# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:07:09 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: methyl (1S,3S,4R)-4-hydroxy-3-[(1S)-1-hydroxypropyl]-2-azabicyclo[2.2.2]octane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](O)[C@@H]1N(C2CCC1(O)CC2)C(=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
 JPD  JPD  'methyl (1S,3S,4R)-4-hydroxy-3-[(1S)-1-hydroxypropyl]-2-azabicyclo[2.2.2]octane-2-carboxylate'  ligand  38  17  .  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_JPD
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
 JPD  C10   C  CT    0   0.244   1.8454  -0.2140  -0.3584
 JPD  C13   C  CH2   0  -0.441   0.8478  -2.5218  -0.0863
 JPD  C17   C  CH3   0  -0.413  -3.5995  -2.0218  -0.7937
 JPD  C03   C  CH1   0   0.074   0.3399   1.7917   0.3871
 JPD  O04   O  OH1   0  -0.658   1.3148   2.7240  -0.0222
 JPD  C05   C  CH1   0  -0.143   0.4580   0.4709  -0.4064
 JPD  N06   N  NT    0  -0.487  -0.5042  -0.5254   0.0771
 JPD  C07   C  CH1   0  -0.146   0.0919  -1.6082   0.8753
 JPD  C08   C  CH2   0  -0.457   1.0861  -1.0143   1.8678
 JPD  C09   C  CH2   0  -0.492   2.2691  -0.3943   1.1015
 JPD  O11   O  OH1   0  -0.673   2.7467   0.5635  -1.1082
 JPD  C12   C  CH2   0  -0.468   1.6963  -1.6096  -0.9879
 JPD  C14   C  C     0   0.761  -1.6550  -0.7116  -0.6174
 JPD  O15   O  O     0  -0.516  -2.0389  -0.0125  -1.5341
 JPD  O16   O  O2    0  -0.477  -2.3533  -1.7538  -0.1609
 JPD  H132  H  HCH2  0   0.240   1.4716  -3.2160   0.4813
 JPD  H131  H  HCH2  0   0.247   0.1591  -3.1271  -0.6772
 JPD  H171  H  HCH3  0   0.247  -4.0116  -2.8853  -0.2791
 JPD  H172  H  HCH3  0   0.233  -4.2905  -1.1848  -0.6959
 JPD  H173  H  HCH3  0   0.234  -3.4742  -2.2616  -1.8494
 JPD  H013  H  HCH3  0   0.225  -2.1997   4.0627   1.1078
 JPD  H011  H  HCH3  0   0.214  -0.8938   3.5399   2.1653
 JPD  H012  H  HCH3  0   0.220  -0.5356   4.4738   0.7154
 JPD  H031  H  HCH1  0   0.217   0.5621   1.5931   1.4402
 JPD  H041  H  HOH1  0   0.437   1.2214   2.8708  -0.9693
 JPD  H051  H  HCH1  0   0.258   0.2373   0.6840  -1.4584
 JPD  H071  H  HCH1  0   0.268  -0.6884  -2.1348   1.4184
 JPD  H081  H  HCH2  0   0.247   0.5816  -0.2794   2.4984
 JPD  H082  H  HCH2  0   0.254   1.4239  -1.8120   2.5301
 JPD  H092  H  HCH2  0   0.241   3.1437  -1.0505   1.1411
 JPD  H091  H  HCH2  0   0.252   2.5718   0.5580   1.5391
 JPD  H111  H  HOH1  0   0.442   3.5750   0.0755  -1.1685
 JPD  H121  H  HCH2  0   0.240   1.2455  -1.5068  -1.9793
 JPD  H122  H  HCH2  0   0.242   2.6913  -2.0373  -1.1414
 JPD  C02   C  CH2   0  -0.446  -1.0622   2.3960   0.3258
 JPD  H021  H  HCH2  0   0.223  -1.7775   1.6758   0.7255
 JPD  C01   C  CH3   0  -0.660  -1.1748   3.6903   1.1205
 JPD  H022  H  HCH2  0   0.217  -1.3452   2.5702  -0.7167

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
 JPD  O11  C10   single  1.407  0.020  1.407
 JPD  C09  C10   single  1.531  0.020  1.531
 JPD  C09  C08   single  1.540  0.020  1.540
 JPD  C12  C10   single  1.538  0.020  1.538
 JPD  C12  C13   single  1.538  0.020  1.538
 JPD  C10  C05   single  1.548  0.020  1.548
 JPD  C08  C07   single  1.525  0.020  1.525
 JPD  C02  C01   single  1.523  0.020  1.523
 JPD  C02  C03   single  1.528  0.020  1.528
 JPD  C13  C07   single  1.527  0.020  1.527
 JPD  C05  C03   single  1.545  0.020  1.545
 JPD  C05  N06   single  1.467  0.020  1.467
 JPD  C03  O04   single  1.410  0.020  1.410
 JPD  C07  N06   single  1.471  0.020  1.471
 JPD  N06  C14   single  1.357  0.020  1.357
 JPD  C14  O16   single  1.335  0.020  1.335
 JPD  C14  O15   double  1.215  0.020  1.215
 JPD  O16  C17   single  1.423  0.020  1.423
 JPD  C13  H132  single  0.970  0.020  1.090
 JPD  C13  H131  single  0.970  0.020  1.090
 JPD  C17  H171  single  0.970  0.020  1.090
 JPD  C17  H172  single  0.970  0.020  1.090
 JPD  C17  H173  single  0.970  0.020  1.090
 JPD  C01  H013  single  0.970  0.020  1.090
 JPD  C01  H011  single  0.970  0.020  1.090
 JPD  C01  H012  single  0.970  0.020  1.090
 JPD  C02  H021  single  0.970  0.020  1.090
 JPD  C02  H022  single  0.970  0.020  1.090
 JPD  C03  H031  single  0.970  0.020  1.090
 JPD  O04  H041  single  0.850  0.020  0.980
 JPD  C05  H051  single  0.970  0.020  1.090
 JPD  C07  H071  single  0.970  0.020  1.090
 JPD  C08  H081  single  0.970  0.020  1.090
 JPD  C08  H082  single  0.970  0.020  1.090
 JPD  C09  H092  single  0.970  0.020  1.090
 JPD  C09  H091  single  0.970  0.020  1.090
 JPD  O11  H111  single  0.850  0.020  0.980
 JPD  C12  H121  single  0.970  0.020  1.090
 JPD  C12  H122  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
 JPD  C12   C10  O11   110.20  3.000
 JPD  C12   C10  C09   108.08  3.000
 JPD  O11   C10  C09   113.33  3.000
 JPD  C12   C10  C05   107.57  3.000
 JPD  C09   C10  C05   109.26  3.000
 JPD  O11   C10  C05   108.25  3.000
 JPD  H131  C13  H132  106.82  3.000
 JPD  H131  C13  C12   111.09  3.000
 JPD  H132  C13  C12   111.50  3.000
 JPD  H131  C13  C07   111.14  3.000
 JPD  H132  C13  C07   109.62  3.000
 JPD  C12   C13  C07   106.71  3.000
 JPD  H173  C17  H172  109.20  3.000
 JPD  H173  C17  H171  109.13  3.000
 JPD  H172  C17  H171  109.12  3.000
 JPD  H173  C17  O16   111.80  3.000
 JPD  H172  C17  O16   111.75  3.000
 JPD  H171  C17  O16   105.74  3.000
 JPD  H031  C03  C05   108.88  3.000
 JPD  H031  C03  O04   105.01  3.000
 JPD  C05   C03  O04   111.30  3.000
 JPD  H031  C03  C02   107.26  3.000
 JPD  O04   C03  C02   111.18  3.000
 JPD  C05   C03  C02   112.80  3.000
 JPD  H041  O04  C03   108.62  3.000
 JPD  H051  C05  N06   108.44  3.000
 JPD  H051  C05  C03   108.14  3.000
 JPD  N06   C05  C03   111.16  3.000
 JPD  H051  C05  C10   107.24  3.000
 JPD  N06   C05  C10   106.09  3.000
 JPD  C03   C05  C10   115.51  3.000
 JPD  C14   N06  C07   121.35  3.000
 JPD  C14   N06  C05   118.73  3.000
 JPD  C07   N06  C05   114.38  3.000
 JPD  H071  C07  C08   109.36  3.000
 JPD  H071  C07  N06   109.68  3.000
 JPD  C08   C07  N06   109.30  3.000
 JPD  H071  C07  C13   112.36  3.000
 JPD  N06   C07  C13   107.42  3.000
 JPD  C08   C07  C13   108.67  3.000
 JPD  H082  C08  H081  106.54  3.000
 JPD  H082  C08  C09   111.03  3.000
 JPD  H081  C08  C09   111.80  3.000
 JPD  H082  C08  C07   108.20  3.000
 JPD  H081  C08  C07   109.67  3.000
 JPD  C09   C08  C07   109.49  3.000
 JPD  H091  C09  H092  106.69  3.000
 JPD  H091  C09  C08   111.41  3.000
 JPD  H092  C09  C08   110.77  3.000
 JPD  H091  C09  C10   110.89  3.000
 JPD  H092  C09  C10   109.06  3.000
 JPD  C08   C09  C10   108.02  3.000
 JPD  H111  O11  C10   107.72  3.000
 JPD  H122  C12  H121  106.53  3.000
 JPD  H122  C12  C13   110.62  3.000
 JPD  H121  C12  C13   111.08  3.000
 JPD  H122  C12  C10   108.91  3.000
 JPD  H121  C12  C10   109.00  3.000
 JPD  C13   C12  C10   110.59  3.000
 JPD  O16   C14  O15   122.81  3.000
 JPD  O15   C14  N06   125.11  3.000
 JPD  O16   C14  N06   112.07  3.000
 JPD  C14   O16  C17   116.94  3.000
 JPD  H022  C02  H021  106.54  3.000
 JPD  H022  C02  C03   109.78  3.000
 JPD  H021  C02  C03   109.02  3.000
 JPD  H022  C02  C01   110.05  3.000
 JPD  H021  C02  C01   108.75  3.000
 JPD  C03   C02  C01   112.52  3.000
 JPD  H012  C01  H011  107.69  3.000
 JPD  H012  C01  H013  107.55  3.000
 JPD  H011  C01  H013  107.46  3.000
 JPD  H012  C01  C02   111.95  3.000
 JPD  H011  C01  C02   111.29  3.000
 JPD  H013  C01  C02   110.70  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
 JPD  Var_01  C07   C08  C09  C10    16.74  30.0  1
 JPD  Var_02  C07   C13  C12  C10    17.77  30.0  1
 JPD  Var_03  O16   C14  N06  C05   172.32  30.0  2
 JPD  Var_04  N06   C14  O16  C17   178.37  30.0  1
 JPD  Var_05  H013  C01  C02  C03  -176.50  30.0  3
 JPD  Var_06  H171  C17  O16  C14  -179.31  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
 JPD  chir_01  C10  C09  C12  C05  negativ
 JPD  chir_02  C03  O04  C05  C02  positiv
 JPD  chir_03  C05  N06  C03  C10  negativ
 JPD  chir_04  C07  N06  C08  C13  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
 JPD  plan-1  N06  0.020
 JPD  plan-1  C14  0.020
 JPD  plan-1  O15  0.020
 JPD  plan-1  O16  0.020

