# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:40:44 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (2~{R},3~{S})-2-ethyl-2-[(2~{E})-2-(6-methoxy-3,4-dihydro-2~{H}-naphthalen-1-ylidene)ethyl]-3-oxidanyl-cyclopentan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@]1(C/C=C/2CCCc3cc(OC)ccc/23)[C@@H](O)CCC1=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
 A6O  A6O  (2~{R},3~{S})-2-ethyl-2-[(2~{E})-2-(6-methoxy-3,4-dihydro-2~{H}-naphthalen-1-ylidene)ethyl]-3-oxidanyl-cyclopentan-1-one  ligand  49  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A6O
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
 A6O  C11  C  C1    0  -0.295  -0.5568  -0.0649   0.8902
 A6O  C12  C  C     0   0.101   0.3602  -0.7045   0.1530
 A6O  C13  C  CR6   0   0.079   1.7619  -0.2324   0.0879
 A6O  C02  C  C     0   0.447  -2.8633  -0.1536  -1.2199
 A6O  C03  C  CH2   0  -0.559  -3.8210  -1.3161  -1.4066
 A6O  C04  C  CH2   0  -0.503  -4.5789  -1.4293  -0.0841
 A6O  C05  C  CH1   0   0.065  -4.4188  -0.0478   0.5658
 A6O  C07  C  CT    0  -0.224  -2.9912   0.3790   0.1981
 A6O  C08  C  CH2   0  -0.418  -2.7175   1.8792   0.2846
 A6O  C09  C  CH3   0  -0.680  -2.9076   2.4700   1.6754
 A6O  C10  C  CH2   0  -0.519  -1.9932  -0.4374   1.0736
 A6O  C14  C  CR16  0  -0.307   2.1037   1.0961   0.3448
 A6O  C15  C  CR16  0  -0.382   3.4137   1.5441   0.3411
 A6O  C16  C  CR6   0   0.382   4.4402   0.6435   0.0623
 A6O  C18  C  CH3   0  -0.436   6.1259   2.2785   0.3967
 A6O  C19  C  CR16  0  -0.393   4.1165  -0.6780  -0.2329
 A6O  C20  C  CR6   0   0.073   2.8014  -1.1223  -0.2335
 A6O  C21  C  CH2   0  -0.503   2.5239  -2.5558  -0.6117
 A6O  C22  C  CH2   0  -0.445   1.1361  -3.0236  -0.2060
 A6O  C23  C  CH2   0  -0.526   0.0952  -1.9787  -0.5960
 A6O  O06  O  OH1   0  -0.668  -5.3004   0.8840  -0.0228
 A6O  O17  O  O2    0  -0.473   5.7491   0.9615   0.0474
 A6O  H2   H  H     0   0.232  -0.2404   0.8138   1.4429
 A6O  H4   H  HCH2  0   0.281  -4.4852  -1.0836  -2.2426
 A6O  H5   H  HCH2  0   0.278  -3.2797  -2.2217  -1.6880
 A6O  H6   H  HCH2  0   0.257  -5.6307  -1.6867  -0.2184
 A6O  H7   H  HCH2  0   0.246  -4.1509  -2.2026   0.5544
 A6O  H8   H  HCH1  0   0.224  -4.5571  -0.0943   1.6533
 A6O  H9   H  HCH2  0   0.233  -1.6953   2.0619  -0.0543
 A6O  H10  H  HCH2  0   0.236  -3.3616   2.4063  -0.4208
 A6O  H11  H  HCH3  0   0.234  -2.6740   3.5350   1.6715
 A6O  H12  H  HCH3  0   0.228  -3.9357   2.3619   2.0228
 A6O  H13  H  HCH3  0   0.222  -2.2597   2.0000   2.4169
 A6O  H14  H  HCH2  0   0.264  -2.1348  -1.5070   0.9082
 A6O  H15  H  HCH2  0   0.264  -2.2674  -0.2677   2.1189
 A6O  H16  H  HCR6  0   0.245   1.3242   1.8220   0.5404
 A6O  H17  H  HCR6  0   0.276   3.6097   2.5872   0.5479
 A6O  H18  H  HCH3  0   0.228   5.7304   3.0181  -0.3042
 A6O  H19  H  HCH3  0   0.228   5.7997   2.5418   1.4063
 A6O  H20  H  HCH3  0   0.259   7.2121   2.3100   0.3601
 A6O  H21  H  HCR6  0   0.251   4.9153  -1.3754  -0.4622
 A6O  H22  H  HCH2  0   0.247   2.6269  -2.6462  -1.6987
 A6O  H23  H  HCH2  0   0.251   3.2909  -3.2054  -0.1841
 A6O  H24  H  HCH2  0   0.241   0.9116  -3.9793  -0.6828
 A6O  H25  H  HCH2  0   0.229   1.0940  -3.1908   0.8738
 A6O  H26  H  HCH2  0   0.240  -0.9095  -2.3550  -0.4060
 A6O  H27  H  HCH2  0   0.240   0.1599  -1.7917  -1.6733
 A6O  H28  H  HOH1  0   0.451  -6.2021   0.5848   0.1305
 A6O  O01  O  O     0  -0.400  -2.1207   0.2791  -2.0666

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
 A6O  C18  O17  single    1.414  0.020  1.414
 A6O  C21  C22  single    1.520  0.020  1.520
 A6O  C21  C20  single    1.508  0.020  1.508
 A6O  C22  C23  single    1.525  0.020  1.525
 A6O  C19  C20  aromatic  1.388  0.020  1.388
 A6O  C19  C16  aromatic  1.392  0.020  1.392
 A6O  O17  C16  single    1.347  0.020  1.347
 A6O  C20  C13  aromatic  1.406  0.020  1.406
 A6O  C16  C15  aromatic  1.394  0.020  1.394
 A6O  C23  C12  single    1.502  0.020  1.502
 A6O  C13  C12  single    1.480  0.020  1.480
 A6O  C13  C14  aromatic  1.396  0.020  1.396
 A6O  C15  C14  aromatic  1.385  0.020  1.385
 A6O  C12  C11  double    1.339  0.020  1.339
 A6O  C11  C10  single    1.495  0.020  1.495
 A6O  C10  C07  single    1.558  0.020  1.558
 A6O  C08  C07  single    1.527  0.020  1.527
 A6O  C08  C09  single    1.523  0.020  1.523
 A6O  C07  C05  single    1.535  0.020  1.535
 A6O  C07  C02  single    1.520  0.020  1.520
 A6O  O06  C05  single    1.411  0.020  1.411
 A6O  C05  C04  single    1.535  0.020  1.535
 A6O  O01  C02  double    1.207  0.020  1.207
 A6O  C02  C03  single    1.518  0.020  1.518
 A6O  C03  C04  single    1.528  0.020  1.528
 A6O  C11  H2   single    0.930  0.020  1.080
 A6O  C03  H4   single    0.970  0.020  1.090
 A6O  C03  H5   single    0.970  0.020  1.090
 A6O  C04  H6   single    0.970  0.020  1.090
 A6O  C04  H7   single    0.970  0.020  1.090
 A6O  C05  H8   single    0.970  0.020  1.090
 A6O  C08  H9   single    0.970  0.020  1.090
 A6O  C08  H10  single    0.970  0.020  1.090
 A6O  C09  H11  single    0.970  0.020  1.090
 A6O  C09  H12  single    0.970  0.020  1.090
 A6O  C09  H13  single    0.970  0.020  1.090
 A6O  C10  H14  single    0.970  0.020  1.090
 A6O  C10  H15  single    0.970  0.020  1.090
 A6O  C14  H16  single    0.930  0.020  1.080
 A6O  C15  H17  single    0.930  0.020  1.080
 A6O  C18  H18  single    0.970  0.020  1.090
 A6O  C18  H19  single    0.970  0.020  1.090
 A6O  C18  H20  single    0.970  0.020  1.090
 A6O  C19  H21  single    0.930  0.020  1.080
 A6O  C21  H22  single    0.970  0.020  1.090
 A6O  C21  H23  single    0.970  0.020  1.090
 A6O  C22  H24  single    0.970  0.020  1.090
 A6O  C22  H25  single    0.970  0.020  1.090
 A6O  C23  H26  single    0.970  0.020  1.090
 A6O  C23  H27  single    0.970  0.020  1.090
 A6O  O06  H28  single    0.850  0.020  0.980

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
 A6O  H2   C11  C10  114.79  3.000
 A6O  H2   C11  C12  117.87  3.000
 A6O  C10  C11  C12  127.33  3.000
 A6O  C23  C12  C13  114.56  3.000
 A6O  C13  C12  C11  121.35  3.000
 A6O  C23  C12  C11  123.99  3.000
 A6O  C20  C13  C14  117.62  3.000
 A6O  C14  C13  C12  121.82  3.000
 A6O  C20  C13  C12  120.55  3.000
 A6O  O01  C02  C07  125.50  3.000
 A6O  O01  C02  C03  125.22  3.000
 A6O  C07  C02  C03  109.27  3.000
 A6O  H5   C03  H4   106.30  3.000
 A6O  H5   C03  C04  114.04  3.000
 A6O  H4   C03  C04  112.10  3.000
 A6O  H5   C03  C02  110.74  3.000
 A6O  H4   C03  C02  108.34  3.000
 A6O  C04  C03  C02  105.26  3.000
 A6O  H7   C04  H6   106.45  3.000
 A6O  H7   C04  C05  110.45  3.000
 A6O  H6   C04  C05  111.40  3.000
 A6O  H7   C04  C03  111.38  3.000
 A6O  H6   C04  C03  112.89  3.000
 A6O  C05  C04  C03  104.35  3.000
 A6O  H8   C05  O06  111.26  3.000
 A6O  H8   C05  C07  111.50  3.000
 A6O  O06  C05  C07  107.31  3.000
 A6O  H8   C05  C04  111.61  3.000
 A6O  O06  C05  C04  110.64  3.000
 A6O  C07  C05  C04  104.23  3.000
 A6O  C10  C07  C08  111.59  3.000
 A6O  C08  C07  C05  115.23  3.000
 A6O  C10  C07  C05  108.39  3.000
 A6O  C05  C07  C02  101.79  3.000
 A6O  C08  C07  C02  112.45  3.000
 A6O  C10  C07  C02  106.65  3.000
 A6O  H10  C08  H9   105.74  3.000
 A6O  H10  C08  C09  109.23  3.000
 A6O  H9   C08  C09  109.59  3.000
 A6O  H10  C08  C07  109.40  3.000
 A6O  H9   C08  C07  108.33  3.000
 A6O  C09  C08  C07  114.22  3.000
 A6O  H13  C09  H12  107.50  3.000
 A6O  H13  C09  H11  107.22  3.000
 A6O  H12  C09  H11  107.46  3.000
 A6O  H13  C09  C08  112.29  3.000
 A6O  H12  C09  C08  111.72  3.000
 A6O  H11  C09  C08  110.42  3.000
 A6O  H15  C10  H14  105.32  3.000
 A6O  H15  C10  C07  107.16  3.000
 A6O  H14  C10  C07  110.19  3.000
 A6O  H15  C10  C11  108.63  3.000
 A6O  H14  C10  C11  110.50  3.000
 A6O  C07  C10  C11  114.57  3.000
 A6O  H16  C14  C15  117.69  3.000
 A6O  H16  C14  C13  119.68  3.000
 A6O  C15  C14  C13  122.63  3.000
 A6O  H17  C15  C16  121.87  3.000
 A6O  H17  C15  C14  118.89  3.000
 A6O  C16  C15  C14  119.23  3.000
 A6O  O17  C16  C19  116.59  3.000
 A6O  O17  C16  C15  124.43  3.000
 A6O  C19  C16  C15  118.98  3.000
 A6O  H20  C18  H19  108.79  3.000
 A6O  H20  C18  H18  108.68  3.000
 A6O  H19  C18  H18  108.74  3.000
 A6O  H20  C18  O17  106.56  3.000
 A6O  H19  C18  O17  111.90  3.000
 A6O  H18  C18  O17  112.06  3.000
 A6O  H21  C19  C20  119.45  3.000
 A6O  H21  C19  C16  118.94  3.000
 A6O  C20  C19  C16  121.61  3.000
 A6O  C21  C20  C19  118.60  3.000
 A6O  C19  C20  C13  119.86  3.000
 A6O  C21  C20  C13  121.53  3.000
 A6O  H23  C21  H22  105.86  3.000
 A6O  H23  C21  C22  110.71  3.000
 A6O  H22  C21  C22  108.99  3.000
 A6O  H23  C21  C20  109.74  3.000
 A6O  H22  C21  C20  108.05  3.000
 A6O  C22  C21  C20  113.18  3.000
 A6O  H25  C22  H24  106.83  3.000
 A6O  H25  C22  C23  109.32  3.000
 A6O  H24  C22  C23  110.35  3.000
 A6O  H25  C22  C21  110.24  3.000
 A6O  H24  C22  C21  109.92  3.000
 A6O  C23  C22  C21  110.12  3.000
 A6O  H27  C23  H26  106.55  3.000
 A6O  H27  C23  C22  109.15  3.000
 A6O  H26  C23  C22  110.37  3.000
 A6O  H27  C23  C12  109.59  3.000
 A6O  H26  C23  C12  111.64  3.000
 A6O  C22  C23  C12  109.47  3.000
 A6O  H28  O06  C05  108.27  3.000
 A6O  C18  O17  C16  118.43  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
 A6O  CONST_01  C16  C19  C20  C13     0.00   0.0  0
 A6O  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 A6O  CONST_03  C19  C20  C13  C14     0.00   0.0  0
 A6O  CONST_04  C19  C16  C15  C14     0.00   0.0  0
 A6O  CONST_05  C20  C19  C16  C15     0.00   0.0  0
 A6O  CONST_06  C20  C13  C14  C15     0.00   0.0  0
 A6O  CONST_07  O17  C16  C15  C14   180.00   0.0  0
 A6O  CONST_08  O17  C16  C19  C20   180.00   0.0  0
 A6O  CONST_09  H16  C14  C13  C12     0.00   0.0  0
 A6O  CONST_10  H21  C19  C20  C13   180.00   0.0  0
 A6O  CONST_11  H17  C15  C14  C13   180.00   0.0  0
 A6O  Var_01    C21  C22  C23  C12   -62.86  30.0  1
 A6O  Var_02    C22  C21  C20  C13   -17.48  30.0  1
 A6O  Var_03    C22  C23  C12  C13    49.68  30.0  1
 A6O  Var_04    C05  C04  C03  C02    21.02  30.0  1
 A6O  Var_05    C07  C02  C03  C04     2.61  30.0  1
 A6O  Var_06    C23  C12  C13  C14   159.45  30.0  1
 A6O  Var_07    C23  C22  C21  C20    46.27  30.0  1
 A6O  Var_08    C07  C10  C11  C12  -100.14  30.0  3
 A6O  Var_09    C10  C11  C12  C13  -178.67  30.0  2
 A6O  Var_10    C19  C16  O17  C18  -177.37  30.0  2
 A6O  Var_11    H11  C09  C08  C07   178.66  30.0  3
 A6O  Var_12    H18  C18  O17  C16   -63.51  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
 A6O  chir_01  C05  C07  O06  C04  negativ
 A6O  chir_02  C07  C05  C02  C10  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
 A6O  plan-1  C02  0.020
 A6O  plan-1  C03  0.020
 A6O  plan-1  C07  0.020
 A6O  plan-1  O01  0.020
 A6O  plan-2  C12  0.020
 A6O  plan-2  C13  0.020
 A6O  plan-2  C14  0.020
 A6O  plan-2  C15  0.020
 A6O  plan-2  C16  0.020
 A6O  plan-2  C19  0.020
 A6O  plan-2  C20  0.020
 A6O  plan-2  C21  0.020
 A6O  plan-2  O17  0.020
 A6O  plan-2  H16  0.020
 A6O  plan-2  H17  0.020
 A6O  plan-2  H21  0.020

