# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 07:08:31 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1CCCCC1
#
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
 RXK  RXK  'cyclohexanecarboxylic acid'  ligand  20  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RXK
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
 RXK  C01  C  CH2    0  -0.437  -12.3037  -30.5400  -42.9640
 RXK  O01  O  O      0  -0.606   -8.9020  -33.1801  -40.4009
 RXK  C02  C  CH2    0  -0.443  -12.4824  -31.9659  -42.4604
 RXK  O02  O  OC    -1  -0.608   -8.8081  -31.1991  -39.3923
 RXK  C03  C  CH2    0  -0.402  -11.1705  -32.5215  -41.8853
 RXK  C04  C  CH1    0  -0.388  -10.2885  -31.4306  -41.2551
 RXK  C05  C  CH2    0  -0.429  -11.1704  -30.3201  -40.6895
 RXK  C06  C  CH2    0  -0.423  -11.9472  -29.6009  -41.8031
 RXK  C07  C  C      0   0.420   -9.2505  -31.9898  -40.2516
 RXK  H1   H  HCH2   0   0.209  -11.5097  -30.5249  -43.7172
 RXK  H2   H  HCH2   0   0.220  -13.2059  -30.1908  -43.4715
 RXK  H3   H  HCH2   0   0.207  -13.2623  -31.9735  -41.6922
 RXK  H5   H  HCH2   0   0.203  -10.6129  -33.0314  -42.6742
 RXK  H6   H  HCH1   0   0.214   -9.6905  -30.9776  -42.0610
 RXK  H7   H  HCH2   0   0.219  -10.5684  -29.6031  -40.1322
 RXK  H8   H  HCH2   0   0.200  -11.8698  -30.7567  -39.9676
 RXK  H9   H  HCH2   0   0.211  -11.3565  -28.7624  -42.1819
 RXK  H10  H  HCH2   0   0.211  -12.8583  -29.1639  -41.3858
 RXK  H11  H  HCH2   0   0.219  -12.8467  -32.6152  -43.2603
 RXK  H12  H  HCH2   0   0.204  -11.4020  -33.2856  -41.1398

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
 RXK  C01  C02  single  1.523  0.020  1.523
 RXK  C01  C06  single  1.535  0.020  1.535
 RXK  C03  C04  single  1.538  0.020  1.538
 RXK  C06  C05  single  1.536  0.020  1.536
 RXK  C04  C05  single  1.527  0.020  1.527
 RXK  C04  C07  single  1.548  0.020  1.548
 RXK  C07  O01  deloc   1.249  0.020  1.249
 RXK  C07  O02  deloc   1.249  0.020  1.249
 RXK  C01  H1   single  0.970  0.020  1.090
 RXK  C01  H2   single  0.970  0.020  1.090
 RXK  C02  H3   single  0.970  0.020  1.090
 RXK  C03  H5   single  0.970  0.020  1.090
 RXK  C04  H6   single  0.970  0.020  1.090
 RXK  C05  H7   single  0.970  0.020  1.090
 RXK  C05  H8   single  0.970  0.020  1.090
 RXK  C06  H9   single  0.970  0.020  1.090
 RXK  C06  H10  single  0.970  0.020  1.090
 RXK  C02  C03  single  1.536  0.020  1.536
 RXK  C02  H11  single  0.970  0.020  1.090
 RXK  C03  H12  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
 RXK  H2   C01  H1   105.96  3.000
 RXK  H2   C01  C06  110.34  3.000
 RXK  H1   C01  C06  110.09  3.000
 RXK  H2   C01  C02  110.86  3.000
 RXK  H1   C01  C02  109.00  3.000
 RXK  C06  C01  C02  110.49  3.000
 RXK  H11  C02  H3   105.78  3.000
 RXK  H11  C02  C03  110.11  3.000
 RXK  H3   C02  C03  110.06  3.000
 RXK  H11  C02  C01  110.70  3.000
 RXK  C03  C02  C01  111.24  3.000
 RXK  H3   C02  C01  108.80  3.000
 RXK  H12  C03  H5   105.93  3.000
 RXK  H12  C03  C04  109.76  3.000
 RXK  H5   C03  C04  109.53  3.000
 RXK  H12  C03  C02  109.12  3.000
 RXK  H5   C03  C02  109.53  3.000
 RXK  C04  C03  C02  112.74  3.000
 RXK  H6   C04  C07  105.00  3.000
 RXK  H6   C04  C05  106.60  3.000
 RXK  C07  C04  C05  114.20  3.000
 RXK  H6   C04  C03  107.66  3.000
 RXK  C07  C04  C03  113.19  3.000
 RXK  C05  C04  C03  109.66  3.000
 RXK  H8   C05  H7   106.13  3.000
 RXK  H8   C05  C06  109.95  3.000
 RXK  H7   C05  C06  110.00  3.000
 RXK  H8   C05  C04  108.84  3.000
 RXK  H7   C05  C04  110.43  3.000
 RXK  C06  C05  C04  111.35  3.000
 RXK  H10  C06  H9   106.02  3.000
 RXK  H10  C06  C05  109.38  3.000
 RXK  H9   C06  C05  109.69  3.000
 RXK  H10  C06  C01  109.85  3.000
 RXK  H9   C06  C01  109.43  3.000
 RXK  C05  C06  C01  112.28  3.000
 RXK  C04  C07  O02  117.05  3.000
 RXK  O02  C07  O01  125.92  3.000
 RXK  C04  C07  O01  116.99  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
 RXK  Var_01  C04  C03  C02  C01   31.10  30.0  1
 RXK  Var_02  C04  C05  C06  C01   32.24  30.0  1
 RXK  Var_03  C05  C06  C01  C02   29.91  30.0  1
 RXK  Var_04  C06  C01  C02  C03  -63.70  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
 RXK  chir_01  C04  C03  C05  C07  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
 RXK  plan-1  O01  0.020
 RXK  plan-1  O02  0.020
 RXK  plan-1  C04  0.020
 RXK  plan-1  C07  0.020

