# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:21:05 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (1R,4R,5R,6R)-4,6-dimethoxy-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1CC[C@@H]2C[C@H]1[C@H](CN2[S](C)(=O)=O)OC
#
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
 JOA  JOA  (1R,4R,5R,6R)-4,6-dimethoxy-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonane  ligand  38  17  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JOA
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
 JOA  C10   C  CH2   0  -0.334   0.5157  -0.8339   0.8730
 JOA  C15   C  CH3   0  -0.804   2.5101   1.7402   1.4277
 JOA  C17   C  CH3   0  -0.407   0.3787  -3.7960   0.2305
 JOA  O02   O  O2    0  -0.494  -3.6067   0.5010  -0.3529
 JOA  C03   C  CH1   0   0.079  -2.5190   0.1125   0.4666
 JOA  C04   C  CH2   0  -0.500  -1.7037   1.3216   0.9356
 JOA  C05   C  CH2   0  -0.436  -0.7946   1.9039  -0.1466
 JOA  C06   C  CH1   0  -0.119  -0.0263   0.8477  -0.9410
 JOA  C07   C  CH2   0  -0.431  -1.0066  -0.1569  -1.5258
 JOA  C08   C  CH1   0  -0.333  -1.7094  -0.8773  -0.3819
 JOA  C09   C  CH1   0   0.071  -0.6768  -1.6762   0.4155
 JOA  N11   N  N     0  -0.600   0.9742   0.0871  -0.1681
 JOA  S12   S  S     0   1.351   2.4998   0.6790  -0.0033
 JOA  O13   O  OS    0  -0.668   2.7846   1.4983  -1.1735
 JOA  O14   O  OS    0  -0.670   3.3795  -0.4440   0.2931
 JOA  O16   O  O2    0  -0.491  -0.2811  -2.7400  -0.4219
 JOA  H102  H  HCH2  0   0.245   0.2426  -0.3103   1.7913
 JOA  H101  H  HCH2  0   0.287   1.3375  -1.4959   1.1425
 JOA  H151  H  HCH3  0   0.289   2.2276   1.1732   2.3124
 JOA  H152  H  HCH3  0   0.307   3.5227   2.1215   1.5508
 JOA  H153  H  HCH3  0   0.288   1.8221   2.5683   1.2752
 JOA  H172  H  HCH3  0   0.207  -0.1795  -4.1461   1.1064
 JOA  H173  H  HCH3  0   0.240   0.4608  -4.6199  -0.4773
 JOA  H171  H  HCH3  0   0.207   1.3910  -3.5349   0.5582
 JOA  H013  H  HCH3  0   0.202  -5.0009   0.5306   1.1891
 JOA  H011  H  HCH3  0   0.204  -4.4224   2.1269   0.6852
 JOA  H012  H  HCH3  0   0.235  -5.5000   1.2097  -0.3697
 JOA  H031  H  HCH1  0   0.221  -2.9046  -0.4146   1.3533
 JOA  H041  H  HCH2  0   0.258  -2.3761   2.1014   1.3008
 JOA  H042  H  HCH2  0   0.237  -1.1229   1.0403   1.8140
 JOA  H051  H  HCH2  0   0.241  -1.3974   2.4615  -0.8684
 JOA  H052  H  HCH2  0   0.243  -0.1142   2.6345   0.2961
 JOA  H061  H  HCH1  0   0.281   0.5051   1.3359  -1.7552
 JOA  H072  H  HCH2  0   0.250  -1.7266   0.3722  -2.1523
 JOA  H071  H  HCH2  0   0.251  -0.4849  -0.8650  -2.1711
 JOA  H081  H  HCH1  0   0.257  -2.4228  -1.6051  -0.7791
 JOA  H091  H  HCH1  0   0.236  -1.1461  -2.0758   1.3274
 JOA  C01   C  CH3   0  -0.402  -4.6672   1.1211   0.3274

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
 JOA  C05  C04   single  1.529  0.020  1.529
 JOA  C05  C06   single  1.529  0.020  1.529
 JOA  O13  S12   double  1.457  0.020  1.457
 JOA  C04  C03   single  1.532  0.020  1.532
 JOA  C06  N11   single  1.475  0.020  1.475
 JOA  C06  C07   single  1.521  0.020  1.521
 JOA  O14  S12   double  1.457  0.020  1.457
 JOA  S12  N11   single  1.645  0.020  1.645
 JOA  S12  C15   single  1.782  0.020  1.782
 JOA  N11  C10   single  1.464  0.020  1.464
 JOA  C03  O02   single  1.416  0.020  1.416
 JOA  C03  C08   single  1.535  0.020  1.535
 JOA  O02  C01   single  1.404  0.020  1.404
 JOA  C07  C08   single  1.524  0.020  1.524
 JOA  C10  C09   single  1.530  0.020  1.530
 JOA  C08  C09   single  1.530  0.020  1.530
 JOA  C09  O16   single  1.411  0.020  1.411
 JOA  O16  C17   single  1.406  0.020  1.406
 JOA  C10  H102  single  0.970  0.020  1.090
 JOA  C10  H101  single  0.970  0.020  1.090
 JOA  C15  H151  single  0.970  0.020  1.090
 JOA  C15  H152  single  0.970  0.020  1.090
 JOA  C15  H153  single  0.970  0.020  1.090
 JOA  C17  H172  single  0.970  0.020  1.090
 JOA  C17  H173  single  0.970  0.020  1.090
 JOA  C17  H171  single  0.970  0.020  1.090
 JOA  C01  H013  single  0.970  0.020  1.090
 JOA  C01  H011  single  0.970  0.020  1.090
 JOA  C01  H012  single  0.970  0.020  1.090
 JOA  C03  H031  single  0.970  0.020  1.090
 JOA  C04  H041  single  0.970  0.020  1.090
 JOA  C04  H042  single  0.970  0.020  1.090
 JOA  C05  H051  single  0.970  0.020  1.090
 JOA  C05  H052  single  0.970  0.020  1.090
 JOA  C06  H061  single  0.970  0.020  1.090
 JOA  C07  H072  single  0.970  0.020  1.090
 JOA  C07  H071  single  0.970  0.020  1.090
 JOA  C08  H081  single  0.970  0.020  1.090
 JOA  C09  H091  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
 JOA  H101  C10  H102  105.79  3.000
 JOA  H101  C10  N11   108.79  3.000
 JOA  H102  C10  N11   112.02  3.000
 JOA  H101  C10  C09   109.12  3.000
 JOA  H102  C10  C09   108.69  3.000
 JOA  N11   C10  C09   112.20  3.000
 JOA  H153  C15  H152  109.73  3.000
 JOA  H153  C15  H151  110.28  3.000
 JOA  H152  C15  H151  109.38  3.000
 JOA  H153  C15  S12   109.72  3.000
 JOA  H152  C15  S12   107.74  3.000
 JOA  H151  C15  S12   109.95  3.000
 JOA  H171  C17  H173  107.75  3.000
 JOA  H171  C17  H172  107.92  3.000
 JOA  H173  C17  H172  108.42  3.000
 JOA  H171  C17  O16   113.18  3.000
 JOA  H173  C17  O16   107.58  3.000
 JOA  H172  C17  O16   111.83  3.000
 JOA  C03   O02  C01   114.89  3.000
 JOA  H031  C03  C08   108.73  3.000
 JOA  H031  C03  C04   108.52  3.000
 JOA  C08   C03  C04   113.42  3.000
 JOA  H031  C03  O02   109.17  3.000
 JOA  C08   C03  O02   105.20  3.000
 JOA  C04   C03  O02   111.68  3.000
 JOA  H042  C04  H041  104.05  3.000
 JOA  H042  C04  C05   110.60  3.000
 JOA  H041  C04  C05   109.31  3.000
 JOA  H042  C04  C03   109.07  3.000
 JOA  H041  C04  C03   109.76  3.000
 JOA  C05   C04  C03   113.61  3.000
 JOA  H052  C05  H051  105.67  3.000
 JOA  H052  C05  C06   111.08  3.000
 JOA  H051  C05  C06   106.64  3.000
 JOA  H052  C05  C04   109.78  3.000
 JOA  H051  C05  C04   109.50  3.000
 JOA  C06   C05  C04   113.80  3.000
 JOA  H061  C06  N11   106.99  3.000
 JOA  H061  C06  C07   108.88  3.000
 JOA  N11   C06  C07   107.34  3.000
 JOA  H061  C06  C05   108.93  3.000
 JOA  C07   C06  C05   109.41  3.000
 JOA  N11   C06  C05   115.14  3.000
 JOA  H071  C07  H072  106.90  3.000
 JOA  H071  C07  C08   110.96  3.000
 JOA  H072  C07  C08   110.85  3.000
 JOA  H071  C07  C06   110.37  3.000
 JOA  H072  C07  C06   109.02  3.000
 JOA  C08   C07  C06   108.73  3.000
 JOA  H081  C08  C09   106.39  3.000
 JOA  H081  C08  C07   110.04  3.000
 JOA  C09   C08  C07   109.08  3.000
 JOA  H081  C08  C03   106.61  3.000
 JOA  C09   C08  C03   113.88  3.000
 JOA  C07   C08  C03   110.70  3.000
 JOA  H091  C09  O16   109.73  3.000
 JOA  H091  C09  C08   109.49  3.000
 JOA  O16   C09  C08   105.89  3.000
 JOA  H091  C09  C10   106.53  3.000
 JOA  O16   C09  C10   111.97  3.000
 JOA  C08   C09  C10   113.24  3.000
 JOA  S12   N11  C06   119.74  3.000
 JOA  S12   N11  C10   116.47  3.000
 JOA  C06   N11  C10   118.98  3.000
 JOA  O14   S12  O13   118.61  3.000
 JOA  O14   S12  N11   107.64  3.000
 JOA  O13   S12  N11   107.65  3.000
 JOA  N11   S12  C15   107.47  3.000
 JOA  O14   S12  C15   106.99  3.000
 JOA  O13   S12  C15   108.01  3.000
 JOA  C09   O16  C17   115.00  3.000
 JOA  H012  C01  H011  107.76  3.000
 JOA  H012  C01  H013  108.29  3.000
 JOA  H011  C01  H013  107.80  3.000
 JOA  H012  C01  O02   107.65  3.000
 JOA  H011  C01  O02   113.27  3.000
 JOA  H013  C01  O02   111.88  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
 JOA  Var_01  C06   C05  C04  C03  -44.44  30.0  3
 JOA  Var_02  C09   C10  N11  C06   43.80  30.0  1
 JOA  Var_03  O13   S12  N11  C10  176.50  30.0  3
 JOA  Var_04  H013  C01  O02  C03  -51.37  30.0  3
 JOA  Var_05  H172  C17  O16  C09   50.64  30.0  3
 JOA  Var_06  H151  C15  S12  N11   59.93  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
 JOA  chir_01  C03  C04  O02  C08  negativ
 JOA  chir_02  C06  N11  C05  C07  positiv
 JOA  chir_03  C08  C09  C07  C03  positiv
 JOA  chir_04  C09  O16  C08  C10  positiv

