# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 17:46:16 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (1S,2S,3S,4S)-3-{[(naphthalen-1-yl)oxy]carbonyl}-2,4-diphenylcyclobutane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1[C@@H]([C@@H]([C@H]1c2ccccc2)C(=O)Oc3cccc4ccccc34)c5ccccc5
#
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
 8KS  8KS  '(1S,2S,3S,4S)-3-{[(naphthalen-1-yl)oxy]carbonyl}-2,4-diphenylcyclobutane-1-carboxylic acid'  ligand  53  32  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8KS
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
 8KS  C12  C  CH1    0  -0.394   1.1041  -0.6403   0.9151
 8KS  C11  C  CR16   0  -0.320   0.7252  -2.5254  -1.8565
 8KS  C10  C  CR16   0  -0.237  -0.1406  -3.2881  -2.6298
 8KS  O15  O  O2     0  -0.492  -0.9224  -0.0940  -0.1660
 8KS  C16  C  C      0   0.341  -2.2909  -0.1309  -0.3235
 8KS  O01  O  O      0  -0.594   4.0084  -0.9208   1.8181
 8KS  C02  C  C      0   0.449   4.1402  -0.9430   0.5776
 8KS  O03  O  OC    -1  -0.607   5.2066  -0.8268  -0.0570
 8KS  C04  C  CH1    0  -0.383   2.8626  -1.0960  -0.2595
 8KS  C05  C  CH1    0  -0.303   1.7689  -1.9636   0.4029
 8KS  C06  C  CR6    0   0.146   0.8855  -2.7823  -0.4958
 8KS  C07  C  CR16   0  -0.292   0.1496  -3.8269   0.0656
 8KS  C08  C  CR16   0  -0.246  -0.7184  -4.5902  -0.7021
 8KS  C09  C  CR16   0  -0.276  -0.8676  -4.3225  -2.0568
 8KS  C13  C  C      0   0.597  -0.3869  -0.6267   0.9487
 8KS  O14  O  O      0  -0.418  -1.0549  -1.0715   1.8422
 8KS  C17  C  C1     0  -0.319  -2.8929  -1.2724  -0.7663
 8KS  C18  C  C1     0  -0.268  -4.2861  -1.2862  -0.9741
 8KS  C19  C  C1     0  -0.320  -5.0355  -0.1680  -0.7332
 8KS  C20  C  C      0   0.108  -4.4240   1.0239  -0.2796
 8KS  C21  C  C1     0  -0.311  -5.1769   2.1952  -0.0277
 8KS  C22  C  C1     0  -0.251  -4.5675   3.3395   0.4069
 8KS  C23  C  C1     0  -0.254  -3.1718   3.3672   0.6082
 8KS  C24  C  C1     0  -0.294  -2.4128   2.2529   0.3764
 8KS  C25  C  C      0   0.036  -3.0198   1.0536  -0.0668
 8KS  C26  C  CH1    0  -0.255   1.9059   0.1268  -0.1396
 8KS  C27  C  CR6    0   0.144   2.4392   1.4850   0.1941
 8KS  C28  C  CR16   0  -0.289   3.4760   2.0340  -0.5605
 8KS  C29  C  CR16   0  -0.246   3.9519   3.3089  -0.2918
 8KS  C30  C  CR16   0  -0.275   3.3960   4.0619   0.7364
 8KS  C31  C  CR16   0  -0.240   2.3613   3.5275   1.4904
 8KS  C32  C  CR16   0  -0.326   1.8899   2.2483   1.2199
 8KS  H1   H  HCH1   0   0.295   1.4754  -0.4430   1.9204
 8KS  H2   H  HCR6   0   0.247   1.2782  -1.7252  -2.3322
 8KS  H3   H  HCR6   0   0.255  -0.2477  -3.0696  -3.6846
 8KS  H5   H  HCH1   0   0.230   3.1195  -1.3679  -1.2840
 8KS  H6   H  HCH1   0   0.258   2.1248  -2.5858   1.2238
 8KS  H7   H  HCR6   0   0.248   0.2627  -4.0478   1.1206
 8KS  H8   H  HCR6   0   0.254  -1.2753  -5.3965  -0.2419
 8KS  H9   H  HCR6   0   0.255  -1.5426  -4.9147  -2.6608
 8KS  H10  H  H      0   0.283  -2.3005  -2.1575  -0.9650
 8KS  H11  H  H      0   0.264  -4.7565  -2.1943  -1.3263
 8KS  H12  H  H      0   0.260  -6.1066  -0.1813  -0.8922
 8KS  H13  H  H      0   0.260  -6.2481   2.1708  -0.1855
 8KS  H14  H  H      0   0.262  -5.1535   4.2290   0.5971
 8KS  H15  H  H      0   0.263  -2.6990   4.2793   0.9474
 8KS  H16  H  H      0   0.244  -1.3423   2.2972   0.5268
 8KS  H17  H  HCH1   0   0.276   1.3331   0.1950  -1.0682
 8KS  H18  H  HCR6   0   0.242   3.9163   1.4553  -1.3627
 8KS  H19  H  HCR6   0   0.251   4.7599   3.7177  -0.8855
 8KS  H20  H  HCR6   0   0.251   3.7670   5.0567   0.9464
 8KS  H21  H  HCR6   0   0.252   1.9190   4.1043   2.2927
 8KS  H22  H  HCR6   0   0.238   1.0862   1.8457   1.8253

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
 8KS  C09  C08  aromatic  1.389  0.020  1.389
 8KS  C09  C10  aromatic  1.388  0.020  1.388
 8KS  C08  C07  aromatic  1.388  0.020  1.388
 8KS  C10  C11  aromatic  1.389  0.020  1.389
 8KS  O01  C02  deloc     1.248  0.020  1.248
 8KS  C07  C06  aromatic  1.396  0.020  1.396
 8KS  O03  C02  deloc     1.246  0.020  1.246
 8KS  C02  C04  single    1.535  0.020  1.535
 8KS  C11  C06  aromatic  1.394  0.020  1.394
 8KS  C06  C05  single    1.503  0.020  1.503
 8KS  C04  C05  single    1.545  0.020  1.545
 8KS  C04  C26  single    1.557  0.020  1.557
 8KS  C23  C22  aromatic  1.410  0.020  1.410
 8KS  C23  C24  aromatic  1.368  0.020  1.368
 8KS  C05  C12  single    1.567  0.020  1.567
 8KS  C22  C21  aromatic  1.367  0.020  1.367
 8KS  C24  C25  aromatic  1.415  0.020  1.415
 8KS  C21  C20  aromatic  1.415  0.020  1.415
 8KS  O14  C13  double    1.201  0.020  1.201
 8KS  C26  C12  single    1.531  0.020  1.531
 8KS  C26  C27  single    1.497  0.020  1.497
 8KS  C12  C13  single    1.491  0.020  1.491
 8KS  C25  C20  aromatic  1.421  0.020  1.421
 8KS  C25  C16  aromatic  1.414  0.020  1.414
 8KS  C13  O15  single    1.346  0.020  1.346
 8KS  C20  C19  aromatic  1.414  0.020  1.414
 8KS  C27  C32  aromatic  1.392  0.020  1.392
 8KS  C27  C28  aromatic  1.395  0.020  1.395
 8KS  C32  C31  aromatic  1.390  0.020  1.390
 8KS  C28  C29  aromatic  1.387  0.020  1.387
 8KS  O15  C16  single    1.378  0.020  1.378
 8KS  C16  C17  aromatic  1.364  0.020  1.364
 8KS  C19  C18  aromatic  1.367  0.020  1.367
 8KS  C31  C30  aromatic  1.387  0.020  1.387
 8KS  C29  C30  aromatic  1.390  0.020  1.390
 8KS  C17  C18  aromatic  1.409  0.020  1.409
 8KS  C12  H1   single    0.970  0.020  1.090
 8KS  C11  H2   single    0.930  0.020  1.080
 8KS  C10  H3   single    0.930  0.020  1.080
 8KS  C04  H5   single    0.970  0.020  1.090
 8KS  C05  H6   single    0.970  0.020  1.090
 8KS  C07  H7   single    0.930  0.020  1.080
 8KS  C08  H8   single    0.930  0.020  1.080
 8KS  C09  H9   single    0.930  0.020  1.080
 8KS  C17  H10  single    0.930  0.020  1.080
 8KS  C18  H11  single    0.930  0.020  1.080
 8KS  C19  H12  single    0.930  0.020  1.080
 8KS  C21  H13  single    0.930  0.020  1.080
 8KS  C22  H14  single    0.930  0.020  1.080
 8KS  C23  H15  single    0.930  0.020  1.080
 8KS  C24  H16  single    0.930  0.020  1.080
 8KS  C26  H17  single    0.970  0.020  1.090
 8KS  C28  H18  single    0.930  0.020  1.080
 8KS  C29  H19  single    0.930  0.020  1.080
 8KS  C30  H20  single    0.930  0.020  1.080
 8KS  C31  H21  single    0.930  0.020  1.080
 8KS  C32  H22  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
 8KS  H1   C12  C26  111.49  3.000
 8KS  H1   C12  C13  108.56  3.000
 8KS  C26  C12  C13  122.31  3.000
 8KS  H1   C12  C05  108.05  3.000
 8KS  C13  C12  C05  116.05  3.000
 8KS  C26  C12  C05   88.61  3.000
 8KS  H2   C11  C06  120.42  3.000
 8KS  H2   C11  C10  118.66  3.000
 8KS  C06  C11  C10  120.92  3.000
 8KS  H3   C10  C09  120.05  3.000
 8KS  H3   C10  C11  119.56  3.000
 8KS  C09  C10  C11  120.39  3.000
 8KS  C13  O15  C16  118.61  3.000
 8KS  C25  C16  C17  122.15  3.000
 8KS  C17  C16  O15  119.85  3.000
 8KS  C25  C16  O15  117.95  3.000
 8KS  C04  C02  O03  116.34  3.000
 8KS  C04  C02  O01  117.13  3.000
 8KS  O03  C02  O01  126.51  3.000
 8KS  H5   C04  C26  114.38  3.000
 8KS  H5   C04  C05  115.43  3.000
 8KS  C26  C04  C05   88.45  3.000
 8KS  H5   C04  C02  109.94  3.000
 8KS  C26  C04  C02  113.02  3.000
 8KS  C05  C04  C02  114.28  3.000
 8KS  H6   C05  C06  109.35  3.000
 8KS  H6   C05  C04  114.35  3.000
 8KS  C06  C05  C04  117.75  3.000
 8KS  H6   C05  C12  111.99  3.000
 8KS  C04  C05  C12   88.07  3.000
 8KS  C06  C05  C12  113.97  3.000
 8KS  C07  C06  C05  118.50  3.000
 8KS  C05  C06  C11  123.43  3.000
 8KS  C07  C06  C11  118.03  3.000
 8KS  H7   C07  C08  119.45  3.000
 8KS  H7   C07  C06  119.28  3.000
 8KS  C08  C07  C06  121.27  3.000
 8KS  H8   C08  C09  120.19  3.000
 8KS  H8   C08  C07  119.76  3.000
 8KS  C09  C08  C07  120.05  3.000
 8KS  H9   C09  C08  120.39  3.000
 8KS  H9   C09  C10  120.27  3.000
 8KS  C08  C09  C10  119.34  3.000
 8KS  O14  C13  O15  122.77  3.000
 8KS  O15  C13  C12  112.49  3.000
 8KS  O14  C13  C12  124.71  3.000
 8KS  H10  C17  C18  120.38  3.000
 8KS  H10  C17  C16  120.11  3.000
 8KS  C18  C17  C16  119.50  3.000
 8KS  H11  C18  C19  120.37  3.000
 8KS  H11  C18  C17  119.10  3.000
 8KS  C19  C18  C17  120.53  3.000
 8KS  H12  C19  C20  119.01  3.000
 8KS  H12  C19  C18  120.41  3.000
 8KS  C20  C19  C18  120.58  3.000
 8KS  C25  C20  C21  118.82  3.000
 8KS  C25  C20  C19  119.54  3.000
 8KS  C21  C20  C19  121.65  3.000
 8KS  H13  C21  C22  120.40  3.000
 8KS  H13  C21  C20  118.79  3.000
 8KS  C22  C21  C20  120.81  3.000
 8KS  H14  C22  C23  119.65  3.000
 8KS  H14  C22  C21  120.16  3.000
 8KS  C23  C22  C21  120.19  3.000
 8KS  H15  C23  C24  119.82  3.000
 8KS  H15  C23  C22  119.59  3.000
 8KS  C24  C23  C22  120.59  3.000
 8KS  H16  C24  C25  120.17  3.000
 8KS  H16  C24  C23  119.48  3.000
 8KS  C25  C24  C23  120.35  3.000
 8KS  C24  C25  C20  119.24  3.000
 8KS  C20  C25  C16  117.70  3.000
 8KS  C24  C25  C16  123.06  3.000
 8KS  H17  C26  C27  108.63  3.000
 8KS  H17  C26  C04  107.79  3.000
 8KS  C27  C26  C04  120.72  3.000
 8KS  H17  C26  C12  110.00  3.000
 8KS  C27  C26  C12  119.19  3.000
 8KS  C04  C26  C12   88.93  3.000
 8KS  C32  C27  C28  118.44  3.000
 8KS  C28  C27  C26  120.09  3.000
 8KS  C32  C27  C26  121.43  3.000
 8KS  H18  C28  C29  119.69  3.000
 8KS  H18  C28  C27  119.52  3.000
 8KS  C29  C28  C27  120.79  3.000
 8KS  H19  C29  C30  119.96  3.000
 8KS  H19  C29  C28  119.79  3.000
 8KS  C30  C29  C28  120.26  3.000
 8KS  H20  C30  C31  120.28  3.000
 8KS  H20  C30  C29  120.28  3.000
 8KS  C31  C30  C29  119.44  3.000
 8KS  H21  C31  C32  119.74  3.000
 8KS  H21  C31  C30  120.15  3.000
 8KS  C32  C31  C30  120.11  3.000
 8KS  H22  C32  C31  119.00  3.000
 8KS  H22  C32  C27  120.05  3.000
 8KS  C31  C32  C27  120.96  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
 8KS  CONST_01  C08  C09  C10  C11    0.00   0.0  0
 8KS  CONST_02  C08  C07  C06  C11    0.00   0.0  0
 8KS  CONST_03  C07  C08  C09  C10    0.00   0.0  0
 8KS  CONST_04  C07  C06  C11  C10    0.00   0.0  0
 8KS  CONST_05  C23  C24  C25  C16  180.00   0.0  0
 8KS  CONST_06  C21  C20  C25  C16  180.00   0.0  0
 8KS  CONST_07  C19  C20  C25  C16    0.00   0.0  0
 8KS  CONST_08  C19  C18  C17  C16    0.00   0.0  0
 8KS  CONST_09  C09  C08  C07  C06    0.00   0.0  0
 8KS  CONST_10  C09  C10  C11  C06    0.00   0.0  0
 8KS  CONST_11  C24  C25  C16  C17  180.00   0.0  0
 8KS  CONST_12  C20  C25  C16  C17    0.00   0.0  0
 8KS  CONST_13  C20  C19  C18  C17    0.00   0.0  0
 8KS  CONST_14  C21  C20  C19  C18  180.00   0.0  0
 8KS  CONST_15  C25  C20  C19  C18    0.00   0.0  0
 8KS  CONST_16  C25  C16  C17  C18    0.00   0.0  0
 8KS  CONST_17  C22  C21  C20  C19  180.00   0.0  0
 8KS  CONST_18  C24  C25  C20  C19  180.00   0.0  0
 8KS  CONST_19  C23  C22  C21  C20    0.00   0.0  0
 8KS  CONST_20  C23  C24  C25  C20    0.00   0.0  0
 8KS  CONST_21  C24  C23  C22  C21    0.00   0.0  0
 8KS  CONST_22  C24  C25  C20  C21    0.00   0.0  0
 8KS  CONST_23  C25  C24  C23  C22    0.00   0.0  0
 8KS  CONST_24  C25  C20  C21  C22    0.00   0.0  0
 8KS  CONST_25  C30  C31  C32  C27    0.00   0.0  0
 8KS  CONST_26  C30  C29  C28  C27    0.00   0.0  0
 8KS  CONST_27  C31  C32  C27  C28    0.00   0.0  0
 8KS  CONST_28  C31  C30  C29  C28    0.00   0.0  0
 8KS  CONST_29  C32  C27  C28  C29    0.00   0.0  0
 8KS  CONST_30  C32  C31  C30  C29    0.00   0.0  0
 8KS  CONST_31  C05  C06  C11  C10  180.00   0.0  0
 8KS  CONST_32  C08  C07  C06  C05  180.00   0.0  0
 8KS  CONST_33  C31  C32  C27  C26  180.00   0.0  0
 8KS  CONST_34  C29  C28  C27  C26  180.00   0.0  0
 8KS  CONST_35  C24  C25  C16  O15    0.00   0.0  0
 8KS  CONST_36  C20  C25  C16  O15  180.00   0.0  0
 8KS  CONST_37  C18  C17  C16  O15  180.00   0.0  0
 8KS  CONST_38  H9   C09  C10  C11  180.00   0.0  0
 8KS  CONST_39  H7   C07  C06  C11  180.00   0.0  0
 8KS  CONST_40  H8   C08  C09  C10  180.00   0.0  0
 8KS  CONST_41  H16  C24  C25  C16    0.00   0.0  0
 8KS  CONST_42  H11  C18  C17  C16  180.00   0.0  0
 8KS  CONST_43  H2   C11  C06  C05    0.00   0.0  0
 8KS  CONST_44  H3   C10  C11  C06  180.00   0.0  0
 8KS  CONST_45  H12  C19  C18  C17  180.00   0.0  0
 8KS  CONST_46  H13  C21  C20  C19    0.00   0.0  0
 8KS  CONST_47  H10  C17  C18  C19  180.00   0.0  0
 8KS  CONST_48  H14  C22  C21  C20  180.00   0.0  0
 8KS  CONST_49  H15  C23  C22  C21  180.00   0.0  0
 8KS  CONST_50  H22  C32  C27  C26    0.00   0.0  0
 8KS  CONST_51  H18  C28  C27  C26    0.00   0.0  0
 8KS  CONST_52  H21  C31  C32  C27  180.00   0.0  0
 8KS  CONST_53  H19  C29  C28  C27  180.00   0.0  0
 8KS  CONST_54  H20  C30  C29  C28  180.00   0.0  0
 8KS  Var_01    C25  C16  O15  C13  102.03  30.0  2
 8KS  Var_02    O14  C13  O15  C16   -3.90  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
 8KS  chir_01  C12  C05  C26  C13  negativ
 8KS  chir_02  C04  C26  C05  C02  positiv
 8KS  chir_03  C05  C12  C04  C06  positiv
 8KS  chir_04  C26  C04  C12  C27  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
 8KS  plan-1  C11  0.020
 8KS  plan-1  C10  0.020
 8KS  plan-1  C05  0.020
 8KS  plan-1  C06  0.020
 8KS  plan-1  C07  0.020
 8KS  plan-1  C08  0.020
 8KS  plan-1  C09  0.020
 8KS  plan-1  H2   0.020
 8KS  plan-1  H3   0.020
 8KS  plan-1  H7   0.020
 8KS  plan-1  H8   0.020
 8KS  plan-1  H9   0.020
 8KS  plan-2  C26  0.020
 8KS  plan-2  C27  0.020
 8KS  plan-2  C28  0.020
 8KS  plan-2  C29  0.020
 8KS  plan-2  C30  0.020
 8KS  plan-2  C31  0.020
 8KS  plan-2  C32  0.020
 8KS  plan-2  H18  0.020
 8KS  plan-2  H19  0.020
 8KS  plan-2  H20  0.020
 8KS  plan-2  H21  0.020
 8KS  plan-2  H22  0.020
 8KS  plan-3  O15  0.020
 8KS  plan-3  C16  0.020
 8KS  plan-3  C17  0.020
 8KS  plan-3  C18  0.020
 8KS  plan-3  C19  0.020
 8KS  plan-3  C20  0.020
 8KS  plan-3  C21  0.020
 8KS  plan-3  C22  0.020
 8KS  plan-3  C23  0.020
 8KS  plan-3  C24  0.020
 8KS  plan-3  C25  0.020
 8KS  plan-3  H10  0.020
 8KS  plan-3  H11  0.020
 8KS  plan-3  H12  0.020
 8KS  plan-3  H13  0.020
 8KS  plan-3  H14  0.020
 8KS  plan-3  H15  0.020
 8KS  plan-3  H16  0.020
 8KS  plan-4  O01  0.020
 8KS  plan-4  C02  0.020
 8KS  plan-4  O03  0.020
 8KS  plan-4  C04  0.020
 8KS  plan-5  C12  0.020
 8KS  plan-5  O15  0.020
 8KS  plan-5  C13  0.020
 8KS  plan-5  O14  0.020

