# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:01:42 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [(5~{S})-5-[3,5-bis(fluoranyl)phenyl]pyrazolidin-1-yl]-[1-(5-methyl-1,3,4-oxadiazol-2-yl)piperidin-4-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(nn1)N2CCC(CC2)C(=O)N3NCC[C@H]3c4cc(F)cc(F)c4
#
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
 JSW  JSW  '[(5~{S})-5-[3,5-bis(fluoranyl)phenyl]pyrazolidin-1-yl]-[1-(5-methyl-1,3,4-oxadiazol-2-yl)piperidin-4-yl]methanone'  ligand  48  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JSW
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
 JSW  C10  C  CH1   0  -0.440   0.0252   2.5103  -0.3477
 JSW  C13  C  C     0   0.581   1.1024   1.5391  -0.7981
 JSW  C17  C  CH2   0  -0.284   4.0832   2.5621   0.8076
 JSW  C20  C  CR6   0   0.197   2.9143  -0.7799  -0.1204
 JSW  C21  C  CR16  0  -0.496   3.2445  -1.7965  -1.0044
 JSW  C22  C  CR6   0   0.560   2.8733  -3.0922  -0.6971
 JSW  C24  C  CR16  0  -0.571   2.1797  -3.4205   0.4503
 JSW  C02  C  CR5   0   0.448  -5.5052  -0.4565  -0.0753
 JSW  C05  C  CR5   0   0.720  -3.5604   0.3118   0.2738
 JSW  C08  C  CH2   0  -0.306  -1.3636   0.8844   1.0061
 JSW  C09  C  CH2   0  -0.450  -0.5086   2.1376   1.0417
 JSW  C11  C  CH2   0  -0.432  -1.1411   2.5879  -1.3298
 JSW  C12  C  CH2   0  -0.306  -2.0555   1.3708  -1.3172
 JSW  C18  C  CH2   0  -0.497   4.4616   1.1173   0.5396
 JSW  C19  C  CR15  0  -0.122   3.3468   0.6363  -0.4045
 JSW  C25  C  CR6   0   0.557   1.8690  -2.3782   1.3054
 JSW  C27  C  CR16  0  -0.473   2.2218  -1.0699   1.0520
 JSW  F23  F  F     0  -0.309   3.1916  -4.0733  -1.5518
 JSW  F26  F  F     0  -0.309   1.1980  -2.6610   2.4301
 JSW  N03  N  N     0  -0.314  -5.1504  -0.8619   1.0828
 JSW  N04  N  N     0  -0.401  -3.8803  -0.3808   1.3229
 JSW  N07  N  NT    0  -0.522  -2.4496   1.0347   0.0488
 JSW  N15  N  NR5   0  -0.370   2.2821   1.5983  -0.1614
 JSW  N16  N  NR15  0  -0.459   2.6237   2.4943   0.8888
 JSW  O06  O  O     0  -0.438  -4.5330   0.2992  -0.6503
 JSW  O14  O  O     0  -0.492   0.9328   0.7190  -1.6955
 JSW  H1   H  HCH1  0   0.283   0.4646   3.5124  -0.2867
 JSW  H2   H  HCH2  0   0.260   4.4855   2.9406   1.7456
 JSW  H3   H  HCH2  0   0.234   4.4244   3.2089  -0.0079
 JSW  H4   H  HCR6  0   0.279   3.7775  -1.5830  -1.9224
 JSW  H5   H  HCR6  0   0.302   1.8926  -4.4401   0.6702
 JSW  H6   H  HCH3  0   0.270  -6.5605  -1.2144  -1.7595
 JSW  H7   H  HCH3  0   0.271  -7.4213  -1.3108  -0.2185
 JSW  H8   H  HCH3  0   0.270  -7.2629   0.2402  -1.0525
 JSW  H9   H  HCH2  0   0.233  -0.7567   0.0036   0.7586
 JSW  H10  H  HCH2  0   0.273  -1.7877   0.7102   1.9930
 JSW  H11  H  HCH2  0   0.264   0.3031   1.9950   1.7564
 JSW  H12  H  HCH2  0   0.252  -1.1104   2.9684   1.4170
 JSW  H13  H  HCH2  0   0.245  -1.7320   3.4700  -1.0711
 JSW  H14  H  HCH2  0   0.253  -0.7835   2.7416  -2.3486
 JSW  H15  H  HCH2  0   0.262  -2.9420   1.6052  -1.9035
 JSW  H16  H  HCH2  0   0.246  -1.5614   0.5166  -1.7856
 JSW  H17  H  HCH2  0   0.275   5.4459   1.0121   0.0890
 JSW  H18  H  HCH2  0   0.260   4.4515   0.5429   1.4668
 JSW  H19  H  HCR5  0   0.285   3.6716   0.7100  -1.4451
 JSW  H20  H  HCR6  0   0.278   1.9667  -0.2905   1.7601
 JSW  H21  H  HNR5  0   0.386   2.2346   3.4030   0.6610
 JSW  C01  C  CH3   0  -0.752  -6.7561  -0.6968  -0.8197

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
 JSW  F26  C25  single    1.340  0.020  1.340
 JSW  C24  C25  aromatic  1.383  0.020  1.383
 JSW  C24  C22  aromatic  1.380  0.020  1.380
 JSW  C25  C27  aromatic  1.379  0.020  1.379
 JSW  F23  C22  single    1.340  0.020  1.340
 JSW  C22  C21  aromatic  1.382  0.020  1.382
 JSW  C27  C20  aromatic  1.392  0.020  1.392
 JSW  C21  C20  aromatic  1.387  0.020  1.387
 JSW  C20  C19  single    1.508  0.020  1.508
 JSW  C19  C18  single    1.538  0.020  1.538
 JSW  C19  N15  single    1.455  0.020  1.455
 JSW  O14  C13  double    1.228  0.020  1.228
 JSW  C18  C17  single    1.517  0.020  1.517
 JSW  N15  C13  single    1.342  0.020  1.342
 JSW  N15  N16  single    1.422  0.020  1.422
 JSW  C13  C10  single    1.519  0.020  1.519
 JSW  C09  C10  single    1.534  0.020  1.534
 JSW  C09  C08  single    1.517  0.020  1.517
 JSW  N16  C17  single    1.463  0.020  1.463
 JSW  C10  C11  single    1.527  0.020  1.527
 JSW  C08  N07  single    1.455  0.020  1.455
 JSW  N04  C05  aromatic  1.297  0.020  1.297
 JSW  N04  N03  aromatic  1.379  0.020  1.379
 JSW  C11  C12  single    1.522  0.020  1.522
 JSW  N07  C05  single    1.344  0.020  1.344
 JSW  N07  C12  single    1.461  0.020  1.461
 JSW  C05  O06  aromatic  1.342  0.020  1.342
 JSW  N03  C02  aromatic  1.277  0.020  1.277
 JSW  C02  O06  aromatic  1.359  0.020  1.359
 JSW  C02  C01  single    1.475  0.020  1.475
 JSW  C10  H1   single    0.970  0.020  1.090
 JSW  C17  H2   single    0.970  0.020  1.090
 JSW  C17  H3   single    0.970  0.020  1.090
 JSW  C21  H4   single    0.930  0.020  1.080
 JSW  C24  H5   single    0.930  0.020  1.080
 JSW  C01  H6   single    0.970  0.020  1.090
 JSW  C01  H7   single    0.970  0.020  1.090
 JSW  C01  H8   single    0.970  0.020  1.090
 JSW  C08  H9   single    0.970  0.020  1.090
 JSW  C08  H10  single    0.970  0.020  1.090
 JSW  C09  H11  single    0.970  0.020  1.090
 JSW  C09  H12  single    0.970  0.020  1.090
 JSW  C11  H13  single    0.970  0.020  1.090
 JSW  C11  H14  single    0.970  0.020  1.090
 JSW  C12  H15  single    0.970  0.020  1.090
 JSW  C12  H16  single    0.970  0.020  1.090
 JSW  C18  H17  single    0.970  0.020  1.090
 JSW  C18  H18  single    0.970  0.020  1.090
 JSW  C19  H19  single    0.970  0.020  1.090
 JSW  C27  H20  single    0.930  0.020  1.080
 JSW  N16  H21  single    0.890  0.020  1.040

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
 JSW  H1   C10  C11  107.19  3.000
 JSW  H1   C10  C09  108.14  3.000
 JSW  C11  C10  C09  109.21  3.000
 JSW  H1   C10  C13  108.48  3.000
 JSW  C11  C10  C13  112.55  3.000
 JSW  C09  C10  C13  111.10  3.000
 JSW  O14  C13  N15  119.86  3.000
 JSW  N15  C13  C10  117.04  3.000
 JSW  O14  C13  C10  123.10  3.000
 JSW  H3   C17  H2   108.73  3.000
 JSW  H3   C17  N16  112.29  3.000
 JSW  H2   C17  N16  109.69  3.000
 JSW  H3   C17  C18  110.67  3.000
 JSW  H2   C17  C18  113.02  3.000
 JSW  N16  C17  C18  102.38  3.000
 JSW  C27  C20  C19  119.80  3.000
 JSW  C19  C20  C21  120.00  3.000
 JSW  C27  C20  C21  120.16  3.000
 JSW  H4   C21  C22  120.36  3.000
 JSW  H4   C21  C20  120.87  3.000
 JSW  C22  C21  C20  118.77  3.000
 JSW  F23  C22  C24  118.40  3.000
 JSW  F23  C22  C21  118.74  3.000
 JSW  C24  C22  C21  122.86  3.000
 JSW  H5   C24  C25  121.65  3.000
 JSW  H5   C24  C22  121.77  3.000
 JSW  C25  C24  C22  116.58  3.000
 JSW  O06  C02  N03  111.19  3.000
 JSW  O06  C02  C01  118.92  3.000
 JSW  N03  C02  C01  129.89  3.000
 JSW  O06  C05  N07  119.26  3.000
 JSW  O06  C05  N04  111.92  3.000
 JSW  N07  C05  N04  128.78  3.000
 JSW  H10  C08  H9   106.94  3.000
 JSW  H10  C08  N07  108.80  3.000
 JSW  H9   C08  N07  110.31  3.000
 JSW  H10  C08  C09  109.30  3.000
 JSW  H9   C08  C09  110.88  3.000
 JSW  N07  C08  C09  110.52  3.000
 JSW  H12  C09  H11  106.52  3.000
 JSW  H12  C09  C08  109.01  3.000
 JSW  H11  C09  C08  109.07  3.000
 JSW  H12  C09  C10  108.54  3.000
 JSW  H11  C09  C10  111.48  3.000
 JSW  C08  C09  C10  112.05  3.000
 JSW  H14  C11  H13  106.54  3.000
 JSW  H14  C11  C12  108.50  3.000
 JSW  H13  C11  C12  108.57  3.000
 JSW  H14  C11  C10  110.96  3.000
 JSW  H13  C11  C10  107.57  3.000
 JSW  C12  C11  C10  114.39  3.000
 JSW  H16  C12  H15  107.81  3.000
 JSW  H16  C12  N07  110.06  3.000
 JSW  H15  C12  N07  109.48  3.000
 JSW  H16  C12  C11  110.48  3.000
 JSW  H15  C12  C11  108.22  3.000
 JSW  N07  C12  C11  110.71  3.000
 JSW  H18  C18  H17  108.04  3.000
 JSW  H18  C18  C19  110.51  3.000
 JSW  H17  C18  C19  111.80  3.000
 JSW  H18  C18  C17  110.42  3.000
 JSW  H17  C18  C17  113.01  3.000
 JSW  C19  C18  C17  103.03  3.000
 JSW  H19  C19  N15  109.39  3.000
 JSW  H19  C19  C18  110.37  3.000
 JSW  N15  C19  C18  102.77  3.000
 JSW  H19  C19  C20  109.15  3.000
 JSW  N15  C19  C20  112.30  3.000
 JSW  C18  C19  C20  112.71  3.000
 JSW  F26  C25  C27  118.87  3.000
 JSW  C27  C25  C24  122.95  3.000
 JSW  F26  C25  C24  118.19  3.000
 JSW  H20  C27  C25  120.16  3.000
 JSW  H20  C27  C20  121.17  3.000
 JSW  C25  C27  C20  118.67  3.000
 JSW  N04  N03  C02  107.63  3.000
 JSW  N03  N04  C05  105.81  3.000
 JSW  C12  N07  C08  115.94  3.000
 JSW  C12  N07  C05  120.20  3.000
 JSW  C08  N07  C05  116.80  3.000
 JSW  N16  N15  C19  111.35  3.000
 JSW  N16  N15  C13  126.11  3.000
 JSW  C19  N15  C13  122.33  3.000
 JSW  H21  N16  N15  107.84  3.000
 JSW  H21  N16  C17  109.18  3.000
 JSW  N15  N16  C17  103.16  3.000
 JSW  C05  O06  C02  103.44  3.000
 JSW  H8   C01  H7   108.61  3.000
 JSW  H8   C01  H6   107.90  3.000
 JSW  H7   C01  H6   108.56  3.000
 JSW  H8   C01  C02  111.21  3.000
 JSW  H7   C01  C02  109.38  3.000
 JSW  H6   C01  C02  111.10  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
 JSW  CONST_01  C24  C25  C27  C20     0.00   0.0  0
 JSW  CONST_02  C24  C22  C21  C20     0.00   0.0  0
 JSW  CONST_03  C25  C24  C22  C21     0.00   0.0  0
 JSW  CONST_04  C25  C27  C20  C21     0.00   0.0  0
 JSW  CONST_05  C27  C25  C24  C22     0.00   0.0  0
 JSW  CONST_06  C27  C20  C21  C22     0.00   0.0  0
 JSW  CONST_07  C05  N04  N03  C02     0.00   0.0  0
 JSW  CONST_08  N04  C05  O06  C02     0.00   0.0  0
 JSW  CONST_09  N03  C02  O06  C05     0.00   0.0  0
 JSW  CONST_10  O06  C05  N04  N03     0.00   0.0  0
 JSW  CONST_11  O06  C02  N03  N04     0.00   0.0  0
 JSW  CONST_12  C19  C20  C21  C22   180.00   0.0  0
 JSW  CONST_13  N07  C05  O06  C02   180.00   0.0  0
 JSW  CONST_14  C25  C27  C20  C19   180.00   0.0  0
 JSW  CONST_15  N07  C05  N04  N03   180.00   0.0  0
 JSW  CONST_16  F26  C25  C27  C20   180.00   0.0  0
 JSW  CONST_17  F23  C22  C21  C20   180.00   0.0  0
 JSW  CONST_18  F26  C25  C24  C22   180.00   0.0  0
 JSW  CONST_19  N04  N03  C02  C01   180.00   0.0  0
 JSW  CONST_20  C05  O06  C02  C01   180.00   0.0  0
 JSW  CONST_21  F23  C22  C24  C25   180.00   0.0  0
 JSW  CONST_22  C19  N15  C13  C10   180.00   0.0  0
 JSW  CONST_23  N16  N15  C13  C10     0.00   0.0  0
 JSW  CONST_24  H5   C24  C22  C21   180.00   0.0  0
 JSW  CONST_25  H20  C27  C20  C21   180.00   0.0  0
 JSW  CONST_26  H4   C21  C22  C24   180.00   0.0  0
 JSW  CONST_27  O14  C13  N15  C19     0.00   0.0  0
 JSW  CONST_28  O14  C13  N15  N16   180.00   0.0  0
 JSW  Var_01    N07  C08  C09  C10   -55.42  30.0  1
 JSW  Var_02    N07  C12  C11  C10    49.51  30.0  1
 JSW  Var_03    C19  N15  N16  C17    29.25  30.0  1
 JSW  Var_04    C09  C08  N07  C05  -153.44  30.0  1
 JSW  Var_05    C11  C12  N07  C05   158.04  30.0  1
 JSW  Var_06    N04  C05  N07  C08     9.90  30.0  2
 JSW  Var_07    N15  N16  C17  C18   -40.86  30.0  1
 JSW  Var_08    N16  C17  C18  C19    37.82  30.0  1
 JSW  Var_09    H6   C01  C02  N03  -119.27  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
 JSW  chir_01  C10  C13  C09  C11  positiv
 JSW  chir_02  C19  N15  C18  C20  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
 JSW  plan-1  C02  0.020
 JSW  plan-1  C05  0.020
 JSW  plan-1  N03  0.020
 JSW  plan-1  N04  0.020
 JSW  plan-1  N07  0.020
 JSW  plan-1  O06  0.020
 JSW  plan-1  C01  0.020
 JSW  plan-2  C20  0.020
 JSW  plan-2  C21  0.020
 JSW  plan-2  C22  0.020
 JSW  plan-2  C24  0.020
 JSW  plan-2  C19  0.020
 JSW  plan-2  C25  0.020
 JSW  plan-2  C27  0.020
 JSW  plan-2  F23  0.020
 JSW  plan-2  F26  0.020
 JSW  plan-2  H4   0.020
 JSW  plan-2  H5   0.020
 JSW  plan-2  H20  0.020
 JSW  plan-3  C10  0.020
 JSW  plan-3  C13  0.020
 JSW  plan-3  C19  0.020
 JSW  plan-3  N15  0.020
 JSW  plan-3  N16  0.020
 JSW  plan-3  O14  0.020

