# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:01:15 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: N-[(1R,2S,4S)-bicyclo[2.2.1]heptan-2-yl]-N'-[(2R)-2-hydroxypropyl]thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)CNC(=S)N[C@H]1C[C@H]2CC[C@@H]1C2
#
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
 JOP  JOP  N-[(1R,2S,4S)-bicyclo[2.2.1]heptan-2-yl]-N'-[(2R)-2-hydroxypropyl]thiourea  ligand  35  15  .  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_JOP
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
 JOP  C10   C  CH2   0  -0.466   2.8239   0.2269  -1.4801
 JOP  C13   C  CH2   0  -0.444   2.5193   1.0597   1.3055
 JOP  C15   C  CH2   0  -0.442   4.0092  -0.5692   0.4215
 JOP  C01   C  CH3   0  -0.688  -5.4935   0.0323  -0.0389
 JOP  C02   C  CH1   0  -0.011  -4.1206   0.4707  -0.5192
 JOP  O03   O  OH1   0  -0.664  -3.9268   1.8670  -0.3829
 JOP  C04   C  CH2   0  -0.252  -3.0277  -0.3144   0.1975
 JOP  N05   N  NH1   0  -0.629  -1.7257   0.1180  -0.2478
 JOP  C06   C  C     0   0.431  -0.5971  -0.5996  -0.1632
 JOP  S07   S  S1    0  -0.457  -0.5796  -2.1842   0.4196
 JOP  N08   N  NH1   0  -0.639   0.5113   0.0200  -0.5941
 JOP  C09   C  CH1   0  -0.028   1.8504  -0.5187  -0.5286
 JOP  C11   C  CH1   0  -0.249   3.9887   0.6102  -0.5591
 JOP  C12   C  CH2   0  -0.442   3.5232   1.7566   0.3487
 JOP  C14   C  CH1   0  -0.258   2.5465  -0.4009   0.8414
 JOP  H102  H  HCH2  0   0.250   3.1485  -0.4273  -2.2906
 JOP  H101  H  HCH2  0   0.234   2.3659   1.1046  -1.9445
 JOP  H132  H  HCH2  0   0.237   2.8472   1.1343   2.3437
 JOP  H131  H  HCH2  0   0.227   1.5184   1.4927   1.2650
 JOP  H152  H  HCH2  0   0.235   4.2195  -1.5296  -0.0567
 JOP  H151  H  HCH2  0   0.236   4.7116  -0.4324   1.2468
 JOP  H012  H  HCH3  0   0.234  -5.6452  -1.0324  -0.2176
 JOP  H013  H  HCH3  0   0.226  -5.6102   0.2093   1.0329
 JOP  H021  H  HCH1  0   0.235  -4.0348   0.2729  -1.5915
 JOP  H031  H  HOH1  0   0.447  -4.0732   2.1052   0.5399
 JOP  H042  H  HCH2  0   0.228  -3.1318  -0.1921   1.2835
 JOP  H041  H  HCH2  0   0.249  -3.1418  -1.3769  -0.0138
 JOP  H051  H  HNH1  0   0.392  -1.6522   1.0953  -0.4934
 JOP  H081  H  HNH1  0   0.391   0.4198   0.9721  -0.9187
 JOP  H091  H  HCH1  0   0.258   1.7905  -1.5732  -0.7994
 JOP  H111  H  HCH1  0   0.227   4.9197   0.8130  -1.0890
 JOP  H121  H  HCH2  0   0.226   3.0688   2.5704  -0.2199
 JOP  H122  H  HCH2  0   0.233   4.3642   2.1798   0.9010
 JOP  H141  H  HCH1  0   0.227   2.1576  -1.1105   1.5709
 JOP  H011  H  HCH3  0   0.244  -6.2798   0.5758  -0.5622

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
 JOP  C01  C02   single  1.519  0.020  1.519
 JOP  C13  C14   single  1.533  0.020  1.533
 JOP  C13  C12   single  1.552  0.020  1.552
 JOP  C14  C15   single  1.531  0.020  1.531
 JOP  C14  C09   single  1.541  0.020  1.541
 JOP  C04  N05   single  1.442  0.020  1.442
 JOP  C04  C02   single  1.525  0.020  1.525
 JOP  N05  C06   single  1.340  0.020  1.340
 JOP  C02  O03   single  1.416  0.020  1.416
 JOP  C06  N08   single  1.341  0.020  1.341
 JOP  C06  S07   double  1.688  0.020  1.688
 JOP  C12  C11   single  1.535  0.020  1.535
 JOP  N08  C09   single  1.445  0.020  1.445
 JOP  C15  C11   single  1.534  0.020  1.534
 JOP  C09  C10   single  1.552  0.020  1.552
 JOP  C11  C10   single  1.534  0.020  1.534
 JOP  C10  H102  single  0.970  0.020  1.090
 JOP  C10  H101  single  0.970  0.020  1.090
 JOP  C13  H132  single  0.970  0.020  1.090
 JOP  C13  H131  single  0.970  0.020  1.090
 JOP  C15  H152  single  0.970  0.020  1.090
 JOP  C15  H151  single  0.970  0.020  1.090
 JOP  C01  H011  single  0.970  0.020  1.090
 JOP  C01  H012  single  0.970  0.020  1.090
 JOP  C01  H013  single  0.970  0.020  1.090
 JOP  C02  H021  single  0.970  0.020  1.090
 JOP  O03  H031  single  0.850  0.020  0.980
 JOP  C04  H042  single  0.970  0.020  1.090
 JOP  C04  H041  single  0.970  0.020  1.090
 JOP  N05  H051  single  0.860  0.020  1.020
 JOP  N08  H081  single  0.860  0.020  1.020
 JOP  C09  H091  single  0.970  0.020  1.090
 JOP  C11  H111  single  0.970  0.020  1.090
 JOP  C12  H121  single  0.970  0.020  1.090
 JOP  C12  H122  single  0.970  0.020  1.090
 JOP  C14  H141  single  0.970  0.020  1.090

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
 JOP  H101  C10  H102  106.88  3.000
 JOP  H101  C10  C11   111.88  3.000
 JOP  H102  C10  C11   111.71  3.000
 JOP  H101  C10  C09   112.54  3.000
 JOP  H102  C10  C09   110.73  3.000
 JOP  C11   C10  C09   103.20  3.000
 JOP  H131  C13  H132  106.48  3.000
 JOP  H131  C13  C14   112.53  3.000
 JOP  H132  C13  C14   110.36  3.000
 JOP  H131  C13  C12   113.09  3.000
 JOP  H132  C13  C12   111.19  3.000
 JOP  C14   C13  C12   103.28  3.000
 JOP  H151  C15  H152  108.47  3.000
 JOP  H151  C15  C14   113.16  3.000
 JOP  H152  C15  C14   113.59  3.000
 JOP  H151  C15  C11   113.28  3.000
 JOP  H152  C15  C11   113.48  3.000
 JOP  C14   C15  C11    94.47  3.000
 JOP  H013  C01  H012  107.71  3.000
 JOP  H013  C01  H011  108.25  3.000
 JOP  H012  C01  H011  107.93  3.000
 JOP  H013  C01  C02   111.10  3.000
 JOP  H012  C01  C02   110.84  3.000
 JOP  H011  C01  C02   110.87  3.000
 JOP  H021  C02  C04   108.15  3.000
 JOP  H021  C02  O03   105.18  3.000
 JOP  C04   C02  O03   111.37  3.000
 JOP  H021  C02  C01   109.19  3.000
 JOP  O03   C02  C01   112.19  3.000
 JOP  C04   C02  C01   110.52  3.000
 JOP  H031  O03  C02   108.36  3.000
 JOP  H041  C04  H042  106.90  3.000
 JOP  H041  C04  N05   109.09  3.000
 JOP  H042  C04  N05   110.95  3.000
 JOP  H041  C04  C02   109.63  3.000
 JOP  H042  C04  C02   109.86  3.000
 JOP  N05   C04  C02   110.34  3.000
 JOP  H051  N05  C06   118.17  3.000
 JOP  H051  N05  C04   115.51  3.000
 JOP  C06   N05  C04   125.46  3.000
 JOP  N08   C06  S07   122.41  3.000
 JOP  S07   C06  N05   122.21  3.000
 JOP  N08   C06  N05   115.37  3.000
 JOP  H081  N08  C09   116.74  3.000
 JOP  H081  N08  C06   117.64  3.000
 JOP  C09   N08  C06   125.40  3.000
 JOP  H091  C09  C14   108.63  3.000
 JOP  H091  C09  N08   107.36  3.000
 JOP  C14   C09  N08   115.49  3.000
 JOP  H091  C09  C10   110.29  3.000
 JOP  N08   C09  C10   111.99  3.000
 JOP  C14   C09  C10   103.00  3.000
 JOP  H111  C11  C12   114.05  3.000
 JOP  H111  C11  C15   116.25  3.000
 JOP  C12   C11  C15   101.55  3.000
 JOP  H111  C11  C10   113.78  3.000
 JOP  C15   C11  C10   101.65  3.000
 JOP  C12   C11  C10   108.15  3.000
 JOP  H122  C12  H121  107.17  3.000
 JOP  H122  C12  C11   110.81  3.000
 JOP  H121  C12  C11   112.02  3.000
 JOP  H122  C12  C13   111.14  3.000
 JOP  H121  C12  C13   112.74  3.000
 JOP  C11   C12  C13   103.03  3.000
 JOP  H141  C14  C09   112.60  3.000
 JOP  H141  C14  C15   116.93  3.000
 JOP  C09   C14  C15   100.33  3.000
 JOP  H141  C14  C13   114.31  3.000
 JOP  C09   C14  C13   109.51  3.000
 JOP  C15   C14  C13   101.81  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
 JOP  CONST_01  C09   N08  C06  N05   180.00   0.0  0
 JOP  CONST_02  C09   N08  C06  S07     0.00   0.0  0
 JOP  CONST_03  N08   C06  N05  C04   180.00   0.0  0
 JOP  CONST_04  S07   C06  N05  C04     0.00   0.0  0
 JOP  CONST_05  H081  N08  C06  N05     0.00   0.0  0
 JOP  CONST_06  H051  N05  C06  S07   180.00   0.0  0
 JOP  Var_01    C14   C13  C12  C11     0.71  30.0  1
 JOP  Var_02    C06   N05  C04  C02  -157.88  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
 JOP  chir_01  C02  C01  C04  O03  positiv
 JOP  chir_02  C09  N08  C14  C10  positiv
 JOP  chir_03  C11  C12  C15  C10  negativ
 JOP  chir_04  C14  C13  C15  C09  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
 JOP  plan-1  C04   0.020
 JOP  plan-1  N05   0.020
 JOP  plan-1  C06   0.020
 JOP  plan-1  S07   0.020
 JOP  plan-1  N08   0.020
 JOP  plan-1  C09   0.020
 JOP  plan-1  H051  0.020
 JOP  plan-1  H081  0.020

