# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 23:31:38 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 4-azanylcyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CC[C@@H](CC1)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
 6RK  6RK  '4-azanylcyclohexane-1-carboxylic acid'  L-peptide  22  10  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6RK
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
 6RK  C1'  C  C      0   0.425   2.2366   0.0406   0.0728
 6RK  O1'  O  O      0  -0.604   2.7294   1.1113  -0.3362
 6RK  O2'  O  OC    -1  -0.624   2.8628  -1.0226   0.2714
 6RK  C1   C  CH1    0  -0.376   0.7241   0.0076   0.3769
 6RK  C2   C  CH2    0  -0.411  -0.0108   1.2965   0.0266
 6RK  C3   C  CH2    0  -0.423  -1.4967   1.2206   0.3658
 6RK  C4   C  CH1    0  -0.073  -2.1772   0.0365  -0.3103
 6RK  C5   C  CH2    0  -0.436  -1.4394  -1.2569   0.0360
 6RK  C6   C  CH2    0  -0.420   0.0459  -1.1849  -0.3013
 6RK  N4   N  NH2    0  -0.794  -3.5989   0.0226   0.0165
 6RK  H2   H  HCH1   0   0.206   0.6272  -0.1468   1.4627
 6RK  H3   H  HCH2   0   0.214   0.4418   2.1444   0.5443
 6RK  H4   H  HCH2   0   0.196   0.1020   1.4984  -1.0441
 6RK  H5   H  HCH2   0   0.198  -1.6210   1.1272   1.4525
 6RK  H6   H  HCH2   0   0.219  -1.9998   2.1468   0.0739
 6RK  H7   H  HCH1   0   0.202  -2.1004   0.1850  -1.3954
 6RK  H8   H  HCH2   0   0.198  -1.5598  -1.4507   1.1097
 6RK  H9   H  HCH2   0   0.217  -1.9072  -2.0979  -0.4863
 6RK  H10  H  HCH2   0   0.199   0.1657  -1.0967  -1.3884
 6RK  H11  H  HCH2   0   0.220   0.5422  -2.1117  -0.0106
 6RK  H12  H  HNH2   0   0.337  -4.0394  -0.7636  -0.4476
 6RK  H13  H  HNH2   0   0.329  -3.7050  -0.1641   1.0083

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
 6RK  N4   C4   single  1.459  0.020  1.459
 6RK  C5   C4   single  1.529  0.020  1.529
 6RK  C5   C6   single  1.525  0.020  1.525
 6RK  C4   C3   single  1.524  0.020  1.524
 6RK  C3   C2   single  1.526  0.020  1.526
 6RK  C6   C1   single  1.530  0.020  1.530
 6RK  C1   C2   single  1.524  0.020  1.524
 6RK  C1   C1'  single  1.543  0.020  1.543
 6RK  O1'  C1'  deloc   1.248  0.020  1.248
 6RK  C1'  O2'  deloc   1.250  0.020  1.250
 6RK  C1   H2   single  0.970  0.020  1.090
 6RK  C2   H3   single  0.970  0.020  1.090
 6RK  C2   H4   single  0.970  0.020  1.090
 6RK  C3   H5   single  0.970  0.020  1.090
 6RK  C3   H6   single  0.970  0.020  1.090
 6RK  C4   H7   single  0.970  0.020  1.090
 6RK  C5   H8   single  0.970  0.020  1.090
 6RK  C5   H9   single  0.970  0.020  1.090
 6RK  C6   H10  single  0.970  0.020  1.090
 6RK  C6   H11  single  0.970  0.020  1.090
 6RK  N4   H12  single  0.890  0.020  1.040
 6RK  N4   H13  single  0.890  0.020  1.040

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
 6RK  C1   C1'  O2'  116.20  3.000
 6RK  O2'  C1'  O1'  125.75  3.000
 6RK  C1   C1'  O1'  118.04  3.000
 6RK  H2   C1   C6   106.78  3.000
 6RK  H2   C1   C2   107.62  3.000
 6RK  C6   C1   C2   110.08  3.000
 6RK  H2   C1   C1'  106.48  3.000
 6RK  C2   C1   C1'  114.15  3.000
 6RK  C6   C1   C1'  111.33  3.000
 6RK  H4   C2   H3   106.12  3.000
 6RK  H4   C2   C3   109.07  3.000
 6RK  H3   C2   C3   109.69  3.000
 6RK  H4   C2   C1   109.32  3.000
 6RK  H3   C2   C1   110.35  3.000
 6RK  C3   C2   C1   112.11  3.000
 6RK  H6   C3   H5   106.51  3.000
 6RK  H6   C3   C4   109.53  3.000
 6RK  H5   C3   C4   108.82  3.000
 6RK  H6   C3   C2   110.27  3.000
 6RK  H5   C3   C2   109.54  3.000
 6RK  C4   C3   C2   112.01  3.000
 6RK  H7   C4   N4   106.91  3.000
 6RK  H7   C4   C5   107.73  3.000
 6RK  N4   C4   C5   114.30  3.000
 6RK  H7   C4   C3   107.58  3.000
 6RK  C5   C4   C3   109.96  3.000
 6RK  N4   C4   C3   110.07  3.000
 6RK  H9   C5   H8   106.51  3.000
 6RK  H9   C5   C6   110.30  3.000
 6RK  H8   C5   C6   109.36  3.000
 6RK  H9   C5   C4   109.61  3.000
 6RK  H8   C5   C4   108.54  3.000
 6RK  C6   C5   C4   112.33  3.000
 6RK  H11  C6   H10  106.42  3.000
 6RK  H11  C6   C5   110.13  3.000
 6RK  H10  C6   C5   109.23  3.000
 6RK  H11  C6   C1   110.02  3.000
 6RK  H10  C6   C1   109.15  3.000
 6RK  C5   C6   C1   111.75  3.000
 6RK  H13  N4   H12  105.03  3.000
 6RK  H13  N4   C4   108.82  3.000
 6RK  H12  N4   C4   109.17  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
 6RK  Var_01  C4  C5  C6  C1   55.57  30.0  1
 6RK  Var_02  C4  C3  C2  C1  -55.96  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
 6RK  chir_01  C1  C6  C2  C1'  positiv
 6RK  chir_02  C4  N4  C5  C3   positiv

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
 6RK  plan-1  C1'  0.020
 6RK  plan-1  O1'  0.020
 6RK  plan-1  O2'  0.020
 6RK  plan-1  C1   0.020

