# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 21:07:51 2021
#   Inital geometry file: a 56 line input string
#   Ligand name: (1~{S},2~{S})-2-azanylcyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCCC[C@@H]1C(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
 E6F  E6F  '(1~{S},2~{S})-2-azanylcyclohexane-1-carboxylic acid'  ligand  23  10  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_E6F
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
 E6F  N    N  NH2   0  -0.801  18.0915  18.6252  -4.2871
 E6F  CA   C  CR16  0  -0.371  19.2899  18.7056  -6.4185
 E6F  C    C  C     0   0.544  18.5093  17.7249  -7.2523
 E6F  O    O  O     0  -0.451  18.3822  16.5515  -6.9913
 E6F  CB   C  CR16  0  -0.067  18.3269  19.4559  -5.4609
 E6F  CG   C  C     0  -0.445  18.9380  20.7976  -5.0343
 E6F  CD   C  C     0  -0.452  20.4530  20.7103  -4.9227
 E6F  CE   C  C     0  -0.432  21.0756  20.4575  -6.3046
 E6F  CZ   C  C     0  -0.445  20.1213  19.6961  -7.2339
 E6F  H1   H  HNH2  0   0.345  17.3609  19.0442  -3.7244
 E6F  H2   H  HNH2  0   0.343  17.7308  17.7203  -4.5662
 E6F  H4   H  HCR6  0   0.267  19.9671  18.1118  -5.7971
 E6F  H6   H  HCR6  0   0.221  17.3986  19.6771  -6.0079
 E6F  H7   H  H     0   0.226  18.6684  21.5665  -5.7634
 E6F  H8   H  H     0   0.236  18.4861  21.1065  -4.0884
 E6F  H9   H  H     0   0.222  20.7114  19.9017  -4.2340
 E6F  H10  H  H     0   0.234  20.8617  21.6234  -4.4864
 E6F  H11  H  H     0   0.227  22.0056  19.8957  -6.1916
 E6F  H12  H  H     0   0.227  21.3434  21.4067  -6.7736
 E6F  H13  H  H     0   0.246  20.6924  19.1799  -8.0081
 E6F  H14  H  H     0   0.233  19.4608  20.3945  -7.7525
 E6F  O2   O  OH1   0  -0.588  17.9298  18.2905  -8.3055
 E6F  H3   H  HOH1  0   0.480  17.4105  17.6322  -8.7914

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
 E6F  CZ  CA   single  1.529  0.020  1.529
 E6F  CZ  CE   single  1.534  0.020  1.534
 E6F  C   O    double  1.209  0.020  1.209
 E6F  C   CA   single  1.505  0.020  1.505
 E6F  CA  CB   single  1.552  0.020  1.552
 E6F  CE  CD   single  1.537  0.020  1.537
 E6F  CB  CG   single  1.535  0.020  1.535
 E6F  CB  N    single  1.457  0.020  1.457
 E6F  CD  CG   single  1.522  0.020  1.522
 E6F  N   H1   single  0.890  0.020  1.040
 E6F  N   H2   single  0.890  0.020  1.040
 E6F  CA  H4   single  0.970  0.020  1.090
 E6F  CB  H6   single  0.970  0.020  1.090
 E6F  CG  H7   single  0.970  0.020  1.090
 E6F  CG  H8   single  0.970  0.020  1.090
 E6F  CD  H9   single  0.970  0.020  1.090
 E6F  CD  H10  single  0.970  0.020  1.090
 E6F  CE  H11  single  0.970  0.020  1.090
 E6F  CE  H12  single  0.970  0.020  1.090
 E6F  CZ  H13  single  0.970  0.020  1.090
 E6F  CZ  H14  single  0.970  0.020  1.090
 E6F  C   O2   single  1.329  0.020  1.329
 E6F  O2  H3   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
 E6F  H2   N   H1   105.41  3.000
 E6F  H2   N   CB   110.17  3.000
 E6F  H1   N   CB   109.16  3.000
 E6F  H4   CA  CZ   108.53  3.000
 E6F  H4   CA  CB   107.22  3.000
 E6F  CZ   CA  CB   110.70  3.000
 E6F  H4   CA  C    106.37  3.000
 E6F  CB   CA  C    109.57  3.000
 E6F  CZ   CA  C    114.12  3.000
 E6F  O2   C   O    122.59  3.000
 E6F  O2   C   CA   112.82  3.000
 E6F  O    C   CA   124.56  3.000
 E6F  H6   CB  CG   107.37  3.000
 E6F  H6   CB  CA   108.31  3.000
 E6F  CG   CB  CA   110.31  3.000
 E6F  H6   CB  N    112.26  3.000
 E6F  CG   CB  N    109.81  3.000
 E6F  CA   CB  N    108.77  3.000
 E6F  H8   CG  H7   106.05  3.000
 E6F  H8   CG  CD   111.37  3.000
 E6F  H7   CG  CD   109.56  3.000
 E6F  H8   CG  CB   108.85  3.000
 E6F  H7   CG  CB   109.34  3.000
 E6F  CD   CG  CB   111.51  3.000
 E6F  H10  CD  H9   106.17  3.000
 E6F  H10  CD  CE   110.21  3.000
 E6F  H9   CD  CE   110.43  3.000
 E6F  H10  CD  CG   110.74  3.000
 E6F  H9   CD  CG   108.91  3.000
 E6F  CE   CD  CG   110.30  3.000
 E6F  H12  CE  H11  106.41  3.000
 E6F  H12  CE  CZ   108.89  3.000
 E6F  H11  CE  CZ   109.69  3.000
 E6F  H12  CE  CD   110.03  3.000
 E6F  H11  CE  CD   109.67  3.000
 E6F  CZ   CE  CD   111.98  3.000
 E6F  H14  CZ  H13  106.37  3.000
 E6F  H14  CZ  CE   110.27  3.000
 E6F  H13  CZ  CE   109.81  3.000
 E6F  H14  CZ  CA   109.79  3.000
 E6F  H13  CZ  CA   110.87  3.000
 E6F  CE   CZ  CA   109.68  3.000
 E6F  H3   O2  C    110.00  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
 E6F  CONST_01  H3  O2  C   CA  180.00   0.0  0
 E6F  Var_01    CD  CE  CZ  CA  -34.51  30.0  1
 E6F  Var_02    CZ  CE  CD  CG  -28.39  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
 E6F  chir_01  CA  CZ  C   CB  positiv
 E6F  chir_02  CB  N   CG  CA  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
 E6F  plan-1  CA  0.020
 E6F  plan-1  C   0.020
 E6F  plan-1  O   0.020
 E6F  plan-1  O2  0.020
 E6F  plan-1  H3  0.020

