# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 05:58:23 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  23  10  .  2022-03-10  2022-11-17
;
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   0.563   2.1867   0.0669  -0.0365
 6RK  O1'  O  O     0  -0.442   2.6903   0.9254  -0.7188
 6RK  O2'  O  OH1   0  -0.597   2.8818  -0.9519   0.4630
 6RK  C1   C  CH1   0  -0.382   0.7282  -0.0087   0.3371
 6RK  C2   C  CH2   0  -0.423  -0.0077   1.2916   0.0340
 6RK  C3   C  CH2   0  -0.431  -1.4825   1.1926   0.4079
 6RK  C4   C  CH1   0  -0.073  -2.1715   0.0281  -0.2937
 6RK  C5   C  CH2   0  -0.443  -1.4210  -1.2733  -0.0088
 6RK  C6   C  CH2   0  -0.431   0.0553  -1.1906  -0.3801
 6RK  N4   N  NH2   0  -0.793  -3.5820  -0.0053   0.0685
 6RK  H1   H  HOH1  0   0.478   3.8063  -0.8909   0.1798
 6RK  H2   H  HCH1  0   0.266   0.6764  -0.2038   1.4155
 6RK  H3   H  HCH2  0   0.240   0.4549   2.1231   0.5701
 6RK  H4   H  HCH2  0   0.222   0.0799   1.5198  -1.0321
 6RK  H5   H  HCH2  0   0.211  -1.5796   1.0655   1.4932
 6RK  H6   H  HCH2  0   0.233  -1.9908   2.1257   0.1546
 6RK  H7   H  HCH1  0   0.212  -2.1211   0.2147  -1.3741
 6RK  H8   H  HCH2  0   0.211  -1.5142  -1.5091   1.0584
 6RK  H9   H  HCH2  0   0.233  -1.8906  -2.0975  -0.5533
 6RK  H10  H  HCH2  0   0.227   0.1566  -1.0594  -1.4627
 6RK  H11  H  HCH2  0   0.246   0.5529  -2.1280  -0.1265
 6RK  H12  H  HNH2  0   0.341  -4.0334  -0.7744  -0.4130
 6RK  H13  H  HNH2  0   0.332  -3.6652  -0.2238   1.0558

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  1.457  0.020  1.457
 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  1.525  0.020  1.525
 6RK  C6   C1   single  1.538  0.020  1.538
 6RK  C1   C2   single  1.524  0.020  1.524
 6RK  C1   C1'  single  1.507  0.020  1.507
 6RK  O1'  C1'  double  1.207  0.020  1.207
 6RK  C1'  O2'  single  1.331  0.020  1.331
 6RK  O2'  H1   single  0.850  0.020  0.980
 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'  111.97  3.000
 6RK  O2'  C1'  O1'  122.61  3.000
 6RK  C1   C1'  O1'  125.42  3.000
 6RK  H1   O2'  C1'  109.91  3.000
 6RK  H2   C1   C6   107.52  3.000
 6RK  H2   C1   C2   108.92  3.000
 6RK  C6   C1   C2   110.59  3.000
 6RK  H2   C1   C1'  107.35  3.000
 6RK  C2   C1   C1'  112.03  3.000
 6RK  C6   C1   C1'  110.26  3.000
 6RK  H4   C2   H3   106.60  3.000
 6RK  H4   C2   C3   109.27  3.000
 6RK  H3   C2   C3   109.80  3.000
 6RK  H4   C2   C1   109.46  3.000
 6RK  H3   C2   C1   110.33  3.000
 6RK  C3   C2   C1   111.27  3.000
 6RK  H6   C3   H5   106.69  3.000
 6RK  H6   C3   C4   109.60  3.000
 6RK  H5   C3   C4   109.07  3.000
 6RK  H6   C3   C2   109.75  3.000
 6RK  H5   C3   C2   109.62  3.000
 6RK  C4   C3   C2   111.96  3.000
 6RK  H7   C4   N4   107.05  3.000
 6RK  H7   C4   C5   107.79  3.000
 6RK  N4   C4   C5   114.17  3.000
 6RK  H7   C4   C3   107.61  3.000
 6RK  C5   C4   C3   110.04  3.000
 6RK  N4   C4   C3   109.93  3.000
 6RK  H9   C5   H8   106.61  3.000
 6RK  H9   C5   C6   109.60  3.000
 6RK  H8   C5   C6   109.32  3.000
 6RK  H9   C5   C4   109.75  3.000
 6RK  H8   C5   C4   108.82  3.000
 6RK  C6   C5   C4   112.57  3.000
 6RK  H11  C6   H10  106.88  3.000
 6RK  H11  C6   C5   109.78  3.000
 6RK  H10  C6   C5   109.68  3.000
 6RK  H11  C6   C1   110.64  3.000
 6RK  H10  C6   C1   109.18  3.000
 6RK  C5   C6   C1   110.60  3.000
 6RK  H13  N4   H12  105.21  3.000
 6RK  H13  N4   C4   109.05  3.000
 6RK  H12  N4   C4   109.31  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  CONST_01  H1  O2'  C1'  C1  180.00   0.0  0
 6RK  Var_01    C4  C5   C6   C1   55.66  30.0  1
 6RK  Var_02    C4  C3   C2   C1  -56.45  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
 6RK  plan-1  H1   0.020

