# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 00:20:06 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (cyclohexylamino)(oxo)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)NC1CCCCC1
#
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
 EKD  EKD  '(cyclohexylamino)(oxo)acetic acid'  ligand  25  12  .  2021-08-08  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EKD
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
 EKD  C02  C  C     0   0.456   2.8372  -0.3041   0.1817
 EKD  C03  C  C     0   0.441   1.5255   0.2640  -0.3810
 EKD  C05  C  CH1   0  -0.069  -0.9150   0.0175  -0.2087
 EKD  C06  C  CH2   0  -0.435  -1.7465  -1.2429  -0.4332
 EKD  C07  C  CH2   0  -0.439  -3.1938  -0.8903  -0.7634
 EKD  C08  C  CH2   0  -0.433  -3.8145  -0.0064   0.3134
 EKD  C09  C  CH2   0  -0.440  -2.9776   1.2478   0.5422
 EKD  C10  C  CH2   0  -0.423  -1.5320   0.8957   0.8797
 EKD  N04  N  NH1   0  -0.623   0.4520  -0.3399   0.1211
 EKD  O01  O  O     0  -0.416   2.8789  -1.1630   1.0238
 EKD  O11  O  O     0  -0.464   1.5355   1.1646  -1.2002
 EKD  O12  O  OH1   0  -0.566   3.8766   0.2724  -0.3743
 EKD  H1   H  HCH1  0   0.245  -0.8836   0.5856  -1.1419
 EKD  H2   H  HCH2  0   0.243  -1.3039  -1.8364  -1.2364
 EKD  H3   H  HCH2  0   0.220  -1.7162  -1.8593   0.4726
 EKD  H4   H  HCH2  0   0.216  -3.2250  -0.3676  -1.7253
 EKD  H5   H  HCH2  0   0.235  -3.7759  -1.8056  -0.8888
 EKD  H6   H  HCH2  0   0.232  -4.8354   0.2656   0.0355
 EKD  H7   H  HCH2  0   0.212  -3.8842  -0.5702   1.2499
 EKD  H8   H  HCH2  0   0.216  -2.9990   1.8689  -0.3595
 EKD  H9   H  HCH2  0   0.234  -3.4075   1.8524   1.3438
 EKD  H10  H  HCH2  0   0.217  -1.4993   0.3565   1.8329
 EKD  H11  H  HCH2  0   0.239  -0.9348   1.8019   1.0043
 EKD  H12  H  HNH1  0   0.407   0.5940  -1.0542   0.8207
 EKD  H13  H  HOH1  0   0.494   4.6989  -0.0920  -0.0113

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
 EKD  O01  C02  double  1.204  0.020  1.204
 EKD  O11  C03  double  1.217  0.020  1.217
 EKD  C02  C03  single  1.536  0.020  1.536
 EKD  C02  O12  single  1.312  0.020  1.312
 EKD  C03  N04  single  1.330  0.020  1.330
 EKD  N04  C05  single  1.451  0.020  1.451
 EKD  C05  C06  single  1.526  0.020  1.526
 EKD  C05  C10  single  1.529  0.020  1.529
 EKD  C06  C07  single  1.526  0.020  1.526
 EKD  C10  C09  single  1.526  0.020  1.526
 EKD  C07  C08  single  1.525  0.020  1.525
 EKD  C09  C08  single  1.525  0.020  1.525
 EKD  C05  H1   single  0.970  0.020  1.090
 EKD  C06  H2   single  0.970  0.020  1.090
 EKD  C06  H3   single  0.970  0.020  1.090
 EKD  C07  H4   single  0.970  0.020  1.090
 EKD  C07  H5   single  0.970  0.020  1.090
 EKD  C08  H6   single  0.970  0.020  1.090
 EKD  C08  H7   single  0.970  0.020  1.090
 EKD  C09  H8   single  0.970  0.020  1.090
 EKD  C09  H9   single  0.970  0.020  1.090
 EKD  C10  H10  single  0.970  0.020  1.090
 EKD  C10  H11  single  0.970  0.020  1.090
 EKD  N04  H12  single  0.860  0.020  1.020
 EKD  O12  H13  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
 EKD  O12  C02  O01  125.63  3.000
 EKD  O12  C02  C03  111.02  3.000
 EKD  O01  C02  C03  123.35  3.000
 EKD  O11  C03  N04  126.62  3.000
 EKD  N04  C03  C02  112.52  3.000
 EKD  O11  C03  C02  120.86  3.000
 EKD  H1   C05  N04  107.16  3.000
 EKD  H1   C05  C10  108.72  3.000
 EKD  N04  C05  C10  111.10  3.000
 EKD  H1   C05  C06  108.62  3.000
 EKD  C10  C05  C06  111.05  3.000
 EKD  N04  C05  C06  110.08  3.000
 EKD  H3   C06  H2   106.91  3.000
 EKD  H3   C06  C07  109.58  3.000
 EKD  H2   C06  C07  110.53  3.000
 EKD  H3   C06  C05  109.13  3.000
 EKD  H2   C06  C05  109.63  3.000
 EKD  C07  C06  C05  110.96  3.000
 EKD  H5   C07  H4   106.50  3.000
 EKD  H5   C07  C08  110.48  3.000
 EKD  H4   C07  C08  109.39  3.000
 EKD  H5   C07  C06  109.68  3.000
 EKD  H4   C07  C06  109.11  3.000
 EKD  C08  C07  C06  111.54  3.000
 EKD  H7   C08  H6   106.63  3.000
 EKD  H7   C08  C09  109.27  3.000
 EKD  H6   C08  C09  110.26  3.000
 EKD  H7   C08  C07  109.34  3.000
 EKD  H6   C08  C07  110.18  3.000
 EKD  C09  C08  C07  111.05  3.000
 EKD  H9   C09  H8   106.43  3.000
 EKD  H9   C09  C10  109.78  3.000
 EKD  H8   C09  C10  109.36  3.000
 EKD  H9   C09  C08  110.44  3.000
 EKD  H8   C09  C08  109.40  3.000
 EKD  C10  C09  C08  111.31  3.000
 EKD  H11  C10  H10  107.02  3.000
 EKD  H11  C10  C09  110.59  3.000
 EKD  H10  C10  C09  109.53  3.000
 EKD  H11  C10  C05  109.71  3.000
 EKD  H10  C10  C05  108.95  3.000
 EKD  C09  C10  C05  110.95  3.000
 EKD  H12  N04  C05  117.66  3.000
 EKD  H12  N04  C03  117.98  3.000
 EKD  C05  N04  C03  124.25  3.000
 EKD  H13  O12  C02  110.36  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
 EKD  CONST_01  C05  N04  C03  C02  180.00   0.0  0
 EKD  CONST_02  O11  C03  N04  C05    0.00   0.0  0
 EKD  CONST_03  H12  N04  C03  C02    0.00   0.0  0
 EKD  CONST_04  H13  O12  C02  C03  180.00   0.0  0
 EKD  Var_01    C08  C07  C06  C05  -55.50  30.0  1
 EKD  Var_02    C08  C09  C10  C05   55.90  30.0  1
 EKD  Var_03    C09  C08  C07  C06   55.25  30.0  1
 EKD  Var_04    C10  C09  C08  C07  -55.40  30.0  1
 EKD  Var_05    O01  C02  C03  N04   -2.84  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
 EKD  chir_01  C05  N04  C06  C10  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
 EKD  plan-1  C02  0.020
 EKD  plan-1  C03  0.020
 EKD  plan-1  C05  0.020
 EKD  plan-1  N04  0.020
 EKD  plan-1  O11  0.020
 EKD  plan-1  H12  0.020
 EKD  plan-2  C02  0.020
 EKD  plan-2  C03  0.020
 EKD  plan-2  O01  0.020
 EKD  plan-2  O12  0.020
 EKD  plan-2  H13  0.020

