# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 08:27:31 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  15  8  .  2021-08-07  2021-08-07  
;
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   0.352  -1.4542  -0.1085   0.0017
 C54  O    O  O      0  -0.420  -1.8857  -1.2762   0.0569
 C54  CA   C  CH1    0  -0.412  -0.0045   0.0699  -0.4883
 C54  CB   C  CH2    0  -0.448   0.9436  -1.1095  -0.1967
 C54  CG   C  CH2    0  -0.470   2.3273  -0.4812   0.0542
 C54  CD   C  C1     0  -0.280   1.9932   0.9432   0.3993
 C54  CN   C  C1     0  -0.252   0.7329   1.2418   0.0986
 C54  HA   H  HCH1   0   0.248  -0.0801   0.2231  -1.5770
 C54  HB2  H  HCH2   0   0.240   0.6065  -1.6245   0.7040
 C54  HB3  H  HCH2   0   0.225   0.9608  -1.8453  -1.0003
 C54  HG2  H  HCH2   0   0.222   2.8802  -0.9934   0.8458
 C54  HG3  H  HCH2   0   0.261   2.9650  -0.5234  -0.8358
 C54  HD2  H  H      0   0.236   2.7220   1.6343   0.8063
 C54  OXT  O  OC    -1  -0.735  -2.0968   0.9345   0.2418
 C54  HN   H  H      0   0.232   0.2760   2.2152   0.2215

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    deloc   1.246  0.020  1.246
 C54  C   CA   single  1.541  0.020  1.541
 C54  CA  CB   single  1.541  0.020  1.541
 C54  CA  CN   single  1.504  0.020  1.504
 C54  CB  CG   single  1.540  0.020  1.540
 C54  CG  CD   single  1.503  0.020  1.503
 C54  CD  CN   double  1.330  0.020  1.330
 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  deloc   1.248  0.020  1.248
 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   116.67  3.000
 C54  OXT  C   O    126.60  3.000
 C54  CA   C   O    116.64  3.000
 C54  HA   CA  CN   108.11  3.000
 C54  HA   CA  CB   109.61  3.000
 C54  CN   CA  CB   102.76  3.000
 C54  HA   CA  C    105.41  3.000
 C54  CN   CA  C    115.31  3.000
 C54  CB   CA  C    115.48  3.000
 C54  HB3  CB  HB2  107.16  3.000
 C54  HB3  CB  CG   112.42  3.000
 C54  HB2  CB  CG   109.62  3.000
 C54  HB3  CB  CA   112.76  3.000
 C54  HB2  CB  CA   109.11  3.000
 C54  CG   CB  CA   105.75  3.000
 C54  HG3  CG  HG2  106.01  3.000
 C54  HG3  CG  CD   110.63  3.000
 C54  HG2  CG  CD   112.97  3.000
 C54  HG3  CG  CB   112.02  3.000
 C54  HG2  CG  CB   112.41  3.000
 C54  CD   CG  CB   102.96  3.000
 C54  HD2  CD  CN   125.39  3.000
 C54  HD2  CD  CG   122.76  3.000
 C54  CN   CD  CG   111.81  3.000
 C54  HN   CN  CD   125.20  3.000
 C54  HN   CN  CA   122.56  3.000
 C54  CD   CN  CA   112.21  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  Var_01  CD  CG  CB  CA   20.36  30.0  1
 C54  Var_02  CN  CD  CG  CB  -13.42  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

