# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 05:02:30 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: (3~{R},4~{R})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(C[C@@H]2[C@H](COC2=O)Cc3ccc4OCOc4c3)cc(OC)c1OC
#
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
 YTN  YTN  "(3~{R},4~{R})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one"
  ligand  53  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YTN
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
 YTN  C01  C  CR56  0   0.322  -18.5652  20.4556  -24.3721
 YTN  C02  C  CR56  0   0.283  -19.6595  21.2759  -24.5939
 YTN  C03  C  CR16  0  -0.329  -19.8352  22.4408  -23.8934
 YTN  C04  C  CR16  0  -0.335  -18.8509  22.7674  -22.9492
 YTN  C05  C  CR6   0   0.136  -17.7465  21.9591  -22.7262
 YTN  C06  C  CR16  0  -0.380  -17.5947  20.7686  -23.4581
 YTN  C07  C  CH2   0   0.068  -19.8651  19.4815  -25.8977
 YTN  C09  C  CR15  0  -0.419  -17.6292  21.6308  -19.4005
 YTN  C10  C  CR15  0  -0.292  -16.6235  21.3853  -20.5244
 YTN  C11  C  CH2   0  -0.520  -16.6901  22.3299  -21.7203
 YTN  C12  C  CR5   0   0.581  -16.9090  21.0455  -18.2035
 YTN  C13  C  CH2   0  -0.153  -15.3119  21.5046  -19.7570
 YTN  C14  C  CR6   0   0.160  -19.3456  19.8757  -20.2385
 YTN  C15  C  CR16  0  -0.454  -20.3162  19.8195  -21.2295
 YTN  C16  C  CR6   0   0.346  -20.6079  18.6163  -21.8667
 YTN  C17  C  CR6   0   0.155  -19.9191  17.4555  -21.5151
 YTN  C18  C  CR6   0   0.352  -18.9374  17.5139  -20.5203
 YTN  C19  C  CR16  0  -0.483  -18.6663  18.7167  -19.8730
 YTN  C20  C  CH3   0  -0.437  -17.3282  16.3344  -19.2419
 YTN  C21  C  CH3   0  -0.411  -19.4620  15.9899  -23.2777
 YTN  C22  C  CH3   0  -0.438  -22.5054  19.4993  -22.9774
 YTN  O01  O  O     0  -0.489  -18.6340  19.3799  -25.1938
 YTN  O02  O  O     0  -0.489  -20.4375  20.7392  -25.5676
 YTN  O03  O  O     0  -0.437  -15.5968  21.0052  -18.4420
 YTN  O04  O  O     0  -0.429  -17.3694  20.6776  -17.1573
 YTN  O05  O  O2    0  -0.463  -18.3221  16.3496  -20.2449
 YTN  O06  O  O2    0  -0.478  -20.2215  16.2712  -22.1119
 YTN  O07  O  O2    0  -0.472  -21.5328  18.4823  -22.8374
 YTN  H1   H  HCR6  0   0.267  -20.6880  23.0855  -24.0597
 YTN  H2   H  HCR6  0   0.247  -18.9595  23.6826  -22.3804
 YTN  H3   H  HCR6  0   0.262  -16.7398  20.1207  -23.3056
 YTN  H4   H  HCH2  0   0.231  -20.5352  18.6736  -25.5891
 YTN  H5   H  HCH2  0   0.264  -19.5995  21.9741  -20.1344
 YTN  H6   H  HCH2  0   0.263  -19.5504  21.2035  -18.5752
 YTN  H7   H  HCR5  0   0.305  -17.6480  22.7135  -19.2014
 YTN  H8   H  HCR5  0   0.279  -16.7217  20.3531  -20.8753
 YTN  H9   H  HCH2  0   0.259  -15.7155  22.3208  -22.2198
 YTN  H10  H  HCH2  0   0.254  -16.8447  23.3534  -21.3695
 YTN  H11  H  HCH2  0   0.260  -14.5043  20.9112  -20.1826
 YTN  H12  H  HCH2  0   0.240  -14.9819  22.5447  -19.6769
 YTN  H13  H  HCR6  0   0.267  -20.8286  20.7294  -21.5117
 YTN  H14  H  HCR6  0   0.274  -17.9302  18.7499  -19.0827
 YTN  H15  H  HCH3  0   0.259  -16.9585  15.3133  -19.1891
 YTN  H16  H  HCH3  0   0.227  -16.4931  16.9982  -19.4816
 YTN  H17  H  HCH3  0   0.227  -17.7291  16.6136  -18.2637
 YTN  H18  H  HCH3  0   0.234  -19.8295  15.0481  -23.6823
 YTN  H19  H  HCH3  0   0.221  -19.5803  16.7653  -24.0386
 YTN  H20  H  HCH3  0   0.219  -18.3977  15.8815  -23.0537
 YTN  H21  H  HCH3  0   0.256  -23.2160  19.1466  -23.7211
 YTN  H22  H  HCH3  0   0.229  -23.0340  19.6808  -22.0380
 YTN  H23  H  HCH3  0   0.229  -22.0784  20.4419  -23.3248
 YTN  H25  H  HCH2  0   0.240  -19.6806  19.4310  -26.9727
 YTN  C08  C  CH2   0  -0.503  -19.0856  21.1988  -19.5660

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
 YTN  C07  O02  single    1.421  0.020  1.421
 YTN  C07  O01  single    1.422  0.020  1.422
 YTN  O02  C02  single    1.357  0.020  1.357
 YTN  O01  C01  single    1.355  0.020  1.355
 YTN  C02  C01  aromatic  1.385  0.020  1.385
 YTN  C02  C03  aromatic  1.371  0.020  1.371
 YTN  C01  C06  aromatic  1.369  0.020  1.369
 YTN  C03  C04  aromatic  1.403  0.020  1.403
 YTN  C06  C05  aromatic  1.406  0.020  1.406
 YTN  O07  C22  single    1.414  0.020  1.414
 YTN  O07  C16  single    1.348  0.020  1.348
 YTN  C04  C05  aromatic  1.387  0.020  1.387
 YTN  C05  C11  single    1.505  0.020  1.505
 YTN  C21  O06  single    1.420  0.020  1.420
 YTN  C16  C15  aromatic  1.392  0.020  1.392
 YTN  C16  C17  aromatic  1.395  0.020  1.395
 YTN  C11  C10  single    1.525  0.020  1.525
 YTN  O06  C17  single    1.360  0.020  1.360
 YTN  C15  C14  aromatic  1.388  0.020  1.388
 YTN  C17  C18  aromatic  1.399  0.020  1.399
 YTN  C10  C13  single    1.524  0.020  1.524
 YTN  C10  C09  single    1.528  0.020  1.528
 YTN  C13  O03  single    1.435  0.020  1.435
 YTN  C14  C08  single    1.507  0.020  1.507
 YTN  C14  C19  aromatic  1.392  0.020  1.392
 YTN  C18  C19  aromatic  1.392  0.020  1.392
 YTN  C18  O05  single    1.345  0.020  1.345
 YTN  C08  C09  single    1.528  0.020  1.528
 YTN  C09  C12  single    1.515  0.020  1.515
 YTN  O05  C20  single    1.412  0.020  1.412
 YTN  O03  C12  single    1.334  0.020  1.334
 YTN  C12  O04  double    1.201  0.020  1.201
 YTN  C03  H1   single    0.930  0.020  1.080
 YTN  C04  H2   single    0.930  0.020  1.080
 YTN  C06  H3   single    0.930  0.020  1.080
 YTN  C07  H4   single    0.970  0.020  1.090
 YTN  C08  H5   single    0.970  0.020  1.090
 YTN  C08  H6   single    0.970  0.020  1.090
 YTN  C09  H7   single    0.970  0.020  1.090
 YTN  C10  H8   single    0.970  0.020  1.090
 YTN  C11  H9   single    0.970  0.020  1.090
 YTN  C11  H10  single    0.970  0.020  1.090
 YTN  C13  H11  single    0.970  0.020  1.090
 YTN  C13  H12  single    0.970  0.020  1.090
 YTN  C15  H13  single    0.930  0.020  1.080
 YTN  C19  H14  single    0.930  0.020  1.080
 YTN  C20  H15  single    0.970  0.020  1.090
 YTN  C20  H16  single    0.970  0.020  1.090
 YTN  C20  H17  single    0.970  0.020  1.090
 YTN  C21  H18  single    0.970  0.020  1.090
 YTN  C21  H19  single    0.970  0.020  1.090
 YTN  C21  H20  single    0.970  0.020  1.090
 YTN  C22  H21  single    0.970  0.020  1.090
 YTN  C22  H22  single    0.970  0.020  1.090
 YTN  C22  H23  single    0.970  0.020  1.090
 YTN  C07  H25  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
 YTN  O01  C01  C06  128.46  3.000
 YTN  C06  C01  C02  122.09  3.000
 YTN  O01  C01  C02  109.44  3.000
 YTN  O02  C02  C03  129.00  3.000
 YTN  C03  C02  C01  121.51  3.000
 YTN  O02  C02  C01  109.48  3.000
 YTN  H1   C03  C04  121.19  3.000
 YTN  H1   C03  C02  121.94  3.000
 YTN  C04  C03  C02  116.87  3.000
 YTN  H2   C04  C05  119.21  3.000
 YTN  H2   C04  C03  118.68  3.000
 YTN  C05  C04  C03  122.11  3.000
 YTN  C11  C05  C06  118.74  3.000
 YTN  C11  C05  C04  121.53  3.000
 YTN  C06  C05  C04  119.73  3.000
 YTN  H3   C06  C05  121.22  3.000
 YTN  H3   C06  C01  121.09  3.000
 YTN  C05  C06  C01  117.69  3.000
 YTN  H25  C07  H4   110.30  3.000
 YTN  H25  C07  O02  109.74  3.000
 YTN  H4   C07  O02  109.96  3.000
 YTN  H25  C07  O01  109.75  3.000
 YTN  H4   C07  O01  109.75  3.000
 YTN  O02  C07  O01  107.28  3.000
 YTN  H7   C09  C12  104.19  3.000
 YTN  H7   C09  C10  107.59  3.000
 YTN  C12  C09  C10  101.90  3.000
 YTN  H7   C09  C08  106.34  3.000
 YTN  C12  C09  C08  115.44  3.000
 YTN  C10  C09  C08  120.14  3.000
 YTN  H8   C10  C13  108.20  3.000
 YTN  H8   C10  C11  109.19  3.000
 YTN  C13  C10  C11  112.57  3.000
 YTN  H8   C10  C09  109.16  3.000
 YTN  C13  C10  C09  100.57  3.000
 YTN  C11  C10  C09  116.65  3.000
 YTN  H10  C11  H9   106.26  3.000
 YTN  H10  C11  C10  109.53  3.000
 YTN  H9   C11  C10  108.27  3.000
 YTN  H10  C11  C05  110.24  3.000
 YTN  H9   C11  C05  108.53  3.000
 YTN  C10  C11  C05  113.71  3.000
 YTN  O04  C12  O03  121.57  3.000
 YTN  O04  C12  C09  128.66  3.000
 YTN  O03  C12  C09  109.76  3.000
 YTN  H12  C13  H11  108.84  3.000
 YTN  H12  C13  O03  108.87  3.000
 YTN  H11  C13  O03  108.41  3.000
 YTN  H12  C13  C10  111.77  3.000
 YTN  H11  C13  C10  113.51  3.000
 YTN  O03  C13  C10  105.26  3.000
 YTN  C19  C14  C15  119.66  3.000
 YTN  C19  C14  C08  121.98  3.000
 YTN  C15  C14  C08  118.34  3.000
 YTN  H13  C15  C16  120.54  3.000
 YTN  H13  C15  C14  118.91  3.000
 YTN  C16  C15  C14  120.54  3.000
 YTN  O07  C16  C17  115.96  3.000
 YTN  C17  C16  C15  120.02  3.000
 YTN  O07  C16  C15  124.02  3.000
 YTN  O06  C17  C18  120.29  3.000
 YTN  C18  C17  C16  119.41  3.000
 YTN  O06  C17  C16  120.28  3.000
 YTN  O05  C18  C19  124.28  3.000
 YTN  O05  C18  C17  115.49  3.000
 YTN  C19  C18  C17  120.22  3.000
 YTN  H14  C19  C18  119.95  3.000
 YTN  H14  C19  C14  119.92  3.000
 YTN  C18  C19  C14  120.14  3.000
 YTN  H17  C20  H16  108.73  3.000
 YTN  H17  C20  H15  108.72  3.000
 YTN  H16  C20  H15  108.73  3.000
 YTN  H17  C20  O05  112.00  3.000
 YTN  H16  C20  O05  112.05  3.000
 YTN  H15  C20  O05  106.49  3.000
 YTN  H20  C21  H19  108.57  3.000
 YTN  H20  C21  H18  108.60  3.000
 YTN  H19  C21  H18  108.57  3.000
 YTN  H20  C21  O06  111.86  3.000
 YTN  H19  C21  O06  111.92  3.000
 YTN  H18  C21  O06  107.22  3.000
 YTN  H23  C22  H22  108.62  3.000
 YTN  H23  C22  H21  108.54  3.000
 YTN  H22  C22  H21  109.00  3.000
 YTN  H23  C22  O07  112.55  3.000
 YTN  H22  C22  O07  111.53  3.000
 YTN  H21  C22  O07  106.49  3.000
 YTN  C07  O01  C01  106.70  3.000
 YTN  C07  O02  C02  106.61  3.000
 YTN  C13  O03  C12  110.39  3.000
 YTN  C20  O05  C18  118.47  3.000
 YTN  C21  O06  C17  114.45  3.000
 YTN  C22  O07  C16  118.15  3.000
 YTN  H6   C08  H5   105.60  3.000
 YTN  H6   C08  C14  109.54  3.000
 YTN  H5   C08  C14  108.09  3.000
 YTN  H6   C08  C09  107.79  3.000
 YTN  H5   C08  C09  107.74  3.000
 YTN  C14  C08  C09  117.45  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
 YTN  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 YTN  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 YTN  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 YTN  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 YTN  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 YTN  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 YTN  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 YTN  CONST_08  C17  C18  C19  C14     0.00   0.0  0
 YTN  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 YTN  CONST_10  C18  C19  C14  C15     0.00   0.0  0
 YTN  CONST_11  C19  C14  C15  C16     0.00   0.0  0
 YTN  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 YTN  CONST_13  C11  C05  C06  C01   180.00   0.0  0
 YTN  CONST_14  C11  C05  C04  C03   180.00   0.0  0
 YTN  CONST_15  C16  C15  C14  C08   180.00   0.0  0
 YTN  CONST_16  C18  C19  C14  C08   180.00   0.0  0
 YTN  CONST_17  O07  C16  C15  C14   180.00   0.0  0
 YTN  CONST_18  O05  C18  C19  C14   180.00   0.0  0
 YTN  CONST_19  O06  C17  C16  C15   180.00   0.0  0
 YTN  CONST_20  O05  C18  C17  C16   180.00   0.0  0
 YTN  CONST_21  O07  C16  C17  C18   180.00   0.0  0
 YTN  CONST_22  O06  C17  C18  C19   180.00   0.0  0
 YTN  CONST_23  H1   C03  C02  C01   180.00   0.0  0
 YTN  CONST_24  H3   C06  C01  C02   180.00   0.0  0
 YTN  CONST_25  H2   C04  C03  C02   180.00   0.0  0
 YTN  CONST_26  H3   C06  C05  C04   180.00   0.0  0
 YTN  CONST_27  H1   C03  C04  C05   180.00   0.0  0
 YTN  CONST_28  H2   C04  C05  C06   180.00   0.0  0
 YTN  CONST_29  H14  C19  C14  C15   180.00   0.0  0
 YTN  CONST_30  H13  C15  C16  C17   180.00   0.0  0
 YTN  CONST_31  H14  C19  C18  C17   180.00   0.0  0
 YTN  CONST_32  H13  C15  C14  C19   180.00   0.0  0
 YTN  CONST_33  H3   C06  C01  O01     0.00   0.0  0
 YTN  CONST_34  H1   C03  C02  O02     0.00   0.0  0
 YTN  Var_01    O02  C07  O01  C01     6.67  30.0  1
 YTN  Var_02    C07  O02  C02  C01     4.59  30.0  1
 YTN  Var_03    O01  C07  O02  C02    -6.91  30.0  1
 YTN  Var_04    C07  O01  C01  C02    -3.93  30.0  1
 YTN  Var_05    C07  O02  C02  C03  -176.03  30.0  1
 YTN  Var_06    C07  O01  C01  C06   177.12  30.0  1
 YTN  Var_07    C13  O03  C12  C09    -1.08  30.0  1
 YTN  Var_08    C12  O03  C13  C10   -20.74  30.0  1
 YTN  Var_09    C10  C11  C05  C04   113.53  30.0  2
 YTN  Var_10    C10  C11  C05  C06   -66.96  30.0  2
 YTN  Var_11    C15  C14  C08  C09  -133.36  30.0  2
 YTN  Var_12    C19  C14  C08  C09    48.14  30.0  2
 YTN  Var_13    O04  C12  O03  C13  -179.73  30.0  1
 YTN  Var_14    H4   C07  O01  C01  -112.78  30.0  1
 YTN  Var_15    H25  C07  O01  C01   125.85  30.0  1
 YTN  Var_16    H4   C07  O02  C02   112.40  30.0  1
 YTN  Var_17    H25  C07  O02  C02  -126.09  30.0  1
 YTN  Var_18    H11  C13  O03  C12  -142.52  30.0  1
 YTN  Var_19    H12  C13  O03  C12    99.22  30.0  1
 YTN  Var_20    C22  O07  C16  C15   -17.75  30.0  2
 YTN  Var_21    C21  O06  C17  C16    90.98  30.0  2
 YTN  Var_22    C22  O07  C16  C17   162.62  30.0  2
 YTN  Var_23    C20  O05  C18  C17  -179.45  30.0  2
 YTN  Var_24    C21  O06  C17  C18   -90.59  30.0  2
 YTN  Var_25    C20  O05  C18  C19    -0.44  30.0  2
 YTN  Var_26    H9   C11  C05  C04  -125.92  30.0  2
 YTN  Var_27    H10  C11  C05  C04    -9.92  30.0  2
 YTN  Var_28    H9   C11  C05  C06    53.60  30.0  2
 YTN  Var_29    H10  C11  C05  C06   169.60  30.0  2
 YTN  Var_30    H5   C08  C14  C15   -11.29  30.0  2
 YTN  Var_31    H6   C08  C14  C15   103.29  30.0  2
 YTN  Var_32    H5   C08  C14  C19   170.21  30.0  2
 YTN  Var_33    H6   C08  C14  C19   -75.21  30.0  2
 YTN  Var_34    H21  C22  O07  C16  -173.26  30.0  3
 YTN  Var_35    H22  C22  O07  C16   -54.46  30.0  3
 YTN  Var_36    H23  C22  O07  C16    67.92  30.0  3
 YTN  Var_37    H18  C21  O06  C17  -177.33  30.0  3
 YTN  Var_38    H19  C21  O06  C17   -58.38  30.0  3
 YTN  Var_39    H20  C21  O06  C17    63.71  30.0  3
 YTN  Var_40    H15  C20  O05  C18  -179.38  30.0  3
 YTN  Var_41    H16  C20  O05  C18   -60.61  30.0  3
 YTN  Var_42    H17  C20  O05  C18    61.89  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
 YTN  chir_01  C09  C10  C08  C12  negativ
 YTN  chir_02  C10  C09  C13  C11  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
 YTN  plan-1  C14  0.020
 YTN  plan-1  C15  0.020
 YTN  plan-1  C16  0.020
 YTN  plan-1  C17  0.020
 YTN  plan-1  C18  0.020
 YTN  plan-1  C19  0.020
 YTN  plan-1  O05  0.020
 YTN  plan-1  O06  0.020
 YTN  plan-1  O07  0.020
 YTN  plan-1  H13  0.020
 YTN  plan-1  H14  0.020
 YTN  plan-1  C08  0.020
 YTN  plan-2  C01  0.020
 YTN  plan-2  C02  0.020
 YTN  plan-2  C03  0.020
 YTN  plan-2  C04  0.020
 YTN  plan-2  C05  0.020
 YTN  plan-2  C06  0.020
 YTN  plan-2  C11  0.020
 YTN  plan-2  O01  0.020
 YTN  plan-2  O02  0.020
 YTN  plan-2  H1   0.020
 YTN  plan-2  H2   0.020
 YTN  plan-2  H3   0.020
 YTN  plan-3  C09  0.020
 YTN  plan-3  C12  0.020
 YTN  plan-3  O03  0.020
 YTN  plan-3  O04  0.020

