# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 20:36:43 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  20  9  .  2022-03-29  2022-11-18
;
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  -0.802  -0.9473  -2.0749   0.3078
 XCP  CB   C  CH1   0  -0.059  -0.9273  -0.7430  -0.2675
 XCP  CG   C  CH2   0  -0.450  -2.2198   0.0251  -0.0178
 XCP  CD   C  CH2   0  -0.446  -1.8502   1.4909  -0.2751
 XCP  CE   C  CH2   0  -0.442  -0.3256   1.5910  -0.0354
 XCP  CA   C  CH1   0  -0.381   0.1002   0.1705   0.3925
 XCP  C    C  C     0   0.556   1.5293  -0.1396   0.0540
 XCP  O    O  O     0  -0.445   1.8952  -0.9873  -0.7247
 XCP  HN   H  HNH2  0   0.345  -1.7134  -2.6002  -0.0964
 XCP  HB   H  HCH1  0   0.203  -0.7363  -0.7447  -1.3525
 XCP  HG   H  HCH2  0   0.238  -3.0445  -0.3234  -0.6423
 XCP  HGA  H  HCH2  0   0.220  -2.5177  -0.1224   1.0245
 XCP  HD   H  HCH2  0   0.233  -2.0886   1.7736  -1.3009
 XCP  HDA  H  HCH2  0   0.237  -2.4083   2.1662   0.3729
 XCP  HE   H  HCH2  0   0.240   0.1858   1.8843  -0.9542
 XCP  HEA  H  HCH2  0   0.248  -0.0668   2.3303   0.7213
 XCP  HA   H  HCH1  0   0.277  -0.0149   0.0750   1.4794
 XCP  HNA  H  HNH2  0   0.343  -0.1099  -2.5726   0.0319
 XCP  OXT  O  OH1   0  -0.594   2.3756   0.6465   0.7121
 XCP  HXT  H  HOH1  0   0.479   3.2880   0.4333   0.4643

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  1.451  0.020  1.451
 XCP  CB   CG   single  1.524  0.020  1.524
 XCP  CG   HGA  single  0.970  0.020  1.090
 XCP  CD   CG   single  1.533  0.020  1.533
 XCP  CD   HD   single  0.970  0.020  1.090
 XCP  CE   CD   single  1.547  0.020  1.547
 XCP  CE   CA   single  1.543  0.020  1.543
 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  single  1.329  0.020  1.329
 XCP  O    C    double  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
 XCP  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
 XCP  HNA  N    HN  105.17  3.000
 XCP  HNA  N    CB  109.38  3.000
 XCP  HN   N    CB  109.16  3.000
 XCP  HB   CB   CA  108.08  3.000
 XCP  HB   CB   CG  108.01  3.000
 XCP  CA   CB   CG  101.46  3.000
 XCP  HB   CB   N   113.04  3.000
 XCP  CA   CB   N   110.40  1.500
 XCP  CG   CB   N   112.70  3.000
 XCP  HGA  CG   HG  107.23  3.000
 XCP  HG   CG   CD  113.03  3.000
 XCP  HGA  CG   CD  110.76  3.000
 XCP  HG   CG   CB  112.71  3.000
 XCP  CD   CG   CB  104.47  3.000
 XCP  HGA  CG   CB  108.60  3.000
 XCP  HDA  CD   HD  106.67  3.000
 XCP  HDA  CD   CE  111.88  3.000
 XCP  HD   CD   CE  110.16  3.000
 XCP  HDA  CD   CG  111.66  3.000
 XCP  CE   CD   CG  105.87  3.000
 XCP  HD   CD   CG  110.67  3.000
 XCP  HEA  CE   HE  106.92  3.000
 XCP  HEA  CE   CA  111.50  3.000
 XCP  HE   CE   CA  110.57  3.000
 XCP  HEA  CE   CD  112.70  3.000
 XCP  HE   CE   CD  110.41  3.000
 XCP  CA   CE   CD  104.80  3.000
 XCP  HA   CA   C   110.00  3.000
 XCP  C    CA   CE  112.97  3.000
 XCP  HA   CA   CE  109.02  3.000
 XCP  C    CA   CB  110.50  1.500
 XCP  HA   CA   CB  109.00  3.000
 XCP  CE   CA   CB  104.20  3.000
 XCP  OXT  C    O   122.78  3.000
 XCP  O    C    CA  120.80  1.700
 XCP  OXT  C    CA  120.80  1.700
 XCP  HXT  OXT  C   110.04  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
 XCP  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 XCP  Var_01    CE   CD   CG  CB  -24.68  30.0  1
 XCP  Var_02    CA   CE   CD  CG   -1.63  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
 XCP  plan-1  HXT  0.020

