# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 12:44:29 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: [cyclohexyl(hydroxy)amino](oxo)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON(C1CCCCC1)C(=O)C(O)=O
#
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
 EKA  EKA  '[cyclohexyl(hydroxy)amino](oxo)acetic acid'  ligand  25  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EKA
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
 EKA  C02  C  C      0   0.351   2.8051   0.0308  -0.0507
 EKA  C03  C  C      0   0.401   1.3209   0.3889   0.1270
 EKA  C06  C  CH1    0  -0.046  -1.0057  -0.5484   0.0246
 EKA  C07  C  CH2    0  -0.440  -1.5887   0.0731   1.2924
 EKA  C08  C  CH2    0  -0.439  -3.1136   0.0001   1.2541
 EKA  C09  C  CH2    0  -0.431  -3.6720   0.6746   0.0050
 EKA  C10  C  CH2    0  -0.438  -3.0673   0.0785  -1.2619
 EKA  C11  C  CH2    0  -0.436  -1.5420   0.1362  -1.2326
 EKA  N04  N  NT     0  -0.226   0.4514  -0.6424   0.0460
 EKA  O01  O  O      0  -0.596   3.3077  -0.6302   0.8718
 EKA  O05  O  OH1    0  -0.552   0.9549  -1.7931  -0.5207
 EKA  O12  O  O      0  -0.513   0.9678   1.5339   0.3811
 EKA  O13  O  OC    -1  -0.594   3.3425   0.5009  -1.0645
 EKA  H1   H  HCH1   0   0.243  -1.3398  -1.5903   0.0046
 EKA  H2   H  HCH2   0   0.232  -1.2025  -0.4525   2.1694
 EKA  H3   H  HCH2   0   0.229  -1.2807   1.1155   1.3810
 EKA  H4   H  HCH2   0   0.211  -3.4310  -1.0483   1.2759
 EKA  H5   H  HCH2   0   0.232  -3.5249   0.4660   2.1524
 EKA  H6   H  HCH2   0   0.229  -4.7608   0.5864  -0.0178
 EKA  H7   H  HCH2   0   0.212  -3.4468   1.7459   0.0427
 EKA  H8   H  HCH2   0   0.212  -3.3873  -0.9645  -1.3625
 EKA  H9   H  HCH2   0   0.232  -3.4412   0.6014  -2.1451
 EKA  H10  H  HCH2   0   0.223  -1.2139   1.1791  -1.2495
 EKA  H11  H  HCH2   0   0.234  -1.1272  -0.3457  -2.1215
 EKA  H12  H  HOH1   0   0.471   1.1596  -2.3838   0.2162

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
 EKA  O01  C02  deloc   1.241  0.020  1.241
 EKA  O12  C03  double  1.225  0.020  1.225
 EKA  C02  C03  single  1.537  0.020  1.537
 EKA  C02  O13  deloc   1.240  0.020  1.240
 EKA  C03  N04  single  1.351  0.020  1.351
 EKA  O05  N04  single  1.378  0.020  1.378
 EKA  N04  C06  single  1.460  0.020  1.460
 EKA  C06  C07  single  1.528  0.020  1.528
 EKA  C06  C11  single  1.529  0.020  1.529
 EKA  C07  C08  single  1.527  0.020  1.527
 EKA  C11  C10  single  1.527  0.020  1.527
 EKA  C08  C09  single  1.526  0.020  1.526
 EKA  C10  C09  single  1.525  0.020  1.525
 EKA  C06  H1   single  0.970  0.020  1.090
 EKA  C07  H2   single  0.970  0.020  1.090
 EKA  C07  H3   single  0.970  0.020  1.090
 EKA  C08  H4   single  0.970  0.020  1.090
 EKA  C08  H5   single  0.970  0.020  1.090
 EKA  C09  H6   single  0.970  0.020  1.090
 EKA  C09  H7   single  0.970  0.020  1.090
 EKA  C10  H8   single  0.970  0.020  1.090
 EKA  C10  H9   single  0.970  0.020  1.090
 EKA  C11  H10  single  0.970  0.020  1.090
 EKA  C11  H11  single  0.970  0.020  1.090
 EKA  O05  H12  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
 EKA  O13  C02  O01  129.34  3.000
 EKA  O13  C02  C03  115.14  3.000
 EKA  O01  C02  C03  115.41  3.000
 EKA  O12  C03  N04  122.71  3.000
 EKA  N04  C03  C02  115.89  3.000
 EKA  O12  C03  C02  121.34  3.000
 EKA  H1   C06  N04  104.10  3.000
 EKA  H1   C06  C11  107.72  3.000
 EKA  N04  C06  C11  113.01  3.000
 EKA  H1   C06  C07  106.62  3.000
 EKA  C11  C06  C07  111.50  3.000
 EKA  N04  C06  C07  113.25  3.000
 EKA  H3   C07  H2   107.14  3.000
 EKA  H3   C07  C08  109.25  3.000
 EKA  H2   C07  C08  110.48  3.000
 EKA  H3   C07  C06  110.40  3.000
 EKA  H2   C07  C06  109.61  3.000
 EKA  C08  C07  C06  109.93  3.000
 EKA  H5   C08  H4   106.43  3.000
 EKA  H5   C08  C09  110.30  3.000
 EKA  H4   C08  C09  109.47  3.000
 EKA  H5   C08  C07  109.58  3.000
 EKA  H4   C08  C07  109.54  3.000
 EKA  C09  C08  C07  111.40  3.000
 EKA  H7   C09  H6   106.53  3.000
 EKA  H7   C09  C10  109.23  3.000
 EKA  H6   C09  C10  110.26  3.000
 EKA  H7   C09  C08  109.20  3.000
 EKA  H6   C09  C08  110.25  3.000
 EKA  C10  C09  C08  111.24  3.000
 EKA  H9   C10  H8   106.35  3.000
 EKA  H9   C10  C11  109.84  3.000
 EKA  H8   C10  C11  109.24  3.000
 EKA  H9   C10  C09  110.41  3.000
 EKA  H8   C10  C09  109.42  3.000
 EKA  C11  C10  C09  111.43  3.000
 EKA  H11  C11  H10  107.10  3.000
 EKA  H11  C11  C10  110.30  3.000
 EKA  H10  C11  C10  109.61  3.000
 EKA  H11  C11  C06  109.77  3.000
 EKA  H10  C11  C06  109.55  3.000
 EKA  C10  C11  C06  110.45  3.000
 EKA  O05  N04  C06  114.35  3.000
 EKA  C06  N04  C03  126.43  3.000
 EKA  O05  N04  C03  115.26  3.000
 EKA  H12  O05  N04  105.92  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
 EKA  CONST_01  C06  N04  C03  C02  180.00   0.0  0
 EKA  CONST_02  O12  C03  N04  C06    0.00   0.0  0
 EKA  CONST_04  O12  C03  N04  O05  180.00   0.0  0
 EKA  Var_01    C09  C08  C07  C06  -56.40  30.0  1
 EKA  Var_02    C09  C10  C11  C06   55.29  30.0  1
 EKA  Var_03    C10  C09  C08  C07   55.73  30.0  1
 EKA  Var_04    C11  C10  C09  C08  -55.04  30.0  1
 EKA  Var_05    O01  C02  C03  N04  -69.19  30.0  2

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
 EKA  chir_01  C06  N04  C07  C11  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
 EKA  plan-1  C02  0.020
 EKA  plan-1  C03  0.020
 EKA  plan-1  C06  0.020
 EKA  plan-1  N04  0.020
 EKA  plan-1  O05  0.020
 EKA  plan-1  O12  0.020
 EKA  plan-2  C02  0.020
 EKA  plan-2  C03  0.020
 EKA  plan-2  O01  0.020
 EKA  plan-2  O13  0.020

