# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 11:33:28 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2~{R})-2-azanyl-2-ethyl-octanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@](N)(CC)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
 R6E  R6E  '(2~{R})-2-azanyl-2-ethyl-octanoic acid'  D-peptide  33  13  .  2022-03-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R6E
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
 R6E  N    N  NH2    0  -0.803   1.6362  -1.3315   1.2722
 R6E  CA   C  CT     0  -0.029   1.6379  -0.2058   0.3299
 R6E  C    C  C      0   0.425   2.8882  -0.2524  -0.6013
 R6E  O    O  O      0  -0.601   2.7423   0.0001  -1.8135
 R6E  CB   C  CH2    0  -0.413   0.3383  -0.2491  -0.4783
 R6E  CB2  C  CH2    0  -0.422   1.7485   1.0744   1.1756
 R6E  CG   C  CH2    0  -0.410  -0.9491  -0.1581   0.3322
 R6E  CG2  C  CH3    0  -0.675   1.7151   2.3795   0.3917
 R6E  CD   C  CH2    0  -0.408  -2.1918  -0.2173  -0.5488
 R6E  CE   C  CH2    0  -0.405  -3.4928  -0.0929   0.2333
 R6E  CZ   C  CH2    0  -0.418  -4.7346  -0.1197  -0.6500
 R6E  CH   C  CH3    0  -0.662  -6.0265   0.0210   0.1431
 R6E  H1   H  HNH2   0   0.324   1.4920  -2.1902   0.7504
 R6E  H2   H  HNH2   0   0.325   2.5774  -1.4127   1.6422
 R6E  H7   H  HCH2   0   0.213   0.3486   0.5504  -1.2211
 R6E  H8   H  HCH2   0   0.201   0.3224  -1.1809  -1.0581
 R6E  H9   H  HCH2   0   0.213   0.9455   1.0755   1.9179
 R6E  H10  H  HCH2   0   0.213   2.6824   1.0201   1.7440
 R6E  H11  H  HCH2   0   0.206  -0.9857  -0.9629   1.0719
 R6E  H12  H  HCH2   0   0.204  -0.9706   0.7767   0.9022
 R6E  H13  H  HCH3   0   0.220   2.5222   2.4422  -0.3391
 R6E  H14  H  HCH3   0   0.216   0.7761   2.5005  -0.1510
 R6E  H15  H  HCH3   0   0.222   1.8131   3.2346   1.0621
 R6E  H16  H  HCH2   0   0.201  -2.1428   0.5833  -1.2961
 R6E  H17  H  HCH2   0   0.202  -2.1952  -1.1564  -1.1144
 R6E  H18  H  HCH2   0   0.204  -3.5551  -0.9020   0.9699
 R6E  H19  H  HCH2   0   0.203  -3.4811   0.8392   0.8103
 R6E  H20  H  HCH2   0   0.209  -4.6681   0.6854  -1.3882
 R6E  H21  H  HCH2   0   0.209  -4.7520  -1.0532  -1.2215
 R6E  H22  H  HCH3   0   0.215  -6.1332  -0.7868   0.8701
 R6E  H23  H  HCH3   0   0.215  -6.0469   0.9628   0.6952
 R6E  H24  H  HCH3   0   0.225  -6.9035  -0.0002  -0.5050
 R6E  OXT  O  OC    -1  -0.619   3.9713  -0.5234  -0.0377

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
 R6E  O    C    deloc   1.231  0.020  1.231
 R6E  C    CA   single  1.525  0.021  1.525
 R6E  CG2  CB2  single  1.523  0.020  1.523
 R6E  CG   CD   single  1.524  0.020  1.524
 R6E  CG   CB   single  1.524  0.020  1.524
 R6E  CB2  CA   single  1.538  0.020  1.538
 R6E  CA   CB   single  1.521  0.033  1.521
 R6E  CA   N    single  1.458  0.019  1.458
 R6E  CD   CE   single  1.523  0.020  1.523
 R6E  CZ   CH   single  1.522  0.020  1.522
 R6E  CZ   CE   single  1.524  0.020  1.524
 R6E  N    H1   single  0.890  0.020  1.040
 R6E  N    H2   single  0.890  0.020  1.040
 R6E  CB   H7   single  0.970  0.020  1.090
 R6E  CB   H8   single  0.970  0.020  1.090
 R6E  CB2  H9   single  0.970  0.020  1.090
 R6E  CB2  H10  single  0.970  0.020  1.090
 R6E  CG   H11  single  0.970  0.020  1.090
 R6E  CG   H12  single  0.970  0.020  1.090
 R6E  CG2  H13  single  0.970  0.020  1.090
 R6E  CG2  H14  single  0.970  0.020  1.090
 R6E  CG2  H15  single  0.970  0.020  1.090
 R6E  CD   H16  single  0.970  0.020  1.090
 R6E  CD   H17  single  0.970  0.020  1.090
 R6E  CE   H18  single  0.970  0.020  1.090
 R6E  CE   H19  single  0.970  0.020  1.090
 R6E  CZ   H20  single  0.970  0.020  1.090
 R6E  CZ   H21  single  0.970  0.020  1.090
 R6E  CH   H22  single  0.970  0.020  1.090
 R6E  CH   H23  single  0.970  0.020  1.090
 R6E  CH   H24  single  0.970  0.020  1.090
 R6E  C    OXT  deloc   1.251  0.020  1.251

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
 R6E  H2   N    H1   104.56  3.000
 R6E  H2   N    CA   107.11  3.000
 R6E  H1   N    CA   108.59  3.000
 R6E  CB2  CA   CB   112.01  3.000
 R6E  CB   CA   C    110.50  1.500
 R6E  CB2  CA   C    107.18  3.000
 R6E  CB   CA   N    110.40  1.500
 R6E  CB2  CA   N    106.58  3.000
 R6E  C    CA   N    111.00  2.800
 R6E  OXT  C    O    125.69  3.000
 R6E  OXT  C    CA   120.80  1.700
 R6E  O    C    CA   120.80  1.700
 R6E  H8   CB   H7   105.22  3.000
 R6E  H8   CB   CG   108.63  3.000
 R6E  H7   CB   CG   109.04  3.000
 R6E  H8   CB   CA   108.37  3.000
 R6E  H7   CB   CA   109.31  3.000
 R6E  CG   CB   CA   115.76  3.000
 R6E  H10  CB2  H9   105.90  3.000
 R6E  H10  CB2  CG2  109.18  3.000
 R6E  H9   CB2  CG2  109.42  3.000
 R6E  H10  CB2  CA   107.79  3.000
 R6E  H9   CB2  CA   108.74  3.000
 R6E  CG2  CB2  CA   115.38  3.000
 R6E  H12  CG   H11  105.99  3.000
 R6E  H12  CG   CD   108.54  3.000
 R6E  H11  CG   CD   109.57  3.000
 R6E  H12  CG   CB   110.14  3.000
 R6E  H11  CG   CB   110.12  3.000
 R6E  CD   CG   CB   112.27  3.000
 R6E  H15  CG2  H14  107.22  3.000
 R6E  H15  CG2  H13  107.47  3.000
 R6E  H14  CG2  H13  107.29  3.000
 R6E  H15  CG2  CB2  110.70  3.000
 R6E  H14  CG2  CB2  111.71  3.000
 R6E  H13  CG2  CB2  112.21  3.000
 R6E  H17  CD   H16  105.90  3.000
 R6E  H17  CD   CE   109.40  3.000
 R6E  H16  CD   CE   109.18  3.000
 R6E  H17  CD   CG   109.51  3.000
 R6E  H16  CD   CG   109.22  3.000
 R6E  CE   CD   CG   113.35  3.000
 R6E  H19  CE   H18  105.94  3.000
 R6E  H19  CE   CZ   109.18  3.000
 R6E  H18  CE   CZ   109.28  3.000
 R6E  H19  CE   CD   109.30  3.000
 R6E  H18  CE   CD   109.48  3.000
 R6E  CZ   CE   CD   113.39  3.000
 R6E  H21  CZ   H20  106.03  3.000
 R6E  H21  CZ   CH   109.71  3.000
 R6E  H20  CZ   CH   109.57  3.000
 R6E  H21  CZ   CE   109.30  3.000
 R6E  H20  CZ   CE   109.18  3.000
 R6E  CH   CZ   CE   112.82  3.000
 R6E  H24  CH   H23  107.59  3.000
 R6E  H24  CH   H22  107.61  3.000
 R6E  H23  CH   H22  107.44  3.000
 R6E  H24  CH   CZ   111.78  3.000
 R6E  H23  CH   CZ   111.04  3.000
 R6E  H22  CH   CZ   111.19  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
 R6E  Var_01  CD   CG   CB   CA  -179.64  30.0  1
 R6E  Var_02  CE   CD   CG   CB  -178.54  30.0  3
 R6E  Var_03  CZ   CE   CD   CG   178.67  30.0  3
 R6E  Var_04  CH   CZ   CE   CD  -179.36  30.0  1
 R6E  Var_05  H13  CG2  CB2  CA   -59.12  30.0  3
 R6E  Var_06  H22  CH   CZ   CE   -59.72  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
 R6E  chir_01  CA  CB2  CB  N  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
 R6E  plan-1  CA   0.020
 R6E  plan-1  C    0.020
 R6E  plan-1  O    0.020
 R6E  plan-1  OXT  0.020

