# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 08:02:29 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2S,4S)-4-methylpiperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCN[C@@H](C1)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
 3A0  3A0  '(2S,4S)-4-methylpiperidine-2-carboxylic acid'  ligand  23  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3A0
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
 3A0  N3   N  NH1   0  -0.602   0.0121   1.4140  -0.1852
 3A0  O4   O  O     0  -0.438  -2.6484   1.0268   0.2359
 3A0  C21  C  CH1   0  -0.192  -0.4953   0.0629  -0.2809
 3A0  C22  C  C     0   0.538  -1.9855   0.0557  -0.0292
 3A0  C33  C  CH2   0  -0.421   0.2372  -0.8242   0.7347
 3A0  C34  C  CH1   0  -0.257   1.7541  -0.7908   0.5218
 3A0  C35  C  CH3   0  -0.666   2.1807  -1.5991  -0.7013
 3A0  C36  C  CH2   0  -0.419   2.2367   0.6604   0.4581
 3A0  C37  C  CH2   0  -0.302   1.4231   1.4821  -0.5292
 3A0  H3   H  HCH1  0   0.245  -0.3532  -0.3695  -1.2879
 3A0  H41  H  HCH2  0   0.236   0.0037  -0.4603   1.7397
 3A0  H42  H  HCH2  0   0.241  -0.1226  -1.8523   0.6689
 3A0  H7   H  HCH1  0   0.237   2.2133  -1.2614   1.3966
 3A0  H44  H  HCH3  0   0.220   1.7566  -1.2183  -1.6317
 3A0  H43  H  HCH3  0   0.229   3.2665  -1.5853  -0.8120
 3A0  H45  H  HCH3  0   0.228   1.8711  -2.6413  -0.6060
 3A0  H46  H  HCH2  0   0.223   2.1490   1.1154   1.4491
 3A0  H47  H  HCH2  0   0.226   3.2944   0.6959   0.1846
 3A0  H48  H  HCH2  0   0.195   1.6190   1.1355  -1.5561
 3A0  H49  H  HCH2  0   0.237   1.7359   2.5272  -0.4895
 3A0  H2   H  HNH1  0   0.352  -0.5122   2.0250  -0.7977
 3A0  OXT  O  OH1   0  -0.595  -2.4986  -1.1632  -0.1521
 3A0  HXT  H  HOH1  0   0.483  -3.4539  -1.1362   0.0065

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
 3A0  N3   C21  single  1.446  0.020  1.446
 3A0  N3   C37  single  1.454  0.020  1.454
 3A0  O4   C22  double  1.205  0.020  1.205
 3A0  C21  C33  single  1.535  0.020  1.535
 3A0  C21  C22  single  1.511  0.020  1.511
 3A0  C33  C34  single  1.532  0.020  1.532
 3A0  C34  C36  single  1.531  0.020  1.531
 3A0  C34  C35  single  1.527  0.020  1.527
 3A0  C36  C37  single  1.520  0.020  1.520
 3A0  C21  H3   single  0.970  0.020  1.090
 3A0  C33  H41  single  0.970  0.020  1.090
 3A0  C33  H42  single  0.970  0.020  1.090
 3A0  C34  H7   single  0.970  0.020  1.090
 3A0  C35  H44  single  0.970  0.020  1.090
 3A0  C35  H43  single  0.970  0.020  1.090
 3A0  C35  H45  single  0.970  0.020  1.090
 3A0  C36  H46  single  0.970  0.020  1.090
 3A0  C36  H47  single  0.970  0.020  1.090
 3A0  C37  H48  single  0.970  0.020  1.090
 3A0  C37  H49  single  0.970  0.020  1.090
 3A0  N3   H2   single  0.890  0.020  1.040
 3A0  C22  OXT  single  1.328  0.020  1.328
 3A0  OXT  HXT  single  0.850  0.020  0.980

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
 3A0  H2   N3   C37  109.35  3.000
 3A0  H2   N3   C21  110.02  3.000
 3A0  C37  N3   C21  111.63  3.000
 3A0  H3   C21  C33  108.39  3.000
 3A0  H3   C21  C22  106.06  3.000
 3A0  C33  C21  C22  110.96  3.000
 3A0  H3   C21  N3   112.38  3.000
 3A0  C22  C21  N3   109.84  3.000
 3A0  C33  C21  N3   109.20  3.000
 3A0  OXT  C22  C21  111.71  3.000
 3A0  OXT  C22  O4   123.18  3.000
 3A0  C21  C22  O4   125.10  3.000
 3A0  H42  C33  H41  107.36  3.000
 3A0  H42  C33  C34  109.79  3.000
 3A0  H41  C33  C34  109.37  3.000
 3A0  H42  C33  C21  110.33  3.000
 3A0  H41  C33  C21  108.28  3.000
 3A0  C34  C33  C21  111.59  3.000
 3A0  H7   C34  C36  107.98  3.000
 3A0  H7   C34  C35  107.18  3.000
 3A0  C36  C34  C35  112.36  3.000
 3A0  H7   C34  C33  107.16  3.000
 3A0  C35  C34  C33  112.11  3.000
 3A0  C36  C34  C33  109.79  3.000
 3A0  H45  C35  H43  107.64  3.000
 3A0  H45  C35  H44  107.31  3.000
 3A0  H43  C35  H44  107.20  3.000
 3A0  H45  C35  C34  110.88  3.000
 3A0  H43  C35  C34  110.64  3.000
 3A0  H44  C35  C34  112.94  3.000
 3A0  H47  C36  H46  106.90  3.000
 3A0  H47  C36  C37  109.74  3.000
 3A0  H46  C36  C37  108.70  3.000
 3A0  H47  C36  C34  110.25  3.000
 3A0  H46  C36  C34  109.35  3.000
 3A0  C37  C36  C34  111.76  3.000
 3A0  H49  C37  H48  106.51  3.000
 3A0  H49  C37  C36  109.91  3.000
 3A0  H48  C37  C36  109.89  3.000
 3A0  H49  C37  N3   108.32  3.000
 3A0  H48  C37  N3   112.24  3.000
 3A0  C36  C37  N3   109.89  3.000
 3A0  HXT  OXT  C22  109.89  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
 3A0  CONST_01  HXT  OXT  C22  C21  180.00   0.0  0
 3A0  Var_01    C34  C36  C37  N3    56.16  30.0  1
 3A0  Var_02    C36  C37  N3   C21  -62.80  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
 3A0  chir_01  C21  N3   C33  C22  negativ
 3A0  chir_02  C34  C33  C36  C35  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
 3A0  plan-1  O4   0.020
 3A0  plan-1  C21  0.020
 3A0  plan-1  C22  0.020
 3A0  plan-1  OXT  0.020
 3A0  plan-1  HXT  0.020

