# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:34:57 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-(4-methoxypiperidin-1-yl)carbonylbenzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1CCN(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
 V3W  V3W  4-(4-methoxypiperidin-1-yl)carbonylbenzaldehyde  ligand  35  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V3W
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
 V3W  C01  C  C1    0   0.117  21.5904  21.8425  -4.0122
 V3W  C02  C  CR6   0  -0.014  22.5555  21.6902  -2.9114
 V3W  C03  C  CR16  0  -0.255  23.1085  22.8011  -2.2746
 V3W  C04  C  CR16  0  -0.246  24.0073  22.6266  -1.2399
 V3W  C05  C  CR6   0  -0.086  24.3478  21.3419  -0.8188
 V3W  C06  C  C     0   0.511  25.3720  21.1844   0.2665
 V3W  C08  C  CH2   0  -0.335  25.8247  20.8040   2.6211
 V3W  C09  C  CH2   0  -0.461  25.6333  22.0526   3.4746
 V3W  C10  C  CH1   0   0.083  24.1814  22.1880   3.9139
 V3W  C13  C  CH2   0  -0.464  23.2496  22.1334   2.7029
 V3W  C14  C  CH2   0  -0.327  23.5204  20.8841   1.8739
 V3W  C16  C  CR16  0  -0.236  23.8015  20.2322  -1.4532
 V3W  C17  C  CR16  0  -0.266  22.9119  20.4092  -2.5008
 V3W  N07  N  NT    0  -0.426  24.9197  20.8289   1.4832
 V3W  O15  O  O     0  -0.472  26.5500  21.3721   0.0003
 V3W  H1   H  H     0   0.199  21.2290  20.8898  -4.4388
 V3W  H4   H  HCR6  0   0.270  22.8354  23.8000  -2.5892
 V3W  H5   H  HCR6  0   0.270  24.4360  23.4897  -0.7464
 V3W  H6   H  HCH2  0   0.252  25.6044  19.9082   3.2088
 V3W  H7   H  HCH2  0   0.271  26.8504  20.7195   2.2732
 V3W  H8   H  HCH2  0   0.248  26.2858  21.9973   4.3490
 V3W  H9   H  HCH2  0   0.234  25.9306  22.9352   2.8997
 V3W  H10  H  HCH1  0   0.194  23.9391  21.3306   4.5654
 V3W  H11  H  HCH3  0   0.233  22.9479  24.4166   5.9780
 V3W  H12  H  HCH3  0   0.206  21.9859  23.6128   4.7333
 V3W  H13  H  HCH3  0   0.202  22.7057  22.6631   6.0443
 V3W  H14  H  HCH2  0   0.232  23.4024  23.0210   2.0802
 V3W  H15  H  HCH2  0   0.250  22.2015  22.1253   3.0102
 V3W  H16  H  HCH2  0   0.279  22.8774  20.8630   0.9983
 V3W  H17  H  HCH2  0   0.254  23.2924  19.9860   2.4550
 V3W  H18  H  HCR6  0   0.272  24.0632  19.2334  -1.1274
 V3W  H19  H  HCR6  0   0.274  22.4853  19.5458  -2.9977
 V3W  O1   O  O     0  -0.372  21.2001  22.9035  -4.4382
 V3W  O11  O  O2    0  -0.487  24.0645  23.3864   4.6434
 V3W  C12  C  CH3   0  -0.404  22.8698  23.5145   5.3721

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
 V3W  C01  C02  single    1.472  0.020  1.472
 V3W  C03  C02  aromatic  1.395  0.020  1.395
 V3W  C03  C04  aromatic  1.382  0.020  1.382
 V3W  C02  C17  aromatic  1.392  0.020  1.392
 V3W  C04  C05  aromatic  1.394  0.020  1.394
 V3W  C17  C16  aromatic  1.386  0.020  1.386
 V3W  C05  C16  aromatic  1.390  0.020  1.390
 V3W  C05  C06  single    1.501  0.020  1.501
 V3W  O15  C06  double    1.222  0.020  1.222
 V3W  C06  N07  single    1.346  0.020  1.346
 V3W  N07  C14  single    1.454  0.020  1.454
 V3W  N07  C08  single    1.454  0.020  1.454
 V3W  C14  C13  single    1.524  0.020  1.524
 V3W  C08  C09  single    1.525  0.020  1.525
 V3W  C13  C10  single    1.529  0.020  1.529
 V3W  C09  C10  single    1.523  0.020  1.523
 V3W  C10  O11  single    1.408  0.020  1.408
 V3W  O11  C12  single    1.405  0.020  1.405
 V3W  C01  H1   single    0.930  0.020  1.080
 V3W  C03  H4   single    0.930  0.020  1.080
 V3W  C04  H5   single    0.930  0.020  1.080
 V3W  C08  H6   single    0.970  0.020  1.090
 V3W  C08  H7   single    0.970  0.020  1.090
 V3W  C09  H8   single    0.970  0.020  1.090
 V3W  C09  H9   single    0.970  0.020  1.090
 V3W  C10  H10  single    0.970  0.020  1.090
 V3W  C12  H11  single    0.970  0.020  1.090
 V3W  C12  H12  single    0.970  0.020  1.090
 V3W  C12  H13  single    0.970  0.020  1.090
 V3W  C13  H14  single    0.970  0.020  1.090
 V3W  C13  H15  single    0.970  0.020  1.090
 V3W  C14  H16  single    0.970  0.020  1.090
 V3W  C14  H17  single    0.970  0.020  1.090
 V3W  C16  H18  single    0.930  0.020  1.080
 V3W  C17  H19  single    0.930  0.020  1.080
 V3W  C01  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
 V3W  O1   C01  H1   121.03  3.000
 V3W  O1   C01  C02  124.50  3.000
 V3W  H1   C01  C02  114.47  3.000
 V3W  C17  C02  C03  119.79  3.000
 V3W  C17  C02  C01  118.94  3.000
 V3W  C03  C02  C01  121.27  3.000
 V3W  H4   C03  C04  119.89  3.000
 V3W  H4   C03  C02  120.15  3.000
 V3W  C04  C03  C02  119.95  3.000
 V3W  H5   C04  C05  120.01  3.000
 V3W  H5   C04  C03  119.88  3.000
 V3W  C05  C04  C03  120.10  3.000
 V3W  C16  C05  C06  120.97  3.000
 V3W  C06  C05  C04  118.81  3.000
 V3W  C16  C05  C04  120.12  3.000
 V3W  O15  C06  N07  124.15  3.000
 V3W  N07  C06  C05  116.89  3.000
 V3W  O15  C06  C05  118.96  3.000
 V3W  H7   C08  H6   107.37  3.000
 V3W  H7   C08  N07  109.78  3.000
 V3W  H6   C08  N07  108.01  3.000
 V3W  H7   C08  C09  111.19  3.000
 V3W  H6   C08  C09  110.16  3.000
 V3W  N07  C08  C09  110.24  3.000
 V3W  H9   C09  H8   107.40  3.000
 V3W  H9   C09  C10  109.80  3.000
 V3W  H8   C09  C10  110.06  3.000
 V3W  H9   C09  C08  109.41  3.000
 V3W  H8   C09  C08  109.37  3.000
 V3W  C10  C09  C08  110.73  3.000
 V3W  H10  C10  O11  109.70  3.000
 V3W  H10  C10  C13  107.81  3.000
 V3W  O11  C10  C13  112.96  3.000
 V3W  H10  C10  C09  108.09  3.000
 V3W  O11  C10  C09  107.72  3.000
 V3W  C13  C10  C09  110.45  3.000
 V3W  H15  C13  H14  107.45  3.000
 V3W  H15  C13  C14  108.51  3.000
 V3W  H14  C13  C14  109.30  3.000
 V3W  H15  C13  C10  111.24  3.000
 V3W  H14  C13  C10  109.66  3.000
 V3W  C14  C13  C10  110.60  3.000
 V3W  H17  C14  H16  106.79  3.000
 V3W  H17  C14  N07  108.19  3.000
 V3W  H16  C14  N07  110.63  3.000
 V3W  H17  C14  C13  110.31  3.000
 V3W  H16  C14  C13  110.44  3.000
 V3W  N07  C14  C13  110.39  3.000
 V3W  H18  C16  C17  120.04  3.000
 V3W  H18  C16  C05  120.27  3.000
 V3W  C17  C16  C05  119.69  3.000
 V3W  H19  C17  C16  119.85  3.000
 V3W  H19  C17  C02  119.81  3.000
 V3W  C16  C17  C02  120.34  3.000
 V3W  C14  N07  C08  112.91  3.000
 V3W  C08  N07  C06  120.19  3.000
 V3W  C14  N07  C06  123.80  3.000
 V3W  C12  O11  C10  114.64  3.000
 V3W  H13  C12  H12  107.84  3.000
 V3W  H13  C12  H11  108.21  3.000
 V3W  H12  C12  H11  107.94  3.000
 V3W  H13  C12  O11  111.97  3.000
 V3W  H12  C12  O11  113.07  3.000
 V3W  H11  C12  O11  107.63  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
 V3W  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 V3W  CONST_02  C05  C16  C17  C02    0.00   0.0  0
 V3W  CONST_03  C16  C17  C02  C03    0.00   0.0  0
 V3W  CONST_04  C16  C05  C04  C03    0.00   0.0  0
 V3W  CONST_05  C17  C02  C03  C04    0.00   0.0  0
 V3W  CONST_06  C17  C16  C05  C04    0.00   0.0  0
 V3W  CONST_07  C04  C03  C02  C01  180.00   0.0  0
 V3W  CONST_08  C16  C17  C02  C01  180.00   0.0  0
 V3W  CONST_09  C06  C05  C04  C03  180.00   0.0  0
 V3W  CONST_10  C17  C16  C05  C06  180.00   0.0  0
 V3W  CONST_11  C14  N07  C06  C05    0.00   0.0  0
 V3W  CONST_12  C08  N07  C06  C05  180.00   0.0  0
 V3W  CONST_13  H5   C04  C03  C02  180.00   0.0  0
 V3W  CONST_14  H18  C16  C17  C02  180.00   0.0  0
 V3W  CONST_15  H19  C17  C02  C03  180.00   0.0  0
 V3W  CONST_16  H4   C03  C04  C05  180.00   0.0  0
 V3W  CONST_17  O15  C06  N07  C08    0.00   0.0  0
 V3W  CONST_18  O15  C06  N07  C14  180.00   0.0  0
 V3W  Var_01    C13  C14  N07  C08   59.61  30.0  1
 V3W  Var_02    C14  N07  C08  C09  -59.62  30.0  1
 V3W  Var_03    N07  C14  C13  C10  -55.66  30.0  1
 V3W  Var_04    N07  C08  C09  C10   55.93  30.0  1
 V3W  Var_05    N07  C06  C05  C04  106.08  30.0  2
 V3W  Var_06    O1   C01  C02  C03   -0.54  30.0  2
 V3W  Var_07    H11  C12  O11  C10  173.54  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
 V3W  chir_01  C10  C13  C09  O11  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
 V3W  plan-1  C01  0.020
 V3W  plan-1  C02  0.020
 V3W  plan-1  C03  0.020
 V3W  plan-1  C04  0.020
 V3W  plan-1  C05  0.020
 V3W  plan-1  C06  0.020
 V3W  plan-1  C16  0.020
 V3W  plan-1  C17  0.020
 V3W  plan-1  H4   0.020
 V3W  plan-1  H5   0.020
 V3W  plan-1  H18  0.020
 V3W  plan-1  H19  0.020
 V3W  plan-2  C05  0.020
 V3W  plan-2  C06  0.020
 V3W  plan-2  C08  0.020
 V3W  plan-2  C14  0.020
 V3W  plan-2  N07  0.020
 V3W  plan-2  O15  0.020
 V3W  plan-3  C01  0.020
 V3W  plan-3  C02  0.020
 V3W  plan-3  H1   0.020
 V3W  plan-3  O1   0.020

