# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:47:22 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: [(1~{S},2~{S},5~{R})-5-methyl-2-propan-2-yl-cyclohexyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H]1CC[C@@H](C)C[C@@H]1CN
#
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
 HZC  HZC  '[(1~{S},2~{S},5~{R})-5-methyl-2-propan-2-yl-cyclohexyl]methanamine'  ligand  35  12  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HZC
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
 HZC  C10  C  CH3   0  -0.662  -3.4842  -15.4308  40.5038
 HZC  C11  C  CH2   0  -0.290  -1.5921  -14.5571  37.6777
 HZC  C1   C  CH2   0  -0.403  -4.0641  -11.8630  36.9258
 HZC  C2   C  CH1   0  -0.232  -2.5553  -11.6754  36.8137
 HZC  C3   C  CH2   0  -0.419  -1.8993  -12.0692  38.1336
 HZC  C4   C  CH1   0  -0.238  -2.2329  -13.4970  38.5784
 HZC  C5   C  CH1   0  -0.183  -3.7625  -13.6532  38.7054
 HZC  C6   C  CH2   0  -0.434  -4.4534  -13.2612  37.3933
 HZC  C7   C  CH3   0  -0.650  -2.1997  -10.2475  36.4226
 HZC  C8   C  CH1   0  -0.226  -4.2156  -15.0307  39.2227
 HZC  C9   C  CH3   0  -0.657  -5.7215  -15.0656  39.4857
 HZC  N12  N  NH2   0  -0.803  -0.1415  -14.4104  37.6228
 HZC  H1   H  HCH3  0   0.224  -3.8622  -16.3815  40.8839
 HZC  H2   H  HCH3  0   0.228  -2.4095  -15.5456  40.3623
 HZC  H3   H  HCH3  0   0.212  -3.6369  -14.6821  41.2856
 HZC  H4   H  HCH2  0   0.195  -2.0600  -14.5457  36.6844
 HZC  H5   H  HCH2  0   0.225  -1.7995  -15.5454  38.0943
 HZC  H7   H  HCH2  0   0.218  -4.5425  -11.6434  35.9666
 HZC  H8   H  HCH1  0   0.211  -2.1865  -12.3416  36.0232
 HZC  H9   H  HCH2  0   0.219  -0.8156  -11.9323  38.0745
 HZC  H10  H  HCH2  0   0.212  -2.2427  -11.3748  38.9103
 HZC  H11  H  HCH1  0   0.220  -1.7930  -13.6273  39.5725
 HZC  H12  H  HCH1  0   0.198  -4.0781  -12.9211  39.4646
 HZC  H13  H  HCH2  0   0.229  -5.5378  -13.2973  37.5138
 HZC  H14  H  HCH2  0   0.206  -4.2146  -13.9943  36.6147
 HZC  H15  H  HCH3  0   0.221  -1.1205  -10.1181  36.3219
 HZC  H16  H  HCH3  0   0.221  -2.6580   -9.9704  35.4712
 HZC  H17  H  HCH3  0   0.209  -2.5492   -9.5380  37.1767
 HZC  H18  H  HCH1  0   0.208  -3.9961  -15.7822  38.4542
 HZC  H19  H  HCH3  0   0.224  -6.0141  -16.0233  39.9196
 HZC  H20  H  HCH3  0   0.210  -6.0084  -14.2828  40.1926
 HZC  H21  H  HCH3  0   0.227  -6.3135  -14.9292  38.5814
 HZC  H22  H  HNH2  0   0.343   0.2540  -15.2212  37.1641
 HZC  H23  H  HNH2  0   0.340   0.1012  -13.6268  37.0297
 HZC  H6   H  HCH2  0   0.199  -4.4549  -11.1265  37.6390

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
 HZC  C7   C2   single  1.523  0.020  1.523
 HZC  C2   C1   single  1.525  0.020  1.525
 HZC  C2   C3   single  1.526  0.020  1.526
 HZC  C1   C6   single  1.525  0.020  1.525
 HZC  C6   C5   single  1.534  0.020  1.534
 HZC  C11  N12  single  1.459  0.020  1.459
 HZC  C11  C4   single  1.532  0.020  1.532
 HZC  C3   C4   single  1.532  0.020  1.532
 HZC  C4   C5   single  1.543  0.020  1.543
 HZC  C5   C8   single  1.540  0.020  1.540
 HZC  C8   C9   single  1.529  0.020  1.529
 HZC  C8   C10  single  1.528  0.020  1.528
 HZC  C10  H1   single  0.970  0.020  1.090
 HZC  C10  H2   single  0.970  0.020  1.090
 HZC  C10  H3   single  0.970  0.020  1.090
 HZC  C11  H4   single  0.970  0.020  1.090
 HZC  C11  H5   single  0.970  0.020  1.090
 HZC  C1   H6   single  0.970  0.020  1.090
 HZC  C1   H7   single  0.970  0.020  1.090
 HZC  C2   H8   single  0.970  0.020  1.090
 HZC  C3   H9   single  0.970  0.020  1.090
 HZC  C3   H10  single  0.970  0.020  1.090
 HZC  C4   H11  single  0.970  0.020  1.090
 HZC  C5   H12  single  0.970  0.020  1.090
 HZC  C6   H13  single  0.970  0.020  1.090
 HZC  C6   H14  single  0.970  0.020  1.090
 HZC  C7   H15  single  0.970  0.020  1.090
 HZC  C7   H16  single  0.970  0.020  1.090
 HZC  C7   H17  single  0.970  0.020  1.090
 HZC  C8   H18  single  0.970  0.020  1.090
 HZC  C9   H19  single  0.970  0.020  1.090
 HZC  C9   H20  single  0.970  0.020  1.090
 HZC  C9   H21  single  0.970  0.020  1.090
 HZC  N12  H22  single  0.890  0.020  1.040
 HZC  N12  H23  single  0.890  0.020  1.040

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
 HZC  H3   C10  H2   107.62  3.000
 HZC  H3   C10  H1   107.41  3.000
 HZC  H2   C10  H1   107.15  3.000
 HZC  H3   C10  C8   110.69  3.000
 HZC  H2   C10  C8   112.99  3.000
 HZC  H1   C10  C8   110.74  3.000
 HZC  H5   C11  H4   105.88  3.000
 HZC  H5   C11  N12  107.10  3.000
 HZC  H4   C11  N12  112.86  3.000
 HZC  H5   C11  C4   108.81  3.000
 HZC  H4   C11  C4   110.27  3.000
 HZC  N12  C11  C4   111.62  3.000
 HZC  H7   C1   H6   106.22  3.000
 HZC  H7   C1   C6   109.95  3.000
 HZC  H6   C1   C6   108.98  3.000
 HZC  H7   C1   C2   110.10  3.000
 HZC  H6   C1   C2   108.53  3.000
 HZC  C6   C1   C2   112.83  3.000
 HZC  H8   C2   C7   107.80  3.000
 HZC  H8   C2   C3   108.78  3.000
 HZC  C7   C2   C3   111.34  3.000
 HZC  H8   C2   C1   108.11  3.000
 HZC  C3   C2   C1   109.28  3.000
 HZC  C7   C2   C1   111.43  3.000
 HZC  H10  C3   H9   105.61  3.000
 HZC  H10  C3   C4   108.44  3.000
 HZC  H9   C3   C4   110.37  3.000
 HZC  H10  C3   C2   108.33  3.000
 HZC  H9   C3   C2   110.30  3.000
 HZC  C4   C3   C2   113.46  3.000
 HZC  H11  C4   C5   108.15  3.000
 HZC  H11  C4   C3   106.67  3.000
 HZC  C5   C4   C3   109.52  3.000
 HZC  H11  C4   C11  106.47  3.000
 HZC  C5   C4   C11  113.15  3.000
 HZC  C3   C4   C11  112.53  3.000
 HZC  H12  C5   C8   106.19  3.000
 HZC  H12  C5   C6   106.91  3.000
 HZC  C8   C5   C6   112.55  3.000
 HZC  H12  C5   C4   105.89  3.000
 HZC  C8   C5   C4   114.21  3.000
 HZC  C6   C5   C4   110.50  3.000
 HZC  H14  C6   H13  105.83  3.000
 HZC  H14  C6   C5   109.80  3.000
 HZC  H13  C6   C5   110.16  3.000
 HZC  H14  C6   C1   109.88  3.000
 HZC  H13  C6   C1   108.53  3.000
 HZC  C5   C6   C1   112.44  3.000
 HZC  H17  C7   H16  107.59  3.000
 HZC  H17  C7   H15  107.63  3.000
 HZC  H16  C7   H15  107.73  3.000
 HZC  H17  C7   C2   110.91  3.000
 HZC  H16  C7   C2   111.34  3.000
 HZC  H15  C7   C2   111.45  3.000
 HZC  H18  C8   C9   107.57  3.000
 HZC  H18  C8   C5   108.58  3.000
 HZC  C9   C8   C5   111.60  3.000
 HZC  H18  C8   C10  108.19  3.000
 HZC  C9   C8   C10  108.73  3.000
 HZC  C5   C8   C10  112.02  3.000
 HZC  H21  C9   H20  107.73  3.000
 HZC  H21  C9   H19  107.11  3.000
 HZC  H20  C9   H19  107.51  3.000
 HZC  H21  C9   C8   112.93  3.000
 HZC  H20  C9   C8   110.69  3.000
 HZC  H19  C9   C8   110.64  3.000
 HZC  H23  N12  H22  105.13  3.000
 HZC  H23  N12  C11  109.77  3.000
 HZC  H22  N12  C11  108.96  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
 HZC  Var_01  C5   C6   C1   C2    54.10  30.0  1
 HZC  Var_02  H22  N12  C11  C4   169.64  30.0  3
 HZC  Var_03  H19  C9   C8   C5  -175.88  30.0  3
 HZC  Var_04  H1   C10  C8   C5   176.68  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
 HZC  chir_01  C2  C7  C1  C3   positiv
 HZC  chir_02  C4  C5  C3  C11  positiv
 HZC  chir_03  C5  C6  C4  C8   positiv

