# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:39:26 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (1R,4R,5R,6R)-4-methoxy-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonan-6-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1CN([C@@H]2CC[C@@H](O)[C@H]1C2)[S](C)(=O)=O
#
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
 JO7  JO7  (1R,4R,5R,6R)-4-methoxy-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonan-6-ol  ligand  35  16  .  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_JO7
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
 JO7  C01   C  CH3   0  -0.411   0.1199   3.5633   0.2199
 JO7  O02   O  O2    0  -0.493   0.4802   2.3716  -0.4346
 JO7  C03   C  CH1   0   0.069   1.0267   1.3858   0.4198
 JO7  C04   C  CH2   0  -0.343  -0.0776   0.6322   1.1587
 JO7  N05   N  N     0  -0.579  -0.7366  -0.3890   0.3439
 JO7  C06   C  CH1   0  -0.141   0.1059  -1.2194  -0.5387
 JO7  C07   C  CH2   0  -0.406   0.9575  -2.2135   0.2521
 JO7  C08   C  CH2   0  -0.517   2.0729  -1.5675   1.0773
 JO7  C09   C  CH1   0   0.070   2.8159  -0.4442   0.3493
 JO7  O10   O  OH1   0  -0.675   3.7398  -0.9666  -0.5896
 JO7  C11   C  CH1   0  -0.322   1.8970   0.4817  -0.4566
 JO7  C12   C  CH2   0  -0.433   1.0050  -0.3325  -1.3889
 JO7  S13   S  S     0   1.342  -2.3320  -0.2408  -0.0075
 JO7  O14   O  OS    0  -0.672  -2.8195  -1.5556  -0.4055
 JO7  O15   O  OS    0  -0.671  -2.9724   0.4262   1.1191
 JO7  C16   C  CH3   0  -0.797  -2.4794   0.8291  -1.4230
 JO7  H012  H  HCH3  0   0.238  -0.2740   4.2471  -0.5307
 JO7  H013  H  HCH3  0   0.206  -0.6543   3.4177   0.9813
 JO7  H011  H  HCH3  0   0.215   0.9817   4.0362   0.7043
 JO7  H031  H  HCH1  0   0.234   1.6584   1.8636   1.1838
 JO7  H041  H  HCH2  0   0.263   0.3292   0.1633   2.0534
 JO7  H042  H  HCH2  0   0.282  -0.8183   1.3373   1.5345
 JO7  H061  H  HCH1  0   0.278  -0.5596  -1.7954  -1.1803
 JO7  H072  H  HCH2  0   0.245   0.3170  -2.8212   0.8936
 JO7  H071  H  HCH2  0   0.235   1.4014  -2.8937  -0.4794
 JO7  H082  H  HCH2  0   0.238   1.6843  -1.1926   2.0236
 JO7  H081  H  HCH2  0   0.251   2.7968  -2.3361   1.3671
 JO7  H091  H  HCH1  0   0.216   3.3475   0.1590   1.1003
 JO7  H101  H  HOH1  0   0.447   4.3116  -1.5900  -0.1311
 JO7  H111  H  HCH1  0   0.257   2.5472   1.1452  -1.0350
 JO7  H121  H  HCH2  0   0.250   1.6045  -0.9562  -2.0536
 JO7  H122  H  HCH2  0   0.249   0.4151   0.3255  -2.0299
 JO7  H163  H  HCH3  0   0.301  -3.5363   0.9224  -1.6666
 JO7  H161  H  HCH3  0   0.289  -2.0628   1.8036  -1.1853
 JO7  H162  H  HCH3  0   0.283  -1.9461   0.3938  -2.2651

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
 JO7  O15  S13   double  1.457  0.020  1.457
 JO7  C01  O02   single  1.406  0.020  1.406
 JO7  C12  C06   single  1.522  0.020  1.522
 JO7  C12  C11   single  1.526  0.020  1.526
 JO7  C04  N05   single  1.463  0.020  1.463
 JO7  C04  C03   single  1.528  0.020  1.528
 JO7  S13  O14   double  1.458  0.020  1.458
 JO7  S13  N05   single  1.640  0.020  1.640
 JO7  S13  C16   single  1.780  0.020  1.780
 JO7  N05  C06   single  1.476  0.020  1.476
 JO7  C06  C07   single  1.529  0.020  1.529
 JO7  C11  C03   single  1.531  0.020  1.531
 JO7  C11  C09   single  1.533  0.020  1.533
 JO7  O02  C03   single  1.414  0.020  1.414
 JO7  O10  C09   single  1.417  0.020  1.417
 JO7  C09  C08   single  1.531  0.020  1.531
 JO7  C07  C08   single  1.530  0.020  1.530
 JO7  C01  H012  single  0.970  0.020  1.090
 JO7  C01  H013  single  0.970  0.020  1.090
 JO7  C01  H011  single  0.970  0.020  1.090
 JO7  C03  H031  single  0.970  0.020  1.090
 JO7  C04  H041  single  0.970  0.020  1.090
 JO7  C04  H042  single  0.970  0.020  1.090
 JO7  C06  H061  single  0.970  0.020  1.090
 JO7  C07  H072  single  0.970  0.020  1.090
 JO7  C07  H071  single  0.970  0.020  1.090
 JO7  C08  H082  single  0.970  0.020  1.090
 JO7  C08  H081  single  0.970  0.020  1.090
 JO7  C09  H091  single  0.970  0.020  1.090
 JO7  O10  H101  single  0.850  0.020  0.980
 JO7  C11  H111  single  0.970  0.020  1.090
 JO7  C12  H121  single  0.970  0.020  1.090
 JO7  C12  H122  single  0.970  0.020  1.090
 JO7  C16  H163  single  0.970  0.020  1.090
 JO7  C16  H161  single  0.970  0.020  1.090
 JO7  C16  H162  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
 JO7  H011  C01  H013  107.81  3.000
 JO7  H011  C01  H012  108.55  3.000
 JO7  H013  C01  H012  107.87  3.000
 JO7  H011  C01  O02   111.71  3.000
 JO7  H013  C01  O02   113.07  3.000
 JO7  H012  C01  O02   107.69  3.000
 JO7  C03   O02  C01   114.11  3.000
 JO7  H031  C03  C11   109.12  3.000
 JO7  H031  C03  C04   107.06  3.000
 JO7  C11   C03  C04   113.37  3.000
 JO7  H031  C03  O02   109.79  3.000
 JO7  C11   C03  O02   106.59  3.000
 JO7  C04   C03  O02   110.90  3.000
 JO7  H042  C04  H041  104.43  3.000
 JO7  H042  C04  N05   109.73  3.000
 JO7  H041  C04  N05   108.98  3.000
 JO7  H042  C04  C03   109.82  3.000
 JO7  H041  C04  C03   109.87  3.000
 JO7  N05   C04  C03   113.61  3.000
 JO7  S13   N05  C06   118.55  3.000
 JO7  C06   N05  C04   117.94  3.000
 JO7  S13   N05  C04   119.62  3.000
 JO7  H061  C06  C12   109.87  3.000
 JO7  H061  C06  C07   107.53  3.000
 JO7  C12   C06  C07   109.79  3.000
 JO7  H061  C06  N05   107.52  3.000
 JO7  C07   C06  N05   111.99  3.000
 JO7  C12   C06  N05   110.08  3.000
 JO7  H071  C07  H072  106.57  3.000
 JO7  H071  C07  C08   109.12  3.000
 JO7  H072  C07  C08   110.23  3.000
 JO7  H071  C07  C06   106.53  3.000
 JO7  H072  C07  C06   109.82  3.000
 JO7  C08   C07  C06   114.22  3.000
 JO7  H081  C08  H082  104.33  3.000
 JO7  H081  C08  C09   108.66  3.000
 JO7  H082  C08  C09   109.49  3.000
 JO7  H081  C08  C07   109.16  3.000
 JO7  H082  C08  C07   110.71  3.000
 JO7  C09   C08  C07   114.02  3.000
 JO7  H091  C09  C11   108.49  3.000
 JO7  H091  C09  O10   109.84  3.000
 JO7  C11   C09  O10   105.37  3.000
 JO7  H091  C09  C08   108.19  3.000
 JO7  O10   C09  C08   111.16  3.000
 JO7  C11   C09  C08   113.71  3.000
 JO7  H101  O10  C09   108.09  3.000
 JO7  H111  C11  C12   110.36  3.000
 JO7  H111  C11  C09   106.73  3.000
 JO7  C12   C11  C09   110.44  3.000
 JO7  H111  C11  C03   106.40  3.000
 JO7  C09   C11  C03   113.36  3.000
 JO7  C12   C11  C03   109.43  3.000
 JO7  H122  C12  H121  106.48  3.000
 JO7  H122  C12  C11   110.68  3.000
 JO7  H121  C12  C11   110.86  3.000
 JO7  H122  C12  C06   111.10  3.000
 JO7  H121  C12  C06   109.37  3.000
 JO7  C11   C12  C06   108.35  3.000
 JO7  C16   S13  O15   107.65  3.000
 JO7  C16   S13  O14   107.29  3.000
 JO7  O15   S13  O14   118.49  3.000
 JO7  C16   S13  N05   107.76  3.000
 JO7  O14   S13  N05   107.59  3.000
 JO7  O15   S13  N05   107.65  3.000
 JO7  H162  C16  H161  109.91  3.000
 JO7  H162  C16  H163  109.69  3.000
 JO7  H161  C16  H163  110.15  3.000
 JO7  H162  C16  S13   109.54  3.000
 JO7  H161  C16  S13   109.48  3.000
 JO7  H163  C16  S13   108.04  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
 JO7  Var_01  C06   N05  C04  C03   40.88  30.0  1
 JO7  Var_02  C09   C08  C07  C06  -41.95  30.0  3
 JO7  Var_03  O15   S13  N05  C04  -32.10  30.0  3
 JO7  Var_04  H012  C01  O02  C03  179.33  30.0  3
 JO7  Var_05  H163  C16  S13  N05  179.42  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
 JO7  chir_01  C03  C04  C11  O02  negativ
 JO7  chir_02  C06  N05  C12  C07  negativ
 JO7  chir_03  C09  O10  C08  C11  positiv
 JO7  chir_04  C11  C12  C03  C09  negativ

