# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:00:41 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 4-cyano-4-phenylpiperidine-1-carbodithioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SC(=S)N1CCC(CC1)(C#N)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
 IT5  IT5  '4-cyano-4-phenylpiperidine-1-carbodithioic acid'  ligand  31  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IT5
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
 IT5  N11   N  NS    0  -0.250   1.4925  -1.9032  -2.5232
 IT5  N22   N  NT    0  -0.351  -1.8668  -0.2373  -0.3387
 IT5  SAB   S  S1    0  -0.322  -3.5428   1.8136  -0.0554
 IT5  SAC   S  S2    0  -0.137  -3.4133  -0.5474   1.7549
 IT5  CAD   C  CSP   0   0.151   1.3036  -1.1991  -1.6330
 IT5  CAE   C  CR16  0  -0.263   4.8710   0.8101   1.1790
 IT5  CAF   C  CR16  0  -0.240   4.5367  -0.5255   0.9916
 IT5  CAG   C  CR16  0  -0.234   3.9711   1.7964   0.8080
 IT5  CAH   C  CR16  0  -0.295   3.3108  -0.8633   0.4418
 IT5  CAI   C  CR16  0  -0.326   2.7415   1.4567   0.2546
 IT5  CAJ   C  CH2   0  -0.335  -1.1946   0.4144  -1.4546
 IT5  CAK   C  CH2   0  -0.360  -1.1565  -1.4374   0.0834
 IT5  CAL   C  CH2   0  -0.436   0.1905   0.8708  -1.0191
 IT5  CAM   C  CH2   0  -0.395   0.2393  -1.0721   0.5691
 IT5  CAN   C  C     0   0.026  -2.8478   0.3512   0.3392
 IT5  CAO   C  CR6   0   0.214   2.3973   0.1229   0.0697
 IT5  CAQ   C  CT    0  -0.305   1.0457  -0.2992  -0.5000
 IT5  HSAC  H  HSH1  0   0.266  -4.3574   0.3372   2.0829
 IT5  HAE   H  HCR6  0   0.262   5.8272   1.0784   1.6085
 IT5  HAF   H  HCR6  0   0.262   5.2314  -1.3065   1.2716
 IT5  HAG   H  HCR6  0   0.262   4.2226   2.8400   0.9439
 IT5  HAH   H  HCR6  0   0.259   3.0713  -1.9108   0.2997
 IT5  HAI   H  HCR6  0   0.264   2.0651   2.2518  -0.0269
 IT5  HAJ   H  HCH2  0   0.278  -1.1457  -0.2976  -2.2822
 IT5  HAJA  H  HCH2  0   0.293  -1.7837   1.2645  -1.7840
 IT5  HAK   H  HCH2  0   0.304  -1.6922  -1.9716   0.8643
 IT5  HAKA  H  HCH2  0   0.288  -1.1100  -2.1166  -0.7715
 IT5  HAL   H  HCH2  0   0.287   0.6881   1.3741  -1.8497
 IT5  HALA  H  HCH2  0   0.275   0.0704   1.6006  -0.2158
 IT5  HAM   H  HCH2  0   0.278   0.1714  -0.4377   1.4557
 IT5  HAMA  H  HCH2  0   0.281   0.7642  -1.9817   0.8627

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
 IT5  N11  CAD   triple    1.151  0.020  1.151
 IT5  CAK  N22   single    1.457  0.020  1.457
 IT5  CAJ  N22   single    1.457  0.020  1.457
 IT5  N22  CAN   single    1.330  0.020  1.330
 IT5  CAN  SAB   double    1.667  0.020  1.667
 IT5  CAN  SAC   single    1.770  0.020  1.770
 IT5  SAC  HSAC  single    1.200  0.020  1.300
 IT5  CAD  CAQ   single    1.470  0.020  1.470
 IT5  CAF  CAE   aromatic  1.389  0.020  1.389
 IT5  CAE  CAG   aromatic  1.386  0.020  1.386
 IT5  CAE  HAE   single    0.930  0.020  1.080
 IT5  CAH  CAF   aromatic  1.385  0.020  1.385
 IT5  CAF  HAF   single    0.930  0.020  1.080
 IT5  CAI  CAG   aromatic  1.391  0.020  1.391
 IT5  CAG  HAG   single    0.930  0.020  1.080
 IT5  CAH  CAO   aromatic  1.395  0.020  1.395
 IT5  CAH  HAH   single    0.930  0.020  1.080
 IT5  CAO  CAI   aromatic  1.390  0.020  1.390
 IT5  CAI  HAI   single    0.930  0.020  1.080
 IT5  CAL  CAJ   single    1.522  0.020  1.522
 IT5  CAJ  HAJ   single    0.970  0.020  1.090
 IT5  CAJ  HAJA  single    0.970  0.020  1.090
 IT5  CAM  CAK   single    1.522  0.020  1.522
 IT5  CAK  HAK   single    0.970  0.020  1.090
 IT5  CAK  HAKA  single    0.970  0.020  1.090
 IT5  CAQ  CAL   single    1.539  0.020  1.539
 IT5  CAL  HAL   single    0.970  0.020  1.090
 IT5  CAL  HALA  single    0.970  0.020  1.090
 IT5  CAQ  CAM   single    1.546  0.020  1.546
 IT5  CAM  HAM   single    0.970  0.020  1.090
 IT5  CAM  HAMA  single    0.970  0.020  1.090
 IT5  CAQ  CAO   single    1.526  0.020  1.526

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
 IT5  CAN   N22  CAK  125.20  3.000
 IT5  CAN   N22  CAJ  122.21  3.000
 IT5  CAK   N22  CAJ  111.44  3.000
 IT5  HSAC  SAC  CAN   94.94  3.000
 IT5  CAQ   CAD  N11  180.00  3.000
 IT5  HAE   CAE  CAG  120.24  3.000
 IT5  HAE   CAE  CAF  120.30  3.000
 IT5  CAG   CAE  CAF  119.46  3.000
 IT5  HAF   CAF  CAH  119.66  3.000
 IT5  HAF   CAF  CAE  120.29  3.000
 IT5  CAH   CAF  CAE  120.05  3.000
 IT5  HAG   CAG  CAI  119.41  3.000
 IT5  HAG   CAG  CAE  120.13  3.000
 IT5  CAI   CAG  CAE  120.46  3.000
 IT5  HAH   CAH  CAO  120.24  3.000
 IT5  HAH   CAH  CAF  118.89  3.000
 IT5  CAO   CAH  CAF  120.86  3.000
 IT5  HAI   CAI  CAO  121.08  3.000
 IT5  HAI   CAI  CAG  118.50  3.000
 IT5  CAO   CAI  CAG  120.42  3.000
 IT5  HAJA  CAJ  HAJ  107.74  3.000
 IT5  HAJA  CAJ  CAL  110.23  3.000
 IT5  HAJ   CAJ  CAL  111.80  3.000
 IT5  HAJA  CAJ  N22  109.42  3.000
 IT5  HAJ   CAJ  N22  108.01  3.000
 IT5  CAL   CAJ  N22  109.57  3.000
 IT5  HAKA  CAK  HAK  106.11  3.000
 IT5  HAKA  CAK  CAM  111.08  3.000
 IT5  HAK   CAK  CAM  109.91  3.000
 IT5  HAKA  CAK  N22  107.81  3.000
 IT5  HAK   CAK  N22  111.87  3.000
 IT5  CAM   CAK  N22  109.98  3.000
 IT5  HALA  CAL  HAL  107.57  3.000
 IT5  HALA  CAL  CAQ  108.72  3.000
 IT5  HAL   CAL  CAQ  110.72  3.000
 IT5  HALA  CAL  CAJ  108.11  3.000
 IT5  HAL   CAL  CAJ  109.60  3.000
 IT5  CAQ   CAL  CAJ  111.97  3.000
 IT5  HAMA  CAM  HAM  107.20  3.000
 IT5  HAMA  CAM  CAQ  110.62  3.000
 IT5  HAM   CAM  CAQ  107.66  3.000
 IT5  HAMA  CAM  CAK  109.10  3.000
 IT5  HAM   CAM  CAK  109.96  3.000
 IT5  CAQ   CAM  CAK  112.18  3.000
 IT5  SAC   CAN  SAB  120.12  3.000
 IT5  SAC   CAN  N22  114.76  3.000
 IT5  SAB   CAN  N22  125.12  3.000
 IT5  CAQ   CAO  CAI  122.30  3.000
 IT5  CAQ   CAO  CAH  118.95  3.000
 IT5  CAI   CAO  CAH  118.74  3.000
 IT5  CAO   CAQ  CAM  110.00  3.000
 IT5  CAO   CAQ  CAL  114.05  3.000
 IT5  CAM   CAQ  CAL  108.87  3.000
 IT5  CAO   CAQ  CAD  107.56  3.000
 IT5  CAM   CAQ  CAD  108.57  3.000
 IT5  CAL   CAQ  CAD  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
 IT5  CONST_01  CAO  CAH  CAF  CAE    0.00   0.0  0
 IT5  CONST_02  CAO  CAI  CAG  CAE    0.00   0.0  0
 IT5  CONST_03  CAI  CAG  CAE  CAF    0.00   0.0  0
 IT5  CONST_04  CAI  CAO  CAH  CAF    0.00   0.0  0
 IT5  CONST_05  CAH  CAF  CAE  CAG    0.00   0.0  0
 IT5  CONST_06  CAH  CAO  CAI  CAG    0.00   0.0  0
 IT5  CONST_07  CAQ  CAO  CAH  CAF  180.00   0.0  0
 IT5  CONST_08  CAQ  CAO  CAI  CAG  180.00   0.0  0
 IT5  CONST_09  HAH  CAH  CAF  CAE  180.00   0.0  0
 IT5  CONST_10  HAI  CAI  CAG  CAE  180.00   0.0  0
 IT5  CONST_11  HAG  CAG  CAE  CAF  180.00   0.0  0
 IT5  CONST_12  HAF  CAF  CAE  CAG  180.00   0.0  0
 IT5  CONST_13  HAE  CAE  CAF  CAH  180.00   0.0  0
 IT5  Var_01    CAQ  CAM  CAK  N22  -55.98  30.0  1
 IT5  Var_02    CAQ  CAL  CAJ  N22   57.67  30.0  1
 IT5  Var_03    CAM  CAK  N22  CAJ   61.97  30.0  1
 IT5  Var_04    CAL  CAJ  N22  CAK  -62.72  30.0  1
 IT5  Var_05    CAK  N22  CAN  SAB  172.76  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
 IT5  chir_01  CAQ  CAL  CAM  CAO  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
 IT5  plan-1  CAE  0.020
 IT5  plan-1  CAF  0.020
 IT5  plan-1  CAG  0.020
 IT5  plan-1  CAH  0.020
 IT5  plan-1  CAI  0.020
 IT5  plan-1  CAO  0.020
 IT5  plan-1  CAQ  0.020
 IT5  plan-1  HAE  0.020
 IT5  plan-1  HAF  0.020
 IT5  plan-1  HAG  0.020
 IT5  plan-1  HAH  0.020
 IT5  plan-1  HAI  0.020
 IT5  plan-2  N22  0.020
 IT5  plan-2  SAB  0.020
 IT5  plan-2  SAC  0.020
 IT5  plan-2  CAN  0.020

