# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 02:42:43 2022
#   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  22  10  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.817  18.1581  18.5623  -4.3421
 E6F  CA   C  CH1    0  -0.379  19.3171  18.7268  -6.4976
 E6F  C    C  C      0   0.425  18.5055  17.7686  -7.3951
 E6F  O    O  O      0  -0.612  17.8418  16.8881  -6.7979
 E6F  CB   C  CH1    0  -0.051  18.3841  19.4369  -5.4882
 E6F  CG   C  CH2    0  -0.438  18.9846  20.7679  -5.0105
 E6F  CD   C  CH2    0  -0.439  20.4993  20.6797  -4.9027
 E6F  CE   C  CH2    0  -0.426  21.1151  20.4833  -6.2962
 E6F  CZ   C  CH2    0  -0.431  20.1587  19.7507  -7.2480
 E6F  H1   H  HNH2   0   0.326  17.3930  18.9295  -3.7883
 E6F  H2   H  HNH2   0   0.336  17.8444  17.6705  -4.7091
 E6F  H4   H  HCH1   0   0.209  20.0015  18.1053  -5.9021
 E6F  H6   H  HCH1   0   0.186  17.4436  19.6765  -6.0113
 E6F  H7   H  HCH2   0   0.211  18.7168  21.5658  -5.7097
 E6F  H8   H  HCH2   0   0.220  18.5322  21.0427  -4.0532
 E6F  H9   H  HCH2   0   0.210  20.7565  19.8389  -4.2526
 E6F  H10  H  HCH2   0   0.220  20.9104  21.5711  -4.4238
 E6F  H11  H  HCH2   0   0.212  22.0492  19.9219  -6.2080
 E6F  H12  H  HCH2   0   0.211  21.3830  21.4522  -6.7256
 E6F  H13  H  HCH2   0   0.216  20.7275  19.2714  -8.0455
 E6F  H14  H  HCH2   0   0.202  19.4984  20.4699  -7.7428
 E6F  O2   O  OC    -1  -0.591  18.5551  17.9318  -8.6295

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  1.523  0.020  1.523
 E6F  CZ  CE   single  1.535  0.020  1.535
 E6F  C   O    deloc   1.254  0.020  1.254
 E6F  C   CA   single  1.544  0.020  1.544
 E6F  CA  CB   single  1.547  0.020  1.547
 E6F  CE  CD   single  1.536  0.020  1.536
 E6F  CB  CG   single  1.536  0.020  1.536
 E6F  CB  N    single  1.459  0.020  1.459
 E6F  CD  CG   single  1.521  0.020  1.521
 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   deloc   1.246  0.020  1.246

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   106.43  3.000
 E6F  H2   N   CB   106.90  3.000
 E6F  H1   N   CB   109.21  3.000
 E6F  H4   CA  CZ   107.63  3.000
 E6F  H4   CA  CB   106.34  3.000
 E6F  CZ   CA  CB   110.25  3.000
 E6F  H4   CA  C    106.93  3.000
 E6F  CB   CA  C    110.31  3.000
 E6F  CZ   CA  C    114.93  3.000
 E6F  O2   C   O    125.79  3.000
 E6F  O2   C   CA   118.28  3.000
 E6F  O    C   CA   115.93  3.000
 E6F  H6   CB  CG   107.02  3.000
 E6F  H6   CB  CA   107.73  3.000
 E6F  CG   CB  CA   111.39  3.000
 E6F  H6   CB  N    111.76  3.000
 E6F  CG   CB  N    109.61  3.000
 E6F  CA   CB  N    109.31  3.000
 E6F  H8   CG  H7   105.95  3.000
 E6F  H8   CG  CD   111.37  3.000
 E6F  H7   CG  CD   109.35  3.000
 E6F  H8   CG  CB   109.15  3.000
 E6F  H7   CG  CB   109.72  3.000
 E6F  CD   CG  CB   111.16  3.000
 E6F  H10  CD  H9   106.16  3.000
 E6F  H10  CD  CE   110.56  3.000
 E6F  H9   CD  CE   110.29  3.000
 E6F  H10  CD  CG   111.01  3.000
 E6F  H9   CD  CG   108.72  3.000
 E6F  CE   CD  CG   110.02  3.000
 E6F  H12  CE  H11  106.11  3.000
 E6F  H12  CE  CZ   109.40  3.000
 E6F  H11  CE  CZ   109.71  3.000
 E6F  H12  CE  CD   109.95  3.000
 E6F  H11  CE  CD   109.57  3.000
 E6F  CZ   CE  CD   111.94  3.000
 E6F  H14  CZ  H13  105.83  3.000
 E6F  H14  CZ  CE   110.03  3.000
 E6F  H13  CZ  CE   109.76  3.000
 E6F  H14  CZ  CA   109.33  3.000
 E6F  H13  CZ  CA   110.67  3.000
 E6F  CE   CZ  CA   111.07  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  Var_01  CD  CE  CZ  CA  -34.08  30.0  1
 E6F  Var_02  CZ  CE  CD  CG  -28.70  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

