# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 04:49:34 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2~{R})-1-methylpiperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCCC[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
 O9B  O9B  '(2~{R})-1-methylpiperidine-2-carboxylic acid'  ligand  22  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_O9B
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
 O9B  N5   N  NT     0  -0.409  -3.6487  36.5936  17.9302
 O9B  C31  C  C      0   0.383  -3.1204  34.8740  16.1710
 O9B  O6   O  O      0  -0.601  -4.3237  34.8279  15.8516
 O9B  C32  C  CH1    0  -0.143  -2.6434  36.0918  17.0052
 O9B  C33  C  CH2    0  -0.437  -2.2289  37.1818  16.0108
 O9B  C34  C  CH2    0  -0.435  -1.7715  38.4551  16.7061
 O9B  C35  C  CH2    0  -0.433  -2.8449  38.9143  17.6790
 O9B  C36  C  CH2    0  -0.269  -3.2024  37.7861  18.6303
 O9B  C37  C  CH3    0  -0.524  -4.0263  35.5855  18.8967
 O9B  O1   O  OC    -1  -0.609  -2.2252  34.0736  15.8319
 O9B  H2   H  HCH1   0   0.158  -1.7363  35.7877  17.5629
 O9B  H3   H  HCH2   0   0.206  -3.0810  37.4082  15.3609
 O9B  H4   H  HCH2   0   0.224  -1.4363  36.7862  15.3721
 O9B  H5   H  HCH2   0   0.205  -0.8435  38.2607  17.2544
 O9B  H6   H  HCH2   0   0.225  -1.5479  39.2340  15.9732
 O9B  H7   H  HCH2   0   0.224  -2.5116  39.7813  18.2537
 O9B  H8   H  HCH2   0   0.210  -3.7385  39.2208  17.1264
 O9B  H9   H  HCH2   0   0.170  -2.3279  37.5706  19.2743
 O9B  H10  H  HCH2   0   0.223  -4.0033  38.1079  19.3019
 O9B  H11  H  HCH3   0   0.221  -4.7897  35.9829  19.5684
 O9B  H12  H  HCH3   0   0.234  -4.4453  34.7122  18.4015
 O9B  H13  H  HCH3   0   0.178  -3.1807  35.2514  19.5209

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
 O9B  C33  C34  single  1.521  0.020  1.521
 O9B  C33  C32  single  1.533  0.020  1.533
 O9B  O6   C31  deloc   1.246  0.020  1.246
 O9B  C31  C32  single  1.551  0.020  1.551
 O9B  C34  C35  single  1.520  0.020  1.520
 O9B  C32  N5   single  1.455  0.020  1.455
 O9B  C35  C36  single  1.518  0.020  1.518
 O9B  N5   C36  single  1.453  0.020  1.453
 O9B  N5   C37  single  1.447  0.020  1.447
 O9B  C31  O1   deloc   1.248  0.020  1.248
 O9B  C32  H2   single  0.970  0.020  1.090
 O9B  C33  H3   single  0.970  0.020  1.090
 O9B  C33  H4   single  0.970  0.020  1.090
 O9B  C34  H5   single  0.970  0.020  1.090
 O9B  C34  H6   single  0.970  0.020  1.090
 O9B  C35  H7   single  0.970  0.020  1.090
 O9B  C35  H8   single  0.970  0.020  1.090
 O9B  C36  H9   single  0.970  0.020  1.090
 O9B  C36  H10  single  0.970  0.020  1.090
 O9B  C37  H11  single  0.970  0.020  1.090
 O9B  C37  H12  single  0.970  0.020  1.090
 O9B  C37  H13  single  0.970  0.020  1.090

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
 O9B  C37  N5   C36  109.28  3.000
 O9B  C37  N5   C32  111.39  3.000
 O9B  C36  N5   C32  112.15  3.000
 O9B  O1   C31  C32  115.41  3.000
 O9B  O1   C31  O6   126.84  3.000
 O9B  C32  C31  O6   117.64  3.000
 O9B  H2   C32  C33  107.49  3.000
 O9B  H2   C32  C31  107.89  3.000
 O9B  C33  C32  C31  107.01  3.000
 O9B  H2   C32  N5   109.90  3.000
 O9B  C31  C32  N5   113.58  3.000
 O9B  C33  C32  N5   110.74  3.000
 O9B  H4   C33  H3   107.01  3.000
 O9B  H4   C33  C34  110.63  3.000
 O9B  H3   C33  C34  109.40  3.000
 O9B  H4   C33  C32  108.55  3.000
 O9B  H3   C33  C32  108.75  3.000
 O9B  C34  C33  C32  112.34  3.000
 O9B  H6   C34  H5   106.79  3.000
 O9B  H6   C34  C35  111.01  3.000
 O9B  H5   C34  C35  109.37  3.000
 O9B  H6   C34  C33  110.59  3.000
 O9B  H5   C34  C33  109.58  3.000
 O9B  C35  C34  C33  109.46  3.000
 O9B  H8   C35  H7   107.01  3.000
 O9B  H8   C35  C36  109.40  3.000
 O9B  H7   C35  C36  109.39  3.000
 O9B  H8   C35  C34  109.77  3.000
 O9B  H7   C35  C34  111.17  3.000
 O9B  C36  C35  C34  110.05  3.000
 O9B  H10  C36  H9   106.17  3.000
 O9B  H10  C36  C35  109.79  3.000
 O9B  H9   C36  C35  108.85  3.000
 O9B  H10  C36  N5   108.21  3.000
 O9B  H9   C36  N5   111.29  3.000
 O9B  C35  C36  N5   112.35  3.000
 O9B  H13  C37  H12  108.05  3.000
 O9B  H13  C37  H11  107.35  3.000
 O9B  H12  C37  H11  107.63  3.000
 O9B  H13  C37  N5   112.90  3.000
 O9B  H12  C37  N5   110.85  3.000
 O9B  H11  C37  N5   109.87  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
 O9B  Var_01  C34  C35  C36  N5    -57.26  30.0  1
 O9B  Var_02  C35  C36  N5   C32    58.46  30.0  1
 O9B  Var_03  C36  C35  C34  C33    54.00  30.0  1
 O9B  Var_04  H11  C37  N5   C32  -179.23  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
 O9B  chir_01  C32  C33  C31  N5  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
 O9B  plan-1  C31  0.020
 O9B  plan-1  O6   0.020
 O9B  plan-1  C32  0.020
 O9B  plan-1  O1   0.020

