# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 19:46:17 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (3-endo)-N-(2-bromophenyl)-9-methyl-9-azabicyclo[3.3.1]nonan-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H]2CCC[C@H]1C[C@H](C2)Nc3ccccc3Br
#
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
 P1M  P1M  (3-endo)-N-(2-bromophenyl)-9-methyl-9-azabicyclo[3.3.1]nonan-3-amine  ligand  39  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1M
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
 P1M  C1   C   CH1   0  -0.097  -1.1562   1.0872  -0.9743
 P1M  C2   C   CH2   0  -0.452  -2.1091   0.1939  -1.7752
 P1M  C3   C   CH1   0  -0.105  -3.1392  -0.5871  -0.9589
 P1M  C4   C   CH2   0  -0.447  -2.6098  -1.7802  -0.1438
 P1M  C7   C   CH1   0  -0.109  -2.9778   0.8872   0.9051
 P1M  C10  C   CR6   0   0.443   1.2305   0.9666  -0.3083
 P1M  C11  C   CR6   0  -0.211   2.4103   0.2299  -0.0770
 P1M  N8   N   NT    0  -0.406  -3.8603   0.3754  -0.1361
 P1M  C13  C   CR16  0  -0.294   3.6792   2.2149   0.4020
 P1M  C14  C   CR16  0  -0.244   2.5338   2.9666   0.1849
 P1M  C15  C   CR16  0  -0.349   1.3383   2.3619  -0.1630
 P1M  C12  C   CR16  0  -0.232   3.6070   0.8361   0.2647
 P1M  C5   C   CH2   0  -0.452  -1.8537  -1.3940   1.1324
 P1M  C8   C   CH2   0  -0.426  -1.8671   1.7132   0.2415
 P1M  C8A  C   CH3   0  -0.524  -5.1397  -0.0976   0.3400
 P1M  N9   N   NH1   0  -0.701   0.0546   0.3608  -0.6352
 P1M  BR1  BR  BR    0  -0.061   2.3832  -1.6610  -0.2298
 P1M  H1   H   HCH1  0   0.244  -0.8734   1.9134  -1.6380
 P1M  H2   H   HCH2  0   0.246  -2.6753   0.8466  -2.4426
 P1M  H3   H   HCH2  0   0.237  -1.5398  -0.4788  -2.4237
 P1M  H4   H   HCH1  0   0.234  -3.8494  -0.9931  -1.6871
 P1M  H5   H   HCH2  0   0.224  -3.4689  -2.3999   0.1295
 P1M  H6   H   HCH2  0   0.225  -1.9820  -2.4105  -0.7805
 P1M  H7   H   HCH2  0   0.224  -1.8150   0.2039   2.5938
 P1M  H8   H   HCH2  0   0.219  -3.3718  -0.5691   2.4228
 P1M  H9   H   HCH1  0   0.232  -3.5579   1.5998   1.5021
 P1M  H11  H   HCR6  0   0.256   4.6139   2.6841   0.6757
 P1M  H12  H   HCR6  0   0.258   2.5641   4.0440   0.2834
 P1M  H13  H   HCR6  0   0.275   0.4723   2.9872  -0.3290
 P1M  H14  H   HCR6  0   0.273   4.4893   0.2320   0.4323
 P1M  H15  H   HCH2  0   0.225  -1.8089  -2.2581   1.7997
 P1M  H16  H   HCH2  0   0.223  -0.8217  -1.1431   0.8968
 P1M  H17  H   HCH2  0   0.237  -1.1355   2.0060   0.9979
 P1M  H18  H   HCH2  0   0.232  -2.3313   2.6400  -0.1059
 P1M  H19  H   HCH3  0   0.228  -5.6357   0.6954   0.9028
 P1M  H20  H   HCH3  0   0.229  -5.7759  -0.3417  -0.5133
 P1M  H21  H   HCH3  0   0.196  -5.1095  -0.9866   0.9845
 P1M  H22  H   HNH1  0   0.381   0.1222  -0.5674  -1.0175
 P1M  C6   C   CH2   0  -0.433  -2.5038  -0.2169   1.8565

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
 P1M  C13  C12  aromatic  1.388  0.020  1.388
 P1M  C13  C14  aromatic  1.387  0.020  1.387
 P1M  C12  C11  aromatic  1.384  0.020  1.384
 P1M  C14  C15  aromatic  1.384  0.020  1.384
 P1M  C11  BR1  single    1.897  0.020  1.897
 P1M  C11  C10  aromatic  1.410  0.020  1.410
 P1M  C15  C10  aromatic  1.407  0.020  1.407
 P1M  C10  N9   single    1.363  0.020  1.363
 P1M  N9   C1   single    1.452  0.020  1.452
 P1M  C8   C1   single    1.541  0.020  1.541
 P1M  C8   C7   single    1.535  0.020  1.535
 P1M  C1   C2   single    1.532  0.020  1.532
 P1M  C7   N8   single    1.458  0.020  1.458
 P1M  C7   C6   single    1.533  0.020  1.533
 P1M  N8   C8A  single    1.445  0.020  1.445
 P1M  N8   C3   single    1.457  0.020  1.457
 P1M  C2   C3   single    1.529  0.020  1.529
 P1M  C6   C5   single    1.527  0.020  1.527
 P1M  C3   C4   single    1.539  0.020  1.539
 P1M  C5   C4   single    1.533  0.020  1.533
 P1M  C1   H1   single    0.970  0.020  1.090
 P1M  C2   H2   single    0.970  0.020  1.090
 P1M  C2   H3   single    0.970  0.020  1.090
 P1M  C3   H4   single    0.970  0.020  1.090
 P1M  C4   H5   single    0.970  0.020  1.090
 P1M  C4   H6   single    0.970  0.020  1.090
 P1M  C6   H7   single    0.970  0.020  1.090
 P1M  C6   H8   single    0.970  0.020  1.090
 P1M  C7   H9   single    0.970  0.020  1.090
 P1M  C13  H11  single    0.930  0.020  1.080
 P1M  C14  H12  single    0.930  0.020  1.080
 P1M  C15  H13  single    0.930  0.020  1.080
 P1M  C12  H14  single    0.930  0.020  1.080
 P1M  C5   H15  single    0.970  0.020  1.090
 P1M  C5   H16  single    0.970  0.020  1.090
 P1M  C8   H17  single    0.970  0.020  1.090
 P1M  C8   H18  single    0.970  0.020  1.090
 P1M  C8A  H19  single    0.970  0.020  1.090
 P1M  C8A  H20  single    0.970  0.020  1.090
 P1M  C8A  H21  single    0.970  0.020  1.090
 P1M  N9   H22  single    0.890  0.020  1.040

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
 P1M  H1   C1   N9   107.64  3.000
 P1M  H1   C1   C8   106.88  3.000
 P1M  N9   C1   C8   113.80  3.000
 P1M  H1   C1   C2   106.45  3.000
 P1M  C8   C1   C2   111.24  3.000
 P1M  N9   C1   C2   110.43  3.000
 P1M  H3   C2   H2   105.97  3.000
 P1M  H3   C2   C3   110.67  3.000
 P1M  H2   C2   C3   106.40  3.000
 P1M  H3   C2   C1   110.16  3.000
 P1M  H2   C2   C1   107.07  3.000
 P1M  C3   C2   C1   115.96  3.000
 P1M  H4   C3   N8   107.42  3.000
 P1M  H4   C3   C4   106.73  3.000
 P1M  N8   C3   C4   112.54  3.000
 P1M  H4   C3   C2   105.74  3.000
 P1M  C4   C3   C2   116.56  3.000
 P1M  N8   C3   C2   107.31  3.000
 P1M  H6   C4   H5   105.64  3.000
 P1M  H6   C4   C5   110.28  3.000
 P1M  H5   C4   C5   108.79  3.000
 P1M  H6   C4   C3   109.62  3.000
 P1M  H5   C4   C3   107.54  3.000
 P1M  C5   C4   C3   114.54  3.000
 P1M  H9   C7   C8   105.59  3.000
 P1M  H9   C7   N8   107.28  3.000
 P1M  C8   C7   N8   108.55  3.000
 P1M  H9   C7   C6   107.10  3.000
 P1M  N8   C7   C6   112.19  3.000
 P1M  C8   C7   C6   115.61  3.000
 P1M  N9   C10  C15  122.13  3.000
 P1M  N9   C10  C11  121.95  3.000
 P1M  C15  C10  C11  115.91  3.000
 P1M  BR1  C11  C12  117.94  3.000
 P1M  BR1  C11  C10  119.70  3.000
 P1M  C12  C11  C10  122.35  3.000
 P1M  C8A  N8   C7   114.56  3.000
 P1M  C8A  N8   C3   114.08  3.000
 P1M  C7   N8   C3   109.61  3.000
 P1M  H11  C13  C12  120.09  3.000
 P1M  H11  C13  C14  121.22  3.000
 P1M  C12  C13  C14  118.69  3.000
 P1M  H12  C14  C15  118.81  3.000
 P1M  H12  C14  C13  120.14  3.000
 P1M  C15  C14  C13  121.05  3.000
 P1M  H13  C15  C14  118.54  3.000
 P1M  H13  C15  C10  119.76  3.000
 P1M  C14  C15  C10  121.70  3.000
 P1M  H14  C12  C13  119.79  3.000
 P1M  H14  C12  C11  119.91  3.000
 P1M  C13  C12  C11  120.30  3.000
 P1M  H16  C5   H15  106.00  3.000
 P1M  H16  C5   C6   109.20  3.000
 P1M  H15  C5   C6   109.72  3.000
 P1M  H16  C5   C4   110.23  3.000
 P1M  H15  C5   C4   109.24  3.000
 P1M  C6   C5   C4   112.27  3.000
 P1M  H18  C8   H17  106.10  3.000
 P1M  H18  C8   C7   106.63  3.000
 P1M  H17  C8   C7   109.24  3.000
 P1M  H18  C8   C1   106.83  3.000
 P1M  H17  C8   C1   110.26  3.000
 P1M  C7   C8   C1   117.14  3.000
 P1M  H21  C8A  H20  107.08  3.000
 P1M  H21  C8A  H19  107.34  3.000
 P1M  H20  C8A  H19  107.49  3.000
 P1M  H21  C8A  N8   115.72  3.000
 P1M  H20  C8A  N8   109.36  3.000
 P1M  H19  C8A  N8   109.54  3.000
 P1M  H22  N9   C10  116.31  3.000
 P1M  H22  N9   C1   115.39  3.000
 P1M  C10  N9   C1   123.59  3.000
 P1M  H8   C6   H7   105.93  3.000
 P1M  H8   C6   C5   109.56  3.000
 P1M  H7   C6   C5   110.38  3.000
 P1M  H8   C6   C7   107.92  3.000
 P1M  H7   C6   C7   109.65  3.000
 P1M  C5   C6   C7   113.12  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
 P1M  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 P1M  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 P1M  CONST_03  C14  C13  C12  C11     0.00   0.0  0
 P1M  CONST_04  C14  C15  C10  C11     0.00   0.0  0
 P1M  CONST_05  C12  C13  C14  C15     0.00   0.0  0
 P1M  CONST_06  C12  C11  C10  C15     0.00   0.0  0
 P1M  CONST_07  BR1  C11  C12  C13   180.00   0.0  0
 P1M  CONST_08  N9   C10  C15  C14   180.00   0.0  0
 P1M  CONST_09  BR1  C11  C10  C15   180.00   0.0  0
 P1M  CONST_10  N9   C10  C11  C12   180.00   0.0  0
 P1M  CONST_11  C11  C10  N9   C1    180.00   0.0  0
 P1M  CONST_12  C15  C10  N9   C1      0.00   0.0  0
 P1M  CONST_13  H14  C12  C11  C10   180.00   0.0  0
 P1M  CONST_14  H12  C14  C15  C10   180.00   0.0  0
 P1M  CONST_15  H11  C13  C12  C11   180.00   0.0  0
 P1M  CONST_16  H13  C15  C10  C11   180.00   0.0  0
 P1M  Var_01    C6   C5   C4   C3     39.42  30.0  3
 P1M  Var_02    C7   C6   C5   C4    -41.58  30.0  3
 P1M  Var_03    H19  C8A  N8   C3   -177.16  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
 P1M  chir_01  C1  N9  C8  C2  positiv
 P1M  chir_02  C3  N8  C4  C2  positiv
 P1M  chir_03  C7  N8  C6  C8  negativ

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
 P1M  plan-1  C10  0.020
 P1M  plan-1  C11  0.020
 P1M  plan-1  C13  0.020
 P1M  plan-1  C14  0.020
 P1M  plan-1  C15  0.020
 P1M  plan-1  C12  0.020
 P1M  plan-1  N9   0.020
 P1M  plan-1  BR1  0.020
 P1M  plan-1  H11  0.020
 P1M  plan-1  H12  0.020
 P1M  plan-1  H13  0.020
 P1M  plan-1  H14  0.020
 P1M  plan-2  C1   0.020
 P1M  plan-2  C10  0.020
 P1M  plan-2  N9   0.020
 P1M  plan-2  H22  0.020

