# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:37:56 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: 4-{[(2S)-2-butyl-6,7-dichloro-2-cyclopentyl-1-oxo-2,3-dihydro-1H-inden-5-yl]oxy}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@]1(Cc2cc(OCCCC(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
 L9Y  L9Y  '4-{[(2S)-2-butyl-6,7-dichloro-2-cyclopentyl-1-oxo-2,3-dihydro-1H-inden-5-yl]oxy}butanoic acid'  ligand  55  28  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L9Y
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
 L9Y  C01   C   CH3    0  -0.662   3.2874   2.7016  -4.7107
 L9Y  C02   C   CH2    0  -0.416   3.9123   2.6213  -3.3252
 L9Y  C03   C   CH2    0  -0.425   3.0536   1.8398  -2.3373
 L9Y  C04   C   CH2    0  -0.411   3.6698   1.8018  -0.9423
 L9Y  C05   C   CT     0  -0.202   2.8335   1.0959   0.1349
 L9Y  C06   C   CH2    0  -0.513   1.4273   1.7144   0.2936
 L9Y  C07   C   CR6    0   0.117   0.4655   0.5831   0.1094
 L9Y  C08   C   CR6    0   0.036   1.1220  -0.5948  -0.2140
 L9Y  C09   C   C      0   0.395   2.5692  -0.3545  -0.2786
 L9Y  C11   C   CR6    0  -0.045   0.3893  -1.7631  -0.4255
 L9Y  C13   C   CR6    0  -0.151  -0.9859  -1.7284  -0.3061
 L9Y  C15   C   CR6    0   0.488  -1.6503  -0.5242   0.0218
 L9Y  C17   C   CH2    0  -0.178  -3.7247   0.5758   0.4061
 L9Y  C18   C   CH2    0  -0.452  -5.1914   0.2089   0.4365
 L9Y  C19   C   CH2    0  -0.593  -6.0419   1.4340   0.7331
 L9Y  C20   C   C      0   0.418  -7.5613   1.1853   0.7842
 L9Y  C23   C   CR16   0  -0.463  -0.9120   0.6370   0.2294
 L9Y  C24   C   CR15   0  -0.217   3.5578   1.1460   1.4991
 L9Y  C25   C   CH2    0  -0.439   5.0104   0.6759   1.5688
 L9Y  C26   C   CH2    0  -0.449   5.3001   0.6432   3.0750
 L9Y  C27   C   CH2    0  -0.441   3.9401   0.3691   3.7600
 L9Y  C28   C   CH2    0  -0.443   2.9036   0.3405   2.6277
 L9Y  O10   O   O      0  -0.391   3.4197  -1.1487  -0.6118
 L9Y  O16   O   O2     0  -0.450  -2.9707  -0.6026   0.1088
 L9Y  O21   O   O      0  -0.605  -7.9663   0.0219   0.5986
 L9Y  O22   O   OC    -1  -0.630  -8.2658   2.1906   1.0122
 L9Y  CL12  CL  CL     0  -0.080   1.1769  -3.2344  -0.8200
 L9Y  CL14  CL  CL     0  -0.072  -1.9342  -3.1403  -0.5503
 L9Y  H012  H   HCH3   0   0.227   3.9147   3.2665  -5.4012
 L9Y  H011  H   HCH3   0   0.217   3.1391   1.7072  -5.1363
 L9Y  H013  H   HCH3   0   0.216   2.3120   3.1909  -4.6739
 L9Y  H022  H   HCH2   0   0.213   4.9008   2.1574  -3.3945
 L9Y  H021  H   HCH2   0   0.213   4.0783   3.6314  -2.9380
 L9Y  H032  H   HCH2   0   0.217   2.0572   2.2911  -2.3081
 L9Y  H031  H   HCH2   0   0.218   2.9133   0.8220  -2.7164
 L9Y  H042  H   HCH2   0   0.237   4.6456   1.3145  -1.0084
 L9Y  H041  H   HCH2   0   0.229   3.8621   2.8250  -0.6004
 L9Y  H062  H   HCH2   0   0.278   1.2904   2.1820   1.2711
 L9Y  H061  H   HCH2   0   0.281   1.2342   2.4979  -0.4424
 L9Y  H171  H   HCH2   0   0.232  -3.5310   1.3371  -0.3572
 L9Y  H172  H   HCH2   0   0.232  -3.4082   0.9818   1.3726
 L9Y  H181  H   HCH2   0   0.227  -5.4789  -0.2223  -0.5251
 L9Y  H182  H   HCH2   0   0.227  -5.3595  -0.5582   1.1955
 L9Y  H191  H   HCH2   0   0.227  -5.7387   1.8756   1.6892
 L9Y  H192  H   HCH2   0   0.226  -5.8488   2.2113  -0.0148
 L9Y  H231  H   HCR6   0   0.295  -1.3961   1.5701   0.4828
 L9Y  H241  H   HCR5   0   0.235   3.5456   2.2048   1.7936
 L9Y  H252  H   HCH2   0   0.226   5.1092  -0.3243   1.1424
 L9Y  H251  H   HCH2   0   0.232   5.6995   1.3281   1.0312
 L9Y  H261  H   HCH2   0   0.229   6.0520  -0.1055   3.3271
 L9Y  H262  H   HCH2   0   0.225   5.6985   1.6067   3.3985
 L9Y  H272  H   HCH2   0   0.229   3.9435  -0.5665   4.3200
 L9Y  H271  H   HCH2   0   0.228   3.7063   1.1579   4.4767
 L9Y  H282  H   HCH2   0   0.237   1.9338   0.7363   2.9332
 L9Y  H281  H   HCH2   0   0.221   2.7382  -0.6917   2.3039

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
 L9Y  C01   C02   single    1.522  0.020  1.522
 L9Y  C02   C03   single    1.524  0.020  1.524
 L9Y  C03   C04   single    1.526  0.020  1.526
 L9Y  C04   C05   single    1.536  0.020  1.536
 L9Y  O10   C09   double    1.210  0.020  1.210
 L9Y  C05   C09   single    1.531  0.020  1.531
 L9Y  C05   C24   single    1.545  0.020  1.545
 L9Y  C05   C06   single    1.544  0.020  1.544
 L9Y  C09   C08   single    1.468  0.020  1.468
 L9Y  C25   C24   single    1.528  0.020  1.528
 L9Y  C25   C26   single    1.534  0.020  1.534
 L9Y  C24   C28   single    1.533  0.020  1.533
 L9Y  CL12  C11   single    1.715  0.020  1.715
 L9Y  C06   C07   single    1.496  0.020  1.496
 L9Y  C08   C11   aromatic  1.395  0.020  1.395
 L9Y  C08   C07   aromatic  1.387  0.020  1.387
 L9Y  C26   C27   single    1.547  0.020  1.547
 L9Y  C28   C27   single    1.535  0.020  1.535
 L9Y  C11   C13   aromatic  1.381  0.020  1.381
 L9Y  C07   C23   aromatic  1.384  0.020  1.384
 L9Y  C13   CL14  single    1.718  0.020  1.718
 L9Y  C13   C15   aromatic  1.414  0.020  1.414
 L9Y  C23   C15   aromatic  1.392  0.020  1.392
 L9Y  C15   O16   single    1.326  0.020  1.326
 L9Y  O16   C17   single    1.430  0.020  1.430
 L9Y  C17   C18   single    1.512  0.020  1.512
 L9Y  C18   C19   single    1.521  0.020  1.521
 L9Y  C19   C20   single    1.540  0.020  1.540
 L9Y  C20   O21   deloc     1.246  0.020  1.246
 L9Y  C20   O22   deloc     1.249  0.020  1.249
 L9Y  C01   H012  single    0.970  0.020  1.090
 L9Y  C01   H011  single    0.970  0.020  1.090
 L9Y  C01   H013  single    0.970  0.020  1.090
 L9Y  C02   H022  single    0.970  0.020  1.090
 L9Y  C02   H021  single    0.970  0.020  1.090
 L9Y  C03   H032  single    0.970  0.020  1.090
 L9Y  C03   H031  single    0.970  0.020  1.090
 L9Y  C04   H042  single    0.970  0.020  1.090
 L9Y  C04   H041  single    0.970  0.020  1.090
 L9Y  C06   H062  single    0.970  0.020  1.090
 L9Y  C06   H061  single    0.970  0.020  1.090
 L9Y  C17   H171  single    0.970  0.020  1.090
 L9Y  C17   H172  single    0.970  0.020  1.090
 L9Y  C18   H181  single    0.970  0.020  1.090
 L9Y  C18   H182  single    0.970  0.020  1.090
 L9Y  C19   H191  single    0.970  0.020  1.090
 L9Y  C19   H192  single    0.970  0.020  1.090
 L9Y  C23   H231  single    0.930  0.020  1.080
 L9Y  C24   H241  single    0.970  0.020  1.090
 L9Y  C25   H252  single    0.970  0.020  1.090
 L9Y  C25   H251  single    0.970  0.020  1.090
 L9Y  C26   H261  single    0.970  0.020  1.090
 L9Y  C26   H262  single    0.970  0.020  1.090
 L9Y  C27   H272  single    0.970  0.020  1.090
 L9Y  C27   H271  single    0.970  0.020  1.090
 L9Y  C28   H282  single    0.970  0.020  1.090
 L9Y  C28   H281  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
 L9Y  H013  C01  H011  107.46  3.000
 L9Y  H013  C01  H012  107.64  3.000
 L9Y  H011  C01  H012  107.64  3.000
 L9Y  H013  C01  C02   111.08  3.000
 L9Y  H011  C01  C02   111.26  3.000
 L9Y  H012  C01  C02   111.56  3.000
 L9Y  H021  C02  H022  106.06  3.000
 L9Y  H021  C02  C03   109.23  3.000
 L9Y  H022  C02  C03   109.43  3.000
 L9Y  H021  C02  C01   109.61  3.000
 L9Y  H022  C02  C01   109.61  3.000
 L9Y  C03   C02  C01   112.69  3.000
 L9Y  H031  C03  H032  106.02  3.000
 L9Y  H031  C03  C04   110.19  3.000
 L9Y  H032  C03  C04   110.71  3.000
 L9Y  H031  C03  C02   108.92  3.000
 L9Y  H032  C03  C02   108.59  3.000
 L9Y  C04   C03  C02   112.20  3.000
 L9Y  H041  C04  H042  106.18  3.000
 L9Y  H041  C04  C05   107.81  3.000
 L9Y  H042  C04  C05   108.89  3.000
 L9Y  H041  C04  C03   109.45  3.000
 L9Y  H042  C04  C03   108.45  3.000
 L9Y  C05   C04  C03   115.65  3.000
 L9Y  C24   C05  C09   110.49  3.000
 L9Y  C24   C05  C06   108.84  3.000
 L9Y  C09   C05  C06   104.47  3.000
 L9Y  C06   C05  C04   112.57  3.000
 L9Y  C24   C05  C04   110.43  3.000
 L9Y  C09   C05  C04   109.88  3.000
 L9Y  H061  C06  H062  105.89  3.000
 L9Y  H061  C06  C07   110.23  3.000
 L9Y  H062  C06  C07   110.69  3.000
 L9Y  H061  C06  C05   112.27  3.000
 L9Y  H062  C06  C05   112.18  3.000
 L9Y  C07   C06  C05   105.65  3.000
 L9Y  C23   C07  C08   121.64  3.000
 L9Y  C23   C07  C06   126.85  3.000
 L9Y  C08   C07  C06   111.51  3.000
 L9Y  C11   C08  C09   130.39  3.000
 L9Y  C11   C08  C07   119.87  3.000
 L9Y  C09   C08  C07   109.74  3.000
 L9Y  O10   C09  C08   126.67  3.000
 L9Y  C08   C09  C05   108.26  3.000
 L9Y  O10   C09  C05   125.07  3.000
 L9Y  CL12  C11  C13   119.92  3.000
 L9Y  C13   C11  C08   119.27  3.000
 L9Y  CL12  C11  C08   120.80  3.000
 L9Y  CL14  C13  C15   118.26  3.000
 L9Y  C15   C13  C11   120.62  3.000
 L9Y  CL14  C13  C11   121.11  3.000
 L9Y  O16   C15  C23   124.61  3.000
 L9Y  O16   C15  C13   115.65  3.000
 L9Y  C23   C15  C13   119.74  3.000
 L9Y  H172  C17  H171  107.84  3.000
 L9Y  H172  C17  O16   109.67  3.000
 L9Y  H171  C17  O16   109.54  3.000
 L9Y  H172  C17  C18   110.65  3.000
 L9Y  H171  C17  C18   110.74  3.000
 L9Y  O16   C17  C18   108.40  3.000
 L9Y  H182  C18  H181  107.10  3.000
 L9Y  H182  C18  C19   110.13  3.000
 L9Y  H181  C18  C19   110.03  3.000
 L9Y  H182  C18  C17   109.49  3.000
 L9Y  H181  C18  C17   109.47  3.000
 L9Y  C19   C18  C17   110.54  3.000
 L9Y  H192  C19  H191  105.12  3.000
 L9Y  H192  C19  C20   108.12  3.000
 L9Y  H191  C19  C20   108.00  3.000
 L9Y  H192  C19  C18   109.86  3.000
 L9Y  H191  C19  C18   109.88  3.000
 L9Y  C20   C19  C18   115.34  3.000
 L9Y  O22   C20  O21   126.56  3.000
 L9Y  O22   C20  C19   115.63  3.000
 L9Y  O21   C20  C19   117.81  3.000
 L9Y  H231  C23  C15   121.16  3.000
 L9Y  H231  C23  C07   119.98  3.000
 L9Y  C15   C23  C07   118.86  3.000
 L9Y  H241  C24  C28   107.71  3.000
 L9Y  H241  C24  C25   107.14  3.000
 L9Y  C28   C24  C25   102.14  3.000
 L9Y  H241  C24  C05   105.22  3.000
 L9Y  C28   C24  C05   115.65  3.000
 L9Y  C25   C24  C05   118.40  3.000
 L9Y  H251  C25  H252  107.35  3.000
 L9Y  H251  C25  C26   112.17  3.000
 L9Y  H252  C25  C26   110.30  3.000
 L9Y  H251  C25  C24   113.21  3.000
 L9Y  H252  C25  C24   110.49  3.000
 L9Y  C26   C25  C24   103.34  3.000
 L9Y  H262  C26  H261  106.61  3.000
 L9Y  H262  C26  C27   110.24  3.000
 L9Y  H261  C26  C27   112.46  3.000
 L9Y  H262  C26  C25   109.94  3.000
 L9Y  H261  C26  C25   111.82  3.000
 L9Y  C27   C26  C25   105.81  3.000
 L9Y  H271  C27  H272  106.47  3.000
 L9Y  H271  C27  C28   110.69  3.000
 L9Y  H272  C27  C28   111.40  3.000
 L9Y  H271  C27  C26   110.56  3.000
 L9Y  H272  C27  C26   112.12  3.000
 L9Y  C28   C27  C26   105.68  3.000
 L9Y  H281  C28  H282  106.90  3.000
 L9Y  H281  C28  C27   109.75  3.000
 L9Y  H282  C28  C27   112.75  3.000
 L9Y  H281  C28  C24   110.02  3.000
 L9Y  H282  C28  C24   113.25  3.000
 L9Y  C27   C28  C24   104.18  3.000
 L9Y  C17   O16  C15   119.35  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
 L9Y  CONST_01  C13   C11  C08  C07     0.00   0.0  0
 L9Y  CONST_02  C13   C15  C23  C07     0.00   0.0  0
 L9Y  CONST_03  C15   C13  C11  C08     0.00   0.0  0
 L9Y  CONST_04  C15   C23  C07  C08     0.00   0.0  0
 L9Y  CONST_05  C23   C07  C08  C11     0.00   0.0  0
 L9Y  CONST_06  C23   C15  C13  C11     0.00   0.0  0
 L9Y  CONST_07  CL12  C11  C08  C07   180.00   0.0  0
 L9Y  CONST_08  O16   C15  C23  C07   180.00   0.0  0
 L9Y  CONST_09  CL14  C13  C11  C08   180.00   0.0  0
 L9Y  CONST_10  CL12  C11  C08  C09     0.00   0.0  0
 L9Y  CONST_11  O16   C15  C13  C11   180.00   0.0  0
 L9Y  CONST_12  CL12  C11  C13  C15   180.00   0.0  0
 L9Y  CONST_13  CL14  C13  C15  C23   180.00   0.0  0
 L9Y  CONST_14  H231  C23  C07  C06     0.00   0.0  0
 L9Y  Var_01    C11   C08  C09  C05  -176.28  30.0  1
 L9Y  Var_02    C08   C07  C06  C05    -3.57  30.0  1
 L9Y  Var_03    C27   C26  C25  C24    28.39  30.0  1
 L9Y  Var_04    C26   C27  C28  C24   -22.85  30.0  1
 L9Y  Var_05    C28   C27  C26  C25    -3.40  30.0  1
 L9Y  Var_06    C23   C15  O16  C17     1.46  30.0  1
 L9Y  Var_07    C05   C04  C03  C02   176.94  30.0  3
 L9Y  Var_08    C18   C17  O16  C15   179.63  30.0  3
 L9Y  Var_09    C04   C03  C02  C01  -178.29  30.0  3
 L9Y  Var_10    C20   C19  C18  C17   179.76  30.0  3
 L9Y  Var_11    O21   C20  C19  C18     0.83  30.0  3
 L9Y  Var_12    O16   C17  C18  C19  -179.32  30.0  1
 L9Y  Var_13    H012  C01  C02  C03   179.83  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
 L9Y  chir_01  C05  C09  C24  C06  positiv
 L9Y  chir_02  C24  C28  C25  C05  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
 L9Y  plan-1  C05   0.020
 L9Y  plan-1  C08   0.020
 L9Y  plan-1  C09   0.020
 L9Y  plan-1  O10   0.020
 L9Y  plan-2  C06   0.020
 L9Y  plan-2  C07   0.020
 L9Y  plan-2  C08   0.020
 L9Y  plan-2  C09   0.020
 L9Y  plan-2  C11   0.020
 L9Y  plan-2  C13   0.020
 L9Y  plan-2  C15   0.020
 L9Y  plan-2  C23   0.020
 L9Y  plan-2  O16   0.020
 L9Y  plan-2  CL12  0.020
 L9Y  plan-2  CL14  0.020
 L9Y  plan-2  H231  0.020
 L9Y  plan-3  C19   0.020
 L9Y  plan-3  C20   0.020
 L9Y  plan-3  O21   0.020
 L9Y  plan-3  O22   0.020

