# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:08:30 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (1S,4R,5S,6R)-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonane-4,6-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N1C[C@H](O)[C@H]2C[C@@H]1CC[C@H]2O
#
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
 JKA  JKA  (1S,4R,5S,6R)-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonane-4,6-diol  ligand  32  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 OK
;

data_comp_JKA
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
 JKA  C10   C  CH2   0  -0.453  -0.8936  -0.6687  -1.6841
 JKA  C13   C  CH2   0  -0.507  -1.7442  -1.4373   1.0224
 JKA  C01   C  CH3   0  -0.782   3.0326   0.8882  -1.2137
 JKA  S02   S  S     0   1.346   2.3576   0.0980   0.2306
 JKA  O03   O  OS    0  -0.668   2.8636  -1.2689   0.2595
 JKA  O04   O  OS    0  -0.668   2.6160   0.9631   1.3747
 JKA  N05   N  N     0  -0.610   0.7432   0.0494  -0.0255
 JKA  C06   C  CH2   0  -0.323  -0.0931   1.1476   0.4535
 JKA  C07   C  CH1   0   0.077  -1.2797   1.4171  -0.4806
 JKA  O08   O  OH1   0  -0.658  -2.1864   2.2885   0.1477
 JKA  C09   C  CH1   0  -0.320  -1.9735   0.1522  -0.9808
 JKA  C11   C  CH1   0  -0.107   0.1357  -1.1284  -0.6608
 JKA  C12   C  CH2   0  -0.416  -0.5227  -2.0632   0.3505
 JKA  C14   C  CH1   0   0.093  -2.6835  -0.7633   0.0219
 JKA  O15   O  OH1   0  -0.667  -3.7191  -0.0583   0.6684
 JKA  H101  H  HCH2  0   0.253  -1.3277  -1.5485  -2.1660
 JKA  H102  H  HCH2  0   0.253  -0.4146  -0.0808  -2.4709
 JKA  H131  H  HCH2  0   0.244  -2.2986  -2.2188   1.5511
 JKA  H132  H  HCH2  0   0.233  -1.4401  -0.7236   1.7894
 JKA  H011  H  HCH3  0   0.286   2.7829   0.2943  -2.0902
 JKA  H012  H  HCH3  0   0.285   2.6117   1.8869  -1.3089
 JKA  H013  H  HCH3  0   0.295   4.1140   0.9512  -1.1040
 JKA  H062  H  HCH2  0   0.246  -0.4562   0.9586   1.4658
 JKA  H061  H  HCH2  0   0.267   0.5022   2.0608   0.5030
 JKA  H071  H  HCH1  0   0.214  -0.8717   1.8883  -1.3874
 JKA  H081  H  HOH1  0   0.449  -1.7688   3.1537   0.2078
 JKA  H091  H  HCH1  0   0.253  -2.7180   0.4646  -1.7206
 JKA  H111  H  HCH1  0   0.275   0.9236  -1.6723  -1.1810
 JKA  H122  H  HCH2  0   0.243   0.2041  -2.3780   1.1012
 JKA  H121  H  HCH2  0   0.228  -0.8264  -2.9657  -0.1890
 JKA  H141  H  HCH1  0   0.197  -3.1134  -1.5678  -0.5973
 JKA  H151  H  HOH1  0   0.444  -4.2160  -0.6900   1.1980

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
 JKA  O04  S02   double  1.457  0.020  1.457
 JKA  C06  N05   single  1.461  0.020  1.461
 JKA  C06  C07   single  1.534  0.020  1.534
 JKA  N05  S02   single  1.635  0.020  1.635
 JKA  N05  C11   single  1.470  0.020  1.470
 JKA  S02  O03   double  1.458  0.020  1.458
 JKA  S02  C01   single  1.779  0.020  1.779
 JKA  C13  C12   single  1.528  0.020  1.528
 JKA  C13  C14   single  1.529  0.020  1.529
 JKA  O15  C14   single  1.410  0.020  1.410
 JKA  C12  C11   single  1.526  0.020  1.526
 JKA  O08  C07   single  1.406  0.020  1.406
 JKA  C07  C09   single  1.527  0.020  1.527
 JKA  C14  C09   single  1.532  0.020  1.532
 JKA  C11  C10   single  1.522  0.020  1.522
 JKA  C09  C10   single  1.528  0.020  1.528
 JKA  C10  H101  single  0.970  0.020  1.090
 JKA  C10  H102  single  0.970  0.020  1.090
 JKA  C13  H131  single  0.970  0.020  1.090
 JKA  C13  H132  single  0.970  0.020  1.090
 JKA  C01  H011  single  0.970  0.020  1.090
 JKA  C01  H012  single  0.970  0.020  1.090
 JKA  C01  H013  single  0.970  0.020  1.090
 JKA  C06  H062  single  0.970  0.020  1.090
 JKA  C06  H061  single  0.970  0.020  1.090
 JKA  C07  H071  single  0.970  0.020  1.090
 JKA  O08  H081  single  0.850  0.020  0.980
 JKA  C09  H091  single  0.970  0.020  1.090
 JKA  C11  H111  single  0.970  0.020  1.090
 JKA  C12  H122  single  0.970  0.020  1.090
 JKA  C12  H121  single  0.970  0.020  1.090
 JKA  C14  H141  single  0.970  0.020  1.090
 JKA  O15  H151  single  0.850  0.020  0.980

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
 JKA  H102  C10  H101  106.84  3.000
 JKA  H102  C10  C11   110.49  3.000
 JKA  H101  C10  C11   108.77  3.000
 JKA  H102  C10  C09   110.62  3.000
 JKA  H101  C10  C09   110.78  3.000
 JKA  C11   C10  C09   109.31  3.000
 JKA  H132  C13  H131  105.59  3.000
 JKA  H132  C13  C14   110.06  3.000
 JKA  H131  C13  C14   108.64  3.000
 JKA  H132  C13  C12   110.75  3.000
 JKA  H131  C13  C12   108.96  3.000
 JKA  C14   C13  C12   112.58  3.000
 JKA  H013  C01  H012  109.87  3.000
 JKA  H013  C01  H011  109.93  3.000
 JKA  H012  C01  H011  109.99  3.000
 JKA  H013  C01  S02   108.71  3.000
 JKA  H012  C01  S02   109.38  3.000
 JKA  H011  C01  S02   108.93  3.000
 JKA  N05   S02  O04   108.40  3.000
 JKA  N05   S02  O03   108.53  3.000
 JKA  O04   S02  O03   118.65  3.000
 JKA  O03   S02  C01   107.51  3.000
 JKA  N05   S02  C01   105.11  3.000
 JKA  O04   S02  C01   107.84  3.000
 JKA  C11   N05  C06   120.50  3.000
 JKA  C11   N05  S02   119.98  3.000
 JKA  C06   N05  S02   119.43  3.000
 JKA  H061  C06  H062  106.52  3.000
 JKA  H061  C06  C07   107.61  3.000
 JKA  H062  C06  C07   109.73  3.000
 JKA  H061  C06  N05   109.37  3.000
 JKA  H062  C06  N05   111.36  3.000
 JKA  C07   C06  N05   112.03  3.000
 JKA  H071  C07  C09   104.67  3.000
 JKA  H071  C07  O08   110.00  3.000
 JKA  C09   C07  O08   111.52  3.000
 JKA  H071  C07  C06   106.87  3.000
 JKA  C09   C07  C06   113.92  3.000
 JKA  O08   C07  C06   109.61  3.000
 JKA  H081  O08  C07   107.77  3.000
 JKA  H091  C09  C14   107.31  3.000
 JKA  H091  C09  C07   107.09  3.000
 JKA  C14   C09  C07   119.42  3.000
 JKA  H091  C09  C10   108.83  3.000
 JKA  C14   C09  C10   107.92  3.000
 JKA  C07   C09  C10   105.95  3.000
 JKA  H111  C11  C12   108.82  3.000
 JKA  H111  C11  N05   107.91  3.000
 JKA  C12   C11  N05   112.50  3.000
 JKA  H111  C11  C10   108.58  3.000
 JKA  C12   C11  C10   109.79  3.000
 JKA  N05   C11  C10   109.15  3.000
 JKA  H121  C12  H122  106.62  3.000
 JKA  H121  C12  C11   107.35  3.000
 JKA  H122  C12  C11   110.19  3.000
 JKA  H121  C12  C13   109.43  3.000
 JKA  H122  C12  C13   110.37  3.000
 JKA  C11   C12  C13   112.66  3.000
 JKA  H141  C14  O15   109.64  3.000
 JKA  H141  C14  C09   104.43  3.000
 JKA  O15   C14  C09   109.98  3.000
 JKA  H141  C14  C13   106.58  3.000
 JKA  C09   C14  C13   114.01  3.000
 JKA  O15   C14  C13   111.82  3.000
 JKA  H151  O15  C14   107.66  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
 JKA  Var_01  C11   N05  C06  C07  -37.63  30.0  3
 JKA  Var_02  C14   C13  C12  C11   46.52  30.0  1
 JKA  Var_03  C06   N05  S02  C01  -91.46  30.0  1
 JKA  Var_04  H011  C01  S02  N05  -60.21  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
 JKA  chir_01  C07  C06  O08  C09  positiv
 JKA  chir_02  C09  C10  C14  C07  negativ
 JKA  chir_03  C11  N05  C10  C12  positiv
 JKA  chir_04  C14  O15  C13  C09  positiv

