# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:48:24 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: cis-1-(2-carboxy-2-oxoethyl)-4-hydroxycyclohexa-2,5-diene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C=C[C@](CC(=O)C(O)=O)(C=C1)C(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
 PRE  PRE  'cis-1-(2-carboxy-2-oxoethyl)-4-hydroxycyclohexa-2,5-diene-1-carboxylic acid'  ligand  24  16  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PRE
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
 PRE  C1   C  CR6    0  -0.335  -0.3494   0.1431   0.5750
 PRE  C2   C  CR16   0  -0.158  -0.0880   1.1990   1.6093
 PRE  C3   C  CR16   0  -0.276   0.5442   0.9991   2.7601
 PRE  C4   C  CR16   0  -0.025   1.0872  -0.3256   3.1877
 PRE  O4   O  OH1    0  -0.676   2.4682  -0.1454   3.4896
 PRE  C5   C  CR16   0  -0.300   0.8824  -1.3732   2.1368
 PRE  C6   C  CR16   0  -0.128   0.2355  -1.1688   0.9949
 PRE  C7   C  C      0   0.452  -1.9059   0.0559   0.4362
 PRE  O71  O  O      0  -0.609  -2.4455   0.9770  -0.2040
 PRE  O72  O  OC    -1  -0.588  -2.4695  -0.8834   1.0221
 PRE  C8   C  CH2    0  -0.519   0.2824   0.6294  -0.7373
 PRE  C1'  C  C      0   0.232  -0.0737  -0.1571  -1.9682
 PRE  O1'  O  O      0  -0.395  -0.7786  -1.1387  -1.9417
 PRE  C2'  C  C      0   0.347   0.5194   0.3436  -3.3202
 PRE  O'L  O  O      0  -0.579   1.3720   1.2442  -3.2348
 PRE  O'M  O  OC    -1  -0.584   0.0800  -0.2123  -4.3361
 PRE  H2   H  HCR6   0   0.242  -0.4564   2.1926   1.3727
 PRE  H3   H  HCR6   0   0.238   0.6786   1.8248   3.4516
 PRE  H4   H  HCR6   0   0.210   0.5619  -0.6384   4.1034
 PRE  HO4  H  HOH1   0   0.448   2.7787  -0.9370   3.9403
 PRE  H5   H  HCR6   0   0.235   1.2776  -2.3605   2.3598
 PRE  H6   H  HCR6   0   0.241   0.1283  -1.9932   0.3003
 PRE  H81  H  HCH2   0   0.264   0.0031   1.6703  -0.9231
 PRE  H82  H  HCH2   0   0.262   1.3731   0.6468  -0.6469

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
 PRE  C1   C2   single  1.501  0.020  1.501
 PRE  C1   C6   single  1.497  0.020  1.497
 PRE  C1   C7   single  1.565  0.020  1.565
 PRE  C1   C8   single  1.535  0.020  1.535
 PRE  C2   C3   double  1.328  0.020  1.328
 PRE  C2   H2   single  0.930  0.020  1.080
 PRE  C3   C4   single  1.494  0.020  1.494
 PRE  C3   H3   single  0.930  0.020  1.080
 PRE  C4   O4   single  1.425  0.020  1.425
 PRE  C4   C5   single  1.498  0.020  1.498
 PRE  C4   H4   single  0.970  0.020  1.090
 PRE  O4   HO4  single  0.850  0.020  0.980
 PRE  C5   C6   double  1.328  0.020  1.328
 PRE  C5   H5   single  0.930  0.020  1.080
 PRE  C6   H6   single  0.930  0.020  1.080
 PRE  C7   O71  deloc   1.245  0.020  1.245
 PRE  C7   O72  deloc   1.242  0.020  1.242
 PRE  C8   C1'  single  1.503  0.020  1.503
 PRE  C8   H81  single  0.970  0.020  1.090
 PRE  C8   H82  single  0.970  0.020  1.090
 PRE  C1'  O1'  double  1.209  0.020  1.209
 PRE  C1'  C2'  single  1.559  0.020  1.559
 PRE  C2'  O'L  deloc   1.243  0.020  1.243
 PRE  C2'  O'M  deloc   1.239  0.020  1.239

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
 PRE  C8   C1   C7   110.55  3.000
 PRE  C8   C1   C6   110.89  3.000
 PRE  C7   C1   C6   111.39  3.000
 PRE  C8   C1   C2   107.13  3.000
 PRE  C7   C1   C2   105.88  3.000
 PRE  C6   C1   C2   110.81  3.000
 PRE  H2   C2   C3   119.21  3.000
 PRE  H2   C2   C1   115.75  3.000
 PRE  C3   C2   C1   125.04  3.000
 PRE  H3   C3   C4   116.56  3.000
 PRE  H3   C3   C2   119.77  3.000
 PRE  C4   C3   C2   123.67  3.000
 PRE  H4   C4   C5   108.64  3.000
 PRE  H4   C4   O4   108.78  3.000
 PRE  C5   C4   O4   111.69  3.000
 PRE  H4   C4   C3   108.45  3.000
 PRE  C5   C4   C3   111.69  3.000
 PRE  O4   C4   C3   107.50  3.000
 PRE  HO4  O4   C4   107.93  3.000
 PRE  H5   C5   C6   119.57  3.000
 PRE  H5   C5   C4   116.21  3.000
 PRE  C6   C5   C4   124.20  3.000
 PRE  H6   C6   C5   118.83  3.000
 PRE  H6   C6   C1   116.65  3.000
 PRE  C5   C6   C1   124.51  3.000
 PRE  O72  C7   O71  127.26  3.000
 PRE  O72  C7   C1   116.84  3.000
 PRE  O71  C7   C1   115.81  3.000
 PRE  H82  C8   H81  104.68  3.000
 PRE  H82  C8   C1'  108.18  3.000
 PRE  H81  C8   C1'  107.36  3.000
 PRE  H82  C8   C1   110.15  3.000
 PRE  H81  C8   C1   109.97  3.000
 PRE  C1'  C8   C1   115.89  3.000
 PRE  C2'  C1'  O1'  120.11  3.000
 PRE  C2'  C1'  C8   116.87  3.000
 PRE  O1'  C1'  C8   123.02  3.000
 PRE  O'M  C2'  O'L  128.67  3.000
 PRE  O'M  C2'  C1'  115.61  3.000
 PRE  O'L  C2'  C1'  115.73  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
 PRE  Var_01  C4   C3   C2   C1  -0.09  30.0  1
 PRE  Var_02  C4   C5   C6   C1   1.75  30.0  1
 PRE  Var_03  O1'  C1'  C8   C1  -2.21  30.0  3
 PRE  Var_04  O'L  C2'  C1'  C8   8.98  30.0  2

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
 PRE  chir_01  C1  C6  C2  C8  negativ
 PRE  chir_02  C4  O4  C3  C5  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
 PRE  plan-1  C8   0.020
 PRE  plan-1  C1'  0.020
 PRE  plan-1  O1'  0.020
 PRE  plan-1  C2'  0.020
 PRE  plan-2  C1   0.020
 PRE  plan-2  C7   0.020
 PRE  plan-2  O71  0.020
 PRE  plan-2  O72  0.020
 PRE  plan-3  C1'  0.020
 PRE  plan-3  C2'  0.020
 PRE  plan-3  O'L  0.020
 PRE  plan-3  O'M  0.020

