# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:39:07 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: phenyl(piperidin-4-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(C1CCNCC1)c2ccccc2
#
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
 3VW  3VW  phenyl(piperidin-4-yl)methanone  ligand  29  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3VW
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
 3VW  CAI  C  CH2   0  -0.422   1.4347  -0.6357   0.8988
 3VW  CAG  C  CH2   0  -0.289   2.7158  -1.4339   0.7045
 3VW  NAK  N  NH1   0  -0.595   3.8161  -0.5467   0.3792
 3VW  CAH  C  CH2   0  -0.298   3.5778   0.1734  -0.8587
 3VW  CAJ  C  CH2   0  -0.404   2.3411   1.0499  -0.7208
 3VW  CAN  C  CH1   0  -0.416   1.1312   0.1907  -0.3644
 3VW  CAL  C  C     0   0.411  -0.1282   1.0001  -0.1562
 3VW  OAA  O  O     0  -0.396  -0.0844   2.1992   0.0267
 3VW  CAM  C  CR6   0  -0.010  -1.4443   0.2928  -0.1309
 3VW  CAE  C  CR16  0  -0.265  -2.5641   0.9814   0.3419
 3VW  CAC  C  CR16  0  -0.241  -3.8055   0.3694   0.3774
 3VW  CAB  C  CR16  0  -0.249  -3.9489  -0.9394  -0.0687
 3VW  CAD  C  CR16  0  -0.240  -2.8447  -1.6322  -0.5448
 3VW  CAF  C  CR16  0  -0.292  -1.5993  -1.0213  -0.5723
 3VW  H1   H  HCH2  0   0.246   0.6151  -1.3191   1.1282
 3VW  H2   H  HCH2  0   0.232   1.5479   0.0373   1.7538
 3VW  H3   H  HCH2  0   0.236   2.9536  -1.9729   1.6240
 3VW  H4   H  HCH2  0   0.190   2.5375  -2.1925  -0.0762
 3VW  H5   H  HNH1  0   0.353   4.6696  -1.0838   0.3005
 3VW  H7   H  HCH2  0   0.234   4.4485   0.7946  -1.0781
 3VW  H8   H  HCH2  0   0.188   3.4405  -0.5021  -1.7200
 3VW  H9   H  HCH2  0   0.223   2.5145   1.7952   0.0586
 3VW  H10  H  HCH2  0   0.236   2.1676   1.5874  -1.6555
 3VW  H11  H  HCH1  0   0.255   0.9656  -0.5154  -1.1867
 3VW  H12  H  HCR6  0   0.261  -2.4594   2.0008   0.6888
 3VW  H13  H  HCR6  0   0.263  -4.6639   0.9120   0.7509
 3VW  H14  H  HCR6  0   0.266  -4.9199  -1.4169  -0.0462
 3VW  H15  H  HCR6  0   0.265  -2.9522  -2.6497  -0.8965
 3VW  H16  H  HCR6  0   0.260  -0.7564  -1.5816  -0.9540

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
 3VW  CAD  CAF  aromatic  1.387  0.020  1.387
 3VW  CAD  CAB  aromatic  1.388  0.020  1.388
 3VW  CAH  CAJ  single    1.522  0.020  1.522
 3VW  CAH  NAK  single    1.452  0.020  1.452
 3VW  CAF  CAM  aromatic  1.395  0.020  1.395
 3VW  CAJ  CAN  single    1.526  0.020  1.526
 3VW  CAN  CAL  single    1.511  0.020  1.511
 3VW  CAN  CAI  single    1.540  0.020  1.540
 3VW  CAM  CAL  single    1.494  0.020  1.494
 3VW  CAM  CAE  aromatic  1.397  0.020  1.397
 3VW  CAB  CAC  aromatic  1.390  0.020  1.390
 3VW  CAL  OAA  double    1.214  0.020  1.214
 3VW  CAC  CAE  aromatic  1.385  0.020  1.385
 3VW  NAK  CAG  single    1.450  0.020  1.450
 3VW  CAG  CAI  single    1.522  0.020  1.522
 3VW  CAI  H1   single    0.970  0.020  1.090
 3VW  CAI  H2   single    0.970  0.020  1.090
 3VW  CAG  H3   single    0.970  0.020  1.090
 3VW  CAG  H4   single    0.970  0.020  1.090
 3VW  NAK  H5   single    0.890  0.020  1.040
 3VW  CAH  H7   single    0.970  0.020  1.090
 3VW  CAH  H8   single    0.970  0.020  1.090
 3VW  CAJ  H9   single    0.970  0.020  1.090
 3VW  CAJ  H10  single    0.970  0.020  1.090
 3VW  CAN  H11  single    0.970  0.020  1.090
 3VW  CAE  H12  single    0.930  0.020  1.080
 3VW  CAC  H13  single    0.930  0.020  1.080
 3VW  CAB  H14  single    0.930  0.020  1.080
 3VW  CAD  H15  single    0.930  0.020  1.080
 3VW  CAF  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
 3VW  H2   CAI  H1   107.37  3.000
 3VW  H2   CAI  CAN  109.36  3.000
 3VW  H1   CAI  CAN  111.12  3.000
 3VW  H2   CAI  CAG  109.59  3.000
 3VW  H1   CAI  CAG  109.30  3.000
 3VW  CAN  CAI  CAG  110.04  3.000
 3VW  H4   CAG  H3   106.96  3.000
 3VW  H4   CAG  NAK  112.61  3.000
 3VW  H3   CAG  NAK  109.00  3.000
 3VW  H4   CAG  CAI  108.36  3.000
 3VW  H3   CAG  CAI  109.55  3.000
 3VW  NAK  CAG  CAI  110.26  3.000
 3VW  H5   NAK  CAH  109.61  3.000
 3VW  H5   NAK  CAG  109.43  3.000
 3VW  CAH  NAK  CAG  111.73  3.000
 3VW  H8   CAH  H7   106.90  3.000
 3VW  H8   CAH  CAJ  108.80  3.000
 3VW  H7   CAH  CAJ  109.79  3.000
 3VW  H8   CAH  NAK  112.48  3.000
 3VW  H7   CAH  NAK  108.82  3.000
 3VW  CAJ  CAH  NAK  109.98  3.000
 3VW  H10  CAJ  H9   107.47  3.000
 3VW  H10  CAJ  CAN  110.54  3.000
 3VW  H9   CAJ  CAN  110.08  3.000
 3VW  H10  CAJ  CAH  109.57  3.000
 3VW  H9   CAJ  CAH  109.19  3.000
 3VW  CAN  CAJ  CAH  109.94  3.000
 3VW  H11  CAN  CAL  108.80  3.000
 3VW  H11  CAN  CAJ  107.89  3.000
 3VW  CAL  CAN  CAJ  113.03  3.000
 3VW  H11  CAN  CAI  107.43  3.000
 3VW  CAL  CAN  CAI  109.80  3.000
 3VW  CAJ  CAN  CAI  109.72  3.000
 3VW  CAM  CAL  OAA  119.79  3.000
 3VW  OAA  CAL  CAN  121.31  3.000
 3VW  CAM  CAL  CAN  118.86  3.000
 3VW  CAF  CAM  CAE  118.84  3.000
 3VW  CAE  CAM  CAL  118.58  3.000
 3VW  CAF  CAM  CAL  122.57  3.000
 3VW  H12  CAE  CAC  119.68  3.000
 3VW  H12  CAE  CAM  119.70  3.000
 3VW  CAC  CAE  CAM  120.63  3.000
 3VW  H13  CAC  CAB  120.07  3.000
 3VW  H13  CAC  CAE  119.90  3.000
 3VW  CAB  CAC  CAE  120.03  3.000
 3VW  H14  CAB  CAD  120.05  3.000
 3VW  H14  CAB  CAC  120.08  3.000
 3VW  CAD  CAB  CAC  119.87  3.000
 3VW  H15  CAD  CAF  119.80  3.000
 3VW  H15  CAD  CAB  120.13  3.000
 3VW  CAF  CAD  CAB  120.08  3.000
 3VW  H16  CAF  CAD  118.58  3.000
 3VW  H16  CAF  CAM  120.86  3.000
 3VW  CAD  CAF  CAM  120.55  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
 3VW  CONST_01  CAB  CAD  CAF  CAM    0.00   0.0  0
 3VW  CONST_02  CAB  CAC  CAE  CAM    0.00   0.0  0
 3VW  CONST_03  CAD  CAF  CAM  CAE    0.00   0.0  0
 3VW  CONST_04  CAD  CAB  CAC  CAE    0.00   0.0  0
 3VW  CONST_05  CAF  CAD  CAB  CAC    0.00   0.0  0
 3VW  CONST_06  CAF  CAM  CAE  CAC    0.00   0.0  0
 3VW  CONST_07  CAD  CAF  CAM  CAL  180.00   0.0  0
 3VW  CONST_08  CAC  CAE  CAM  CAL  180.00   0.0  0
 3VW  CONST_09  H15  CAD  CAF  CAM  180.00   0.0  0
 3VW  CONST_10  H13  CAC  CAE  CAM  180.00   0.0  0
 3VW  CONST_11  H16  CAF  CAM  CAE  180.00   0.0  0
 3VW  CONST_12  H14  CAB  CAC  CAE  180.00   0.0  0
 3VW  CONST_13  H12  CAE  CAC  CAB  180.00   0.0  0
 3VW  Var_01    CAH  NAK  CAG  CAI  -61.36  30.0  1
 3VW  Var_02    CAJ  CAH  NAK  CAG   61.92  30.0  1
 3VW  Var_03    CAN  CAJ  CAH  NAK  -58.26  30.0  1
 3VW  Var_04    CAN  CAI  CAG  NAK   56.88  30.0  1
 3VW  Var_05    CAF  CAM  CAL  CAN  -14.22  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
 3VW  chir_01  CAN  CAJ  CAL  CAI  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
 3VW  plan-1  CAL  0.020
 3VW  plan-1  CAM  0.020
 3VW  plan-1  CAE  0.020
 3VW  plan-1  CAC  0.020
 3VW  plan-1  CAB  0.020
 3VW  plan-1  CAD  0.020
 3VW  plan-1  CAF  0.020
 3VW  plan-1  H12  0.020
 3VW  plan-1  H13  0.020
 3VW  plan-1  H14  0.020
 3VW  plan-1  H15  0.020
 3VW  plan-1  H16  0.020
 3VW  plan-2  CAN  0.020
 3VW  plan-2  CAL  0.020
 3VW  plan-2  OAA  0.020
 3VW  plan-2  CAM  0.020

