# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 00:17:49 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: ~{N}-(1-pyrimidin-2-ylpiperidin-4-yl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC1CCN(CC1)c2ncccn2
#
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
 9W2  9W2  ~{N}-(1-pyrimidin-2-ylpiperidin-4-yl)ethanamide  ligand  32  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9W2
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
 9W2  C10  C  CH2   0  -0.459  -0.7775   1.4743   0.7247
 9W2  N12  N  N     0  -0.473   2.8943   0.6346   0.8808
 9W2  C13  C  CR16  0  -0.009   4.1816   0.7443   0.6073
 9W2  C15  C  CR16  0  -0.009   3.9522  -0.7154  -1.2059
 9W2  C01  C  CH3   0  -0.778  -4.8264  -1.0843   0.9652
 9W2  C02  C  C     0   0.526  -3.9430  -0.3001   0.0264
 9W2  O03  O  O     0  -0.511  -4.3115   0.0038  -1.1015
 9W2  N04  N  NH1   0  -0.629  -2.7401   0.0436   0.5158
 9W2  C05  C  CH1   0  -0.106  -1.7533   0.7989  -0.2383
 9W2  C06  C  CH2   0  -0.430  -0.9855  -0.0927  -1.2201
 9W2  C07  C  CH2   0  -0.322  -0.0512  -1.0496  -0.4917
 9W2  N08  N  NT    0  -0.483   0.8544  -0.3156   0.3722
 9W2  C09  C  CH2   0  -0.330   0.1800   0.4799   1.3781
 9W2  C11  C  CR6   0   0.637   2.1687  -0.1669   0.0871
 9W2  C14  C  CR16  0  -0.403   4.7927   0.0810  -0.4448
 9W2  N16  N  N     0  -0.473   2.6615  -0.8464  -0.9586
 9W2  H1   H  HCH2  0   0.250  -0.1928   2.2077   0.1641
 9W2  H2   H  HCH2  0   0.253  -1.3225   2.0248   1.4955
 9W2  H3   H  HCR6  0   0.267   4.7561   1.3950   1.2585
 9W2  H4   H  HCR6  0   0.267   4.3359  -1.2715  -2.0552
 9W2  H5   H  HCH3  0   0.265  -5.1051  -2.0270   0.4949
 9W2  H6   H  HCH3  0   0.248  -4.3607  -1.3022   1.9244
 9W2  H7   H  HCH3  0   0.265  -5.7462  -0.5286   1.1473
 9W2  H8   H  HNH1  0   0.398  -2.5117  -0.2443   1.4531
 9W2  H9   H  HCH1  0   0.263  -2.2839   1.5707  -0.7996
 9W2  H10  H  HCH2  0   0.247  -1.6838  -0.6541  -1.8428
 9W2  H11  H  HCH2  0   0.235  -0.4005   0.5443  -1.8902
 9W2  H12  H  HCH2  0   0.238  -0.6283  -1.7475   0.1242
 9W2  H13  H  HCH2  0   0.273   0.5200  -1.6442  -1.1975
 9W2  H14  H  HCH2  0   0.278   0.9135   1.0058   1.9811
 9W2  H15  H  HCH2  0   0.238  -0.3560  -0.1964   2.0541
 9W2  H16  H  HCR6  0   0.269   5.8460   0.1801  -0.6579

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
 9W2  C14  C13  aromatic  1.386  0.020  1.386
 9W2  C14  C15  aromatic  1.386  0.020  1.386
 9W2  C13  N12  aromatic  1.321  0.020  1.321
 9W2  C15  N16  aromatic  1.321  0.020  1.321
 9W2  C01  C02  single    1.509  0.020  1.509
 9W2  N12  C11  aromatic  1.341  0.020  1.341
 9W2  N04  C02  single    1.343  0.020  1.343
 9W2  N04  C05  single    1.454  0.020  1.454
 9W2  N16  C11  aromatic  1.341  0.020  1.341
 9W2  C11  N08  single    1.353  0.020  1.353
 9W2  C06  C05  single    1.532  0.020  1.532
 9W2  C06  C07  single    1.523  0.020  1.523
 9W2  C02  O03  double    1.225  0.020  1.225
 9W2  C10  C05  single    1.528  0.020  1.528
 9W2  C10  C09  single    1.527  0.020  1.527
 9W2  N08  C07  single    1.451  0.020  1.451
 9W2  N08  C09  single    1.449  0.020  1.449
 9W2  C10  H1   single    0.970  0.020  1.090
 9W2  C10  H2   single    0.970  0.020  1.090
 9W2  C13  H3   single    0.930  0.020  1.080
 9W2  C15  H4   single    0.930  0.020  1.080
 9W2  C01  H5   single    0.970  0.020  1.090
 9W2  C01  H6   single    0.970  0.020  1.090
 9W2  C01  H7   single    0.970  0.020  1.090
 9W2  N04  H8   single    0.860  0.020  1.020
 9W2  C05  H9   single    0.970  0.020  1.090
 9W2  C06  H10  single    0.970  0.020  1.090
 9W2  C06  H11  single    0.970  0.020  1.090
 9W2  C07  H12  single    0.970  0.020  1.090
 9W2  C07  H13  single    0.970  0.020  1.090
 9W2  C09  H14  single    0.970  0.020  1.090
 9W2  C09  H15  single    0.970  0.020  1.090
 9W2  C14  H16  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
 9W2  H2   C10  H1   106.90  3.000
 9W2  H2   C10  C09  109.81  3.000
 9W2  H1   C10  C09  108.72  3.000
 9W2  H2   C10  C05  110.40  3.000
 9W2  H1   C10  C05  108.36  3.000
 9W2  C09  C10  C05  112.47  3.000
 9W2  C11  N12  C13  117.03  3.000
 9W2  H3   C13  C14  120.61  3.000
 9W2  H3   C13  N12  116.20  3.000
 9W2  C14  C13  N12  123.18  3.000
 9W2  H4   C15  N16  116.18  3.000
 9W2  H4   C15  C14  120.66  3.000
 9W2  N16  C15  C14  123.16  3.000
 9W2  H7   C01  H6   108.42  3.000
 9W2  H7   C01  H5   107.29  3.000
 9W2  H6   C01  H5   108.46  3.000
 9W2  H7   C01  C02  109.45  3.000
 9W2  H6   C01  C02  113.70  3.000
 9W2  H5   C01  C02  109.32  3.000
 9W2  N04  C02  O03  122.78  3.000
 9W2  O03  C02  C01  121.71  3.000
 9W2  N04  C02  C01  115.50  3.000
 9W2  H8   N04  C05  118.52  3.000
 9W2  H8   N04  C02  117.98  3.000
 9W2  C05  N04  C02  123.49  3.000
 9W2  H9   C05  C06  108.98  3.000
 9W2  H9   C05  N04  107.70  3.000
 9W2  C06  C05  N04  111.73  3.000
 9W2  H9   C05  C10  108.77  3.000
 9W2  C06  C05  C10  109.93  3.000
 9W2  N04  C05  C10  109.65  3.000
 9W2  H11  C06  H10  106.99  3.000
 9W2  H11  C06  C07  109.31  3.000
 9W2  H10  C06  C07  110.02  3.000
 9W2  H11  C06  C05  108.76  3.000
 9W2  H10  C06  C05  110.14  3.000
 9W2  C07  C06  C05  111.50  3.000
 9W2  H13  C07  H12  107.09  3.000
 9W2  H13  C07  N08  109.62  3.000
 9W2  H12  C07  N08  108.45  3.000
 9W2  H13  C07  C06  110.85  3.000
 9W2  H12  C07  C06  110.25  3.000
 9W2  N08  C07  C06  110.48  3.000
 9W2  C11  N08  C09  122.55  3.000
 9W2  C09  N08  C07  113.61  3.000
 9W2  C11  N08  C07  122.45  3.000
 9W2  H15  C09  H14  106.67  3.000
 9W2  H15  C09  N08  108.48  3.000
 9W2  H14  C09  N08  109.71  3.000
 9W2  H15  C09  C10  111.04  3.000
 9W2  H14  C09  C10  110.23  3.000
 9W2  N08  C09  C10  110.62  3.000
 9W2  N16  C11  N08  117.75  3.000
 9W2  N08  C11  N12  117.81  3.000
 9W2  N16  C11  N12  124.43  3.000
 9W2  H16  C14  C15  122.44  3.000
 9W2  H16  C14  C13  122.43  3.000
 9W2  C15  C14  C13  115.13  3.000
 9W2  C11  N16  C15  117.06  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
 9W2  CONST_01  C15  C14  C13  N12    0.00   0.0  0
 9W2  CONST_02  C15  N16  C11  N12    0.00   0.0  0
 9W2  CONST_03  N16  C15  C14  C13    0.00   0.0  0
 9W2  CONST_04  N16  C11  N12  C13    0.00   0.0  0
 9W2  CONST_05  C14  C13  N12  C11    0.00   0.0  0
 9W2  CONST_06  C14  C15  N16  C11    0.00   0.0  0
 9W2  CONST_07  N08  C11  N12  C13  180.00   0.0  0
 9W2  CONST_08  N08  C11  N16  C15  180.00   0.0  0
 9W2  CONST_09  H16  C14  C13  N12  180.00   0.0  0
 9W2  CONST_10  H4   C15  C14  C13  180.00   0.0  0
 9W2  CONST_11  H3   C13  C14  C15  180.00   0.0  0
 9W2  CONST_12  C05  N04  C02  C01  180.00   0.0  0
 9W2  CONST_13  C05  N04  C02  O03    0.00   0.0  0
 9W2  CONST_14  H8   N04  C02  C01    0.00   0.0  0
 9W2  Var_01    C11  N08  C09  C10  109.07  30.0  1
 9W2  Var_02    N08  C07  C06  C05  -55.70  30.0  1
 9W2  Var_03    N08  C09  C10  C05   53.25  30.0  1
 9W2  Var_04    H5   C01  C02  O03   57.29  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
 9W2  chir_01  C05  N04  C06  C10  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
 9W2  plan-1  N12  0.020
 9W2  plan-1  C13  0.020
 9W2  plan-1  C15  0.020
 9W2  plan-1  N08  0.020
 9W2  plan-1  C11  0.020
 9W2  plan-1  C14  0.020
 9W2  plan-1  N16  0.020
 9W2  plan-1  H3   0.020
 9W2  plan-1  H4   0.020
 9W2  plan-1  H16  0.020
 9W2  plan-2  C01  0.020
 9W2  plan-2  C02  0.020
 9W2  plan-2  O03  0.020
 9W2  plan-2  N04  0.020
 9W2  plan-2  C05  0.020
 9W2  plan-2  H8   0.020

