30   108.45  3.000
 2D9  C25   S28  O29   108.36  3.000
 2D9  O30   S28  O29   118.70  3.000
 2D9  C25   S28  C31   103.94  3.000
 2D9  O30   S28  C31   108.15  3.000
 2D9  O29   S28  C31   108.26  3.000
 2D9  C24   C25  C26   121.11  3.000
 2D9  C24   C25  S28   119.52  3.000
 2D9  C26   C25  S28   119.37  3.000
 2D9  H26   C26  C27   119.89  3.000
 2D9  H26   C26  C25   120.95  3.000
 2D9  C27   C26  C25   119.16  3.000
 2D9  H27   C27  C19   119.34  3.000
 2D9  H27   C27  C26   119.87  3.000
 2D9  C19   C27  C26   120.78  3.000
 2D9  H24   C24  C23   119.98  3.000
 2D9  H24   C24  C25   121.04  3.000
 2D9  C23   C24  C25   118.98  3.000
 2D9  H23   C23  C19   119.81  3.000
 2D9  H23   C23  C24   119.24  3.000
 2D9  C19   C23  C24   120.95  3.000
 2D9  C18   C19  C23   120.54  3.000
 2D9  C18   C19  C27   120.42  3.000
 2D9  C23   C19  C27   119.02  3.000
 2D9  H182  C18  H181  106.12  3.000
 2D9  H182  C18  N15   108.05  3.000
 2D9  H181  C18  N15   112.70  3.000
 2D9  H182  C18  C19   107.90  3.000
 2D9  H181  C18  C19   109.51  3.000
 2D9  N15   C18  C19   112.26  3.000
 2D9  C14   N15  C16   110.44  3.000
 2D9  C14   N15  C18   112.59  3.000
 2D9  C16   N15  C18   112.99  3.000
 2D9  H162  C16  H161  107.17  3.000
 2D9  H162  C16  C17   108.54  3.000
 2D9  H161  C16  C17   109.39  3.000
 2D9  H162  C16  N15   109.37  3.000
 2D9  H161  C16  N15   112.20  3.000
 2D9  C17   C16  N15   110.07  3.000
 2D9  H172  C17  H171  107.76  3.000
 2D9  H172  C17  N12   110.29  3.000
 2D9  H171  C17  N12   109.06  3.000
 2D9  H172  C17  C16   109.94  3.000
 2D9  H171  C17  C16   109.66  3.000
 2D9  N12   C17  C16   110.10  3.000
 2D9  H142  C14  H141  106.99  3.000
 2D9  H142  C14  C13   109.71  3.000
 2D9  H141  C14  C13   108.22  3.000
 2D9  H142  C14  N15   111.61  3.000
 2D9  H141  C14  N15   109.72  3.000
 2D9  C13   C14  N15   110.47  3.000
 2D9  H132  C13  H131  108.14  3.000
 2D9  H132  C13  N12   110.98  3.000
 2D9  H131  C13  N12   108.84  3.000
 2D9  H132  C13  C14   109.15  3.000
 2D9  H131  C13  C14   109.64  3.000
 2D9  N12   C13  C14   110.07  3.000
 2D9  C3    N12  C13   113.89  3.000
 2D9  C3    N12  C17   113.24  3.000
 2D9  C13   N12  C17   110.74  3.000
 2D9  C4    C3   C2    105.13  3.000
 2D9  C4    C3   N12   125.20  3.000
 2D9  C2    C3   N12   129.67  3.000
 2D9  H2    C2   N1    120.60  3.000
 2D9  H2    C2   C3    128.43  3.000
 2D9  N1    C2   C3    110.96  3.000
 2D9  N5    N1   C2    105.18  3.000
 2D9  H5    N5   C4    126.70  3.000
 2D9  H5    N5   N1    119.26  3.000
 2D9  C4    N5   N1    113.89  3.000
 2D9  C6    C4   N5    122.61  3.000
 2D9  C6    C4   C3    132.56  3.000
 2D9  N5    C4   C3    104.82  3.000
 2D9  C11   C6   C7    118.19  3.000
 2D9  C11   C6   C4    122.15  3.000
 2D9  C7    C6   C4    119.61  3.000
 2D9  H7    C7   C8    118.60  3.000
 2D9  H7    C7   C6    119.86  3.000
 2D9  C8    C7   C6    121.54  3.000
 2D9  C9    C8   CL20  119.14  3.000
 2D9  C9    C8   C7    120.56  3.000
 2D9  CL20  C8   C7    120.30  3.000
 2D9  C10   C9   O21   118.20  3.000
 2D9  C10   C9   C8    118.38  3.000
 2D9  O21   C9   C8    123.41  3.000
 2D9  H21   O21  C9    111.14  3.000
 2D9  H10   C10  C11   119.15  3.000
 2D9  H10   C10  C9    119.16  3.000
 2D9  C11   C10  C9    121.69  3.000
 2D9  O22   C11  C10   117.28  3.000
 2D9  O22   C11  C6    123.08  3.000
 2D9  C10   C11  C6    119.62  3.000
 2D9  H22   O22  C11   111.55  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
 2D9  CONST_01  C19   C27  C26  C25      0.00   0.0  0
 2D9  CONST_02  C19   C23  C24  C25      0.00   0.0  0
 2D9  CONST_03  C23   C24  C25  C26      0.00   0.0  0
 2D9  CONST_04  C23   C19  C27  C26      0.00   0.0  0
 2D9  CONST_05  C24   C25  C26  C27      0.00   0.0  0
 2D9  CONST_06  C24   C23  C19  C27      0.00   0.0  0
 2D9  CONST_07  N5    N1   C2   C3       0.00   0.0  0
 2D9  CONST_08  N1    N5   C4   C3       0.00   0.0  0
 2D9  CONST_11  N5    C4   C3   C2       0.00   0.0  0
 2D9  CONST_12  C6    C4   C3   C2     180.00   0.0  0
 2D9  CONST_13  C4    N5   N1   C2       0.00   0.0  0
 2D9  CONST_14  C4    C3   C2   N1       0.00   0.0  0
 2D9  CONST_15  C6    C4   N5   N1     180.00   0.0  0
 2D9  CONST_18  C8    C7   C6   C4     180.00   0.0  0
 2D9  CONST_19  C10   C11  C6   C4     180.00   0.0  0
 2D9  CONST_20  C9    C8   C7   C6       0.00   0.0  0
 2D9  CONST_21  C9    C10  C11  C6       0.00   0.0  0
 2D9  CONST_22  C10   C11  C6   C7       0.00   0.0  0
 2D9  CONST_23  C10   C9   C8   C7       0.00   0.0  0
 2D9  CONST_24  C11   C6   C7   C8       0.00   0.0  0
 2D9  CONST_25  C11   C10  C9   C8       0.00   0.0  0
 2D9  CONST_26  N1    C2   C3   N12    180.00   0.0  0
 2D9  CONST_27  N5    C4   C3   N12    180.00   0.0  0
 2D9  CONST_28  C6    C4   C3   N12      0.00   0.0  0
 2D9  CONST_29  C27   C26  C25  S28    180.00   0.0  0
 2D9  CONST_30  C23   C24  C25  S28    180.00   0.0  0
 2D9  CONST_31  C18   C19  C27  C26    180.00   0.0  0
 2D9  CONST_32  C18   C19  C23  C24    180.00   0.0  0
 2D9  CONST_33  O22   C11  C6   C4       0.00   0.0  0
 2D9  CONST_34  CL20  C8   C7   C6     180.00   0.0  0
 2D9  CONST_35  O22   C11  C6   C7     180.00   0.0  0
 2D9  CONST_36  O21   C9   C8   C7     180.00   0.0  0
 2D9  CONST_37  C10   C9   C8   CL20   180.00   0.0  0
 2D9  CONST_38  O22   C11  C10  C9     180.00   0.0  0
 2D9  CONST_39  C11   C10  C9   O21    180.00   0.0  0
 2D9  CONST_40  H27   C27  C26  C25    180.00   0.0  0
 2D9  CONST_41  H23   C23  C24  C25    180.00   0.0  0
 2D9  CONST_42  H24   C24  C25  C26    180.00   0.0  0
 2D9  CONST_43  H26   C26  C25  C24    180.00   0.0  0
 2D9  CONST_44  H2    C2   C3   N12      0.00   0.0  0
 2D9  CONST_45  H5    N5   C4   C3     180.00   0.0  0
 2D9  CONST_46  H7    C7   C6   C4       0.00   0.0  0
 2D9  CONST_47  H10   C10  C11  C6     180.00   0.0  0
 2D9  Var_01    N12   C17  C16  N15     57.88  30.0  1
 2D9  Var_02    N12   C13  C14  N15    -57.51  30.0  1
 2D9  Var_03    C13   C14  N15  C16     59.17  30.0  1
 2D9  Var_04    C13   N12  C17  C16    -56.85  30.0  1
 2D9  Var_05    C14   N15  C16  C17    -59.26  30.0  1
 2D9  Var_06    C14   C13  N12  C17     56.51  30.0  1
 2D9  Var_07    C2    C3   N12  C17     98.83  30.0  2
 2D9  Var_08    N15   C18  C19  C27     37.09  30.0  2
 2D9  Var_09    C16   N15  C18  C19   -162.59  30.0  3
 2D9  Var_10    C26   C25  S28  C31     88.50  30.0  2
 2D9  Var_11    H311  C31  S28  C25    -58.21  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
 2D9  plan-1  N12   0.020
 2D9  plan-1  C3    0.020
 2D9  plan-1  C2    0.020
 2D9  plan-1  N1    0.020
 2D9  plan-1  N5    0.020
 2D9  plan-1  C4    0.020
 2D9  plan-1  C6    0.020
 2D9  plan-1  H2    0.020
 2D9  plan-1  H5    0.020
 2D9  plan-2  S28   0.020
 2D9  plan-2  C25   0.020
 2D9  plan-2  C26   0.020
 2D9  plan-2  C27   0.020
 2D9  plan-2  C24   0.020
 2D9  plan-2  C23   0.020
 2D9  plan-2  C19   0.020
 2D9  plan-2  C18   0.020
 2D9  plan-2  H26   0.020
 2D9  plan-2  H27   0.020
 2D9  plan-2  H24   0.020
 2D9  plan-2  H23   0.020
 2D9  plan-3  C4    0.020
 2D9  plan-3  C6    0.020
 2D9  plan-3  C7    0.020
 2D9  plan-3  C8    0.020
 2D9  plan-3  CL20  0.020
 2D9  plan-3  C9    0.020
 2D9  plan-3  O21   0.020
 2D9  plan-3  C10   0.020
 2D9  plan-3  C11   0.020
 2D9  plan-3  O22   0.020
 2D9  plan-3  H7    0.020
 2D9  plan-3  H10   0.020

