# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:21:39 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: (3R)-N-methyl-1-(pyridazin-3-yl)piperidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1CCCN(C1)c2cccnn2
#
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
 W0J  W0J  (3R)-N-methyl-1-(pyridazin-3-yl)piperidin-3-amine  ligand  30  14  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W0J
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
 W0J  N1   N  NT    0  -0.494  14.5218  38.2362  -21.3682
 W0J  N3   N  N     0  -0.345  16.7946  38.2865  -21.6301
 W0J  C4   C  CH2   0  -0.269  14.5863  36.8520  -20.9190
 W0J  C5   C  CH2   0  -0.343  13.1969  38.8122  -21.3680
 W0J  C6   C  CR6   0   0.495  15.6129  38.8688  -21.8597
 W0J  C7   C  CR16  0  -0.298  15.5334  40.0798  -22.5902
 W0J  C8   C  CR16  0  -0.252  16.7036  40.6295  -23.0251
 W0J  C1   C  CH1   0  -0.056  12.3059  38.1460  -22.4266
 W0J  C3   C  CH2   0  -0.492  13.2514  36.1584  -21.2026
 W0J  C2   C  CH2   0  -0.453  12.6882  36.6607  -22.5252
 W0J  N2   N  N     0  -0.249  17.9098  38.8239  -22.0719
 W0J  C9   C  CR16  0  -0.123  17.8963  39.9570  -22.7354
 W0J  H1   H  HCH2  0   0.243  15.3798  36.3468  -21.4686
 W0J  H2   H  HCH2  0   0.234  14.8446  36.7905  -19.8563
 W0J  H3   H  HCH2  0   0.269  13.2489  39.8911  -21.4978
 W0J  H4   H  HCH2  0   0.260  12.7516  38.6538  -20.3803
 W0J  H5   H  HCR6  0   0.278  14.5880  40.5473  -22.8239
 W0J  H6   H  HCR6  0   0.280  16.7123  41.5493  -23.5937
 W0J  H7   H  HCH3  0   0.237   9.3656  39.6653  -21.8624
 W0J  H8   H  HCH3  0   0.227  10.8865  40.1904  -21.1664
 W0J  H9   H  HCH3  0   0.194  10.6707  40.2231  -22.9189
 W0J  H12  H  HCH1  0   0.208  12.5041  38.6307  -23.3978
 W0J  H13  H  HCH2  0   0.233  12.5305  36.3370  -20.4009
 W0J  H14  H  HCH2  0   0.252  13.4200  35.0809  -21.2303
 W0J  H15  H  HCH2  0   0.242  11.8185  36.0733  -22.8303
 W0J  H16  H  HCH2  0   0.231  13.4380  36.5247  -23.3090
 W0J  H17  H  HCR6  0   0.271  18.8565  40.3406  -23.0541
 W0J  N    N  NH1   0  -0.600  10.9122  38.2788  -22.0410
 W0J  H10  H  HNH1  0   0.347  10.3504  37.7684  -22.7105
 W0J  C    C  CH3   0  -0.529  10.4456  39.6518  -22.0068

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
 W0J  C8  C9   aromatic  1.399  0.020  1.399
 W0J  C8  C7   aromatic  1.364  0.020  1.364
 W0J  C2  C1   single    1.537  0.020  1.537
 W0J  C2  C3   single    1.523  0.020  1.523
 W0J  C9  N2   aromatic  1.313  0.020  1.313
 W0J  C7  C6   aromatic  1.417  0.020  1.417
 W0J  C1  C5   single    1.536  0.020  1.536
 W0J  C1  N    single    1.452  0.020  1.452
 W0J  N2  N3   aromatic  1.314  0.020  1.314
 W0J  C6  N3   aromatic  1.337  0.020  1.337
 W0J  C6  N1   single    1.354  0.020  1.354
 W0J  C5  N1   single    1.445  0.020  1.445
 W0J  N1  C4   single    1.457  0.020  1.457
 W0J  C   N    single    1.451  0.020  1.451
 W0J  C3  C4   single    1.531  0.020  1.531
 W0J  C4  H1   single    0.970  0.020  1.090
 W0J  C4  H2   single    0.970  0.020  1.090
 W0J  C5  H3   single    0.970  0.020  1.090
 W0J  C5  H4   single    0.970  0.020  1.090
 W0J  C7  H5   single    0.930  0.020  1.080
 W0J  C8  H6   single    0.930  0.020  1.080
 W0J  C   H7   single    0.970  0.020  1.090
 W0J  C   H8   single    0.970  0.020  1.090
 W0J  C   H9   single    0.970  0.020  1.090
 W0J  N   H10  single    0.890  0.020  1.040
 W0J  C1  H12  single    0.970  0.020  1.090
 W0J  C3  H13  single    0.970  0.020  1.090
 W0J  C3  H14  single    0.970  0.020  1.090
 W0J  C2  H15  single    0.970  0.020  1.090
 W0J  C2  H16  single    0.970  0.020  1.090
 W0J  C9  H17  single    0.930  0.020  1.080

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
 W0J  C6   N1  C5   123.57  3.000
 W0J  C5   N1  C4   114.80  3.000
 W0J  C6   N1  C4   121.36  3.000
 W0J  N2   N3  C6   120.93  3.000
 W0J  H2   C4  H1   106.96  3.000
 W0J  H2   C4  C3   111.10  3.000
 W0J  H1   C4  C3   109.36  3.000
 W0J  H2   C4  N1   111.28  3.000
 W0J  H1   C4  N1   108.50  3.000
 W0J  C3   C4  N1   109.56  3.000
 W0J  H4   C5  H3   105.69  3.000
 W0J  H4   C5  C1   108.86  3.000
 W0J  H3   C5  C1   112.07  3.000
 W0J  H4   C5  N1   108.38  3.000
 W0J  H3   C5  N1   110.58  3.000
 W0J  C1   C5  N1   111.04  3.000
 W0J  C7   C6  N3   120.69  3.000
 W0J  N3   C6  N1   116.52  3.000
 W0J  C7   C6  N1   122.79  3.000
 W0J  H5   C7  C8   120.49  3.000
 W0J  H5   C7  C6   122.05  3.000
 W0J  C8   C7  C6   117.44  3.000
 W0J  H6   C8  C9   120.71  3.000
 W0J  H6   C8  C7   121.16  3.000
 W0J  C9   C8  C7   118.13  3.000
 W0J  H12  C1  C2   108.87  3.000
 W0J  H12  C1  N    111.47  3.000
 W0J  C2   C1  N    110.13  3.000
 W0J  H12  C1  C5   108.18  3.000
 W0J  N    C1  C5   109.52  3.000
 W0J  C2   C1  C5   108.61  3.000
 W0J  H14  C3  H13  106.38  3.000
 W0J  H14  C3  C2   111.15  3.000
 W0J  H13  C3  C2   109.83  3.000
 W0J  H14  C3  C4   108.51  3.000
 W0J  H13  C3  C4   111.43  3.000
 W0J  C2   C3  C4   109.51  3.000
 W0J  H16  C2  H15  106.19  3.000
 W0J  H16  C2  C3   109.15  3.000
 W0J  H15  C2  C3   111.07  3.000
 W0J  H16  C2  C1   109.68  3.000
 W0J  H15  C2  C1   109.84  3.000
 W0J  C3   C2  C1   110.80  3.000
 W0J  C9   N2  N3   120.92  3.000
 W0J  H17  C9  N2   116.46  3.000
 W0J  H17  C9  C8   121.67  3.000
 W0J  N2   C9  C8   121.87  3.000
 W0J  H10  N   C1   108.12  3.000
 W0J  H10  N   C    108.32  3.000
 W0J  C1   N   C    113.68  3.000
 W0J  H9   C   H8   107.44  3.000
 W0J  H9   C   H7   107.84  3.000
 W0J  H8   C   H7   107.00  3.000
 W0J  H9   C   N    113.98  3.000
 W0J  H8   C   N    110.82  3.000
 W0J  H7   C   N    109.50  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
 W0J  CONST_01  C8   C9  N2  N3    0.00   0.0  0
 W0J  CONST_02  C8   C7  C6  N3    0.00   0.0  0
 W0J  CONST_03  C9   C8  C7  C6    0.00   0.0  0
 W0J  CONST_04  C9   N2  N3  C6    0.00   0.0  0
 W0J  CONST_05  N2   C9  C8  C7    0.00   0.0  0
 W0J  CONST_06  N2   N3  C6  C7    0.00   0.0  0
 W0J  CONST_07  C8   C7  C6  N1  180.00   0.0  0
 W0J  CONST_08  N2   N3  C6  N1  180.00   0.0  0
 W0J  CONST_09  H5   C7  C6  N1    0.00   0.0  0
 W0J  CONST_10  H17  C9  N2  N3  180.00   0.0  0
 W0J  CONST_11  H6   C8  C7  C6  180.00   0.0  0
 W0J  Var_01    C2   C3  C4  N1   36.99  30.0  1
 W0J  Var_02    C5   N1  C6  N3  171.38  30.0  2
 W0J  Var_03    C1   C5  N1  C4  -67.47  30.0  1
 W0J  Var_04    C1   C2  C3  C4  -66.49  30.0  1
 W0J  Var_05    C3   C4  N1  C5   27.39  30.0  1
 W0J  Var_06    H7   C   N   C1  171.36  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
 W0J  chir_01  C1  C2  C5  N  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
 W0J  plan-1  N1   0.020
 W0J  plan-1  N3   0.020
 W0J  plan-1  C6   0.020
 W0J  plan-1  C7   0.020
 W0J  plan-1  C8   0.020
 W0J  plan-1  N2   0.020
 W0J  plan-1  C9   0.020
 W0J  plan-1  H5   0.020
 W0J  plan-1  H6   0.020
 W0J  plan-1  H17  0.020

