# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:30:01 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  24  12  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.332   2.8898  -0.3550   0.1302
 EKD  C03  C  C      0   0.349   1.5539   0.1999  -0.4522
 EKD  C05  C  CH1    0  -0.054  -0.9010  -0.0038  -0.2363
 EKD  C06  C  CH2    0  -0.433  -1.7552  -1.2555  -0.4264
 EKD  C07  C  CH2    0  -0.437  -3.2039  -0.8960  -0.7426
 EKD  C08  C  CH2    0  -0.431  -3.8000   0.0164   0.3245
 EKD  C09  C  CH2    0  -0.438  -2.9467   1.2657   0.5165
 EKD  C10  C  CH2    0  -0.424  -1.5000   0.9043   0.8387
 EKD  N04  N  NH1    0  -0.617   0.4628  -0.3645   0.0785
 EKD  O01  O  O      0  -0.591   2.7816  -1.2171   1.0225
 EKD  O11  O  O      0  -0.508   1.5319   1.0669  -1.3163
 EKD  O12  O  OC    -1  -0.578   3.9190   0.1271  -0.3567
 EKD  H1   H  HCH1   0   0.229  -0.8782   0.5471  -1.1809
 EKD  H2   H  HCH2   0   0.235  -1.3305  -1.8701  -1.2237
 EKD  H3   H  HCH2   0   0.213  -1.7189  -1.8572   0.4895
 EKD  H4   H  HCH2   0   0.213  -3.2452  -0.3926  -1.7144
 EKD  H5   H  HCH2   0   0.231  -3.7990  -1.8067  -0.8400
 EKD  H6   H  HCH2   0   0.229  -4.8224   0.2931   0.0564
 EKD  H7   H  HCH2   0   0.210  -3.8617  -0.5280   1.2731
 EKD  H8   H  HCH2   0   0.212  -2.9749   1.8689  -0.3974
 EKD  H9   H  HCH2   0   0.230  -3.3604   1.8911   1.3109
 EKD  H10  H  HCH2   0   0.211  -1.4586   0.3872   1.8042
 EKD  H11  H  HCH2   0   0.233  -0.8912   1.8065   0.9351
 EKD  H12  H  HNH1   0   0.383   0.6312  -1.0428   0.8069

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  deloc   1.245  0.020  1.245
 EKD  O11  C03  double  1.224  0.020  1.224
 EKD  C02  C03  single  1.559  0.020  1.559
 EKD  C02  O12  deloc   1.236  0.020  1.236
 EKD  C03  N04  single  1.338  0.020  1.338
 EKD  N04  C05  single  1.445  0.020  1.445
 EKD  C05  C06  single  1.527  0.020  1.527
 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

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  128.63  3.000
 EKD  O12  C02  C03  115.29  3.000
 EKD  O01  C02  C03  116.07  3.000
 EKD  O11  C03  N04  124.32  3.000
 EKD  N04  C03  C02  113.60  3.000
 EKD  O11  C03  C02  122.08  3.000
 EKD  H1   C05  N04  107.11  3.000
 EKD  H1   C05  C10  108.43  3.000
 EKD  N04  C05  C10  111.39  3.000
 EKD  H1   C05  C06  108.48  3.000
 EKD  C10  C05  C06  110.80  3.000
 EKD  N04  C05  C06  110.50  3.000
 EKD  H3   C06  H2   106.74  3.000
 EKD  H3   C06  C07  109.50  3.000
 EKD  H2   C06  C07  110.51  3.000
 EKD  H3   C06  C05  109.11  3.000
 EKD  H2   C06  C05  109.54  3.000
 EKD  C07  C06  C05  111.33  3.000
 EKD  H5   C07  H4   106.47  3.000
 EKD  H5   C07  C08  110.38  3.000
 EKD  H4   C07  C08  109.33  3.000
 EKD  H5   C07  C06  109.84  3.000
 EKD  H4   C07  C06  109.15  3.000
 EKD  C08  C07  C06  111.53  3.000
 EKD  H7   C08  H6   106.59  3.000
 EKD  H7   C08  C09  109.25  3.000
 EKD  H6   C08  C09  110.30  3.000
 EKD  H7   C08  C07  109.30  3.000
 EKD  H6   C08  C07  110.22  3.000
 EKD  C09  C08  C07  111.07  3.000
 EKD  H9   C09  H8   106.36  3.000
 EKD  H9   C09  C10  109.95  3.000
 EKD  H8   C09  C10  109.33  3.000
 EKD  H9   C09  C08  110.41  3.000
 EKD  H8   C09  C08  109.37  3.000
 EKD  C10  C09  C08  111.29  3.000
 EKD  H11  C10  H10  106.91  3.000
 EKD  H11  C10  C09  110.58  3.000
 EKD  H10  C10  C09  109.49  3.000
 EKD  H11  C10  C05  109.51  3.000
 EKD  H10  C10  C05  108.92  3.000
 EKD  C09  C10  C05  111.32  3.000
 EKD  H12  N04  C05  118.84  3.000
 EKD  H12  N04  C03  115.69  3.000
 EKD  C05  N04  C03  125.29  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  Var_01    C08  C07  C06  C05  -55.38  30.0  1
 EKD  Var_02    C08  C09  C10  C05   55.80  30.0  1
 EKD  Var_03    C09  C08  C07  C06   55.13  30.0  1
 EKD  Var_04    C10  C09  C08  C07  -55.29  30.0  1
 EKD  Var_05    O01  C02  C03  N04   -1.54  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
 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

