# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:43:27 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (1R,3R,4S)-3-(methoxymethyl)-2-(methylsulfonyl)-2-azabicyclo[2.2.2]octan-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H]1N(C2CCC1(O)CC2)[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
 JKJ  JKJ  (1R,3R,4S)-3-(methoxymethyl)-2-(methylsulfonyl)-2-azabicyclo[2.2.2]octan-4-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_JKJ
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
 JKJ  C01   C  CH3   0  -0.399  -2.0949   3.1173  -0.7500
 JKJ  O02   O  O2    0  -0.483  -1.4823   2.0473  -0.0765
 JKJ  C03   C  CH2   0  -0.105  -0.1017   1.9783  -0.3207
 JKJ  C04   C  CH1   0  -0.103   0.4636   0.7724   0.4153
 JKJ  N05   N  N     0  -0.612  -0.0502  -0.4919  -0.1290
 JKJ  C06   C  CH1   0  -0.137   0.9394  -1.3148  -0.8448
 JKJ  C07   C  CH2   0  -0.426   1.9703  -1.8290   0.1546
 JKJ  C08   C  CH2   0  -0.458   2.4308  -0.6312   1.0058
 JKJ  C09   C  CT    0   0.208   2.0007   0.6822   0.3420
 JKJ  O10   O  OH1   0  -0.677   2.4949   1.8021   1.0368
 JKJ  C11   C  CH2   0  -0.494   2.4489   0.6533  -1.1227
 JKJ  C12   C  CH2   0  -0.442   1.6335  -0.4198  -1.8670
 JKJ  S13   S  S     0   1.357  -1.4000  -1.2042   0.4795
 JKJ  O14   O  OS    0  -0.673  -1.1725  -2.6437   0.5775
 JKJ  O15   O  OS    0  -0.665  -1.8101  -0.4926   1.6822
 JKJ  C16   C  CH3   0  -0.785  -2.6399  -0.9713  -0.7715
 JKJ  H013  H  HCH3  0   0.209  -1.6986   4.0863  -0.4241
 JKJ  H011  H  HCH3  0   0.205  -1.9648   3.0483  -1.8366
 JKJ  H012  H  HCH3  0   0.235  -3.1611   3.0883  -0.5286
 JKJ  H031  H  HCH2  0   0.203   0.0909   1.8926  -1.3989
 JKJ  H032  H  HCH2  0   0.211   0.3990   2.8908   0.0285
 JKJ  H041  H  HCH1  0   0.273   0.1948   0.8569   1.4722
 JKJ  H061  H  HCH1  0   0.269   0.4306  -2.1294  -1.3580
 JKJ  H072  H  HCH2  0   0.249   1.5414  -2.6125   0.7777
 JKJ  H071  H  HCH2  0   0.236   2.8061  -2.2738  -0.3894
 JKJ  H082  H  HCH2  0   0.241   2.0086  -0.6807   2.0131
 JKJ  H081  H  HCH2  0   0.245   3.5183  -0.6318   1.1184
 JKJ  H101  H  HOH1  0   0.449   3.4557   1.7988   0.9681
 JKJ  H112  H  HCH2  0   0.254   2.3239   1.6360  -1.5809
 JKJ  H111  H  HCH2  0   0.247   3.5182   0.4249  -1.1608
 JKJ  H122  H  HCH2  0   0.255   2.2784  -1.0372  -2.4932
 JKJ  H121  H  HCH2  0   0.248   0.8879   0.0314  -2.5244
 JKJ  H162  H  HCH3  0   0.282  -2.2992  -1.4323  -1.6962
 JKJ  H163  H  HCH3  0   0.289  -3.5563  -1.4532  -0.4347
 JKJ  H161  H  HCH3  0   0.292  -2.7999   0.0920  -0.9167

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
 JKJ  C01  O02   single  1.405  0.020  1.405
 JKJ  O02  C03   single  1.404  0.020  1.404
 JKJ  O15  S13   double  1.456  0.020  1.456
 JKJ  C03  C04   single  1.522  0.020  1.522
 JKJ  C12  C11   single  1.540  0.020  1.540
 JKJ  C12  C06   single  1.526  0.020  1.526
 JKJ  S13  N05   single  1.643  0.020  1.643
 JKJ  S13  O14   double  1.461  0.020  1.461
 JKJ  S13  C16   single  1.777  0.020  1.777
 JKJ  C11  C09   single  1.532  0.020  1.532
 JKJ  N05  C04   single  1.469  0.020  1.469
 JKJ  N05  C06   single  1.473  0.020  1.473
 JKJ  C04  C09   single  1.542  0.020  1.542
 JKJ  C06  C07   single  1.525  0.020  1.525
 JKJ  C09  O10   single  1.408  0.020  1.408
 JKJ  C09  C08   single  1.533  0.020  1.533
 JKJ  C07  C08   single  1.540  0.020  1.540
 JKJ  C01  H013  single  0.970  0.020  1.090
 JKJ  C01  H011  single  0.970  0.020  1.090
 JKJ  C01  H012  single  0.970  0.020  1.090
 JKJ  C03  H031  single  0.970  0.020  1.090
 JKJ  C03  H032  single  0.970  0.020  1.090
 JKJ  C04  H041  single  0.970  0.020  1.090
 JKJ  C06  H061  single  0.970  0.020  1.090
 JKJ  C07  H072  single  0.970  0.020  1.090
 JKJ  C07  H071  single  0.970  0.020  1.090
 JKJ  C08  H082  single  0.970  0.020  1.090
 JKJ  C08  H081  single  0.970  0.020  1.090
 JKJ  O10  H101  single  0.850  0.020  0.980
 JKJ  C11  H112  single  0.970  0.020  1.090
 JKJ  C11  H111  single  0.970  0.020  1.090
 JKJ  C12  H122  single  0.970  0.020  1.090
 JKJ  C12  H121  single  0.970  0.020  1.090
 JKJ  C16  H162  single  0.970  0.020  1.090
 JKJ  C16  H163  single  0.970  0.020  1.090
 JKJ  C16  H161  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
 JKJ  H012  C01  H011  108.41  3.000
 JKJ  H012  C01  H013  108.47  3.000
 JKJ  H011  C01  H013  107.90  3.000
 JKJ  H012  C01  O02   108.01  3.000
 JKJ  H011  C01  O02   112.04  3.000
 JKJ  H013  C01  O02   111.90  3.000
 JKJ  C03   O02  C01   112.52  3.000
 JKJ  H032  C03  H031  107.28  3.000
 JKJ  H032  C03  C04   109.60  3.000
 JKJ  H031  C03  C04   110.35  3.000
 JKJ  H032  C03  O02   110.63  3.000
 JKJ  H031  C03  O02   110.30  3.000
 JKJ  C04   C03  O02   108.68  3.000
 JKJ  H041  C04  C09   107.19  3.000
 JKJ  H041  C04  N05   109.79  3.000
 JKJ  C09   C04  N05   106.30  3.000
 JKJ  H041  C04  C03   108.35  3.000
 JKJ  C09   C04  C03   113.19  3.000
 JKJ  N05   C04  C03   111.89  3.000
 JKJ  S13   N05  C06   119.33  3.000
 JKJ  C06   N05  C04   115.21  3.000
 JKJ  S13   N05  C04   121.54  3.000
 JKJ  H061  C06  C12   109.61  3.000
 JKJ  H061  C06  C07   111.86  3.000
 JKJ  C12   C06  C07   109.22  3.000
 JKJ  H061  C06  N05   109.46  3.000
 JKJ  C07   C06  N05   108.91  3.000
 JKJ  C12   C06  N05   107.68  3.000
 JKJ  H071  C07  H072  107.06  3.000
 JKJ  H071  C07  C08   111.30  3.000
 JKJ  H072  C07  C08   111.16  3.000
 JKJ  H071  C07  C06   109.17  3.000
 JKJ  H072  C07  C06   110.57  3.000
 JKJ  C08   C07  C06   107.58  3.000
 JKJ  H081  C08  H082  106.81  3.000
 JKJ  H081  C08  C09   108.91  3.000
 JKJ  H082  C08  C09   109.23  3.000
 JKJ  H081  C08  C07   110.73  3.000
 JKJ  H082  C08  C07   111.02  3.000
 JKJ  C09   C08  C07   110.07  3.000
 JKJ  C11   C09  O10   112.60  3.000
 JKJ  O10   C09  C08   111.68  3.000
 JKJ  C11   C09  C08   108.40  3.000
 JKJ  C08   C09  C04   108.01  3.000
 JKJ  O10   C09  C04   106.27  3.000
 JKJ  C11   C09  C04   109.77  3.000
 JKJ  H101  O10  C09   108.20  3.000
 JKJ  H111  C11  H112  106.57  3.000
 JKJ  H111  C11  C12   110.82  3.000
 JKJ  H112  C11  C12   111.34  3.000
 JKJ  H111  C11  C09   108.85  3.000
 JKJ  H112  C11  C09   110.54  3.000
 JKJ  C12   C11  C09   108.69  3.000
 JKJ  H121  C12  H122  106.98  3.000
 JKJ  H121  C12  C11   111.39  3.000
 JKJ  H122  C12  C11   111.04  3.000
 JKJ  H121  C12  C06   109.58  3.000
 JKJ  H122  C12  C06   108.77  3.000
 JKJ  C11   C12  C06   109.02  3.000
 JKJ  C16   S13  O15   108.72  3.000
 JKJ  C16   S13  O14   106.57  3.000
 JKJ  O15   S13  O14   118.03  3.000
 JKJ  C16   S13  N05   104.82  3.000
 JKJ  O14   S13  N05   108.91  3.000
 JKJ  O15   S13  N05   108.99  3.000
 JKJ  H161  C16  H163  110.55  3.000
 JKJ  H161  C16  H162  110.35  3.000
 JKJ  H163  C16  H162  109.81  3.000
 JKJ  H161  C16  S13   109.00  3.000
 JKJ  H163  C16  S13   108.15  3.000
 JKJ  H162  C16  S13   108.93  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
 JKJ  Var_01  C09   C11  C12  C06   -14.50  30.0  3
 JKJ  Var_02  C09   C08  C07  C06   -14.77  30.0  1
 JKJ  Var_03  O15   S13  N05  C04    -7.97  30.0  2
 JKJ  Var_04  C04   C03  O02  C01  -178.44  30.0  3
 JKJ  Var_05  H162  C16  S13  N05    58.98  30.0  3
 JKJ  Var_06  H013  C01  O02  C03   -61.94  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
 JKJ  chir_01  C04  C03  N05  C09  negativ
 JKJ  chir_02  C06  N05  C12  C07  negativ
 JKJ  chir_03  C09  C08  C04  C11  positiv

