# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 13:50:04 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2~{S})-1-(4-fluorophenyl)sulfonyl-~{N}-(2-methyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc2CCCc2c1NC(=O)[C@@H]3CCCN3[S](=O)(=O)c4ccc(F)cc4
#
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
 JR5  JR5  (2~{S})-1-(4-fluorophenyl)sulfonyl-~{N}-(2-methyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)pyrrolidine-2-carboxamide  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 PERFECT
;

data_comp_JR5
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
 JR5  C01  C  CH3   0  -0.520  -2.7650   1.3333  -2.9217
 JR5  C04  C  CR55  0   0.229  -4.3142  -0.1695  -0.2010
 JR5  C05  C  CR55  0  -0.103  -3.2836   0.4296   0.5202
 JR5  C06  C  CR5   0   0.515  -2.5545   1.0970  -0.4297
 JR5  C08  C  C     0   0.525  -0.1955   1.4314  -0.7147
 JR5  C10  C  CR15  0  -0.162   0.9635   2.3755  -0.4392
 JR5  C11  C  CH2   0  -0.483   1.4872   2.9859  -1.7575
 JR5  C12  C  CH2   0  -0.457   3.0089   2.8834  -1.6620
 JR5  C13  C  CH2   0  -0.270   3.2246   1.5977  -0.8813
 JR5  C18  C  CR6   0  -0.191   1.9546  -0.9591   0.8914
 JR5  C19  C  CR16  0  -0.223   3.1075  -1.6153   0.4765
 JR5  C20  C  CR16  0  -0.405   3.0314  -2.9288   0.0449
 JR5  C21  C  CR6   0   0.549   1.8002  -3.5580   0.0575
 JR5  C23  C  CR16  0  -0.409   0.6474  -2.9261   0.4855
 JR5  C24  C  CR16  0  -0.193   0.7277  -1.6087   0.9034
 JR5  C25  C  CH2   0  -0.506  -3.3533   0.0913   1.9708
 JR5  C26  C  CH2   0  -0.463  -4.7909  -0.4891   2.0824
 JR5  C27  C  CH2   0  -0.499  -5.2070  -0.9873   0.6744
 JR5  F22  F  F     0  -0.304   1.7240  -4.8276  -0.3537
 JR5  N02  N  NR5   0  -0.298  -3.1778   0.8769  -1.6183
 JR5  N03  N  N     0  -0.317  -4.2484   0.0861  -1.4917
 JR5  N14  N  NR5   0  -0.607   2.1246   1.6600   0.0755
 JR5  O09  O  O     0  -0.440  -0.0322   0.3708  -1.2824
 JR5  O16  O  OS    0  -0.650   0.8254   1.0784   2.0915
 JR5  O17  O  OS    0  -0.648   3.3380   0.8644   2.1021
 JR5  S15  S  S     0   1.388   2.0649   0.7286   1.4130
 JR5  H1   H  HCH3  0   0.254  -2.1666   0.5801  -3.4332
 JR5  H2   H  HCH3  0   0.265  -3.6474   1.5553  -3.5159
 JR5  H3   H  HCH3  0   0.252  -2.1768   2.2421  -2.8230
 JR5  H4   H  HCR5  0   0.291   0.6725   3.1643   0.2577
 JR5  H5   H  HCH2  0   0.260   1.1301   2.4103  -2.6124
 JR5  H6   H  HCH2  0   0.275   1.1375   4.0092  -1.8789
 JR5  H7   H  HCH2  0   0.261   3.4847   2.8568  -2.6410
 JR5  H8   H  HCH2  0   0.251   3.4184   3.7273  -1.1053
 JR5  H9   H  HCH2  0   0.245   3.1409   0.7185  -1.5279
 JR5  H10  H  HCH2  0   0.270   4.1863   1.5666  -0.3717
 JR5  H11  H  HCR6  0   0.293   4.0696  -1.1207   0.4901
 JR5  H12  H  HCR6  0   0.295   3.9174  -3.4547  -0.2840
 JR5  H13  H  HCR6  0   0.293  -0.2976  -3.4526   0.4925
 JR5  H14  H  HCR6  0   0.286  -0.1656  -1.1060   1.2449
 JR5  H15  H  HCH2  0   0.242  -2.6014  -0.6574   2.2377
 JR5  H16  H  HCH2  0   0.247  -3.2072   0.9401   2.6396
 JR5  H17  H  HCH2  0   0.239  -4.8600  -1.2740   2.8345
 JR5  H18  H  HCH2  0   0.242  -5.4677   0.3106   2.3880
 JR5  H19  H  HCH2  0   0.252  -6.2713  -0.8431   0.4852
 JR5  H20  H  HCH2  0   0.248  -4.9997  -2.0542   0.5520
 JR5  H21  H  HNH1  0   0.418  -1.4616   2.7174   0.2445
 JR5  N07  N  NH1   0  -0.740  -1.4102   1.8847  -0.3238

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
 JR5  C12  C11  single    1.528  0.020  1.528
 JR5  C12  C13  single    1.520  0.020  1.520
 JR5  C11  C10  single    1.544  0.020  1.544
 JR5  C13  N14  single    1.459  0.020  1.459
 JR5  C10  N14  single    1.458  0.020  1.458
 JR5  C10  C08  single    1.520  0.020  1.520
 JR5  N14  S15  single    1.631  0.020  1.631
 JR5  O09  C08  double    1.214  0.020  1.214
 JR5  C08  N07  single    1.354  0.020  1.354
 JR5  N07  C06  single    1.393  0.020  1.393
 JR5  O17  S15  double    1.454  0.020  1.454
 JR5  S15  C18  single    1.770  0.020  1.770
 JR5  S15  O16  double    1.456  0.020  1.456
 JR5  C24  C18  aromatic  1.388  0.020  1.388
 JR5  C24  C23  aromatic  1.384  0.020  1.384
 JR5  C06  C05  aromatic  1.371  0.020  1.371
 JR5  C06  N02  aromatic  1.360  0.020  1.360
 JR5  C01  N02  single    1.441  0.020  1.441
 JR5  C25  C05  single    1.491  0.020  1.491
 JR5  C25  C26  single    1.554  0.020  1.554
 JR5  C05  C04  aromatic  1.393  0.020  1.393
 JR5  N02  N03  aromatic  1.337  0.020  1.337
 JR5  C18  C19  aromatic  1.390  0.020  1.390
 JR5  C23  C21  aromatic  1.383  0.020  1.383
 JR5  C04  N03  aromatic  1.317  0.020  1.317
 JR5  C04  C27  single    1.494  0.020  1.494
 JR5  C27  C26  single    1.550  0.020  1.550
 JR5  C19  C20  aromatic  1.385  0.020  1.385
 JR5  C21  C20  aromatic  1.383  0.020  1.383
 JR5  C21  F22  single    1.337  0.020  1.337
 JR5  C01  H1   single    0.970  0.020  1.090
 JR5  C01  H2   single    0.970  0.020  1.090
 JR5  C01  H3   single    0.970  0.020  1.090
 JR5  C10  H4   single    0.970  0.020  1.090
 JR5  C11  H5   single    0.970  0.020  1.090
 JR5  C11  H6   single    0.970  0.020  1.090
 JR5  C12  H7   single    0.970  0.020  1.090
 JR5  C12  H8   single    0.970  0.020  1.090
 JR5  C13  H9   single    0.970  0.020  1.090
 JR5  C13  H10  single    0.970  0.020  1.090
 JR5  C19  H11  single    0.930  0.020  1.080
 JR5  C20  H12  single    0.930  0.020  1.080
 JR5  C23  H13  single    0.930  0.020  1.080
 JR5  C24  H14  single    0.930  0.020  1.080
 JR5  C25  H15  single    0.970  0.020  1.090
 JR5  C25  H16  single    0.970  0.020  1.090
 JR5  C26  H17  single    0.970  0.020  1.090
 JR5  C26  H18  single    0.970  0.020  1.090
 JR5  C27  H19  single    0.970  0.020  1.090
 JR5  C27  H20  single    0.970  0.020  1.090
 JR5  N07  H21  single    0.860  0.020  1.020

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
 JR5  H3   C01  H2   108.56  3.000
 JR5  H3   C01  H1   108.87  3.000
 JR5  H2   C01  H1   109.30  3.000
 JR5  H3   C01  N02  109.73  3.000
 JR5  H2   C01  N02  109.06  3.000
 JR5  H1   C01  N02  111.28  3.000
 JR5  N03  C04  C27  135.24  3.000
 JR5  C27  C04  C05  111.97  3.000
 JR5  N03  C04  C05  112.75  3.000
 JR5  C25  C05  C06  144.03  3.000
 JR5  C25  C05  C04  111.81  3.000
 JR5  C06  C05  C04  104.13  3.000
 JR5  N07  C06  N02  122.30  3.000
 JR5  N02  C06  C05  106.44  3.000
 JR5  N07  C06  C05  131.26  3.000
 JR5  O09  C08  N07  123.24  3.000
 JR5  N07  C08  C10  115.07  3.000
 JR5  O09  C08  C10  121.66  3.000
 JR5  H4   C10  N14  109.96  3.000
 JR5  H4   C10  C11  110.47  3.000
 JR5  N14  C10  C11  103.02  3.000
 JR5  H4   C10  C08  111.17  3.000
 JR5  N14  C10  C08  111.50  3.000
 JR5  C11  C10  C08  110.45  3.000
 JR5  H6   C11  H5   107.68  3.000
 JR5  H6   C11  C12  112.95  3.000
 JR5  H5   C11  C12  109.85  3.000
 JR5  H6   C11  C10  110.97  3.000
 JR5  H5   C11  C10  110.46  3.000
 JR5  C12  C11  C10  104.94  3.000
 JR5  H8   C12  H7   108.29  3.000
 JR5  H8   C12  C13  109.82  3.000
 JR5  H7   C12  C13  112.29  3.000
 JR5  H8   C12  C11  110.73  3.000
 JR5  H7   C12  C11  112.37  3.000
 JR5  C13  C12  C11  103.31  3.000
 JR5  H10  C13  H9   108.73  3.000
 JR5  H10  C13  N14  111.11  3.000
 JR5  H9   C13  N14  111.35  3.000
 JR5  H10  C13  C12  112.96  3.000
 JR5  H9   C13  C12  111.42  3.000
 JR5  N14  C13  C12  101.17  3.000
 JR5  S15  C18  C24  119.92  3.000
 JR5  C24  C18  C19  120.98  3.000
 JR5  S15  C18  C19  119.10  3.000
 JR5  H11  C19  C20  119.11  3.000
 JR5  H11  C19  C18  121.20  3.000
 JR5  C20  C19  C18  119.69  3.000
 JR5  H12  C20  C21  120.72  3.000
 JR5  H12  C20  C19  120.73  3.000
 JR5  C21  C20  C19  118.54  3.000
 JR5  F22  C21  C23  118.80  3.000
 JR5  F22  C21  C20  118.70  3.000
 JR5  C23  C21  C20  122.50  3.000
 JR5  H13  C23  C24  120.79  3.000
 JR5  H13  C23  C21  120.52  3.000
 JR5  C24  C23  C21  118.69  3.000
 JR5  H14  C24  C23  119.36  3.000
 JR5  H14  C24  C18  121.04  3.000
 JR5  C23  C24  C18  119.60  3.000
 JR5  H16  C25  H15  106.91  3.000
 JR5  H16  C25  C26  111.75  3.000
 JR5  H15  C25  C26  111.26  3.000
 JR5  H16  C25  C05  114.44  3.000
 JR5  H15  C25  C05  111.13  3.000
 JR5  C26  C25  C05  101.41  3.000
 JR5  H18  C26  H17  107.18  3.000
 JR5  H18  C26  C27  108.86  3.000
 JR5  H17  C26  C27  112.24  3.000
 JR5  H18  C26  C25  108.67  3.000
 JR5  H17  C26  C25  112.17  3.000
 JR5  C27  C26  C25  107.64  3.000
 JR5  H20  C27  H19  107.13  3.000
 JR5  H20  C27  C26  111.36  3.000
 JR5  H19  C27  C26  112.15  3.000
 JR5  H20  C27  C04  110.80  3.000
 JR5  H19  C27  C04  114.15  3.000
 JR5  C26  C27  C04  101.29  3.000
 JR5  N03  N02  C06  112.33  3.000
 JR5  N03  N02  C01  120.15  3.000
 JR5  C06  N02  C01  127.43  3.000
 JR5  N02  N03  C04  104.33  3.000
 JR5  S15  N14  C13  122.74  3.000
 JR5  S15  N14  C10  122.74  3.000
 JR5  C13  N14  C10  112.94  3.000
 JR5  O17  S15  O16  120.15  3.000
 JR5  O16  S15  N14  106.03  3.000
 JR5  O17  S15  N14  107.65  3.000
 JR5  O16  S15  C18  108.26  3.000
 JR5  O17  S15  C18  106.46  3.000
 JR5  N14  S15  C18  107.77  3.000
 JR5  H21  N07  C08  118.97  3.000
 JR5  H21  N07  C06  117.86  3.000
 JR5  C08  N07  C06  121.70  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
 JR5  CONST_01  N02  C06  C05  C04    0.00   0.0  0
 JR5  CONST_02  C06  N02  N03  C04    0.00   0.0  0
 JR5  CONST_03  N03  N02  C06  C05    0.00   0.0  0
 JR5  CONST_04  N02  N03  C04  C05    0.00   0.0  0
 JR5  CONST_05  N03  C04  C05  C06    0.00   0.0  0
 JR5  CONST_06  C21  C23  C24  C18    0.00   0.0  0
 JR5  CONST_07  C21  C20  C19  C18    0.00   0.0  0
 JR5  CONST_08  C23  C24  C18  C19    0.00   0.0  0
 JR5  CONST_09  C23  C21  C20  C19    0.00   0.0  0
 JR5  CONST_10  C24  C18  C19  C20    0.00   0.0  0
 JR5  CONST_11  C24  C23  C21  C20    0.00   0.0  0
 JR5  CONST_12  C05  C06  N02  C01  180.00   0.0  0
 JR5  CONST_13  C04  N03  N02  C01  180.00   0.0  0
 JR5  CONST_14  N07  C06  C05  C04  180.00   0.0  0
 JR5  CONST_15  F22  C21  C20  C19  180.00   0.0  0
 JR5  CONST_16  S15  C18  C19  C20  180.00   0.0  0
 JR5  CONST_17  S15  C18  C24  C23  180.00   0.0  0
 JR5  CONST_18  F22  C21  C23  C24  180.00   0.0  0
 JR5  CONST_19  N07  C06  C05  C25    0.00   0.0  0
 JR5  CONST_20  N07  C06  N02  N03  180.00   0.0  0
 JR5  CONST_21  H13  C23  C24  C18  180.00   0.0  0
 JR5  CONST_22  H12  C20  C19  C18  180.00   0.0  0
 JR5  CONST_23  H14  C24  C18  C19  180.00   0.0  0
 JR5  CONST_24  H11  C19  C20  C21  180.00   0.0  0
 JR5  CONST_25  C10  C08  N07  C06  180.00   0.0  0
 JR5  CONST_29  O09  C08  N07  C06    0.00   0.0  0
 JR5  Var_01    C26  C25  C05  C04  -14.54  30.0  1
 JR5  Var_02    C25  C26  C27  C04  -23.28  30.0  1
 JR5  Var_03    C27  C26  C25  C05   23.31  30.0  1
 JR5  Var_04    C26  C27  C04  C05   14.61  30.0  1
 JR5  Var_05    C13  C12  C11  C10   33.48  30.0  1
 JR5  Var_06    C12  C13  N14  C10   29.63  30.0  1
 JR5  Var_07    N14  C13  C12  C11  -37.53  30.0  1
 JR5  Var_08    C18  S15  N14  C10  100.74  30.0  3
 JR5  Var_09    N14  S15  C18  C19   79.33  30.0  3
 JR5  Var_10    H1   C01  N02  C06   93.86  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
 JR5  chir_01  C10  C11  N14  C08  positiv

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
 JR5  plan-1  C18  0.020
 JR5  plan-1  C19  0.020
 JR5  plan-1  C20  0.020
 JR5  plan-1  C21  0.020
 JR5  plan-1  C23  0.020
 JR5  plan-1  C24  0.020
 JR5  plan-1  F22  0.020
 JR5  plan-1  S15  0.020
 JR5  plan-1  H11  0.020
 JR5  plan-1  H12  0.020
 JR5  plan-1  H13  0.020
 JR5  plan-1  H14  0.020
 JR5  plan-2  C06  0.020
 JR5  plan-2  C08  0.020
 JR5  plan-2  C10  0.020
 JR5  plan-2  O09  0.020
 JR5  plan-2  H21  0.020
 JR5  plan-2  N07  0.020
 JR5  plan-3  C01  0.020
 JR5  plan-3  C04  0.020
 JR5  plan-3  C05  0.020
 JR5  plan-3  C06  0.020
 JR5  plan-3  C25  0.020
 JR5  plan-3  C27  0.020
 JR5  plan-3  N02  0.020
 JR5  plan-3  N03  0.020
 JR5  plan-3  N07  0.020

