# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 02:17:00 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (4S)-4-cyclohexyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1C[C@H](CN1)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
 PH6  PH6  (4S)-4-cyclohexyl-L-proline  L-peptide  32  14  .  2016-04-26  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PH6
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
 PH6  C    C  C      0   0.401  143.0125  -17.3415  100.0257
 PH6  O    O  O      0  -0.597  144.1545  -16.9737   99.6911
 PH6  CA   C  CH1    0  -0.249  142.0355  -16.2889  100.5929
 PH6  CB   C  CH2    0  -0.433  140.9485  -15.9548   99.5622
 PH6  CG   C  CH1    0  -0.252  141.6212  -14.8972   98.6810
 PH6  CD   C  CH2    0  -0.281  142.6270  -14.2232   99.6509
 PH6  N    N  NH1    0  -0.579  142.6546  -14.9999  100.8941
 PH6  C1   C  CH1    0  -0.216  140.6479  -13.9257   98.0189
 PH6  C6   C  CH2    0  -0.448  141.3710  -12.8778   97.1454
 PH6  C5   C  CH2    0  -0.444  141.4274  -13.3121   95.6857
 PH6  C4   C  CH2    0  -0.424  140.0165  -13.3672   95.0842
 PH6  C3   C  CH2    0  -0.442  138.9698  -13.7737   96.1330
 PH6  C2   C  CH2    0  -0.429  139.5928  -14.6773   97.1905
 PH6  OXT  O  OC    -1  -0.622  142.5425  -18.4959   99.9319
 PH6  HA   H  HCH1   0   0.221  141.5971  -16.6959  101.5092
 PH6  HB2  H  HCH2   0   0.221  140.5932  -16.8218   99.0046
 PH6  HB3  H  HCH2   0   0.211  140.0822  -15.5190  100.0735
 PH6  H    H  HNH1   0   0.332  142.0540  -14.5321  101.5612
 PH6  HG2  H  HCH1   0   0.218  142.1817  -15.4079   97.8877
 PH6  HD2  H  HCH2   0   0.204  143.6212  -14.1825   99.2019
 PH6  HD3  H  HCH2   0   0.209  142.3406  -13.1905   99.8679
 PH6  H1   H  HCH1   0   0.207  140.1250  -13.3909   98.8227
 PH6  H61  H  HCH2   0   0.217  140.8477  -11.9186   97.2050
 PH6  H62  H  HCH2   0   0.234  142.3771  -12.6904   97.5284
 PH6  H21  H  HCH2   0   0.208  140.0538  -15.5385   96.6925
 PH6  H22  H  HCH2   0   0.227  138.8254  -15.0883   97.8504
 PH6  H51  H  HCH2   0   0.225  142.0586  -12.6349   95.1062
 PH6  H52  H  HCH2   0   0.215  141.9029  -14.2953   95.6203
 PH6  H41  H  HCH2   0   0.215  139.7546  -12.3937   94.6622
 PH6  H42  H  HCH2   0   0.216  140.0017  -14.0736   94.2504
 PH6  H31  H  HCH2   0   0.212  138.5627  -12.8839   96.6229
 PH6  H32  H  HCH2   0   0.224  138.1232  -14.2666   95.6505

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
 PH6  C   O    deloc   1.231  0.020  1.231
 PH6  C   CA   single  1.525  0.021  1.525
 PH6  C   OXT  deloc   1.250  0.020  1.250
 PH6  CA  CB   single  1.530  0.020  1.530
 PH6  CA  N    single  1.466  0.015  1.466
 PH6  CB  CG   single  1.532  0.020  1.532
 PH6  CG  CD   single  1.551  0.020  1.551
 PH6  CG  C1   single  1.526  0.020  1.526
 PH6  CD  N    single  1.473  0.014  1.473
 PH6  C1  C6   single  1.544  0.020  1.544
 PH6  C1  C2   single  1.538  0.020  1.538
 PH6  C6  C5   single  1.524  0.020  1.524
 PH6  C5  C4   single  1.535  0.020  1.535
 PH6  C4  C3   single  1.536  0.020  1.536
 PH6  C3  C2   single  1.524  0.020  1.524
 PH6  CA  HA   single  0.970  0.020  0.970
 PH6  CB  HB2  single  0.970  0.020  1.090
 PH6  CB  HB3  single  0.970  0.020  1.090
 PH6  N   H    single  0.860  0.020  1.020
 PH6  CG  HG2  single  0.970  0.020  1.090
 PH6  CD  HD2  single  0.970  0.020  1.090
 PH6  CD  HD3  single  0.970  0.020  1.090
 PH6  C1  H1   single  0.970  0.020  1.090
 PH6  C6  H61  single  0.970  0.020  1.090
 PH6  C6  H62  single  0.970  0.020  1.090
 PH6  C2  H21  single  0.970  0.020  1.090
 PH6  C2  H22  single  0.970  0.020  1.090
 PH6  C5  H51  single  0.970  0.020  1.090
 PH6  C5  H52  single  0.970  0.020  1.090
 PH6  C4  H41  single  0.970  0.020  1.090
 PH6  C4  H42  single  0.970  0.020  1.090
 PH6  C3  H31  single  0.970  0.020  1.090
 PH6  C3  H32  single  0.970  0.020  1.090

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
 PH6  OXT  C   CA   114.78  3.000
 PH6  OXT  C   O    126.68  3.000
 PH6  CA   C   O    119.00  3.000
 PH6  HA   CA  N    110.00  3.000
 PH6  HA   CA  CB   109.00  3.000
 PH6  N    CA  CB   103.00  1.100
 PH6  HA   CA  C    109.00  3.000
 PH6  N    CA  C    112.10  2.500
 PH6  CB   CA  C    110.10  1.900
 PH6  HB3  CB  HB2  107.29  3.000
 PH6  HB3  CB  CG   109.92  3.000
 PH6  HB2  CB  CG   113.44  3.000
 PH6  HB3  CB  CA   109.45  3.000
 PH6  HB2  CB  CA   113.65  3.000
 PH6  CG   CB  CA   103.04  3.000
 PH6  HG2  CG  C1   107.96  3.000
 PH6  HG2  CG  CD   108.85  3.000
 PH6  C1   CG  CD   114.09  3.000
 PH6  HG2  CG  CB   108.58  3.000
 PH6  C1   CG  CB   114.13  3.000
 PH6  CD   CG  CB   103.00  3.000
 PH6  HD3  CD  HD2  106.56  3.000
 PH6  HD3  CD  N    109.70  3.000
 PH6  HD2  CD  N    110.58  3.000
 PH6  HD3  CD  CG   111.38  3.000
 PH6  HD2  CD  CG   110.45  3.000
 PH6  N    CD  CG   103.20  1.500
 PH6  H    N   CD   107.63  3.000
 PH6  H    N   CA   106.99  3.000
 PH6  CD   N   CA   106.53  3.000
 PH6  H1   C1  C2   107.80  3.000
 PH6  H1   C1  C6   107.86  3.000
 PH6  C2   C1  C6   110.39  3.000
 PH6  H1   C1  CG   107.22  3.000
 PH6  C2   C1  CG   111.11  3.000
 PH6  C6   C1  CG   112.26  3.000
 PH6  H62  C6  H61  105.72  3.000
 PH6  H62  C6  C5   110.52  3.000
 PH6  H61  C6  C5   108.64  3.000
 PH6  H62  C6  C1   110.44  3.000
 PH6  H61  C6  C1   109.89  3.000
 PH6  C5   C6  C1   111.45  3.000
 PH6  H52  C5  H51  105.92  3.000
 PH6  H52  C5  C4   110.11  3.000
 PH6  H51  C5  C4   110.22  3.000
 PH6  H52  C5  C6   109.23  3.000
 PH6  H51  C5  C6   110.67  3.000
 PH6  C4   C5  C6   110.59  3.000
 PH6  H42  C4  H41  106.13  3.000
 PH6  H42  C4  C3   109.91  3.000
 PH6  H41  C4  C3   109.64  3.000
 PH6  H42  C4  C5   109.55  3.000
 PH6  H41  C4  C5   109.85  3.000
 PH6  C3   C4  C5   111.61  3.000
 PH6  H32  C3  H31  106.04  3.000
 PH6  H32  C3  C2   110.85  3.000
 PH6  H31  C3  C2   108.87  3.000
 PH6  H32  C3  C4   110.24  3.000
 PH6  H31  C3  C4   110.11  3.000
 PH6  C2   C3  C4   110.61  3.000
 PH6  H22  C2  H21  105.92  3.000
 PH6  H22  C2  C3   110.80  3.000
 PH6  H21  C2  C3   108.81  3.000
 PH6  H22  C2  C1   109.91  3.000
 PH6  H21  C2  C1   109.88  3.000
 PH6  C3   C2  C1   111.37  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
 PH6  Var_01  CG  CD  N   CA   15.97  30.0  1
 PH6  Var_02  C4  C5  C6  C1   65.46  30.0  1
 PH6  Var_03  C4  C3  C2  C1   65.79  30.0  1
 PH6  Var_04  C3  C4  C5  C6  -32.62  30.0  1
 PH6  Var_05  C2  C3  C4  C5  -29.68  30.0  1

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
 PH6  chir_01  CA  C   CB  N   positiv
 PH6  chir_02  CG  CB  CD  C1  positiv
 PH6  chir_03  C1  C2  C6  CG  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
 PH6  plan-1  C    0.020
 PH6  plan-1  O    0.020
 PH6  plan-1  CA   0.020
 PH6  plan-1  OXT  0.020

