# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 23:02:20 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-cyclohexylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCC1CCCCC1
#
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
 87X  87X  '5-cyclohexylpentanoic acid'  ligand  33  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_87X
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
 87X  C    C  C     0   0.549   4.4309  -0.0056   0.0125
 87X  O    O  O     0  -0.446   4.6655  -0.9754   0.6903
 87X  C12  C  CH2   0  -0.580   3.0606   0.4734  -0.3761
 87X  C13  C  CH2   0  -0.416   1.9273  -0.3841   0.1625
 87X  C14  C  CH2   0  -0.421   0.5672   0.1483  -0.2692
 87X  C15  C  CH2   0  -0.405  -0.5895  -0.7337   0.1867
 87X  C16  C  CH1   0  -0.218  -1.9673  -0.2117  -0.2203
 87X  C21  C  CH2   0  -0.416  -3.0366  -1.2966  -0.0915
 87X  C20  C  CH2   0  -0.431  -4.4156  -0.7955  -0.5083
 87X  C19  C  CH2   0  -0.428  -4.8182   0.4454   0.2817
 87X  C18  C  CH2   0  -0.429  -3.7593   1.5370   0.1695
 87X  C17  C  CH2   0  -0.420  -2.3818   1.0251   0.5797
 87X  O1   O  OH1   0  -0.599   5.3871   0.7751  -0.4850
 87X  H1   H  HCH2  0   0.275   2.9538   1.5094  -0.0382
 87X  H2   H  HCH2  0   0.275   3.0162   0.5207  -1.4690
 87X  H3   H  HCH2  0   0.223   2.0448  -1.4132  -0.1877
 87X  H4   H  HCH2  0   0.225   1.9758  -0.4217   1.2539
 87X  H5   H  HCH2  0   0.217   0.4408   1.1664   0.1118
 87X  H6   H  HCH2  0   0.211   0.5386   0.2305  -1.3613
 87X  H7   H  HCH2  0   0.213  -0.4461  -1.7361  -0.2327
 87X  H8   H  HCH2  0   0.205  -0.5544  -0.8561   1.2757
 87X  H9   H  HCH1  0   0.199  -1.9180   0.0757  -1.2804
 87X  H10  H  HCH2  0   0.220  -2.7527  -2.1646  -0.6941
 87X  H11  H  HCH2  0   0.202  -3.0726  -1.6434   0.9489
 87X  H12  H  HCH2  0   0.206  -4.4042  -0.5543  -1.5771
 87X  H13  H  HCH2  0   0.223  -5.1599  -1.5852  -0.3785
 87X  H14  H  HCH2  0   0.223  -5.7862   0.8177  -0.0635
 87X  H15  H  HCH2  0   0.206  -4.9487   0.1751   1.3354
 87X  H16  H  HCH2  0   0.206  -3.7180   1.8960  -0.8650
 87X  H17  H  HCH2  0   0.223  -4.0378   2.3982   0.7826
 87X  H18  H  HCH2  0   0.202  -2.3947   0.7657   1.6457
 87X  H19  H  HCH2  0   0.225  -1.6422   1.8225   0.4669
 87X  H20  H  HOH1  0   0.478   6.2570   0.4422  -0.2186

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
 87X  C20  C19  single  1.525  0.020  1.525
 87X  C20  C21  single  1.525  0.020  1.525
 87X  C19  C18  single  1.525  0.020  1.525
 87X  C21  C16  single  1.529  0.020  1.529
 87X  C18  C17  single  1.526  0.020  1.526
 87X  C17  C16  single  1.530  0.020  1.530
 87X  C16  C15  single  1.528  0.020  1.528
 87X  C15  C14  single  1.524  0.020  1.524
 87X  C14  C13  single  1.523  0.020  1.523
 87X  C13  C12  single  1.520  0.020  1.520
 87X  O    C    double  1.206  0.020  1.206
 87X  C    C12  single  1.503  0.020  1.503
 87X  C    O1   single  1.331  0.020  1.331
 87X  C12  H1   single  0.970  0.020  1.090
 87X  C12  H2   single  0.970  0.020  1.090
 87X  C13  H3   single  0.970  0.020  1.090
 87X  C13  H4   single  0.970  0.020  1.090
 87X  C14  H5   single  0.970  0.020  1.090
 87X  C14  H6   single  0.970  0.020  1.090
 87X  C15  H7   single  0.970  0.020  1.090
 87X  C15  H8   single  0.970  0.020  1.090
 87X  C16  H9   single  0.970  0.020  1.090
 87X  C21  H10  single  0.970  0.020  1.090
 87X  C21  H11  single  0.970  0.020  1.090
 87X  C20  H12  single  0.970  0.020  1.090
 87X  C20  H13  single  0.970  0.020  1.090
 87X  C19  H14  single  0.970  0.020  1.090
 87X  C19  H15  single  0.970  0.020  1.090
 87X  C18  H16  single  0.970  0.020  1.090
 87X  C18  H17  single  0.970  0.020  1.090
 87X  C17  H18  single  0.970  0.020  1.090
 87X  C17  H19  single  0.970  0.020  1.090
 87X  O1   H20  single  0.850  0.020  0.980

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
 87X  O1   C    C12  111.81  3.000
 87X  O1   C    O    122.81  3.000
 87X  C12  C    O    125.37  3.000
 87X  H2   C12  H1   105.26  3.000
 87X  H2   C12  C13  110.36  3.000
 87X  H1   C12  C13  110.59  3.000
 87X  H2   C12  C    107.99  3.000
 87X  H1   C12  C    108.10  3.000
 87X  C13  C12  C    114.11  3.000
 87X  H4   C13  H3   106.42  3.000
 87X  H4   C13  C14  109.55  3.000
 87X  H3   C13  C14  109.52  3.000
 87X  H4   C13  C12  109.89  3.000
 87X  H3   C13  C12  109.72  3.000
 87X  C14  C13  C12  111.61  3.000
 87X  H6   C14  H5   105.92  3.000
 87X  H6   C14  C15  108.76  3.000
 87X  H5   C14  C15  110.27  3.000
 87X  H6   C14  C13  109.40  3.000
 87X  H5   C14  C13  109.25  3.000
 87X  C15  C14  C13  112.99  3.000
 87X  H8   C15  H7   105.88  3.000
 87X  H8   C15  C16  109.36  3.000
 87X  H7   C15  C16  109.17  3.000
 87X  H8   C15  C14  109.71  3.000
 87X  H7   C15  C14  108.39  3.000
 87X  C16  C15  C14  114.00  3.000
 87X  H9   C16  C17  107.76  3.000
 87X  H9   C16  C21  107.34  3.000
 87X  C17  C16  C21  109.88  3.000
 87X  H9   C16  C15  107.79  3.000
 87X  C17  C16  C15  112.39  3.000
 87X  C21  C16  C15  111.45  3.000
 87X  H11  C21  H10  106.25  3.000
 87X  H11  C21  C20  109.47  3.000
 87X  H10  C21  C20  110.17  3.000
 87X  H11  C21  C16  109.09  3.000
 87X  H10  C21  C16  109.57  3.000
 87X  C20  C21  C16  112.10  3.000
 87X  H13  C20  H12  106.37  3.000
 87X  H13  C20  C19  110.28  3.000
 87X  H12  C20  C19  109.20  3.000
 87X  H13  C20  C21  110.24  3.000
 87X  H12  C20  C21  109.24  3.000
 87X  C19  C20  C21  111.37  3.000
 87X  H15  C19  H14  106.40  3.000
 87X  H15  C19  C18  109.27  3.000
 87X  H14  C19  C18  110.36  3.000
 87X  H15  C19  C20  109.20  3.000
 87X  H14  C19  C20  110.33  3.000
 87X  C18  C19  C20  111.16  3.000
 87X  H17  C18  H16  106.32  3.000
 87X  H17  C18  C17  110.09  3.000
 87X  H16  C18  C17  109.25  3.000
 87X  H17  C18  C19  110.23  3.000
 87X  H16  C18  C19  109.28  3.000
 87X  C17  C18  C19  111.53  3.000
 87X  H19  C17  H18  106.30  3.000
 87X  H19  C17  C18  109.77  3.000
 87X  H18  C17  C18  109.26  3.000
 87X  H19  C17  C16  110.63  3.000
 87X  H18  C17  C16  108.67  3.000
 87X  C18  C17  C16  112.04  3.000
 87X  H20  O1   C    109.93  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
 87X  CONST_01  H20  O1   C    O       0.00   0.0  0
 87X  Var_01    C19  C20  C21  C16   -55.70  30.0  1
 87X  Var_02    C19  C18  C17  C16    55.40  30.0  1
 87X  Var_03    C17  C18  C19  C20   -54.43  30.0  1
 87X  Var_04    C16  C15  C14  C13   179.32  30.0  1
 87X  Var_05    C14  C13  C12  C    -179.77  30.0  1
 87X  Var_06    C13  C12  C    O      -0.11  30.0  3
 87X  Var_07    C15  C14  C13  C12   176.69  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
 87X  chir_01  C16  C21  C17  C15  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
 87X  plan-1  C    0.020
 87X  plan-1  O    0.020
 87X  plan-1  C12  0.020
 87X  plan-1  O1   0.020
 87X  plan-1  H20  0.020

