# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 00:17:52 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (1R,2R)-2-aminocyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCC[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
 XZP  XZP  '(1R,2R)-2-aminocyclopentane-1-carboxylic acid'  ligand  20  9  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XZP
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
 XZP  O    O  O     0  -0.443  -1.9016  -0.8481  -0.8224
 XZP  C    C  C     0   0.562  -1.5262  -0.1245   0.0671
 XZP  CA   C  CH1   0  -0.388  -0.0960   0.2206   0.3675
 XZP  CB   C  CH1   0  -0.063   0.9234  -0.7428  -0.2347
 XZP  N    N  NH2   0  -0.798   0.9323  -2.0176   0.4559
 XZP  CG   C  CH2   0  -0.452   2.2403   0.0701  -0.2460
 XZP  CD   C  CH2   0  -0.453   1.8445   1.5505  -0.0793
 XZP  CE   C  CH2   0  -0.435   0.3181   1.5813  -0.2051
 XZP  O1   O  OH1   0  -0.598  -2.3672   0.5020   0.8863
 XZP  H1   H  HCH1  0   0.268   0.0347   0.2517   1.4560
 XZP  H2   H  HCH1  0   0.233   0.6258  -0.9395  -1.2683
 XZP  H3   H  HNH2  0   0.346   1.5437  -2.6636  -0.0273
 XZP  H4   H  HNH2  0   0.335   1.3352  -1.8992   1.3791
 XZP  H6   H  HCH2  0   0.227   2.8866  -0.2582   0.5711
 XZP  H7   H  HCH2  0   0.232   2.7940  -0.1029  -1.1698
 XZP  H8   H  HCH2  0   0.232   2.1344   1.9100   0.9098
 XZP  H9   H  HCH2  0   0.236   2.3254   2.2039  -0.8075
 XZP  H10  H  HCH2  0   0.232   0.0217   1.6441  -1.2561
 XZP  H11  H  HCH2  0   0.249  -0.1372   2.4234   0.3154
 XZP  H12  H  HOH1  0   0.477  -3.2817   0.2913   0.6446

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
 XZP  O   C    double  1.206  0.020  1.206
 XZP  C   CA   single  1.502  0.020  1.502
 XZP  N   CB   single  1.450  0.020  1.450
 XZP  CB  CA   single  1.526  0.020  1.526
 XZP  CB  CG   single  1.548  0.020  1.548
 XZP  CA  CE   single  1.533  0.020  1.533
 XZP  CG  CD   single  1.541  0.020  1.541
 XZP  CE  CD   single  1.532  0.020  1.532
 XZP  C   O1   single  1.331  0.020  1.331
 XZP  CA  H1   single  0.970  0.020  1.090
 XZP  CB  H2   single  0.970  0.020  1.090
 XZP  N   H3   single  0.890  0.020  1.040
 XZP  N   H4   single  0.890  0.020  1.040
 XZP  CG  H6   single  0.970  0.020  1.090
 XZP  CG  H7   single  0.970  0.020  1.090
 XZP  CD  H8   single  0.970  0.020  1.090
 XZP  CD  H9   single  0.970  0.020  1.090
 XZP  CE  H10  single  0.970  0.020  1.090
 XZP  CE  H11  single  0.970  0.020  1.090
 XZP  O1  H12  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
 XZP  O1   C   CA   111.75  3.000
 XZP  O1   C   O    122.66  3.000
 XZP  CA   C   O    125.57  3.000
 XZP  H1   CA  CE   108.25  3.000
 XZP  H1   CA  CB   109.26  3.000
 XZP  CE   CA  CB   103.44  3.000
 XZP  H1   CA  C    108.58  3.000
 XZP  CE   CA  C    112.74  3.000
 XZP  CB   CA  C    114.34  3.000
 XZP  H2   CB  CG   108.62  3.000
 XZP  H2   CB  N    107.08  3.000
 XZP  CG   CB  N    117.39  3.000
 XZP  H2   CB  CA   107.74  3.000
 XZP  CG   CB  CA   103.87  3.000
 XZP  N    CB  CA   111.78  3.000
 XZP  H4   N   H3   105.60  3.000
 XZP  H4   N   CB   109.48  3.000
 XZP  H3   N   CB   109.73  3.000
 XZP  H7   CG  H6   106.59  3.000
 XZP  H7   CG  CD   111.98  3.000
 XZP  H6   CG  CD   111.08  3.000
 XZP  H7   CG  CB   110.78  3.000
 XZP  H6   CG  CB   109.89  3.000
 XZP  CD   CG  CB   106.57  3.000
 XZP  H9   CD  H8   106.90  3.000
 XZP  H9   CD  CE   111.88  3.000
 XZP  H8   CD  CE   109.42  3.000
 XZP  H9   CD  CG   112.96  3.000
 XZP  H8   CD  CG   110.25  3.000
 XZP  CE   CD  CG   105.44  3.000
 XZP  H11  CE  H10  107.54  3.000
 XZP  H11  CE  CD   113.12  3.000
 XZP  H10  CE  CD   110.50  3.000
 XZP  H11  CE  CA   113.24  3.000
 XZP  H10  CE  CA   109.67  3.000
 XZP  CD   CE  CA   102.75  3.000
 XZP  H12  O1  C    109.90  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
 XZP  CONST_01  H12  O1  C   CA  180.00   0.0  0
 XZP  Var_01    CG   CD  CE  CA   31.53  30.0  1
 XZP  Var_02    CE   CD  CG  CB   -8.94  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
 XZP  chir_01  CA  C  CB  CE  negativ
 XZP  chir_02  CB  N  CA  CG  negativ

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
 XZP  plan-1  O    0.020
 XZP  plan-1  C    0.020
 XZP  plan-1  CA   0.020
 XZP  plan-1  O1   0.020
 XZP  plan-1  H12  0.020

