# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:42:59 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: (1R)-cyclopent-2-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCC=C1
#
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
 C54  C54  '(1R)-cyclopent-2-ene-1-carboxylic acid'  ligand  16  8  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C54
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
 C54  C    C  C     0   0.558  -1.4095  -0.1817   0.0194
 C54  O    O  O     0  -0.438  -1.8223  -1.1987   0.5177
 C54  CA   C  CR15  0  -0.414  -0.0137   0.0361  -0.5106
 C54  CB   C  CH2   0  -0.449   0.9405  -1.1477  -0.2893
 C54  CG   C  CH2   0  -0.474   2.3148  -0.5172  -0.0057
 C54  CD   C  CR15  0  -0.227   1.9695   0.8791   0.4202
 C54  CN   C  CR15  0  -0.215   0.7074   1.1904   0.1494
 C54  HA   H  HCR5  0   0.296  -0.1282   0.2546  -1.5816
 C54  HB2  H  HCH2  0   0.244   0.6171  -1.7204   0.5801
 C54  HB3  H  HCH2  0   0.245   0.9549  -1.8292  -1.1386
 C54  HG2  H  HCH2  0   0.242   2.8748  -1.0674   0.7528
 C54  HG3  H  HCH2  0   0.241   2.9476  -0.4942  -0.8986
 C54  HD2  H  HCR5  0   0.248   2.6906   1.5595   0.8555
 C54  OXT  O  OH1   0  -0.594  -2.1611   0.9028  -0.1391
 C54  HXT  H  HOH1  0   0.480  -3.0525   0.7422   0.2054
 C54  HN   H  HCR5  0   0.256   0.2478   2.1550   0.3202

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
 C54  C    O    double  1.205  0.020  1.205
 C54  C    CA   single  1.509  0.020  1.509
 C54  CA   CB   single  1.537  0.020  1.537
 C54  CA   CN   single  1.513  0.020  1.513
 C54  CB   CG   single  1.538  0.020  1.538
 C54  CG   CD   single  1.500  0.020  1.500
 C54  CD   CN   double  1.328  0.020  1.328
 C54  CA   HA   single  0.970  0.020  1.090
 C54  CB   HB2  single  0.970  0.020  1.090
 C54  CB   HB3  single  0.970  0.020  1.090
 C54  CG   HG2  single  0.970  0.020  1.090
 C54  CG   HG3  single  0.970  0.020  1.090
 C54  CD   HD2  single  0.930  0.020  1.080
 C54  C    OXT  single  1.329  0.020  1.329
 C54  OXT  HXT  single  0.850  0.020  0.980
 C54  CN   HN   single  0.930  0.020  1.080

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
 C54  OXT  C    CA   111.32  3.000
 C54  OXT  C    O    122.97  3.000
 C54  CA   C    O    125.72  3.000
 C54  HA   CA   CN   108.86  3.000
 C54  HA   CA   CB   110.99  3.000
 C54  CN   CA   CB   103.25  3.000
 C54  HA   CA   C    105.94  3.000
 C54  CN   CA   C    113.45  3.000
 C54  CB   CA   C    114.37  3.000
 C54  HB3  CB   HB2  107.29  3.000
 C54  HB3  CB   CG   112.86  3.000
 C54  HB2  CB   CG   109.47  3.000
 C54  HB3  CB   CA   112.21  3.000
 C54  HB2  CB   CA   109.59  3.000
 C54  CG   CB   CA   105.40  3.000
 C54  HG3  CG   HG2  106.31  3.000
 C54  HG3  CG   CD   110.19  3.000
 C54  HG2  CG   CD   112.96  3.000
 C54  HG3  CG   CB   112.00  3.000
 C54  HG2  CG   CB   112.32  3.000
 C54  CD   CG   CB   103.19  3.000
 C54  HD2  CD   CN   124.59  3.000
 C54  HD2  CD   CG   123.07  3.000
 C54  CN   CD   CG   112.28  3.000
 C54  HN   CN   CD   125.49  3.000
 C54  HN   CN   CA   123.14  3.000
 C54  CD   CN   CA   111.30  3.000
 C54  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
 C54  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 C54  Var_01    CD   CG   CB  CA   20.40  30.0  1
 C54  Var_02    CN   CD   CG  CB  -13.20  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
 C54  chir_01  CA  C  CB  CN  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
 C54  plan-1  C    0.020
 C54  plan-1  O    0.020
 C54  plan-1  CA   0.020
 C54  plan-1  OXT  0.020
 C54  plan-1  HXT  0.020

