# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:24:05 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (1S,2S)-2-aminocyclopentanecarboxylic 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
 XCP  XCP  '(1S,2S)-2-aminocyclopentanecarboxylic acid'  peptide  19  9  .  2022-03-29  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XCP
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
 XCP  N    N  NH2    0  -0.816  -1.0453  -1.9870   0.4560
 XCP  CB   C  CH1    0  -0.051  -0.8875  -0.7503  -0.2943
 XCP  CG   C  CH2    0  -0.444  -2.2107   0.0398  -0.4085
 XCP  CD   C  CH2    0  -0.446  -1.8905   1.4860   0.0132
 XCP  CE   C  CH2    0  -0.425  -0.3688   1.5868  -0.0800
 XCP  CA   C  CH1    0  -0.382   0.0938   0.2125   0.3888
 XCP  C    C  C      0   0.423   1.5759  -0.1187   0.1725
 XCP  O    O  O      0  -0.612   1.8891  -1.3315   0.1813
 XCP  HN   H  HNH2   0   0.329  -1.6132  -2.6366  -0.0751
 XCP  HB   H  HCH1   0   0.183  -0.5124  -0.9323  -1.3144
 XCP  HG   H  HCH2   0   0.218  -2.5954   0.0025  -1.4295
 XCP  HGA  H  HCH2   0   0.218  -2.9751  -0.4044   0.2316
 XCP  HD   H  HCH2   0   0.221  -2.4101   2.2310  -0.5919
 XCP  HDA  H  HCH2   0   0.213  -2.1993   1.6501   1.0490
 XCP  HE   H  HCH2   0   0.203  -0.0613   1.7519  -1.1174
 XCP  HEA  H  HCH2   0   0.218   0.0431   2.4055   0.5110
 XCP  HA   H  HCH1   0   0.219  -0.1013   0.1412   1.4700
 XCP  HNA  H  HNH2   0   0.335  -0.1262  -2.4087   0.5275
 XCP  OXT  O  OC    -1  -0.606   2.3649   0.8359   0.0295

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
 XCP  N    HN   single  0.890  0.020  1.040
 XCP  N    HNA  single  0.890  0.020  1.040
 XCP  CB   N    single  1.455  0.020  1.455
 XCP  CB   CG   single  1.545  0.020  1.545
 XCP  CG   HGA  single  0.970  0.020  1.090
 XCP  CD   CG   single  1.540  0.020  1.540
 XCP  CD   HD   single  0.970  0.020  1.090
 XCP  CE   CD   single  1.528  0.020  1.528
 XCP  CE   CA   single  1.524  0.020  1.524
 XCP  CE   HE   single  0.970  0.020  1.090
 XCP  CA   CB   single  1.521  0.033  1.521
 XCP  CA   HA   single  0.970  0.020  0.970
 XCP  C    CA   single  1.525  0.021  1.525
 XCP  C    OXT  deloc   1.247  0.020  1.247
 XCP  O    C    deloc   1.231  0.020  1.231
 XCP  HB   CB   single  0.970  0.020  1.090
 XCP  HG   CG   single  0.970  0.020  1.090
 XCP  HDA  CD   single  0.970  0.020  1.090
 XCP  HEA  CE   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
 XCP  HNA  N   HN  106.17  3.000
 XCP  HNA  N   CB  106.95  3.000
 XCP  HN   N   CB  109.59  3.000
 XCP  HB   CB  CA  107.34  3.000
 XCP  HB   CB  CG  107.90  3.000
 XCP  CA   CB  CG  105.04  3.000
 XCP  HB   CB  N   111.95  3.000
 XCP  CA   CB  N   110.40  1.500
 XCP  CG   CB  N   112.32  3.000
 XCP  HGA  CG  HG  106.73  3.000
 XCP  HG   CG  CD  111.19  3.000
 XCP  HGA  CG  CD  111.54  3.000
 XCP  HG   CG  CB  110.69  3.000
 XCP  CD   CG  CB  106.37  3.000
 XCP  HGA  CG  CB  110.38  3.000
 XCP  HDA  CD  HD  106.75  3.000
 XCP  HDA  CD  CE  109.22  3.000
 XCP  HD   CD  CE  113.29  3.000
 XCP  HDA  CD  CG  109.98  3.000
 XCP  CE   CD  CG  104.62  3.000
 XCP  HD   CD  CG  112.96  3.000
 XCP  HEA  CE  HE  107.12  3.000
 XCP  HEA  CE  CA  113.30  3.000
 XCP  HE   CE  CA  110.02  3.000
 XCP  HEA  CE  CD  113.12  3.000
 XCP  HE   CE  CD  110.34  3.000
 XCP  CA   CE  CD  102.95  3.000
 XCP  HA   CA  C   110.00  3.000
 XCP  C    CA  CE  116.40  3.000
 XCP  HA   CA  CE  107.86  3.000
 XCP  C    CA  CB  110.50  1.500
 XCP  HA   CA  CB  109.00  3.000
 XCP  CE   CA  CB  103.57  3.000
 XCP  OXT  C   O   125.73  3.000
 XCP  O    C   CA  120.80  1.700
 XCP  OXT  C   CA  120.80  1.700

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
 XCP  Var_01  CE  CD  CG  CB   17.46  30.0  1
 XCP  Var_02  CA  CE  CD  CG  -36.71  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
 XCP  chir_01  CB  N   CG  CA  negativ
 XCP  chir_02  CA  CE  CB  C   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
 XCP  plan-1  CA   0.020
 XCP  plan-1  C    0.020
 XCP  plan-1  O    0.020
 XCP  plan-1  OXT  0.020

