# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:18:49 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/C[C@@H]1[C@H](CCC1=O)CC(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
 JAA  JAA  '{(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid'  ligand  32  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JAA
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
 JAA  O01  O  O      0  -0.412   1.0075   3.2165  -0.1365
 JAA  O02  O  O      0  -0.441  -3.2282  -1.2639  -1.3072
 JAA  O03  O  OC    -1  -0.756  -3.0901  -2.5926   0.4746
 JAA  C04  C  CH1    0  -0.230  -1.0807   0.3436  -0.3745
 JAA  C05  C  CH1    0  -0.334   0.3124   0.8921  -0.0402
 JAA  C06  C  CH2    0  -0.445  -2.0186   1.3569   0.2914
 JAA  C07  C  CH2    0  -0.558  -1.3540   2.7060   0.0416
 JAA  C08  C  C      0   0.420   0.1256   2.3950  -0.0470
 JAA  C09  C  CH2    0  -0.514   1.4563   0.3927  -0.9264
 JAA  C10  C  CH2    0  -0.611  -1.2976  -1.0869   0.0810
 JAA  C11  C  C1     0  -0.211   2.8183   0.6198  -0.3401
 JAA  C12  C  C      0   0.382  -2.6668  -1.6917  -0.2792
 JAA  C13  C  C1     0  -0.213   3.5354  -0.2766   0.3359
 JAA  C14  C  CH2    0  -0.503   3.1522  -1.6918   0.6440
 JAA  C15  C  CH3    0  -0.674   4.0020  -2.6979  -0.1297
 JAA  H2   H  HCH1   0   0.218  -1.2256   0.3988  -1.4596
 JAA  H3   H  HCH1   0   0.294   0.5300   0.6256   1.0062
 JAA  H6   H  HCH2   0   0.257  -1.6574   3.1169  -0.9277
 JAA  H7   H  HCH2   0   0.252  -1.5611   3.4737   0.7889
 JAA  H8   H  HCH2   0   0.231   1.2998  -0.6715  -1.1163
 JAA  H9   H  HCH2   0   0.265   1.3902   0.8825  -1.9017
 JAA  H10  H  HCH2   0   0.228  -0.5340  -1.7354  -0.3670
 JAA  H11  H  HCH2   0   0.220  -1.1380  -1.1540   1.1627
 JAA  H12  H  H      0   0.253   3.2333   1.6131  -0.4698
 JAA  H14  H  H      0   0.248   4.5127   0.0277   0.7016
 JAA  H16  H  HCH2   0   0.238   3.2810  -1.8664   1.7163
 JAA  H17  H  HCH2   0   0.260   2.0951  -1.8656   0.4354
 JAA  H18  H  HCH3   0   0.258   3.8577  -2.5850  -1.2047
 JAA  H19  H  HCH3   0   0.183   5.0646  -2.5620   0.0772
 JAA  H20  H  HCH3   0   0.209   3.7422  -3.7226   0.1371
 JAA  H4   H  HCH2   0   0.263  -3.0328   1.2976  -0.1001
 JAA  H5   H  HCH2   0   0.224  -2.0691   1.1546   1.3661

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
 JAA  C06  C07  single  1.525  0.020  1.525
 JAA  C06  C04  single  1.533  0.020  1.533
 JAA  C07  C08  single  1.514  0.020  1.514
 JAA  O01  C08  double  1.209  0.020  1.209
 JAA  C08  C05  single  1.515  0.020  1.515
 JAA  C04  C05  single  1.534  0.020  1.534
 JAA  C04  C10  single  1.517  0.020  1.517
 JAA  C05  C09  single  1.531  0.020  1.531
 JAA  C10  C12  single  1.540  0.020  1.540
 JAA  O02  C12  deloc   1.247  0.020  1.247
 JAA  C12  O03  deloc   1.249  0.020  1.249
 JAA  C09  C11  single  1.500  0.020  1.500
 JAA  C11  C13  double  1.332  0.020  1.332
 JAA  C13  C14  single  1.498  0.020  1.498
 JAA  C14  C15  single  1.527  0.020  1.527
 JAA  C04  H2   single  0.970  0.020  1.090
 JAA  C05  H3   single  0.970  0.020  1.090
 JAA  C06  H4   single  0.970  0.020  1.090
 JAA  C06  H5   single  0.970  0.020  1.090
 JAA  C07  H6   single  0.970  0.020  1.090
 JAA  C07  H7   single  0.970  0.020  1.090
 JAA  C09  H8   single  0.970  0.020  1.090
 JAA  C09  H9   single  0.970  0.020  1.090
 JAA  C10  H10  single  0.970  0.020  1.090
 JAA  C10  H11  single  0.970  0.020  1.090
 JAA  C11  H12  single  0.930  0.020  1.080
 JAA  C13  H14  single  0.930  0.020  1.080
 JAA  C14  H16  single  0.970  0.020  1.090
 JAA  C14  H17  single  0.970  0.020  1.090
 JAA  C15  H18  single  0.970  0.020  1.090
 JAA  C15  H19  single  0.970  0.020  1.090
 JAA  C15  H20  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
 JAA  H2   C04  C10  109.02  3.000
 JAA  H2   C04  C06  108.41  3.000
 JAA  C10  C04  C06  113.92  3.000
 JAA  H2   C04  C05  108.53  3.000
 JAA  C10  C04  C05  113.68  3.000
 JAA  C06  C04  C05  102.98  3.000
 JAA  H3   C05  C09  108.87  3.000
 JAA  H3   C05  C08  105.59  3.000
 JAA  C09  C05  C08  114.41  3.000
 JAA  H3   C05  C04  107.45  3.000
 JAA  C09  C05  C04  115.84  3.000
 JAA  C08  C05  C04  103.99  3.000
 JAA  H5   C06  H4   107.45  3.000
 JAA  H5   C06  C07  110.15  3.000
 JAA  H4   C06  C07  113.29  3.000
 JAA  H5   C06  C04  109.42  3.000
 JAA  H4   C06  C04  112.20  3.000
 JAA  C07  C06  C04  104.30  3.000
 JAA  H7   C07  H6   106.83  3.000
 JAA  H7   C07  C08  111.72  3.000
 JAA  H6   C07  C08  107.21  3.000
 JAA  H7   C07  C06  115.32  3.000
 JAA  H6   C07  C06  110.86  3.000
 JAA  C08  C07  C06  104.70  3.000
 JAA  C07  C08  C05  108.90  3.000
 JAA  C05  C08  O01  125.79  3.000
 JAA  C07  C08  O01  125.29  3.000
 JAA  H9   C09  H8   105.83  3.000
 JAA  H9   C09  C11  109.61  3.000
 JAA  H8   C09  C11  110.22  3.000
 JAA  H9   C09  C05  108.97  3.000
 JAA  H8   C09  C05  108.14  3.000
 JAA  C11  C09  C05  113.75  3.000
 JAA  H11  C10  H10  105.40  3.000
 JAA  H11  C10  C12  109.66  3.000
 JAA  H10  C10  C12  106.93  3.000
 JAA  H11  C10  C04  109.47  3.000
 JAA  H10  C10  C04  109.59  3.000
 JAA  C12  C10  C04  115.30  3.000
 JAA  H12  C11  C13  118.10  3.000
 JAA  H12  C11  C09  116.07  3.000
 JAA  C13  C11  C09  125.82  3.000
 JAA  C10  C12  O03  116.34  3.000
 JAA  O03  C12  O02  126.34  3.000
 JAA  C10  C12  O02  117.29  3.000
 JAA  H14  C13  C14  115.17  3.000
 JAA  H14  C13  C11  117.80  3.000
 JAA  C14  C13  C11  127.03  3.000
 JAA  H17  C14  H16  106.02  3.000
 JAA  H17  C14  C15  109.70  3.000
 JAA  H16  C14  C15  109.02  3.000
 JAA  H17  C14  C13  111.03  3.000
 JAA  H16  C14  C13  108.80  3.000
 JAA  C15  C14  C13  112.07  3.000
 JAA  H20  C15  H19  107.63  3.000
 JAA  H20  C15  H18  107.88  3.000
 JAA  H19  C15  H18  107.63  3.000
 JAA  H20  C15  C14  111.26  3.000
 JAA  H19  C15  C14  111.33  3.000
 JAA  H18  C15  C14  110.94  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
 JAA  Var_01  C08  C07  C06  C04  -28.77  30.0  1
 JAA  Var_02  C06  C07  C08  C05    7.45  30.0  1
 JAA  Var_03  C04  C10  C12  O02   29.01  30.0  2
 JAA  Var_04  C13  C11  C09  C05   97.14  30.0  3
 JAA  Var_05  C14  C13  C11  C09    0.63   0.0  2
 JAA  Var_06  C15  C14  C13  C11  110.53  30.0  3
 JAA  Var_07  H18  C15  C14  C13  -62.40  30.0  3

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
 JAA  chir_01  C04  C06  C05  C10  negativ
 JAA  chir_02  C05  C09  C04  C08  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
 JAA  plan-1  O01  0.020
 JAA  plan-1  C05  0.020
 JAA  plan-1  C07  0.020
 JAA  plan-1  C08  0.020
 JAA  plan-2  O02  0.020
 JAA  plan-2  O03  0.020
 JAA  plan-2  C10  0.020
 JAA  plan-2  C12  0.020
 JAA  plan-3  C09  0.020
 JAA  plan-3  C11  0.020
 JAA  plan-3  C13  0.020
 JAA  plan-3  C14  0.020
 JAA  plan-3  H12  0.020
 JAA  plan-3  H14  0.020

