# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 19:19:21 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-[[6,7-bis(chloranyl)-2-cyclopentyl-2-methyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(Cc2cc(OCC(O)=O)c(Cl)c(Cl)c2C1=O)C3CCCC3
#
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
 O7Z  O7Z  '2-[[6,7-bis(chloranyl)-2-cyclopentyl-2-methyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid'  ligand  40  23  .  2021-08-17  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O7Z
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
 O7Z  C02  C   C      0   0.388  -4.9256  -2.0691  -0.2085
 O7Z  C04  C   CH2    0  -0.344  -3.4519  -1.8571   0.1782
 O7Z  O01  O   O      0  -0.584  -5.5269  -1.1425  -0.7666
 O7Z  O03  O   OC    -1  -0.619  -5.3513  -3.2004   0.0931
 O7Z  O05  O   O2     0  -0.428  -3.0417  -0.5303  -0.1298
 O7Z  H1   H   HCH2   0   0.242  -3.3241  -2.0518   1.2484
 O7Z  H2   H   HCH2   0   0.242  -2.8320  -2.5806  -0.3631
 O7Z  C1   C   C      0   0.487  -1.7860  -0.1772   0.0895
 O7Z  C2   C   C1     0  -0.464  -0.7985  -1.0188   0.5978
 O7Z  C3   C   CR5    0   0.120   0.4825  -0.5247   0.7632
 O7Z  C4   C   CR5    0   0.018   0.8048   0.7858   0.4423
 O7Z  C5   C   C      0  -0.041  -0.1795   1.6412  -0.0528
 O7Z  C6   C   C      0  -0.157  -1.4623   1.1632  -0.2304
 O7Z  C7   C   CR5    0   0.425   2.2308   1.0176   0.6946
 O7Z  C8   C   CR5    0  -0.217   2.8660  -0.3180   1.0936
 O7Z  C9   C   CH2    0  -0.516   1.6690  -1.2626   1.3036
 O7Z  C10  C   CH1    0  -0.207   3.7657  -0.7515  -0.0824
 O7Z  C11  C   CH2    0  -0.446   4.5186  -2.0734   0.1346
 O7Z  C12  C   CH2    0  -0.444   4.8274  -2.6156  -1.2785
 O7Z  C13  C   CH2    0  -0.445   4.1321  -1.6589  -2.2635
 O7Z  C14  C   CH2    0  -0.439   3.0669  -0.9551  -1.4282
 O7Z  C15  C   CH3    0  -0.658   3.6998  -0.1419   2.3606
 O7Z  O1   O   O      0  -0.395   2.8340   2.0611   0.5927
 O7Z  CL2  CL  CL     0  -0.082   0.1940   3.2671  -0.4514
 O7Z  CL1  CL  CL     0  -0.072  -2.7070   2.1733  -0.8476
 O7Z  H4   H   H      0   0.292  -1.0186  -2.0434   0.8627
 O7Z  H5   H   HCH2   0   0.284   1.5147  -1.4726   2.3656
 O7Z  H6   H   HCH2   0   0.270   1.7909  -2.2332   0.8184
 O7Z  H7   H   HCH1   0   0.237   4.5104   0.0431  -0.2153
 O7Z  H8   H   HCH2   0   0.238   5.4211  -1.9320   0.7298
 O7Z  H9   H   HCH2   0   0.229   3.8930  -2.7833   0.6818
 O7Z  H10  H   HCH2   0   0.229   5.9000  -2.6711  -1.4673
 O7Z  H11  H   HCH2   0   0.227   4.4403  -3.6295  -1.3898
 O7Z  H12  H   HCH2   0   0.222   4.8435  -0.9234  -2.6467
 O7Z  H13  H   HCH2   0   0.231   3.7154  -2.1763  -3.1285
 O7Z  H14  H   HCH2   0   0.223   2.1948  -1.6079  -1.3165
 O7Z  H15  H   HCH2   0   0.235   2.7186  -0.0245  -1.8814
 O7Z  H16  H   HCH3   0   0.238   3.0988   0.2571   3.1796
 O7Z  H17  H   HCH3   0   0.243   4.1087  -1.0981   2.6883
 O7Z  H18  H   HCH3   0   0.235   4.5326   0.5408   2.1893

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
 O7Z  C04  O05  single    1.423  0.020  1.423
 O7Z  C04  C02  single    1.538  0.020  1.538
 O7Z  O01  C02  deloc     1.238  0.020  1.238
 O7Z  C02  O03  deloc     1.246  0.020  1.246
 O7Z  C04  H1   single    0.970  0.020  1.090
 O7Z  C04  H2   single    0.970  0.020  1.090
 O7Z  O05  C1   single    1.323  0.020  1.323
 O7Z  C1   C2   aromatic  1.393  0.020  1.393
 O7Z  C2   C3   aromatic  1.383  0.020  1.383
 O7Z  C3   C4   aromatic  1.387  0.020  1.387
 O7Z  C4   C5   aromatic  1.395  0.020  1.395
 O7Z  C5   C6   aromatic  1.380  0.020  1.380
 O7Z  C6   C1   aromatic  1.416  0.020  1.416
 O7Z  C4   C7   single    1.467  0.020  1.467
 O7Z  C7   C8   single    1.532  0.020  1.532
 O7Z  C8   C9   single    1.539  0.020  1.539
 O7Z  C9   C3   single    1.498  0.020  1.498
 O7Z  C8   C10  single    1.543  0.020  1.543
 O7Z  C10  C11  single    1.537  0.020  1.537
 O7Z  C11  C12  single    1.545  0.020  1.545
 O7Z  C12  C13  single    1.539  0.020  1.539
 O7Z  C13  C14  single    1.526  0.020  1.526
 O7Z  C14  C10  single    1.530  0.020  1.530
 O7Z  C8   C15  single    1.527  0.020  1.527
 O7Z  C7   O1   double    1.210  0.020  1.210
 O7Z  C5   CL2  single    1.715  0.020  1.715
 O7Z  C6   CL1  single    1.718  0.020  1.718
 O7Z  C2   H4   single    0.930  0.020  1.080
 O7Z  C9   H5   single    0.970  0.020  1.090
 O7Z  C9   H6   single    0.970  0.020  1.090
 O7Z  C10  H7   single    0.970  0.020  1.090
 O7Z  C11  H8   single    0.970  0.020  1.090
 O7Z  C11  H9   single    0.970  0.020  1.090
 O7Z  C12  H10  single    0.970  0.020  1.090
 O7Z  C12  H11  single    0.970  0.020  1.090
 O7Z  C13  H12  single    0.970  0.020  1.090
 O7Z  C13  H13  single    0.970  0.020  1.090
 O7Z  C14  H14  single    0.970  0.020  1.090
 O7Z  C14  H15  single    0.970  0.020  1.090
 O7Z  C15  H16  single    0.970  0.020  1.090
 O7Z  C15  H17  single    0.970  0.020  1.090
 O7Z  C15  H18  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
 O7Z  O03  C02  O01  128.54  3.000
 O7Z  O03  C02  C04  113.05  3.000
 O7Z  O01  C02  C04  118.41  3.000
 O7Z  H2   C04  H1   107.42  3.000
 O7Z  H2   C04  O05  110.23  3.000
 O7Z  H1   C04  O05  110.10  3.000
 O7Z  H2   C04  C02  109.08  3.000
 O7Z  H1   C04  C02  109.45  3.000
 O7Z  O05  C04  C02  110.51  3.000
 O7Z  C1   O05  C04  119.13  3.000
 O7Z  C6   C1   C2   119.49  3.000
 O7Z  C6   C1   O05  115.62  3.000
 O7Z  C2   C1   O05  124.89  3.000
 O7Z  H4   C2   C3   119.87  3.000
 O7Z  H4   C2   C1   121.17  3.000
 O7Z  C3   C2   C1   118.96  3.000
 O7Z  C9   C3   C4   111.40  3.000
 O7Z  C9   C3   C2   126.92  3.000
 O7Z  C4   C3   C2   121.67  3.000
 O7Z  C7   C4   C5   130.56  3.000
 O7Z  C7   C4   C3   109.60  3.000
 O7Z  C5   C4   C3   119.84  3.000
 O7Z  CL2  C5   C6   120.05  3.000
 O7Z  CL2  C5   C4   120.67  3.000
 O7Z  C6   C5   C4   119.28  3.000
 O7Z  CL1  C6   C5   121.06  3.000
 O7Z  CL1  C6   C1   118.18  3.000
 O7Z  C5   C6   C1   120.75  3.000
 O7Z  O1   C7   C8   124.57  3.000
 O7Z  O1   C7   C4   127.35  3.000
 O7Z  C8   C7   C4   108.07  3.000
 O7Z  C15  C8   C10  110.27  3.000
 O7Z  C15  C8   C9   112.48  3.000
 O7Z  C10  C8   C9   112.65  3.000
 O7Z  C15  C8   C7   110.00  3.000
 O7Z  C10  C8   C7   106.75  3.000
 O7Z  C9   C8   C7   104.37  3.000
 O7Z  H6   C9   H5   106.05  3.000
 O7Z  H6   C9   C8   113.46  3.000
 O7Z  H5   C9   C8   111.10  3.000
 O7Z  H6   C9   C3   111.47  3.000
 O7Z  H5   C9   C3   109.46  3.000
 O7Z  C8   C9   C3   105.33  3.000
 O7Z  H7   C10  C14  107.45  3.000
 O7Z  H7   C10  C11  107.92  3.000
 O7Z  C14  C10  C11  103.50  3.000
 O7Z  H7   C10  C8   106.54  3.000
 O7Z  C14  C10  C8   116.20  3.000
 O7Z  C11  C10  C8   114.82  3.000
 O7Z  H9   C11  H8   106.54  3.000
 O7Z  H9   C11  C12  110.15  3.000
 O7Z  H8   C11  C12  112.30  3.000
 O7Z  H9   C11  C10  110.43  3.000
 O7Z  H8   C11  C10  111.78  3.000
 O7Z  C12  C11  C10  105.70  3.000
 O7Z  H11  C12  H10  106.50  3.000
 O7Z  H11  C12  C13  110.61  3.000
 O7Z  H10  C12  C13  111.42  3.000
 O7Z  H11  C12  C11  110.40  3.000
 O7Z  H10  C12  C11  111.90  3.000
 O7Z  C13  C12  C11  106.08  3.000
 O7Z  H13  C13  H12  106.85  3.000
 O7Z  H13  C13  C14  112.72  3.000
 O7Z  H12  C13  C14  109.64  3.000
 O7Z  H13  C13  C12  112.66  3.000
 O7Z  H12  C13  C12  110.41  3.000
 O7Z  C14  C13  C12  104.58  3.000
 O7Z  H15  C14  H14  107.24  3.000
 O7Z  H15  C14  C13  112.86  3.000
 O7Z  H14  C14  C13  109.68  3.000
 O7Z  H15  C14  C10  113.41  3.000
 O7Z  H14  C14  C10  110.69  3.000
 O7Z  C13  C14  C10  102.95  3.000
 O7Z  H18  C15  H17  108.05  3.000
 O7Z  H18  C15  H16  108.04  3.000
 O7Z  H17  C15  H16  107.55  3.000
 O7Z  H18  C15  C8   111.03  3.000
 O7Z  H17  C15  C8   110.67  3.000
 O7Z  H16  C15  C8   111.35  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
 O7Z  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 O7Z  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 O7Z  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 O7Z  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 O7Z  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 O7Z  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 O7Z  CONST_07  C3   C2   C1   O05  180.00   0.0  0
 O7Z  CONST_08  C5   C6   C1   O05  180.00   0.0  0
 O7Z  CONST_09  CL2  C5   C6   C1   180.00   0.0  0
 O7Z  CONST_10  CL1  C6   C1   C2   180.00   0.0  0
 O7Z  CONST_11  CL2  C5   C4   C3   180.00   0.0  0
 O7Z  CONST_12  CL1  C6   C5   C4   180.00   0.0  0
 O7Z  CONST_13  CL2  C5   C4   C7     0.00   0.0  0
 O7Z  CONST_14  H4   C2   C3   C4   180.00   0.0  0
 O7Z  Var_01    C8   C9   C3   C2   172.55  30.0  1
 O7Z  Var_02    C8   C7   C4   C3     5.37  30.0  1
 O7Z  Var_03    C13  C12  C11  C10   -5.08  30.0  1
 O7Z  Var_04    C12  C13  C14  C10   38.03  30.0  1
 O7Z  Var_05    C14  C13  C12  C11  -20.32  30.0  1
 O7Z  Var_06    C2   C1   O05  C04    0.69  30.0  2
 O7Z  Var_07    O05  C04  C02  O01    3.27  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
 O7Z  chir_01  C8   C9   C10  C7  negativ
 O7Z  chir_02  C10  C14  C11  C8  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
 O7Z  plan-1  C4   0.020
 O7Z  plan-1  C7   0.020
 O7Z  plan-1  C8   0.020
 O7Z  plan-1  O1   0.020
 O7Z  plan-2  O05  0.020
 O7Z  plan-2  C1   0.020
 O7Z  plan-2  C2   0.020
 O7Z  plan-2  C3   0.020
 O7Z  plan-2  C4   0.020
 O7Z  plan-2  C5   0.020
 O7Z  plan-2  C6   0.020
 O7Z  plan-2  C7   0.020
 O7Z  plan-2  C9   0.020
 O7Z  plan-2  CL2  0.020
 O7Z  plan-2  CL1  0.020
 O7Z  plan-2  H4   0.020
 O7Z  plan-3  C02  0.020
 O7Z  plan-3  C04  0.020
 O7Z  plan-3  O01  0.020
 O7Z  plan-3  O03  0.020

