# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:05:32 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (3-exo)-8-methyl-8-azabicyclo[3.2.1]octan-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H]2CC[C@@H]1CC(O)C2
#
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
 PTO  PTO  (3-exo)-8-methyl-8-azabicyclo[3.2.1]octan-3-ol  ligand  25  10  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PTO
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
 PTO  C1   C  CR15  0  -0.131   0.6057  -1.1303   0.0299
 PTO  C2   C  CH2   0  -0.434  -0.8844  -1.2467   0.3469
 PTO  C3   C  CH1   0   0.051  -1.6319   0.0057  -0.0925
 PTO  C4   C  CH2   0  -0.450  -0.8709   1.2655   0.3205
 PTO  C5   C  CR15  0  -0.130   0.6188   1.1367   0.0059
 PTO  C6   C  CH2   0  -0.472   0.8672   0.7579  -1.4744
 PTO  C7   C  CH2   0  -0.474   0.8574  -0.7850  -1.4582
 PTO  N8   N  NR5   0  -0.396   1.1377   0.0082   0.7774
 PTO  C9   C  CH3   0  -0.526   2.5835   0.0007   0.8718
 PTO  O3   O  OH1   0  -0.677  -2.9358  -0.0406   0.4555
 PTO  H1   H  HCR5  0   0.237   1.1117  -2.0498   0.3326
 PTO  H21  H  HCH2  0   0.231  -1.3056  -2.1271  -0.1461
 PTO  H22  H  HCH2  0   0.223  -1.0022  -1.3869   1.4256
 PTO  H3   H  HCH1  0   0.199  -1.6972  -0.0070  -1.1901
 PTO  H41  H  HCH2  0   0.222  -0.9899   1.4251   1.3963
 PTO  H42  H  HCH2  0   0.228  -1.2892   2.1395  -0.1884
 PTO  H5   H  HCR5  0   0.236   1.1315   2.0579   0.2915
 PTO  H61  H  HCH2  0   0.238   0.1105   1.1798  -2.1383
 PTO  H62  H  HCH2  0   0.241   1.8307   1.1409  -1.8134
 PTO  H71  H  HCH2  0   0.238   0.0938  -1.2102  -2.1119
 PTO  H72  H  HCH2  0   0.241   1.8151  -1.1876  -1.7910
 PTO  H91  H  HCH3  0   0.231   2.9190   0.8875   1.4119
 PTO  H92  H  HCH3  0   0.231   2.9083  -0.8721   1.4405
 PTO  H93  H  HCH3  0   0.198   3.1155  -0.0181  -0.0898
 PTO  HO3  H  HOH1  0   0.446  -3.4296   0.7114   0.1140

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
 PTO  C1  C2   single  1.528  0.020  1.528
 PTO  C1  C7   single  1.548  0.020  1.548
 PTO  C1  N8   single  1.462  0.020  1.462
 PTO  C1  H1   single  0.970  0.020  1.090
 PTO  C2  C3   single  1.523  0.020  1.523
 PTO  C2  H21  single  0.970  0.020  1.090
 PTO  C2  H22  single  0.970  0.020  1.090
 PTO  C3  C4   single  1.529  0.020  1.529
 PTO  C3  O3   single  1.415  0.020  1.415
 PTO  C3  H3   single  0.970  0.020  1.090
 PTO  C4  C5   single  1.528  0.020  1.528
 PTO  C4  H41  single  0.970  0.020  1.090
 PTO  C4  H42  single  0.970  0.020  1.090
 PTO  C5  C6   single  1.548  0.020  1.548
 PTO  C5  N8   single  1.462  0.020  1.462
 PTO  C5  H5   single  0.970  0.020  1.090
 PTO  C6  C7   single  1.543  0.020  1.543
 PTO  C6  H61  single  0.970  0.020  1.090
 PTO  C6  H62  single  0.970  0.020  1.090
 PTO  C7  H71  single  0.970  0.020  1.090
 PTO  C7  H72  single  0.970  0.020  1.090
 PTO  N8  C9   single  1.449  0.020  1.449
 PTO  C9  H91  single  0.970  0.020  1.090
 PTO  C9  H92  single  0.970  0.020  1.090
 PTO  C9  H93  single  0.970  0.020  1.090
 PTO  O3  HO3  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
 PTO  H1   C1  N8   110.20  3.000
 PTO  H1   C1  C7   112.26  3.000
 PTO  N8   C1  C7   104.98  3.000
 PTO  H1   C1  C2   109.28  3.000
 PTO  N8   C1  C2   107.94  3.000
 PTO  C7   C1  C2   112.02  3.000
 PTO  H22  C2  H21  107.45  3.000
 PTO  H22  C2  C3   109.68  3.000
 PTO  H21  C2  C3   110.05  3.000
 PTO  H22  C2  C1   108.62  3.000
 PTO  H21  C2  C1   110.09  3.000
 PTO  C3   C2  C1   110.86  3.000
 PTO  H3   C3  O3   109.35  3.000
 PTO  H3   C3  C4   107.98  3.000
 PTO  O3   C3  C4   112.40  3.000
 PTO  H3   C3  C2   107.91  3.000
 PTO  O3   C3  C2   108.28  3.000
 PTO  C4   C3  C2   110.81  3.000
 PTO  H42  C4  H41  107.40  3.000
 PTO  H42  C4  C5   110.13  3.000
 PTO  H41  C4  C5   108.71  3.000
 PTO  H42  C4  C3   110.02  3.000
 PTO  H41  C4  C3   109.38  3.000
 PTO  C5   C4  C3   111.11  3.000
 PTO  H5   C5  N8   110.26  3.000
 PTO  H5   C5  C6   112.40  3.000
 PTO  N8   C5  C6   105.00  3.000
 PTO  H5   C5  C4   109.43  3.000
 PTO  N8   C5  C4   107.60  3.000
 PTO  C6   C5  C4   111.96  3.000
 PTO  H62  C6  H61  106.72  3.000
 PTO  H62  C6  C7   111.10  3.000
 PTO  H61  C6  C7   112.86  3.000
 PTO  H62  C6  C5   110.67  3.000
 PTO  H61  C6  C5   112.07  3.000
 PTO  C7   C6  C5   103.51  3.000
 PTO  H72  C7  H71  106.72  3.000
 PTO  H72  C7  C6   111.12  3.000
 PTO  H71  C7  C6   112.81  3.000
 PTO  H72  C7  C1   110.70  3.000
 PTO  H71  C7  C1   112.03  3.000
 PTO  C6   C7  C1   103.54  3.000
 PTO  C9   N8  C5   113.11  3.000
 PTO  C9   N8  C1   113.10  3.000
 PTO  C5   N8  C1   101.66  3.000
 PTO  H93  C9  H92  107.35  3.000
 PTO  H93  C9  H91  107.35  3.000
 PTO  H92  C9  H91  107.48  3.000
 PTO  H93  C9  N8   115.22  3.000
 PTO  H92  C9  N8   109.58  3.000
 PTO  H91  C9  N8   109.56  3.000
 PTO  HO3  O3  C3   108.05  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
 PTO  Var_01  C5   C6  C7  C1   -0.05  30.0  3
 PTO  Var_02  H91  C9  N8  C1  178.27  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
 PTO  chir_01  C1  C2  C7  N8  negativ
 PTO  chir_02  C3  O3  C2  C4  positiv
 PTO  chir_03  C5  N8  C6  C4  negativ

