# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 00:42:15 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-[4-(2-hydroxyethyl)piperidin-1-yl]carbonylbenzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCC1CCN(CC1)C(=O)c2ccc(C=O)cc2
#
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
 V4K  V4K  4-[4-(2-hydroxyethyl)piperidin-1-yl]carbonylbenzaldehyde  ligand  38  19  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V4K
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
 V4K  C02  C  CH2   0  -0.162  17.8977  15.8323  -1.8873
 V4K  C03  C  CH2   0  -0.450  16.4534  16.2925  -1.9147
 V4K  C04  C  CH1   0  -0.214  16.1805  17.5928  -1.1644
 V4K  C05  C  CH2   0  -0.440  16.6025  17.5179   0.3123
 V4K  C06  C  CH2   0  -0.328  15.7557  18.4499   1.1789
 V4K  C09  C  CR6   0  -0.063  16.6523  21.1433   1.8666
 V4K  C10  C  CR16  0  -0.239  17.9628  20.7092   1.6966
 V4K  C11  C  CR16  0  -0.264  18.9273  21.0422   2.6341
 V4K  C12  C  CR6   0  -0.016  18.5881  21.7981   3.7518
 V4K  C13  C  CR16  0  -0.255  17.2733  22.2330   3.9214
 V4K  C14  C  CR16  0  -0.257  16.3165  21.9199   2.9754
 V4K  C15  C  C1    0   0.118  19.6354  22.1285   4.7325
 V4K  C17  C  CH2   0  -0.268  14.4961  19.3976  -0.7053
 V4K  C18  C  CH2   0  -0.485  14.7067  17.9825  -1.2407
 V4K  N07  N  NT    0  -0.449  15.3684  19.6397   0.4398
 V4K  O01  O  OH1   0  -0.668  18.7136  16.8229  -2.4766
 V4K  O16  O  O     0  -0.483  15.0676  21.8706   0.2927
 V4K  H1   H  HCH2  0   0.201  17.9742  14.8792  -2.4271
 V4K  H2   H  HCH2  0   0.196  18.2015  15.6281  -0.8524
 V4K  H3   H  HCH2  0   0.227  16.1284  16.3990  -2.9546
 V4K  H4   H  HCH2  0   0.221  15.8419  15.4931  -1.4829
 V4K  H5   H  HCH1  0   0.229  16.7537  18.3939  -1.6436
 V4K  H6   H  HCH2  0   0.232  16.4789  16.4989   0.6903
 V4K  H7   H  HCH2  0   0.238  17.6619  17.7628   0.4140
 V4K  H8   H  HCH2  0   0.276  16.2763  18.7266   2.0920
 V4K  H9   H  HCH2  0   0.260  14.8410  17.9400   1.4945
 V4K  H10  H  HCR6  0   0.276  18.2363  20.1220   0.8289
 V4K  H11  H  HCR6  0   0.273  19.9503  20.7118   2.4960
 V4K  H12  H  HCR6  0   0.269  17.0034  22.8226   4.7880
 V4K  H13  H  HCR6  0   0.268  15.3002  22.2703   3.1012
 V4K  H14  H  H     0   0.200  20.6377  21.7383   4.4809
 V4K  H17  H  HCH2  0   0.245  14.7444  20.1201  -1.4831
 V4K  H18  H  HCH2  0   0.242  13.4486  19.5607  -0.4333
 V4K  H19  H  HCH2  0   0.251  14.3490  17.9514  -2.2720
 V4K  H20  H  HCH2  0   0.231  14.1023  17.2581  -0.6859
 V4K  H21  H  HOH1  0   0.450  19.6298  16.5437  -2.3971
 V4K  O1   O  O     0  -0.371  19.4517  22.7711   5.7386
 V4K  C08  C  C     0   0.512  15.6186  20.9052   0.8076

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
 V4K  O01  C02  single    1.412  0.020  1.412
 V4K  C03  C02  single    1.516  0.020  1.516
 V4K  C03  C04  single    1.526  0.020  1.526
 V4K  C18  C04  single    1.526  0.020  1.526
 V4K  C18  C17  single    1.528  0.020  1.528
 V4K  C04  C05  single    1.538  0.020  1.538
 V4K  C17  N07  single    1.460  0.020  1.460
 V4K  O16  C08  double    1.225  0.020  1.225
 V4K  N07  C08  single    1.341  0.020  1.341
 V4K  N07  C06  single    1.453  0.020  1.453
 V4K  C08  C09  single    1.499  0.020  1.499
 V4K  C05  C06  single    1.529  0.020  1.529
 V4K  C10  C09  aromatic  1.391  0.020  1.391
 V4K  C10  C11  aromatic  1.386  0.020  1.386
 V4K  C09  C14  aromatic  1.395  0.020  1.395
 V4K  C11  C12  aromatic  1.391  0.020  1.391
 V4K  C14  C13  aromatic  1.381  0.020  1.381
 V4K  C12  C13  aromatic  1.395  0.020  1.395
 V4K  C12  C15  single    1.472  0.020  1.472
 V4K  C02  H1   single    0.970  0.020  1.090
 V4K  C02  H2   single    0.970  0.020  1.090
 V4K  C03  H3   single    0.970  0.020  1.090
 V4K  C03  H4   single    0.970  0.020  1.090
 V4K  C04  H5   single    0.970  0.020  1.090
 V4K  C05  H6   single    0.970  0.020  1.090
 V4K  C05  H7   single    0.970  0.020  1.090
 V4K  C06  H8   single    0.970  0.020  1.090
 V4K  C06  H9   single    0.970  0.020  1.090
 V4K  C10  H10  single    0.930  0.020  1.080
 V4K  C11  H11  single    0.930  0.020  1.080
 V4K  C13  H12  single    0.930  0.020  1.080
 V4K  C14  H13  single    0.930  0.020  1.080
 V4K  C15  H14  single    0.930  0.020  1.080
 V4K  C17  H17  single    0.970  0.020  1.090
 V4K  C17  H18  single    0.970  0.020  1.090
 V4K  C18  H19  single    0.970  0.020  1.090
 V4K  C18  H20  single    0.970  0.020  1.090
 V4K  O01  H21  single    0.850  0.020  0.980
 V4K  C15  O1   double    1.208  0.020  1.208

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
 V4K  H2   C02  H1   106.43  3.000
 V4K  H2   C02  O01  111.35  3.000
 V4K  H1   C02  O01  111.31  3.000
 V4K  H2   C02  C03  109.71  3.000
 V4K  H1   C02  C03  108.72  3.000
 V4K  O01  C02  C03  109.26  3.000
 V4K  H4   C03  H3   106.24  3.000
 V4K  H4   C03  C04  109.16  3.000
 V4K  H3   C03  C04  109.34  3.000
 V4K  H4   C03  C02  107.65  3.000
 V4K  H3   C03  C02  109.25  3.000
 V4K  C04  C03  C02  114.85  3.000
 V4K  H5   C04  C18  107.26  3.000
 V4K  H5   C04  C05  108.19  3.000
 V4K  C18  C04  C05  108.99  3.000
 V4K  H5   C04  C03  108.33  3.000
 V4K  C05  C04  C03  112.43  3.000
 V4K  C18  C04  C03  111.45  3.000
 V4K  H7   C05  H6   106.64  3.000
 V4K  H7   C05  C06  110.36  3.000
 V4K  H6   C05  C06  108.03  3.000
 V4K  H7   C05  C04  110.17  3.000
 V4K  H6   C05  C04  110.26  3.000
 V4K  C06  C05  C04  111.26  3.000
 V4K  H9   C06  H8   106.07  3.000
 V4K  H9   C06  N07  107.80  3.000
 V4K  H8   C06  N07  110.27  3.000
 V4K  H9   C06  C05  110.04  3.000
 V4K  H8   C06  C05  111.48  3.000
 V4K  N07  C06  C05  111.01  3.000
 V4K  C14  C09  C10  119.85  3.000
 V4K  C14  C09  C08  118.95  3.000
 V4K  C10  C09  C08  120.92  3.000
 V4K  H10  C10  C11  119.78  3.000
 V4K  H10  C10  C09  120.34  3.000
 V4K  C11  C10  C09  119.87  3.000
 V4K  H11  C11  C12  119.87  3.000
 V4K  H11  C11  C10  119.84  3.000
 V4K  C12  C11  C10  120.29  3.000
 V4K  C15  C12  C13  121.30  3.000
 V4K  C15  C12  C11  118.92  3.000
 V4K  C13  C12  C11  119.78  3.000
 V4K  H12  C13  C14  119.94  3.000
 V4K  H12  C13  C12  120.14  3.000
 V4K  C14  C13  C12  119.92  3.000
 V4K  H13  C14  C13  119.83  3.000
 V4K  H13  C14  C09  119.92  3.000
 V4K  C13  C14  C09  120.25  3.000
 V4K  O1   C15  H14  121.04  3.000
 V4K  O1   C15  C12  124.47  3.000
 V4K  H14  C15  C12  114.49  3.000
 V4K  H18  C17  H17  107.24  3.000
 V4K  H18  C17  N07  110.63  3.000
 V4K  H17  C17  N07  108.28  3.000
 V4K  H18  C17  C18  110.92  3.000
 V4K  H17  C17  C18  109.42  3.000
 V4K  N07  C17  C18  110.26  3.000
 V4K  H20  C18  H19  106.20  3.000
 V4K  H20  C18  C17  111.06  3.000
 V4K  H19  C18  C17  108.20  3.000
 V4K  H20  C18  C04  109.81  3.000
 V4K  H19  C18  C04  110.87  3.000
 V4K  C17  C18  C04  110.61  3.000
 V4K  C17  N07  C08  118.88  3.000
 V4K  C08  N07  C06  125.68  3.000
 V4K  C17  N07  C06  114.99  3.000
 V4K  H21  O01  C02  108.21  3.000
 V4K  O16  C08  N07  122.98  3.000
 V4K  N07  C08  C09  118.18  3.000
 V4K  O16  C08  C09  118.81  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
 V4K  CONST_01  C12  C11  C10  C09     0.00   0.0  0
 V4K  CONST_02  C12  C13  C14  C09     0.00   0.0  0
 V4K  CONST_03  C13  C14  C09  C10     0.00   0.0  0
 V4K  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 V4K  CONST_05  C14  C09  C10  C11     0.00   0.0  0
 V4K  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 V4K  CONST_07  C11  C10  C09  C08   180.00   0.0  0
 V4K  CONST_08  C13  C14  C09  C08   180.00   0.0  0
 V4K  CONST_09  C15  C12  C11  C10   180.00   0.0  0
 V4K  CONST_10  C15  C12  C13  C14   180.00   0.0  0
 V4K  CONST_12  C17  N07  C08  C09   180.00   0.0  0
 V4K  CONST_13  H11  C11  C10  C09   180.00   0.0  0
 V4K  CONST_14  H12  C13  C14  C09   180.00   0.0  0
 V4K  CONST_15  H13  C14  C09  C10   180.00   0.0  0
 V4K  CONST_16  H10  C10  C11  C12   180.00   0.0  0
 V4K  CONST_17  O16  C08  N07  C06   180.00   0.0  0
 V4K  CONST_18  O16  C08  N07  C17     0.00   0.0  0
 V4K  Var_01    N07  C17  C18  C04   -37.59  30.0  1
 V4K  Var_02    N07  C06  C05  C04   -32.77  30.0  1
 V4K  Var_03    C17  N07  C06  C05    64.35  30.0  1
 V4K  Var_04    C18  C17  N07  C06   -26.17  30.0  1
 V4K  Var_05    N07  C08  C09  C10    58.53  30.0  2
 V4K  Var_06    O1   C15  C12  C11  -179.62  30.0  2
 V4K  Var_07    O01  C02  C03  C04   -60.04  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
 V4K  chir_01  C04  C03  C18  C05  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
 V4K  plan-1  C09  0.020
 V4K  plan-1  C10  0.020
 V4K  plan-1  C11  0.020
 V4K  plan-1  C12  0.020
 V4K  plan-1  C13  0.020
 V4K  plan-1  C14  0.020
 V4K  plan-1  C15  0.020
 V4K  plan-1  H10  0.020
 V4K  plan-1  H11  0.020
 V4K  plan-1  H12  0.020
 V4K  plan-1  H13  0.020
 V4K  plan-1  C08  0.020
 V4K  plan-2  C06  0.020
 V4K  plan-2  C09  0.020
 V4K  plan-2  C17  0.020
 V4K  plan-2  N07  0.020
 V4K  plan-2  O16  0.020
 V4K  plan-2  C08  0.020
 V4K  plan-3  C12  0.020
 V4K  plan-3  C15  0.020
 V4K  plan-3  H14  0.020
 V4K  plan-3  O1   0.020

