# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 20:10:06 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 4'-[(3,6,9,12-tetraoxapentadec-14-yn-1-yl)oxy][1,1'-biphenyl]-4-yl sulfurofluoridate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: F[S](=O)(=O)Oc1ccc(cc1)c2ccc(OCCOCCOCCOCCOCC#C)cc2
#
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
 YWZ  YWZ  '4'-[(3,6,9,12-tetraoxapentadec-14-yn-1-yl)oxy][1,1'-biphenyl]-4-yl sulfurofluoridate'  ligand  60  33  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YWZ
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
 YWZ  O1   O  OS    0  -0.574  -10.7439  -1.7087   0.6048
 YWZ  O2   O  OS    0  -0.582   -9.6016   0.2470  -0.4924
 YWZ  O3   O  OC2   0  -0.584   -8.3968  -1.3484   1.0005
 YWZ  O4   O  O2    0  -0.468    0.5820   2.2517  -0.5692
 YWZ  O5   O  O2    0  -0.484    3.3817   2.1254  -0.4564
 YWZ  C6   C  CR6   0   0.287   -7.1343  -0.8113   0.7045
 YWZ  C7   C  CR16  0  -0.271   -6.2071  -1.6147   0.0693
 YWZ  C8   C  CR16  0  -0.315   -4.9369  -1.1094  -0.1550
 YWZ  C9   C  CR6   0   0.109   -4.5918   0.1860   0.2370
 YWZ  C10  C  CR6   0   0.069   -3.2356   0.7135   0.0003
 YWZ  C11  C  CR16  0  -0.292   -2.6323   1.5858   0.9117
 YWZ  C12  C  CR16  0  -0.333   -1.3621   2.0812   0.6991
 YWZ  C13  C  CR6   0   0.385   -0.6453   1.7201  -0.4443
 YWZ  C14  C  CH2   0  -0.223    1.3696   1.9122  -1.6973
 YWZ  C15  C  CH2   0  -0.159    2.6937   2.6186  -1.5747
 YWZ  C16  C  CH2   0  -0.170    4.6127   2.7684  -0.2405
 YWZ  C25  C  CR16  0  -0.369   -1.2306   0.8539  -1.3651
 YWZ  C26  C  CR16  0  -0.295   -2.5085   0.3630  -1.1341
 YWZ  C27  C  CR16  0  -0.318   -5.5625   0.9652   0.8709
 YWZ  C28  C  CR16  0  -0.265   -6.8355   0.4748   1.1112
 YWZ  S    S  S     0   1.744   -9.6042  -1.0894   0.0132
 YWZ  H3   H  HCR6  0   0.290   -6.4551  -2.6261  -0.2232
 YWZ  H4   H  HCR6  0   0.269   -4.2008  -1.7477  -0.6256
 YWZ  H5   H  HCR6  0   0.259   -3.1528   1.8715   1.8175
 YWZ  H6   H  HCR6  0   0.265   -0.9087   2.7466   1.4230
 YWZ  H7   H  HCH2  0   0.234    1.5200   0.8284  -1.7540
 YWZ  H8   H  HCH2  0   0.237    0.8836   2.2322  -2.6251
 YWZ  H9   H  HCH2  0   0.212    2.5327   3.7033  -1.4981
 YWZ  H10  H  HCH2  0   0.216    3.2567   2.4450  -2.5021
 YWZ  H11  H  HCH2  0   0.207    5.2810   2.6443  -1.1045
 YWZ  H12  H  HCH2  0   0.209    4.4741   3.8489  -0.0973
 YWZ  H14  H  HCR6  0   0.282   -0.7158   0.5548  -2.2680
 YWZ  H15  H  HCR6  0   0.260   -2.9471  -0.2923  -1.8764
 YWZ  H16  H  HCR6  0   0.269   -5.3332   1.9790   1.1717
 YWZ  H17  H  HCR6  0   0.290   -7.5738   1.0863   1.6125
 YWZ  F1   F  F     0  -0.393   -9.1431  -2.0113  -1.1906
 YWZ  C1   C  CH2   0  -0.168    5.2602   2.2101   1.0002
 YWZ  O6   O  O2    0  -0.485    5.5985   0.8628   0.7927
 YWZ  C3   C  CH2   0  -0.169    6.1890   0.2692   1.9205
 YWZ  C4   C  CH2   0  -0.170    6.5397  -1.1646   1.6173
 YWZ  O7   O  O2    0  -0.485    7.5432  -1.2108   0.6352
 YWZ  C17  C  CH2   0  -0.167    7.9255  -2.5222   0.3110
 YWZ  C18  C  CH2   0  -0.178    9.0019  -2.4935  -0.7419
 YWZ  O8   O  O2    0  -0.483   10.1622  -1.8944  -0.2105
 YWZ  C20  C  CH2   0  -0.272   11.2066  -1.8490  -1.1475
 YWZ  C21  C  CSP   0   0.233   12.3578  -1.1821  -0.5504
 YWZ  C22  C  CSP1  0  -0.512   13.3146  -0.6355  -0.0726
 YWZ  H1   H  HCH2  0   0.208    6.1513   2.8125   1.2252
 YWZ  H2   H  HCH2  0   0.205    4.5778   2.3202   1.8556
 YWZ  H13  H  HCH2  0   0.205    7.0904   0.8179   2.2301
 YWZ  H18  H  HCH2  0   0.207    5.5022   0.2768   2.7785
 YWZ  H19  H  HCH2  0   0.208    6.8762  -1.6378   2.5500
 YWZ  H20  H  HCH2  0   0.205    5.6417  -1.7090   1.2911
 YWZ  H21  H  HCH2  0   0.207    8.2853  -3.0615   1.1992
 YWZ  H22  H  HCH2  0   0.210    7.0773  -3.0973  -0.0858
 YWZ  H23  H  HCH2  0   0.215    9.2005  -3.5264  -1.0583
 YWZ  H24  H  HCH2  0   0.214    8.6517  -1.9468  -1.6284
 YWZ  H25  H  HCH2  0   0.245   11.5023  -2.8567  -1.4702
 YWZ  H26  H  HCH2  0   0.245   10.9078  -1.3067  -2.0551
 YWZ  H27  H  H     0   0.281   14.1623  -0.1482   0.3522

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
 YWZ  C16  O5   single    1.406  0.020  1.406
 YWZ  O5   C15  single    1.403  0.020  1.403
 YWZ  C15  C14  single    1.506  0.020  1.506
 YWZ  C14  O4   single    1.417  0.020  1.417
 YWZ  O4   C13  single    1.343  0.020  1.343
 YWZ  C13  C12  aromatic  1.397  0.020  1.397
 YWZ  C13  C25  aromatic  1.393  0.020  1.393
 YWZ  C12  C11  aromatic  1.380  0.020  1.380
 YWZ  C25  C26  aromatic  1.388  0.020  1.388
 YWZ  C11  C10  aromatic  1.398  0.020  1.398
 YWZ  C26  C10  aromatic  1.392  0.020  1.392
 YWZ  C10  C9   single    1.474  0.020  1.474
 YWZ  C8   C9   aromatic  1.397  0.020  1.397
 YWZ  C8   C7   aromatic  1.385  0.020  1.385
 YWZ  C9   C27  aromatic  1.397  0.020  1.397
 YWZ  C7   C6   aromatic  1.382  0.020  1.382
 YWZ  C27  C28  aromatic  1.385  0.020  1.385
 YWZ  C6   C28  aromatic  1.382  0.020  1.382
 YWZ  C6   O3   single    1.404  0.020  1.404
 YWZ  O3   S    single    1.581  0.020  1.581
 YWZ  O1   S    deloc     1.426  0.020  1.426
 YWZ  S    O2   deloc     1.429  0.020  1.429
 YWZ  C7   H3   single    0.929  0.020  1.085
 YWZ  C8   H4   single    0.929  0.020  1.085
 YWZ  C11  H5   single    0.929  0.020  1.085
 YWZ  C12  H6   single    0.929  0.020  1.085
 YWZ  C14  H7   single    0.939  0.020  1.096
 YWZ  C14  H8   single    0.939  0.020  1.096
 YWZ  C15  H9   single    0.939  0.020  1.096
 YWZ  C15  H10  single    0.939  0.020  1.096
 YWZ  C16  H11  single    0.939  0.020  1.096
 YWZ  C16  H12  single    0.939  0.020  1.096
 YWZ  C25  H14  single    0.929  0.020  1.085
 YWZ  C26  H15  single    0.929  0.020  1.085
 YWZ  C27  H16  single    0.929  0.020  1.085
 YWZ  C28  H17  single    0.929  0.020  1.085
 YWZ  S    F1   single    1.585  0.020  1.585
 YWZ  C16  C1   single    1.507  0.020  1.507
 YWZ  C1   O6   single    1.405  0.020  1.405
 YWZ  O6   C3   single    1.405  0.020  1.405
 YWZ  C3   C4   single    1.507  0.020  1.507
 YWZ  C4   O7   single    1.405  0.020  1.405
 YWZ  O7   C17  single    1.404  0.020  1.404
 YWZ  C17  C18  single    1.506  0.020  1.506
 YWZ  C18  O8   single    1.410  0.020  1.410
 YWZ  O8   C20  single    1.404  0.020  1.404
 YWZ  C20  C21  single    1.458  0.020  1.458
 YWZ  C21  C22  triple    1.201  0.020  1.201
 YWZ  C1   H1   single    0.939  0.020  1.096
 YWZ  C1   H2   single    0.939  0.020  1.096
 YWZ  C3   H13  single    0.939  0.020  1.096
 YWZ  C3   H18  single    0.939  0.020  1.096
 YWZ  C4   H19  single    0.939  0.020  1.096
 YWZ  C4   H20  single    0.939  0.020  1.096
 YWZ  C17  H21  single    0.939  0.020  1.096
 YWZ  C17  H22  single    0.939  0.020  1.096
 YWZ  C18  H23  single    0.939  0.020  1.096
 YWZ  C18  H24  single    0.939  0.020  1.096
 YWZ  C20  H25  single    0.939  0.020  1.096
 YWZ  C20  H26  single    0.939  0.020  1.096
 YWZ  C22  H27  single    0.913  0.020  1.066

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
 YWZ  S    O3   C6   119.51  3.000
 YWZ  C14  O4   C13  119.14  3.000
 YWZ  C16  O5   C15  113.03  3.000
 YWZ  C28  C6   C7   122.11  3.000
 YWZ  C28  C6   O3   119.26  3.000
 YWZ  C7   C6   O3   118.56  3.000
 YWZ  H3   C7   C8   120.49  3.000
 YWZ  H3   C7   C6   120.95  3.000
 YWZ  C8   C7   C6   118.54  3.000
 YWZ  H4   C8   C9   120.07  3.000
 YWZ  H4   C8   C7   118.63  3.000
 YWZ  C9   C8   C7   121.29  3.000
 YWZ  C27  C9   C10  120.83  3.000
 YWZ  C27  C9   C8   118.23  3.000
 YWZ  C10  C9   C8   120.94  3.000
 YWZ  C26  C10  C11  117.56  3.000
 YWZ  C26  C10  C9   121.41  3.000
 YWZ  C11  C10  C9   121.03  3.000
 YWZ  H5   C11  C12  118.46  3.000
 YWZ  H5   C11  C10  120.15  3.000
 YWZ  C12  C11  C10  121.37  3.000
 YWZ  H6   C12  C13  119.42  3.000
 YWZ  H6   C12  C11  120.20  3.000
 YWZ  C13  C12  C11  120.37  3.000
 YWZ  C25  C13  C12  119.09  3.000
 YWZ  C25  C13  O4   124.64  3.000
 YWZ  C12  C13  O4   116.27  3.000
 YWZ  H8   C14  H7   107.83  3.000
 YWZ  H8   C14  C15  108.79  3.000
 YWZ  H7   C14  C15  110.34  3.000
 YWZ  H8   C14  O4   110.96  3.000
 YWZ  H7   C14  O4   110.76  3.000
 YWZ  C15  C14  O4   108.15  3.000
 YWZ  H10  C15  H9   106.84  3.000
 YWZ  H10  C15  C14  107.92  3.000
 YWZ  H9   C15  C14  109.86  3.000
 YWZ  H10  C15  O5   111.48  3.000
 YWZ  H9   C15  O5   111.30  3.000
 YWZ  C14  C15  O5   109.35  3.000
 YWZ  C1   C16  H12  108.14  3.000
 YWZ  C1   C16  H11  110.12  3.000
 YWZ  H12  C16  H11  106.87  3.000
 YWZ  C1   C16  O5   109.47  3.000
 YWZ  H12  C16  O5   111.07  3.000
 YWZ  H11  C16  O5   111.10  3.000
 YWZ  H14  C25  C26  118.63  3.000
 YWZ  H14  C25  C13  121.59  3.000
 YWZ  C26  C25  C13  119.78  3.000
 YWZ  H15  C26  C25  118.21  3.000
 YWZ  H15  C26  C10  119.95  3.000
 YWZ  C25  C26  C10  121.82  3.000
 YWZ  H16  C27  C28  118.58  3.000
 YWZ  H16  C27  C9   120.10  3.000
 YWZ  C28  C27  C9   121.32  3.000
 YWZ  H17  C28  C27  120.49  3.000
 YWZ  H17  C28  C6   120.99  3.000
 YWZ  C27  C28  C6   118.51  3.000
 YWZ  F1   S    O3    99.03  3.000
 YWZ  F1   S    O2   105.95  3.000
 YWZ  O3   S    O2   111.89  3.000
 YWZ  F1   S    O1   107.17  3.000
 YWZ  O2   S    O1   123.68  3.000
 YWZ  O3   S    O1   106.27  3.000
 YWZ  H2   C1   H1   106.80  3.000
 YWZ  H2   C1   O6   111.13  3.000
 YWZ  H1   C1   O6   111.15  3.000
 YWZ  H2   C1   C16  109.68  3.000
 YWZ  H1   C1   C16  108.29  3.000
 YWZ  O6   C1   C16  109.71  3.000
 YWZ  C3   O6   C1   112.83  3.000
 YWZ  H18  C3   H13  106.79  3.000
 YWZ  H18  C3   C4   108.00  3.000
 YWZ  H13  C3   C4   109.91  3.000
 YWZ  H18  C3   O6   111.17  3.000
 YWZ  H13  C3   O6   111.09  3.000
 YWZ  C4   C3   O6   109.78  3.000
 YWZ  H20  C4   H19  106.78  3.000
 YWZ  H20  C4   O7   111.08  3.000
 YWZ  H19  C4   O7   111.13  3.000
 YWZ  H20  C4   C3   109.92  3.000
 YWZ  H19  C4   C3   108.08  3.000
 YWZ  O7   C4   C3   109.77  3.000
 YWZ  C17  O7   C4   112.75  3.000
 YWZ  H22  C17  H21  106.71  3.000
 YWZ  H22  C17  C18  108.01  3.000
 YWZ  H21  C17  C18  109.89  3.000
 YWZ  H22  C17  O7   111.23  3.000
 YWZ  H21  C17  O7   111.14  3.000
 YWZ  C18  C17  O7   109.77  3.000
 YWZ  H24  C18  H23  107.04  3.000
 YWZ  H24  C18  O8   110.79  3.000
 YWZ  H23  C18  O8   111.06  3.000
 YWZ  H24  C18  C17  110.22  3.000
 YWZ  H23  C18  C17  108.22  3.000
 YWZ  O8   C18  C17  109.44  3.000
 YWZ  C20  O8   C18  111.99  3.000
 YWZ  H26  C20  H25  106.45  3.000
 YWZ  H26  C20  C21  109.10  3.000
 YWZ  H25  C20  C21  109.10  3.000
 YWZ  H26  C20  O8   111.41  3.000
 YWZ  H25  C20  O8   111.51  3.000
 YWZ  C21  C20  O8   109.20  3.000
 YWZ  C22  C21  C20  180.00  3.000
 YWZ  H27  C22  C21  180.00  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
 YWZ  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 YWZ  CONST_02  C9   C27  C28  C6      0.00   0.0  0
 YWZ  CONST_03  C10  C9   C8   C7    180.00   0.0  0
 YWZ  CONST_04  C27  C9   C8   C7      0.00   0.0  0
 YWZ  CONST_05  C27  C28  C6   C7      0.00   0.0  0
 YWZ  CONST_08  C28  C27  C9   C8      0.00   0.0  0
 YWZ  CONST_09  C28  C6   C7   C8      0.00   0.0  0
 YWZ  CONST_10  C12  C11  C10  C9    180.00   0.0  0
 YWZ  CONST_11  C25  C26  C10  C9    180.00   0.0  0
 YWZ  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 YWZ  CONST_13  C13  C25  C26  C10     0.00   0.0  0
 YWZ  CONST_14  C28  C27  C9   C10   180.00   0.0  0
 YWZ  CONST_15  C25  C13  C12  C11     0.00   0.0  0
 YWZ  CONST_16  C25  C26  C10  C11     0.00   0.0  0
 YWZ  CONST_18  C26  C25  C13  C12     0.00   0.0  0
 YWZ  CONST_19  C26  C10  C11  C12     0.00   0.0  0
 YWZ  CONST_21  C8   C7   C6   O3    180.00   0.0  0
 YWZ  CONST_22  C27  C28  C6   O3    180.00   0.0  0
 YWZ  CONST_23  C11  C12  C13  O4    180.00   0.0  0
 YWZ  CONST_24  C26  C25  C13  O4    180.00   0.0  0
 YWZ  CONST_25  H4   C8   C7   C6    180.00   0.0  0
 YWZ  CONST_26  H16  C27  C28  C6    180.00   0.0  0
 YWZ  CONST_27  H17  C28  C6   C7    180.00   0.0  0
 YWZ  CONST_28  H5   C11  C10  C9      0.00   0.0  0
 YWZ  CONST_29  H15  C26  C10  C9      0.00   0.0  0
 YWZ  CONST_30  H3   C7   C8   C9    180.00   0.0  0
 YWZ  CONST_31  H6   C12  C11  C10   180.00   0.0  0
 YWZ  CONST_32  H14  C25  C26  C10   180.00   0.0  0
 YWZ  Var_01    C25  C13  O4   C14    -0.92  30.0  2
 YWZ  Var_02    F1   S    O3   C6     71.23  30.0  3
 YWZ  Var_03    C15  C14  O4   C13  -178.94  30.0  2
 YWZ  Var_04    O5   C15  C14  O4     64.84  30.0  1
 YWZ  Var_05    O6   C1   C16  O5     65.86  30.0  3
 YWZ  Var_06    C1   C16  O5   C15   178.18  30.0  1
 YWZ  Var_07    C4   C3   O6   C1   -179.25  30.0  3
 YWZ  Var_08    O7   C4   C3   O6     65.91  30.0  3
 YWZ  Var_09    C18  C17  O7   C4   -179.90  30.0  3
 YWZ  Var_10    O8   C18  C17  O7     65.18  30.0  3
 YWZ  Var_11    C21  C20  O8   C18   178.21  30.0  3

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
 YWZ  plan-1  O3   0.020
 YWZ  plan-1  C6   0.020
 YWZ  plan-1  C7   0.020
 YWZ  plan-1  C8   0.020
 YWZ  plan-1  C9   0.020
 YWZ  plan-1  C10  0.020
 YWZ  plan-1  C27  0.020
 YWZ  plan-1  C28  0.020
 YWZ  plan-1  H3   0.020
 YWZ  plan-1  H4   0.020
 YWZ  plan-1  H16  0.020
 YWZ  plan-1  H17  0.020
 YWZ  plan-2  O4   0.020
 YWZ  plan-2  C9   0.020
 YWZ  plan-2  C10  0.020
 YWZ  plan-2  C11  0.020
 YWZ  plan-2  C12  0.020
 YWZ  plan-2  C13  0.020
 YWZ  plan-2  C25  0.020
 YWZ  plan-2  C26  0.020
 YWZ  plan-2  H5   0.020
 YWZ  plan-2  H6   0.020
 YWZ  plan-2  H14  0.020
 YWZ  plan-2  H15  0.020

