# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:27:28 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (4-azanylpiperidin-1-yl)-cyclopropyl-methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1CCN(CC1)C(=O)C2CC2
#
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
 5WZ  5WZ  (4-azanylpiperidin-1-yl)-cyclopropyl-methanone  ligand  28  12  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5WZ
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
 5WZ  C4   C  CH2   0  -0.435   2.0045  -1.0114   0.4727
 5WZ  C5   C  C     0   0.589  -1.2932  -0.4807  -0.0114
 5WZ  C6   C  CH1   0  -0.426  -2.2582   0.6406  -0.2027
 5WZ  N1   N  NT    0  -0.461  -0.0978  -0.4190  -0.6434
 5WZ  C7   C  CH2   0  -0.467  -2.9411   1.1762   1.0331
 5WZ  C8   C  CH2   0  -0.462  -3.7130   0.3617   0.0608
 5WZ  O    O  O     0  -0.515  -1.6017  -1.4374   0.6934
 5WZ  C2   C  CH2   0  -0.327   0.4944   0.7715  -1.2326
 5WZ  C1   C  CH2   0  -0.429   1.6059   1.3121  -0.3395
 5WZ  C3   C  CH2   0  -0.326   0.8814  -1.4773  -0.4449
 5WZ  C    C  CH1   0  -0.068   2.6661   0.2483  -0.0758
 5WZ  N    N  NH2   0  -0.801   3.6514   0.7482   0.8701
 5WZ  H1   H  HCH2  0   0.224   1.6065  -0.8101   1.4722
 5WZ  H2   H  HCH2  0   0.237   2.7424  -1.8125   0.5734
 5WZ  H3   H  HCH1  0   0.284  -2.0661   1.3666  -0.9789
 5WZ  H4   H  HCH2  0   0.256  -2.6753   0.7250   1.9801
 5WZ  H5   H  HCH2  0   0.260  -3.1145   2.2434   1.0740
 5WZ  H6   H  HCH2  0   0.259  -4.4222   0.8665  -0.5818
 5WZ  H7   H  HCH2  0   0.255  -3.9866  -0.6462   0.3404
 5WZ  H8   H  HCH2  0   0.244   0.9008   0.5019  -2.2125
 5WZ  H9   H  HCH2  0   0.266  -0.2521   1.5397  -1.4056
 5WZ  H10  H  HCH2  0   0.239   2.0547   2.1867  -0.8184
 5WZ  H11  H  HCH2  0   0.224   1.1793   1.6442   0.6124
 5WZ  H12  H  HCH2  0   0.239   1.2912  -1.7431  -1.4246
 5WZ  H13  H  HCH2  0   0.264   0.3916  -2.3617  -0.0487
 5WZ  H14  H  HCH1  0   0.192   3.1127  -0.0162  -1.0498
 5WZ  H15  H  HNH2  0   0.342   4.3712   0.0479   1.0062
 5WZ  H16  H  HNH2  0   0.342   4.1273   1.5482   0.4696

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
 5WZ  C1  C    single  1.525  0.020  1.525
 5WZ  C1  C2   single  1.525  0.020  1.525
 5WZ  N   C    single  1.454  0.020  1.454
 5WZ  C   C4   single  1.525  0.020  1.525
 5WZ  C2  N1   single  1.454  0.020  1.454
 5WZ  O   C5   double  1.228  0.020  1.228
 5WZ  N1  C5   single  1.354  0.020  1.354
 5WZ  N1  C3   single  1.455  0.020  1.455
 5WZ  C5  C6   single  1.492  0.020  1.492
 5WZ  C4  C3   single  1.523  0.020  1.523
 5WZ  C7  C6   single  1.510  0.020  1.510
 5WZ  C7  C8   single  1.485  0.020  1.485
 5WZ  C6  C8   single  1.505  0.020  1.505
 5WZ  C4  H1   single  0.970  0.020  1.090
 5WZ  C4  H2   single  0.970  0.020  1.090
 5WZ  C6  H3   single  0.970  0.020  1.090
 5WZ  C7  H4   single  0.970  0.020  1.090
 5WZ  C7  H5   single  0.970  0.020  1.090
 5WZ  C8  H6   single  0.970  0.020  1.090
 5WZ  C8  H7   single  0.970  0.020  1.090
 5WZ  C2  H8   single  0.970  0.020  1.090
 5WZ  C2  H9   single  0.970  0.020  1.090
 5WZ  C1  H10  single  0.970  0.020  1.090
 5WZ  C1  H11  single  0.970  0.020  1.090
 5WZ  C3  H12  single  0.970  0.020  1.090
 5WZ  C3  H13  single  0.970  0.020  1.090
 5WZ  C   H14  single  0.970  0.020  1.090
 5WZ  N   H15  single  0.890  0.020  1.040
 5WZ  N   H16  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
 5WZ  H2   C4  H1   107.21  3.000
 5WZ  H2   C4  C    110.21  3.000
 5WZ  H1   C4  C    109.53  3.000
 5WZ  H2   C4  C3   109.20  3.000
 5WZ  H1   C4  C3   109.77  3.000
 5WZ  C    C4  C3   110.85  3.000
 5WZ  O    C5  N1   121.70  3.000
 5WZ  N1   C5  C6   118.50  3.000
 5WZ  O    C5  C6   119.79  3.000
 5WZ  H3   C6  C8   114.99  3.000
 5WZ  H3   C6  C7   115.48  3.000
 5WZ  C8   C6  C7    59.01  3.000
 5WZ  H3   C6  C5   118.84  3.000
 5WZ  C8   C6  C5   117.63  3.000
 5WZ  C7   C6  C5   117.02  3.000
 5WZ  C3   N1  C2   112.12  3.000
 5WZ  C3   N1  C5   119.83  3.000
 5WZ  C2   N1  C5   125.88  3.000
 5WZ  H5   C7  H4   114.68  3.000
 5WZ  H5   C7  C8   118.85  3.000
 5WZ  H4   C7  C8   118.17  3.000
 5WZ  H5   C7  C6   116.95  3.000
 5WZ  H4   C7  C6   117.20  3.000
 5WZ  C8   C7  C6    60.30  3.000
 5WZ  H7   C8  H6   115.00  3.000
 5WZ  H7   C8  C7   118.27  3.000
 5WZ  H6   C8  C7   118.27  3.000
 5WZ  H7   C8  C6   117.57  3.000
 5WZ  H6   C8  C6   116.31  3.000
 5WZ  C7   C8  C6    60.68  3.000
 5WZ  H9   C2  H8   106.69  3.000
 5WZ  H9   C2  C1   110.12  3.000
 5WZ  H8   C2  C1   109.94  3.000
 5WZ  H9   C2  N1   111.34  3.000
 5WZ  H8   C2  N1   108.20  3.000
 5WZ  C1   C2  N1   110.47  3.000
 5WZ  H11  C1  H10  107.34  3.000
 5WZ  H11  C1  C    109.40  3.000
 5WZ  H10  C1  C    110.38  3.000
 5WZ  H11  C1  C2   109.44  3.000
 5WZ  H10  C1  C2   109.04  3.000
 5WZ  C    C1  C2   111.15  3.000
 5WZ  H13  C3  H12  107.32  3.000
 5WZ  H13  C3  N1   109.79  3.000
 5WZ  H12  C3  N1   107.84  3.000
 5WZ  H13  C3  C4   111.22  3.000
 5WZ  H12  C3  C4   109.71  3.000
 5WZ  N1   C3  C4   110.84  3.000
 5WZ  H14  C   N    112.47  3.000
 5WZ  H14  C   C1   107.21  3.000
 5WZ  N    C   C1   110.11  3.000
 5WZ  H14  C   C4   107.16  3.000
 5WZ  N    C   C4   110.12  3.000
 5WZ  C1   C   C4   109.68  3.000
 5WZ  H16  N   H15  105.37  3.000
 5WZ  H16  N   C    109.41  3.000
 5WZ  H15  N   C    109.33  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
 5WZ  CONST_02  C3  N1  C5  C6   180.00   0.0  0
 5WZ  CONST_04  C3  N1  C5  O      0.00   0.0  0
 5WZ  Var_01    C2  N1  C3  C4    59.42  30.0  1
 5WZ  Var_02    C   C1  C2  N1    56.35  30.0  1
 5WZ  Var_03    C   C4  C3  N1   -56.31  30.0  1
 5WZ  Var_04    C3  N1  C2  C1   -59.22  30.0  1
 5WZ  Var_05    C8  C7  C6  C5  -107.52  30.0  1
 5WZ  Var_06    C7  C6  C5  N1  -134.48  30.0  3
 5WZ  Var_07    H6  C8  C7  C6  -105.98  30.0  1

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
 5WZ  chir_02  C   C1  N   C4  negativ
 5WZ  chir_03  C6  C5  C7  C8  both

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
 5WZ  plan-1  C5  0.020
 5WZ  plan-1  C6  0.020
 5WZ  plan-1  N1  0.020
 5WZ  plan-1  O   0.020
 5WZ  plan-1  C2  0.020
 5WZ  plan-1  C3  0.020

