# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:51:53 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: cis-4-cyano-4-[3-(cyclopentyloxy)-4-methoxyphenyl]cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC2CCCC2)[C@]3(CC[C@@H](CC3)C(O)=O)C#N
#
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
 CIO  CIO  'cis-4-cyano-4-[3-(cyclopentyloxy)-4-methoxyphenyl]cyclohexanecarboxylic acid'  ligand  49  25  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CIO
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
 CIO  O25   O  OC    -1  -0.619  -0.4882  -1.5294  -6.3625
 CIO  C23   C  C      0   0.432   0.0360  -0.4747  -5.9474
 CIO  O24   O  O      0  -0.601   0.2305   0.5603  -6.6153
 CIO  C4    C  CH1    0  -0.381   0.4996  -0.4781  -4.4749
 CIO  C5    C  CH2    0  -0.422   0.9661   0.8815  -3.9719
 CIO  C6    C  CH2    0  -0.435   1.4466   0.8175  -2.5267
 CIO  C3    C  CH2    0  -0.435  -0.5767  -1.0423  -3.5490
 CIO  C2    C  CH2    0  -0.394  -0.1183  -1.0950  -2.0977
 CIO  C1    C  CT     0  -0.286   0.3742   0.2717  -1.5678
 CIO  C21   C  CSP    0   0.144  -0.7533   1.2134  -1.5725
 CIO  N22   N  NS     0  -0.270  -1.6406   1.9473  -1.5750
 CIO  C7    C  CR6    0   0.216   0.8465   0.1407  -0.1233
 CIO  C8    C  CR16   0  -0.354   2.1622   0.3207   0.2520
 CIO  C9    C  CR16   0  -0.368   2.5461   0.1606   1.5850
 CIO  C10   C  CR6    0   0.282   1.6193  -0.1698   2.5558
 CIO  O11   O  O2     0  -0.459   1.8906  -0.3383   3.8624
 CIO  C12   C  CH3    0  -0.437   3.2277  -0.1794   4.2885
 CIO  C13   C  CR6    0   0.349   0.2687  -0.3533   2.1840
 CIO  C20   C  CR16   0  -0.431  -0.0927  -0.1998   0.8583
 CIO  O14   O  O2     0  -0.473  -0.5626  -0.6891   3.1835
 CIO  C15   C  CH1    0  -0.030  -1.9659  -0.7840   2.9425
 CIO  C16   C  CH2    0  -0.480  -2.6007   0.5946   2.7857
 CIO  C17   C  CH2    0  -0.440  -2.6512   1.1602   4.2143
 CIO  C18   C  CH2    0  -0.449  -2.6098  -0.0647   5.1569
 CIO  C19   C  CH2    0  -0.454  -2.5884  -1.2904   4.2336
 CIO  H4    H  HCH1   0   0.220   1.3599  -1.1626  -4.4202
 CIO  H51   H  HCH2   0   0.216   0.1584   1.6140  -4.0704
 CIO  H52   H  HCH2   0   0.233   1.7847   1.2534  -4.5896
 CIO  H61   H  HCH2   0   0.254   1.7850   1.7999  -2.1899
 CIO  H62   H  HCH2   0   0.246   2.3083   0.1459  -2.4703
 CIO  H31   H  HCH2   0   0.238  -0.8552  -2.0467  -3.8685
 CIO  H32   H  HCH2   0   0.217  -1.4846  -0.4321  -3.6238
 CIO  H21   H  HCH2   0   0.245   0.7227  -1.7868  -1.9935
 CIO  H22   H  HCH2   0   0.250  -0.9182  -1.4758  -1.4590
 CIO  H8    H  HCR6   0   0.257   2.9219   0.5876  -0.4685
 CIO  H9    H  HCR6   0   0.281   3.5866   0.3080   1.8406
 CIO  H121  H  HCH3   0   0.259   3.2328  -0.3495   5.3624
 CIO  H122  H  HCH3   0   0.227   3.8970  -0.9031   3.8152
 CIO  H123  H  HCH3   0   0.227   3.6038   0.8280   4.0907
 CIO  H20   H  HCR6   0   0.276  -1.1256  -0.3367   0.5643
 CIO  H15   H  HCH1   0   0.248  -2.1578  -1.4537   2.0971
 CIO  H161  H  HCH2   0   0.251  -2.0748   1.2463   2.0861
 CIO  H162  H  HCH2   0   0.242  -3.6093   0.4540   2.3893
 CIO  H171  H  HCH2   0   0.232  -3.5464   1.7640   4.3641
 CIO  H172  H  HCH2   0   0.232  -1.7997   1.8168   4.3967
 CIO  H181  H  HCH2   0   0.232  -3.4626  -0.0913   5.8348
 CIO  H182  H  HCH2   0   0.232  -1.7141  -0.0408   5.7780
 CIO  H191  H  HCH2   0   0.238  -3.6049  -1.6208   4.0085
 CIO  H192  H  HCH2   0   0.245  -2.0559  -2.1471   4.6494

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
 CIO  O25  C23   deloc     1.249  0.020  1.249
 CIO  C23  O24   deloc     1.247  0.020  1.247
 CIO  C23  C4    single    1.544  0.020  1.544
 CIO  C4   C5    single    1.523  0.020  1.523
 CIO  C4   C3    single    1.528  0.020  1.528
 CIO  C4   H4    single    0.970  0.020  1.090
 CIO  C5   C6    single    1.524  0.020  1.524
 CIO  C5   H51   single    0.970  0.020  1.090
 CIO  C5   H52   single    0.970  0.020  1.090
 CIO  C6   C1    single    1.539  0.020  1.539
 CIO  C6   H61   single    0.970  0.020  1.090
 CIO  C6   H62   single    0.970  0.020  1.090
 CIO  C3   C2    single    1.523  0.020  1.523
 CIO  C3   H31   single    0.970  0.020  1.090
 CIO  C3   H32   single    0.970  0.020  1.090
 CIO  C2   C1    single    1.546  0.020  1.546
 CIO  C2   H21   single    0.970  0.020  1.090
 CIO  C2   H22   single    0.970  0.020  1.090
 CIO  C1   C21   single    1.469  0.020  1.469
 CIO  C1   C7    single    1.525  0.020  1.525
 CIO  C21  N22   triple    1.151  0.020  1.151
 CIO  C7   C8    aromatic  1.380  0.020  1.380
 CIO  C7   C20   aromatic  1.401  0.020  1.401
 CIO  C8   C9    aromatic  1.396  0.020  1.396
 CIO  C8   H8    single    0.930  0.020  1.080
 CIO  C9   C10   aromatic  1.382  0.020  1.382
 CIO  C9   H9    single    0.930  0.020  1.080
 CIO  C10  O11   single    1.345  0.020  1.345
 CIO  C10  C13   aromatic  1.413  0.020  1.413
 CIO  O11  C12   single    1.412  0.020  1.412
 CIO  C12  H121  single    0.970  0.020  1.090
 CIO  C12  H122  single    0.970  0.020  1.090
 CIO  C12  H123  single    0.970  0.020  1.090
 CIO  C13  C20   aromatic  1.383  0.020  1.383
 CIO  C13  O14   single    1.343  0.020  1.343
 CIO  C20  H20   single    0.930  0.020  1.080
 CIO  O14  C15   single    1.427  0.020  1.427
 CIO  C15  C16   single    1.526  0.020  1.526
 CIO  C15  C19   single    1.520  0.020  1.520
 CIO  C15  H15   single    0.970  0.020  1.090
 CIO  C16  C17   single    1.537  0.020  1.537
 CIO  C16  H161  single    0.970  0.020  1.090
 CIO  C16  H162  single    0.970  0.020  1.090
 CIO  C17  C18   single    1.546  0.020  1.546
 CIO  C17  H171  single    0.970  0.020  1.090
 CIO  C17  H172  single    0.970  0.020  1.090
 CIO  C18  C19   single    1.535  0.020  1.535
 CIO  C18  H181  single    0.970  0.020  1.090
 CIO  C18  H182  single    0.970  0.020  1.090
 CIO  C19  H191  single    0.970  0.020  1.090
 CIO  C19  H192  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
 CIO  C4    C23  O24   117.77  3.000
 CIO  C4    C23  O25   116.18  3.000
 CIO  O24   C23  O25   126.05  3.000
 CIO  H4    C4   C3    106.91  3.000
 CIO  H4    C4   C5    107.42  3.000
 CIO  C3    C4   C5    110.20  3.000
 CIO  H4    C4   C23   106.47  3.000
 CIO  C3    C4   C23   111.55  3.000
 CIO  C5    C4   C23   113.89  3.000
 CIO  H52   C5   H51   105.94  3.000
 CIO  H52   C5   C6    108.33  3.000
 CIO  H51   C5   C6    110.24  3.000
 CIO  H52   C5   C4    110.32  3.000
 CIO  H51   C5   C4    109.98  3.000
 CIO  C6    C5   C4    111.85  3.000
 CIO  H62   C6   H61   107.00  3.000
 CIO  H62   C6   C1    107.40  3.000
 CIO  H61   C6   C1    110.05  3.000
 CIO  H62   C6   C5    108.84  3.000
 CIO  H61   C6   C5    110.62  3.000
 CIO  C1    C6   C5    112.71  3.000
 CIO  H32   C3   H31   106.33  3.000
 CIO  H32   C3   C2    109.48  3.000
 CIO  H31   C3   C2    108.93  3.000
 CIO  H32   C3   C4    109.66  3.000
 CIO  H31   C3   C4    110.03  3.000
 CIO  C2    C3   C4    112.23  3.000
 CIO  H22   C2   H21   106.67  3.000
 CIO  H22   C2   C1    109.94  3.000
 CIO  H21   C2   C1    106.35  3.000
 CIO  H22   C2   C3    110.42  3.000
 CIO  H21   C2   C3    110.12  3.000
 CIO  C1    C2   C3    113.07  3.000
 CIO  C7    C1   C21   107.20  3.000
 CIO  C7    C1   C2    110.32  3.000
 CIO  C21   C1   C2    108.73  3.000
 CIO  C7    C1   C6    113.88  3.000
 CIO  C21   C1   C6    107.79  3.000
 CIO  C2    C1   C6    108.78  3.000
 CIO  N22   C21  C1    180.00  3.000
 CIO  C20   C7   C8    118.71  3.000
 CIO  C20   C7   C1    118.49  3.000
 CIO  C8    C7   C1    122.79  3.000
 CIO  H8    C8   C9    118.13  3.000
 CIO  H8    C8   C7    121.41  3.000
 CIO  C9    C8   C7    120.45  3.000
 CIO  H9    C9   C10   120.77  3.000
 CIO  H9    C9   C8    118.33  3.000
 CIO  C10   C9   C8    120.90  3.000
 CIO  C13   C10  O11   115.60  3.000
 CIO  C13   C10  C9    119.16  3.000
 CIO  O11   C10  C9    125.24  3.000
 CIO  C12   O11  C10   118.03  3.000
 CIO  H123  C12  H122  108.72  3.000
 CIO  H123  C12  H121  108.74  3.000
 CIO  H122  C12  H121  108.73  3.000
 CIO  H123  C12  O11   112.01  3.000
 CIO  H122  C12  O11   111.99  3.000
 CIO  H121  C12  O11   106.54  3.000
 CIO  O14   C13  C20   125.43  3.000
 CIO  O14   C13  C10   115.37  3.000
 CIO  C20   C13  C10   119.20  3.000
 CIO  H20   C20  C13   119.72  3.000
 CIO  H20   C20  C7    118.70  3.000
 CIO  C13   C20  C7    121.58  3.000
 CIO  C15   O14  C13   119.98  3.000
 CIO  H15   C15  C19   112.34  3.000
 CIO  H15   C15  C16   113.59  3.000
 CIO  C19   C15  C16   102.58  3.000
 CIO  H15   C15  O14   110.08  3.000
 CIO  C19   C15  O14   106.34  3.000
 CIO  C16   C15  O14   111.49  3.000
 CIO  H162  C16  H161  106.80  3.000
 CIO  H162  C16  C17   110.74  3.000
 CIO  H161  C16  C17   113.07  3.000
 CIO  H162  C16  C15   107.76  3.000
 CIO  H161  C16  C15   113.89  3.000
 CIO  C17   C16  C15   104.51  3.000
 CIO  H172  C17  H171  106.54  3.000
 CIO  H172  C17  C18   110.74  3.000
 CIO  H171  C17  C18   112.15  3.000
 CIO  H172  C17  C16   110.57  3.000
 CIO  H171  C17  C16   111.00  3.000
 CIO  C18   C17  C16   105.91  3.000
 CIO  H182  C18  H181  106.81  3.000
 CIO  H182  C18  C19   110.42  3.000
 CIO  H181  C18  C19   111.45  3.000
 CIO  H182  C18  C17   110.60  3.000
 CIO  H181  C18  C17   112.19  3.000
 CIO  C19   C18  C17   105.44  3.000
 CIO  H192  C19  H191  107.17  3.000
 CIO  H192  C19  C18   113.86  3.000
 CIO  H191  C19  C18   110.64  3.000
 CIO  H192  C19  C15   112.67  3.000
 CIO  H191  C19  C15   107.87  3.000
 CIO  C18   C19  C15   104.52  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
 CIO  CONST_01  C10   C9   C8   C7     0.00   0.0  0
 CIO  CONST_02  C10   C13  C20  C7     0.00   0.0  0
 CIO  CONST_03  C13   C20  C7   C8     0.00   0.0  0
 CIO  CONST_04  C13   C10  C9   C8     0.00   0.0  0
 CIO  CONST_05  C20   C7   C8   C9     0.00   0.0  0
 CIO  CONST_06  C20   C13  C10  C9     0.00   0.0  0
 CIO  CONST_07  C9    C8   C7   C1   180.00   0.0  0
 CIO  CONST_08  C13   C20  C7   C1   180.00   0.0  0
 CIO  CONST_09  O14   C13  C20  C7   180.00   0.0  0
 CIO  CONST_10  O11   C10  C9   C8   180.00   0.0  0
 CIO  CONST_11  O14   C13  C10  C9   180.00   0.0  0
 CIO  CONST_12  C20   C13  C10  O11  180.00   0.0  0
 CIO  CONST_13  H8    C8   C7   C1     0.00   0.0  0
 CIO  CONST_14  H20   C20  C7   C1     0.00   0.0  0
 CIO  CONST_15  H9    C9   C8   C7   180.00   0.0  0
 CIO  Var_01    C1    C6   C5   C4   -56.87  30.0  1
 CIO  Var_02    C1    C2   C3   C4    54.77  30.0  1
 CIO  Var_03    C18   C17  C16  C15  -22.80  30.0  1
 CIO  Var_04    C17   C18  C19  C15   26.17  30.0  1
 CIO  Var_05    C19   C18  C17  C16   -1.99  30.0  1
 CIO  Var_06    C13   C10  O11  C12  179.42  30.0  2
 CIO  Var_07    H121  C12  O11  C10  179.69  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
 CIO  chir_01  C4   C23  C5   C3   negativ
 CIO  chir_02  C1   C7   C2   C6   positiv
 CIO  chir_03  C15  O14  C19  C16  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
 CIO  plan-1  O25  0.020
 CIO  plan-1  C23  0.020
 CIO  plan-1  O24  0.020
 CIO  plan-1  C4   0.020
 CIO  plan-2  C1   0.020
 CIO  plan-2  C7   0.020
 CIO  plan-2  C8   0.020
 CIO  plan-2  C9   0.020
 CIO  plan-2  C10  0.020
 CIO  plan-2  O11  0.020
 CIO  plan-2  C13  0.020
 CIO  plan-2  C20  0.020
 CIO  plan-2  O14  0.020
 CIO  plan-2  H8   0.020
 CIO  plan-2  H9   0.020
 CIO  plan-2  H20  0.020

