# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 03:11:39 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: (3~{S},4~{S})-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
 YTC  YTC  "(3~{S},4~{S})-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_YTC
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
 YTC  C01  C  CH3   0  -0.436  -17.3234  15.9149  -19.7497
 YTC  C03  C  CR6   0   0.354  -19.0383  17.2490  -20.6990
 YTC  C04  C  CR16  0  -0.484  -18.4873  18.4282  -20.1994
 YTC  C05  C  CR6   0   0.175  -19.0923  19.6487  -20.4727
 YTC  C06  C  CR16  0  -0.474  -20.2637  19.6898  -21.2211
 YTC  C07  C  CR6   0   0.348  -20.8283  18.5149  -21.7082
 YTC  C08  C  CR6   0   0.153  -20.2148  17.2861  -21.4496
 YTC  C10  C  CH3   0  -0.411  -20.3049  15.7379  -23.1955
 YTC  C12  C  CH3   0  -0.442  -22.6946  19.6483  -22.6356
 YTC  C13  C  CH2   0  -0.497  -18.5298  20.9489  -19.9572
 YTC  C14  C  CH1   0  -0.449  -17.0006  21.0374  -19.8509
 YTC  C15  C  CH1   0  -0.292  -16.3893  22.3692  -20.2927
 YTC  C16  C  CH2   0  -0.152  -15.1962  22.5163  -19.3481
 YTC  C18  C  C     0   0.600  -16.5000  20.8815  -18.4332
 YTC  C20  C  CH2   0  -0.513  -15.9702  22.4225  -21.7635
 YTC  C21  C  CR6   0   0.112  -17.0867  22.0531  -22.7016
 YTC  C22  C  CR16  0  -0.386  -17.1887  20.7295  -23.1582
 YTC  C23  C  CR56  0   0.328  -18.2677  20.4067  -23.9410
 YTC  C24  C  CR56  0   0.289  -19.2272  21.3407  -24.2881
 YTC  C25  C  CR16  0  -0.332  -19.1485  22.6442  -23.8655
 YTC  C26  C  CR16  0  -0.318  -18.0524  22.9843  -23.0633
 YTC  C28  C  CH2   0   0.061  -19.7220  19.4279  -25.3036
 YTC  O02  O  O2    0  -0.464  -18.5140  16.0253  -20.5015
 YTC  O09  O  O2    0  -0.479  -20.7681  16.1324  -21.9132
 YTC  O11  O  O2    0  -0.468  -21.9568  18.4591  -22.4390
 YTC  O17  O  O2    0  -0.439  -15.5117  21.7385  -18.1864
 YTC  O19  O  O     0  -0.427  -16.8912  20.1166  -17.5931
 YTC  O27  O  O     0  -0.491  -20.1909  20.7416  -25.0335
 YTC  O29  O  O     0  -0.486  -18.6029  19.1998  -24.4591
 YTC  H1   H  HCH3  0   0.258  -17.0783  14.8561  -19.7145
 YTC  H2   H  HCH3  0   0.227  -16.4931  16.4528  -20.2148
 YTC  H3   H  HCH3  0   0.227  -17.4484  16.2799  -18.7267
 YTC  H4   H  HCR6  0   0.270  -17.5882  18.3957  -19.5997
 YTC  H5   H  HCR6  0   0.267  -20.7181  20.6494  -21.4297
 YTC  H6   H  HCH3  0   0.234  -20.8067  14.8046  -23.4465
 YTC  H7   H  HCH3  0   0.222  -20.5462  16.4785  -23.9624
 YTC  H8   H  HCH3  0   0.218  -19.2256  15.5660  -23.2041
 YTC  H9   H  HCH3  0   0.257  -23.5857  19.3675  -23.1923
 YTC  H10  H  HCH3  0   0.227  -22.9996  20.1004  -21.6881
 YTC  H11  H  HCH3  0   0.229  -22.1386  20.3868  -23.2168
 YTC  H12  H  HCH2  0   0.271  -18.8752  21.7497  -20.6112
 YTC  H13  H  HCH2  0   0.266  -18.9763  21.1634  -18.9813
 YTC  H14  H  HCH1  0   0.308  -16.5377  20.2264  -20.4287
 YTC  H15  H  HCH1  0   0.273  -17.1077  23.1713  -20.0946
 YTC  H16  H  HCH2  0   0.239  -14.2777  22.1205  -19.7892
 YTC  H17  H  HCH2  0   0.257  -15.0163  23.5428  -19.0334
 YTC  H18  H  HCH2  0   0.250  -15.1328  21.7349  -21.9098
 YTC  H19  H  HCH2  0   0.261  -15.5984  23.4250  -21.9897
 YTC  H20  H  HCR6  0   0.264  -16.4486  19.9862  -22.8887
 YTC  H21  H  HCR6  0   0.268  -19.8970  23.3777  -24.1336
 YTC  H22  H  HCR6  0   0.248  -17.9634  24.0042  -22.7088
 YTC  H23  H  HCH2  0   0.234  -19.4165  19.3509  -26.3533
 YTC  H24  H  HCH2  0   0.242  -20.5060  18.7027  -25.0826

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
 YTC  C28  O29  single    1.420  0.020  1.420
 YTC  C28  O27  single    1.421  0.020  1.421
 YTC  O29  C23  single    1.355  0.020  1.355
 YTC  O27  C24  single    1.358  0.020  1.358
 YTC  C23  C24  aromatic  1.383  0.020  1.383
 YTC  C23  C22  aromatic  1.372  0.020  1.372
 YTC  C24  C25  aromatic  1.373  0.020  1.373
 YTC  C22  C21  aromatic  1.404  0.020  1.404
 YTC  C25  C26  aromatic  1.400  0.020  1.400
 YTC  C12  O11  single    1.413  0.020  1.413
 YTC  O11  C07  single    1.346  0.020  1.346
 YTC  C21  C26  aromatic  1.389  0.020  1.389
 YTC  C21  C20  single    1.504  0.020  1.504
 YTC  C10  O09  single    1.419  0.020  1.419
 YTC  C20  C15  single    1.530  0.020  1.530
 YTC  C07  C06  aromatic  1.392  0.020  1.392
 YTC  C07  C08  aromatic  1.398  0.020  1.398
 YTC  O09  C08  single    1.361  0.020  1.361
 YTC  C06  C05  aromatic  1.391  0.020  1.391
 YTC  C08  C03  aromatic  1.396  0.020  1.396
 YTC  C15  C14  single    1.531  0.020  1.531
 YTC  C15  C16  single    1.529  0.020  1.529
 YTC  C05  C13  single    1.508  0.020  1.508
 YTC  C05  C04  aromatic  1.389  0.020  1.389
 YTC  C03  C04  aromatic  1.394  0.020  1.394
 YTC  C03  O02  single    1.346  0.020  1.346
 YTC  C14  C13  single    1.535  0.020  1.535
 YTC  C14  C18  single    1.512  0.020  1.512
 YTC  C16  O17  single    1.433  0.020  1.433
 YTC  O02  C01  single    1.412  0.020  1.412
 YTC  C18  O17  single    1.331  0.020  1.331
 YTC  C18  O19  double    1.202  0.020  1.202
 YTC  C01  H1   single    0.970  0.020  1.090
 YTC  C01  H2   single    0.970  0.020  1.090
 YTC  C01  H3   single    0.970  0.020  1.090
 YTC  C04  H4   single    0.930  0.020  1.080
 YTC  C06  H5   single    0.930  0.020  1.080
 YTC  C10  H6   single    0.970  0.020  1.090
 YTC  C10  H7   single    0.970  0.020  1.090
 YTC  C10  H8   single    0.970  0.020  1.090
 YTC  C12  H9   single    0.970  0.020  1.090
 YTC  C12  H10  single    0.970  0.020  1.090
 YTC  C12  H11  single    0.970  0.020  1.090
 YTC  C13  H12  single    0.970  0.020  1.090
 YTC  C13  H13  single    0.970  0.020  1.090
 YTC  C14  H14  single    0.970  0.020  1.090
 YTC  C15  H15  single    0.970  0.020  1.090
 YTC  C16  H16  single    0.970  0.020  1.090
 YTC  C16  H17  single    0.970  0.020  1.090
 YTC  C20  H18  single    0.970  0.020  1.090
 YTC  C20  H19  single    0.970  0.020  1.090
 YTC  C22  H20  single    0.930  0.020  1.080
 YTC  C25  H21  single    0.930  0.020  1.080
 YTC  C26  H22  single    0.930  0.020  1.080
 YTC  C28  H23  single    0.970  0.020  1.090
 YTC  C28  H24  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
 YTC  H3   C01  H2   108.71  3.000
 YTC  H3   C01  H1   108.70  3.000
 YTC  H2   C01  H1   108.76  3.000
 YTC  H3   C01  O02  112.06  3.000
 YTC  H2   C01  O02  112.04  3.000
 YTC  H1   C01  O02  106.46  3.000
 YTC  O02  C03  C08  115.55  3.000
 YTC  O02  C03  C04  124.23  3.000
 YTC  C08  C03  C04  120.21  3.000
 YTC  H4   C04  C05  119.84  3.000
 YTC  H4   C04  C03  120.12  3.000
 YTC  C05  C04  C03  120.03  3.000
 YTC  C13  C05  C06  118.22  3.000
 YTC  C13  C05  C04  121.87  3.000
 YTC  C06  C05  C04  119.91  3.000
 YTC  H5   C06  C07  120.72  3.000
 YTC  H5   C06  C05  118.92  3.000
 YTC  C07  C06  C05  120.34  3.000
 YTC  O11  C07  C08  115.60  3.000
 YTC  C08  C07  C06  119.97  3.000
 YTC  O11  C07  C06  124.43  3.000
 YTC  O09  C08  C07  120.25  3.000
 YTC  O09  C08  C03  120.22  3.000
 YTC  C07  C08  C03  119.52  3.000
 YTC  H8   C10  H7   108.60  3.000
 YTC  H8   C10  H6   108.57  3.000
 YTC  H7   C10  H6   108.50  3.000
 YTC  H8   C10  O09  111.91  3.000
 YTC  H7   C10  O09  111.93  3.000
 YTC  H6   C10  O09  107.23  3.000
 YTC  H11  C12  H10  108.88  3.000
 YTC  H11  C12  H9   108.63  3.000
 YTC  H10  C12  H9   108.77  3.000
 YTC  H11  C12  O11  112.16  3.000
 YTC  H10  C12  O11  111.90  3.000
 YTC  H9   C12  O11  106.36  3.000
 YTC  H13  C13  H12  105.17  3.000
 YTC  H13  C13  C14  109.46  3.000
 YTC  H12  C13  C14  108.35  3.000
 YTC  H13  C13  C05  108.77  3.000
 YTC  H12  C13  C05  108.07  3.000
 YTC  C14  C13  C05  116.43  3.000
 YTC  H14  C14  C18  106.12  3.000
 YTC  H14  C14  C15  108.80  3.000
 YTC  C18  C14  C15  103.19  3.000
 YTC  H14  C14  C13  109.92  3.000
 YTC  C18  C14  C13  112.88  3.000
 YTC  C15  C14  C13  115.34  3.000
 YTC  H15  C15  C20  109.15  3.000
 YTC  H15  C15  C16  109.26  3.000
 YTC  C20  C15  C16  112.13  3.000
 YTC  H15  C15  C14  108.86  3.000
 YTC  C16  C15  C14  102.54  3.000
 YTC  C20  C15  C14  114.65  3.000
 YTC  H17  C16  H16  108.61  3.000
 YTC  H17  C16  O17  108.29  3.000
 YTC  H16  C16  O17  108.39  3.000
 YTC  H17  C16  C15  113.47  3.000
 YTC  H16  C16  C15  111.82  3.000
 YTC  O17  C16  C15  106.07  3.000
 YTC  O19  C18  O17  121.46  3.000
 YTC  O19  C18  C14  127.85  3.000
 YTC  O17  C18  C14  110.69  3.000
 YTC  H19  C20  H18  106.77  3.000
 YTC  H19  C20  C21  110.40  3.000
 YTC  H18  C20  C21  109.30  3.000
 YTC  H19  C20  C15  108.91  3.000
 YTC  H18  C20  C15  108.45  3.000
 YTC  C21  C20  C15  112.81  3.000
 YTC  C26  C21  C22  119.78  3.000
 YTC  C26  C21  C20  120.91  3.000
 YTC  C22  C21  C20  119.23  3.000
 YTC  H20  C22  C23  121.20  3.000
 YTC  H20  C22  C21  121.10  3.000
 YTC  C23  C22  C21  117.69  3.000
 YTC  O29  C23  C24  109.49  3.000
 YTC  C24  C23  C22  122.00  3.000
 YTC  O29  C23  C22  128.48  3.000
 YTC  O27  C24  C25  128.96  3.000
 YTC  C25  C24  C23  121.61  3.000
 YTC  O27  C24  C23  109.40  3.000
 YTC  H21  C25  C26  121.26  3.000
 YTC  H21  C25  C24  121.87  3.000
 YTC  C26  C25  C24  116.87  3.000
 YTC  H22  C26  C25  118.72  3.000
 YTC  H22  C26  C21  119.24  3.000
 YTC  C25  C26  C21  122.03  3.000
 YTC  H24  C28  H23  110.36  3.000
 YTC  H24  C28  O29  109.82  3.000
 YTC  H23  C28  O29  109.79  3.000
 YTC  H24  C28  O27  109.82  3.000
 YTC  H23  C28  O27  109.82  3.000
 YTC  O29  C28  O27  107.18  3.000
 YTC  C03  O02  C01  118.52  3.000
 YTC  C10  O09  C08  114.26  3.000
 YTC  C12  O11  C07  118.59  3.000
 YTC  C18  O17  C16  111.25  3.000
 YTC  C28  O27  C24  106.15  3.000
 YTC  C28  O29  C23  106.21  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
 YTC  CONST_01  C06  C07  C08  C03     0.00   0.0  0
 YTC  CONST_02  C06  C05  C04  C03     0.00   0.0  0
 YTC  CONST_03  C07  C06  C05  C04     0.00   0.0  0
 YTC  CONST_04  C07  C08  C03  C04     0.00   0.0  0
 YTC  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 YTC  CONST_06  C08  C03  C04  C05     0.00   0.0  0
 YTC  CONST_07  C24  C23  C22  C21     0.00   0.0  0
 YTC  CONST_08  C24  C25  C26  C21     0.00   0.0  0
 YTC  CONST_09  C25  C24  C23  C22     0.00   0.0  0
 YTC  CONST_10  C25  C26  C21  C22     0.00   0.0  0
 YTC  CONST_11  C26  C25  C24  C23     0.00   0.0  0
 YTC  CONST_12  C26  C21  C22  C23     0.00   0.0  0
 YTC  CONST_13  O11  C07  C08  C03   180.00   0.0  0
 YTC  CONST_14  C13  C05  C04  C03   180.00   0.0  0
 YTC  CONST_15  O09  C08  C03  C04   180.00   0.0  0
 YTC  CONST_16  O11  C07  C06  C05   180.00   0.0  0
 YTC  CONST_17  O02  C03  C04  C05   180.00   0.0  0
 YTC  CONST_18  O09  C08  C07  C06   180.00   0.0  0
 YTC  CONST_19  C13  C05  C06  C07   180.00   0.0  0
 YTC  CONST_20  O02  C03  C08  C07   180.00   0.0  0
 YTC  CONST_21  C23  C22  C21  C20   180.00   0.0  0
 YTC  CONST_22  C25  C26  C21  C20   180.00   0.0  0
 YTC  CONST_23  H5   C06  C05  C04   180.00   0.0  0
 YTC  CONST_24  H4   C04  C05  C06   180.00   0.0  0
 YTC  CONST_25  H5   C06  C07  C08   180.00   0.0  0
 YTC  CONST_26  H4   C04  C03  C08   180.00   0.0  0
 YTC  CONST_27  H21  C25  C26  C21   180.00   0.0  0
 YTC  CONST_28  H22  C26  C21  C22   180.00   0.0  0
 YTC  CONST_29  H21  C25  C24  C23   180.00   0.0  0
 YTC  CONST_30  H20  C22  C23  C24   180.00   0.0  0
 YTC  CONST_31  H22  C26  C25  C24   180.00   0.0  0
 YTC  CONST_32  H20  C22  C21  C26   180.00   0.0  0
 YTC  CONST_33  H21  C25  C24  O27     0.00   0.0  0
 YTC  CONST_34  H20  C22  C23  O29     0.00   0.0  0
 YTC  Var_01    C16  O17  C18  C14    -1.80  30.0  1
 YTC  Var_02    C18  O17  C16  C15    17.05  30.0  1
 YTC  Var_03    C28  O29  C23  C22  -174.04  30.0  1
 YTC  Var_04    O27  C28  O29  C23   -12.17  30.0  1
 YTC  Var_05    C28  O27  C24  C23    -7.66  30.0  1
 YTC  Var_06    O29  C28  O27  C24    12.19  30.0  1
 YTC  Var_07    C28  O29  C23  C24     7.60  30.0  1
 YTC  Var_08    C28  O27  C24  C25   174.03  30.0  1
 YTC  Var_09    C14  C13  C05  C04    33.86  30.0  2
 YTC  Var_10    C14  C13  C05  C06  -147.30  30.0  2
 YTC  Var_11    C22  C21  C20  C15   -95.04  30.0  2
 YTC  Var_12    C26  C21  C20  C15    81.57  30.0  2
 YTC  Var_13    O19  C18  O17  C16   178.29  30.0  1
 YTC  Var_14    H16  C16  O17  C18  -103.18  30.0  1
 YTC  Var_15    H17  C16  O17  C18   139.17  30.0  1
 YTC  Var_16    H23  C28  O29  C23   107.07  30.0  1
 YTC  Var_17    H24  C28  O29  C23  -131.42  30.0  1
 YTC  Var_18    H23  C28  O27  C24  -107.03  30.0  1
 YTC  Var_19    H24  C28  O27  C24   131.44  30.0  1
 YTC  Var_20    C08  C03  O02  C01  -179.98  30.0  3
 YTC  Var_21    C04  C03  O02  C01    -0.49  30.0  3
 YTC  Var_22    C10  O09  C08  C03   -89.75  30.0  3
 YTC  Var_23    C12  O11  C07  C06    -5.87  30.0  2
 YTC  Var_24    C10  O09  C08  C07    90.98  30.0  3
 YTC  Var_25    C12  O11  C07  C08   174.33  30.0  2
 YTC  Var_26    H12  C13  C05  C04   155.99  30.0  2
 YTC  Var_27    H13  C13  C05  C04   -90.33  30.0  2
 YTC  Var_28    H12  C13  C05  C06   -25.17  30.0  2
 YTC  Var_29    H13  C13  C05  C06    88.51  30.0  2
 YTC  Var_30    H18  C20  C21  C22    25.69  30.0  2
 YTC  Var_31    H19  C20  C21  C22   142.86  30.0  2
 YTC  Var_32    H18  C20  C21  C26  -157.69  30.0  2
 YTC  Var_33    H19  C20  C21  C26   -40.53  30.0  2
 YTC  Var_34    H1   C01  O02  C03  -179.91  30.0  3
 YTC  Var_35    H2   C01  O02  C03   -61.14  30.0  3
 YTC  Var_36    H3   C01  O02  C03    61.38  30.0  3
 YTC  Var_37    H9   C12  O11  C07  -176.60  30.0  3
 YTC  Var_38    H10  C12  O11  C07   -57.95  30.0  3
 YTC  Var_39    H11  C12  O11  C07    64.77  30.0  3
 YTC  Var_40    H6   C10  O09  C08   179.28  30.0  3
 YTC  Var_41    H7   C10  O09  C08   -61.85  30.0  3
 YTC  Var_42    H8   C10  O09  C08    60.32  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
 YTC  chir_01  C14  C15  C13  C18  positiv
 YTC  chir_02  C15  C20  C14  C16  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
 YTC  plan-1  C03  0.020
 YTC  plan-1  C04  0.020
 YTC  plan-1  C05  0.020
 YTC  plan-1  C06  0.020
 YTC  plan-1  C07  0.020
 YTC  plan-1  C08  0.020
 YTC  plan-1  C13  0.020
 YTC  plan-1  O02  0.020
 YTC  plan-1  O09  0.020
 YTC  plan-1  O11  0.020
 YTC  plan-1  H4   0.020
 YTC  plan-1  H5   0.020
 YTC  plan-2  C20  0.020
 YTC  plan-2  C21  0.020
 YTC  plan-2  C22  0.020
 YTC  plan-2  C23  0.020
 YTC  plan-2  C24  0.020
 YTC  plan-2  C25  0.020
 YTC  plan-2  C26  0.020
 YTC  plan-2  O27  0.020
 YTC  plan-2  O29  0.020
 YTC  plan-2  H20  0.020
 YTC  plan-2  H21  0.020
 YTC  plan-2  H22  0.020
 YTC  plan-3  C14  0.020
 YTC  plan-3  C18  0.020
 YTC  plan-3  O17  0.020
 YTC  plan-3  O19  0.020

