# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 03:23:38 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 3-[(3~{S})-3-methoxypiperidin-1-yl]-4-nitro-benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1CCCN(C1)c2cc(C=O)ccc2[N](=O)=O
#
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
 TWQ  TWQ  3-[(3~{S})-3-methoxypiperidin-1-yl]-4-nitro-benzaldehyde  ligand  35  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TWQ
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
 TWQ  C01  C  CH3   0  -0.404  21.0081  20.3823   1.2647
 TWQ  C03  C  CH1   0   0.050  22.5986  18.6658   1.6668
 TWQ  C04  C  CH2   0  -0.464  22.8138  17.1942   1.3470
 TWQ  C05  C  CH2   0  -0.444  23.2738  16.9981  -0.0942
 TWQ  C06  C  CH2   0  -0.357  24.4715  17.8947  -0.3897
 TWQ  C08  C  CR6   0   0.437  23.8081  20.1708  -1.0137
 TWQ  C09  C  CR6   0   0.155  23.9637  21.5658  -0.9056
 TWQ  C13  C  CR16  0  -0.250  23.4461  22.4608  -1.8374
 TWQ  C14  C  CR16  0  -0.307  22.8258  21.9952  -2.9739
 TWQ  C15  C  CR6   0   0.026  22.7202  20.6161  -3.1537
 TWQ  C16  C  C1    0   0.123  22.0722  20.0494  -4.3555
 TWQ  C17  C  CR16  0  -0.389  23.1882  19.7341  -2.1966
 TWQ  C18  C  CH2   0  -0.383  23.8664  19.4631   1.3414
 TWQ  N07  N  NT    0  -0.486  24.2421  19.2923  -0.0534
 TWQ  N10  N  N     0   0.327  24.7638  22.1603   0.1550
 TWQ  O02  O  O2    0  -0.480  21.4936  19.1110   0.9143
 TWQ  O11  O  O     0  -0.363  25.8327  21.6582   0.4064
 TWQ  O12  O  O     0  -0.368  24.3328  23.1540   0.6935
 TWQ  H1   H  HCH3  0   0.236  20.0540  20.5230   0.7577
 TWQ  H2   H  HCH3  0   0.207  20.8408  20.4742   2.3443
 TWQ  H3   H  HCH3  0   0.205  21.6727  21.1976   0.9574
 TWQ  H4   H  HCH1  0   0.226  22.3985  18.7842   2.7430
 TWQ  H5   H  HCH2  0   0.246  21.9012  16.6294   1.5484
 TWQ  H6   H  HCH2  0   0.232  23.5778  16.8107   2.0295
 TWQ  H7   H  HCH2  0   0.233  22.4553  17.2077  -0.7861
 TWQ  H8   H  HCH2  0   0.242  23.5623  15.9579  -0.2586
 TWQ  H9   H  HCH2  0   0.266  24.7893  17.8148  -1.4291
 TWQ  H10  H  HCH2  0   0.259  25.3221  17.5615   0.2145
 TWQ  H11  H  HCR6  0   0.293  23.5757  23.5242  -1.6899
 TWQ  H12  H  HCR6  0   0.273  22.4440  22.6864  -3.7120
 TWQ  H13  H  H     0   0.205  22.0441  18.9459  -4.3869
 TWQ  H16  H  HCR6  0   0.292  23.0371  18.6749  -2.3588
 TWQ  H17  H  HCH2  0   0.259  24.6819  19.1087   1.9783
 TWQ  H18  H  HCH2  0   0.266  23.7140  20.5085   1.6000
 TWQ  O1   O  O     0  -0.362  21.6038  20.7123  -5.2474

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
 TWQ  C16  C15  single    1.478  0.020  1.478
 TWQ  C14  C15  aromatic  1.395  0.020  1.395
 TWQ  C14  C13  aromatic  1.376  0.020  1.376
 TWQ  C15  C17  aromatic  1.383  0.020  1.383
 TWQ  C13  C09  aromatic  1.392  0.020  1.392
 TWQ  C17  C08  aromatic  1.405  0.020  1.405
 TWQ  C08  C09  aromatic  1.408  0.020  1.408
 TWQ  C08  N07  single    1.372  0.020  1.372
 TWQ  C09  N10  single    1.455  0.020  1.455
 TWQ  C06  N07  single    1.456  0.020  1.456
 TWQ  C06  C05  single    1.525  0.020  1.525
 TWQ  N07  C18  single    1.455  0.020  1.455
 TWQ  N10  O12  double    1.210  0.020  1.210
 TWQ  N10  O11  double    1.207  0.020  1.207
 TWQ  C05  C04  single    1.525  0.020  1.525
 TWQ  C01  O02  single    1.405  0.020  1.405
 TWQ  C18  C03  single    1.533  0.020  1.533
 TWQ  O02  C03  single    1.409  0.020  1.409
 TWQ  C04  C03  single    1.521  0.020  1.521
 TWQ  C01  H1   single    0.970  0.020  1.090
 TWQ  C01  H2   single    0.970  0.020  1.090
 TWQ  C01  H3   single    0.970  0.020  1.090
 TWQ  C03  H4   single    0.970  0.020  1.090
 TWQ  C04  H5   single    0.970  0.020  1.090
 TWQ  C04  H6   single    0.970  0.020  1.090
 TWQ  C05  H7   single    0.970  0.020  1.090
 TWQ  C05  H8   single    0.970  0.020  1.090
 TWQ  C06  H9   single    0.970  0.020  1.090
 TWQ  C06  H10  single    0.970  0.020  1.090
 TWQ  C13  H11  single    0.930  0.020  1.080
 TWQ  C14  H12  single    0.930  0.020  1.080
 TWQ  C16  H13  single    0.930  0.020  1.080
 TWQ  C17  H16  single    0.930  0.020  1.080
 TWQ  C18  H17  single    0.970  0.020  1.090
 TWQ  C18  H18  single    0.970  0.020  1.090
 TWQ  C16  O1   double    1.206  0.020  1.206

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
 TWQ  H3   C01  H2   107.84  3.000
 TWQ  H3   C01  H1   107.73  3.000
 TWQ  H2   C01  H1   108.29  3.000
 TWQ  H3   C01  O02  113.18  3.000
 TWQ  H2   C01  O02  111.97  3.000
 TWQ  H1   C01  O02  107.66  3.000
 TWQ  H4   C03  O02  110.21  3.000
 TWQ  H4   C03  C18  107.58  3.000
 TWQ  O02  C03  C18  111.78  3.000
 TWQ  H4   C03  C04  109.58  3.000
 TWQ  O02  C03  C04  107.71  3.000
 TWQ  C18  C03  C04  109.97  3.000
 TWQ  H6   C04  H5   106.70  3.000
 TWQ  H6   C04  C05  109.50  3.000
 TWQ  H5   C04  C05  111.09  3.000
 TWQ  H6   C04  C03  107.86  3.000
 TWQ  H5   C04  C03  110.08  3.000
 TWQ  C05  C04  C03  111.45  3.000
 TWQ  H8   C05  H7   106.59  3.000
 TWQ  H8   C05  C06  108.87  3.000
 TWQ  H7   C05  C06  110.67  3.000
 TWQ  H8   C05  C04  110.15  3.000
 TWQ  H7   C05  C04  110.36  3.000
 TWQ  C06  C05  C04  110.14  3.000
 TWQ  H10  C06  H9   106.10  3.000
 TWQ  H10  C06  N07  106.68  3.000
 TWQ  H9   C06  N07  109.67  3.000
 TWQ  H10  C06  C05  108.91  3.000
 TWQ  H9   C06  C05  111.76  3.000
 TWQ  N07  C06  C05  113.33  3.000
 TWQ  N07  C08  C17  121.99  3.000
 TWQ  N07  C08  C09  123.08  3.000
 TWQ  C17  C08  C09  114.92  3.000
 TWQ  N10  C09  C13  115.44  3.000
 TWQ  N10  C09  C08  121.43  3.000
 TWQ  C13  C09  C08  123.00  3.000
 TWQ  H11  C13  C14  119.97  3.000
 TWQ  H11  C13  C09  119.76  3.000
 TWQ  C14  C13  C09  120.20  3.000
 TWQ  H12  C14  C15  121.16  3.000
 TWQ  H12  C14  C13  120.46  3.000
 TWQ  C15  C14  C13  118.37  3.000
 TWQ  C17  C15  C16  117.80  3.000
 TWQ  C17  C15  C14  121.04  3.000
 TWQ  C16  C15  C14  121.13  3.000
 TWQ  O1   C16  H13  121.22  3.000
 TWQ  O1   C16  C15  124.11  3.000
 TWQ  H13  C16  C15  114.67  3.000
 TWQ  H16  C17  C15  118.24  3.000
 TWQ  H16  C17  C08  119.47  3.000
 TWQ  C15  C17  C08  122.25  3.000
 TWQ  H18  C18  H17  106.11  3.000
 TWQ  H18  C18  N07  112.15  3.000
 TWQ  H17  C18  N07  109.13  3.000
 TWQ  H18  C18  C03  109.49  3.000
 TWQ  H17  C18  C03  108.94  3.000
 TWQ  N07  C18  C03  110.86  3.000
 TWQ  C18  N07  C08  120.95  3.000
 TWQ  C18  N07  C06  112.02  3.000
 TWQ  C08  N07  C06  120.20  3.000
 TWQ  O12  N10  O11  124.36  3.000
 TWQ  O11  N10  C09  117.94  3.000
 TWQ  O12  N10  C09  117.65  3.000
 TWQ  C03  O02  C01  115.06  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
 TWQ  CONST_01  C14  C15  C17  C08     0.00   0.0  0
 TWQ  CONST_02  C14  C13  C09  C08     0.00   0.0  0
 TWQ  CONST_03  C15  C14  C13  C09     0.00   0.0  0
 TWQ  CONST_04  C15  C17  C08  C09     0.00   0.0  0
 TWQ  CONST_05  C17  C15  C14  C13     0.00   0.0  0
 TWQ  CONST_06  C17  C08  C09  C13     0.00   0.0  0
 TWQ  CONST_07  N07  C08  C09  C13   180.00   0.0  0
 TWQ  CONST_08  N07  C08  C17  C15   180.00   0.0  0
 TWQ  CONST_09  C16  C15  C17  C08   180.00   0.0  0
 TWQ  CONST_10  C16  C15  C14  C13   180.00   0.0  0
 TWQ  CONST_11  N10  C09  C13  C14   180.00   0.0  0
 TWQ  CONST_12  N10  C09  C08  C17   180.00   0.0  0
 TWQ  CONST_13  N10  C09  C08  N07     0.00   0.0  0
 TWQ  CONST_14  H11  C13  C09  C08   180.00   0.0  0
 TWQ  CONST_15  H12  C14  C13  C09   180.00   0.0  0
 TWQ  CONST_16  H16  C17  C08  C09   180.00   0.0  0
 TWQ  Var_01    C08  N07  C18  C03    92.64  30.0  1
 TWQ  Var_02    C06  C05  C04  C03    51.60  30.0  1
 TWQ  Var_03    N07  C06  C05  C04   -52.44  30.0  1
 TWQ  Var_04    C17  C08  N07  C06    19.77  30.0  2
 TWQ  Var_05    O1   C16  C15  C14     0.27  30.0  2
 TWQ  Var_06    H1   C01  O02  C03  -169.07  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
 TWQ  chir_01  C03  C18  O02  C04  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
 TWQ  plan-1  C08  0.020
 TWQ  plan-1  C09  0.020
 TWQ  plan-1  C13  0.020
 TWQ  plan-1  C14  0.020
 TWQ  plan-1  C15  0.020
 TWQ  plan-1  C16  0.020
 TWQ  plan-1  C17  0.020
 TWQ  plan-1  N07  0.020
 TWQ  plan-1  N10  0.020
 TWQ  plan-1  H11  0.020
 TWQ  plan-1  H12  0.020
 TWQ  plan-1  H16  0.020
 TWQ  plan-2  C09  0.020
 TWQ  plan-2  N10  0.020
 TWQ  plan-2  O11  0.020
 TWQ  plan-2  O12  0.020
 TWQ  plan-3  C15  0.020
 TWQ  plan-3  C16  0.020
 TWQ  plan-3  H13  0.020
 TWQ  plan-3  O1   0.020

