# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 02:45:49 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (5R)-2-[(2-chlorophenyl)sulfanyl]-5-[2,6-dichloro-3-(tetrahydro-2H-pyran-4-ylamino)phenyl]-3-hydroxycyclohex-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(Sc2ccccc2Cl)C(=O)C[C@@H](C1)c3c(Cl)ccc(NC4CCOCC4)c3Cl
#
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
 W13  W13  (5R)-2-[(2-chlorophenyl)sulfanyl]-5-[2,6-dichloro-3-(tetrahydro-2H-pyran-4-ylamino)phenyl]-3-hydroxycyclohex-2-en-1-one  ligand  53  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W13
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
 W13  C4    C   CR16  0  -0.388   4.2432   1.5325   0.5181
 W13  C5    C   CR6   0   0.516   3.7432   0.2308   0.3972
 W13  C11   C   CH2   0  -0.184   7.9801  -0.5123  -1.2036
 W13  C7    C   CH1   0  -0.097   5.9952  -0.7986   0.2913
 W13  C8    C   CH2   0  -0.466   6.5983  -2.1412   0.6894
 W13  C9    C   CH2   0  -0.184   8.1064  -2.1184   0.4935
 W13  C12   C   CH2   0  -0.460   6.4634  -0.4368  -1.1202
 W13  C13   C   CR6   0  -0.298   2.3435   0.1013   0.2893
 W13  C3    C   CR16  0  -0.167   3.3953   2.6180   0.5280
 W13  C2    C   CR6   0  -0.200   2.0261   2.4490   0.4133
 W13  N6    N   NH1   0  -0.698   4.5554  -0.8635   0.4262
 W13  O10   O   O2    0  -0.482   8.4663  -1.7822  -0.8276
 W13  CL14  CL  CL    0  -0.122   1.7399  -1.5302   0.1586
 W13  C15   C   CR6   0   0.393   1.4534   1.1802   0.2937
 W13  C16   C   CH1   0  -0.416  -0.0371   0.9434   0.1845
 W13  C17   C   CH2   0  -0.544  -0.8181   1.3832   1.4221
 W13  C18   C   C     0   0.442  -2.2805   1.0272   1.3135
 W13  C19   C   C     0  -0.471  -2.8569   0.9975  -0.0266
 W13  S20   S   S2    0   0.082  -4.5932   0.7820  -0.1809
 W13  C21   C   CR6   0  -0.028  -4.7938  -0.9757  -0.0855
 W13  C22   C   CR6   0  -0.064  -6.0912  -1.4834  -0.0754
 W13  CL23  CL  CL    0  -0.116  -7.4311  -0.3885  -0.1696
 W13  C24   C   CR16  0  -0.199  -6.3363  -2.8445   0.0045
 W13  C25   C   CR16  0  -0.275  -5.2693  -3.7268   0.0769
 W13  C26   C   CR16  0  -0.232  -3.9709  -3.2378   0.0645
 W13  C27   C   CR16  0  -0.243  -3.7345  -1.8742  -0.0173
 W13  C28   C   C     0   0.491  -2.1124   1.2319  -1.1462
 W13  O29   O   OH1   0  -0.562  -2.6126   1.2532  -2.3602
 W13  C30   C   CH2   0  -0.507  -0.6472   1.5053  -1.0978
 W13  O31   O   O     0  -0.416  -2.9540   0.8057   2.3018
 W13  H1    H   HCR6  0   0.282   5.3062   1.7050   0.6063
 W13  H3    H   HCH2  0   0.200   8.4212   0.2705  -0.5684
 W13  H4    H   HCH1  0   0.241   6.3768  -0.0489   0.9935
 W13  H5    H   HCH2  0   0.252   6.3731  -2.3663   1.7341
 W13  H6    H   HCH2  0   0.233   6.1587  -2.9385   0.0803
 W13  H7    H   HCH2  0   0.200   8.5541  -1.4087   1.2051
 W13  H8    H   HCH2  0   0.241   8.5323  -3.1008   0.7026
 W13  H9    H   HCH2  0   0.246   6.1388   0.5684  -1.3997
 W13  H10   H   HCH2  0   0.232   6.0136  -1.1316  -1.8361
 W13  H11   H   HCR6  0   0.283   3.8098   3.6125   0.6215
 W13  H12   H   HNH1  0   0.378   4.1470  -1.7279   0.1055
 W13  H13   H   HCH1  0   0.284  -0.1821  -0.1341   0.1169
 W13  H14   H   HCH2  0   0.282  -0.4090   0.9156   2.3187
 W13  H15   H   HCH2  0   0.279  -0.7673   2.4644   1.5724
 W13  H16   H   HCR6  0   0.284  -7.3549  -3.2082   0.0106
 W13  H17   H   HCR6  0   0.270  -5.4558  -4.7901   0.1407
 W13  H18   H   HCR6  0   0.269  -3.1323  -3.9188   0.1180
 W13  H19   H   HCR6  0   0.260  -2.7162  -1.5093  -0.0351
 W13  H20   H   HOH1  0   0.484  -3.5768   1.1119  -2.3297
 W13  H21   H   HCH2  0   0.291  -0.5083   2.5852  -1.1938
 W13  H22   H   HCH2  0   0.297  -0.1747   1.0495  -1.9703
 W13  CL1   CL  CL    0  -0.132   1.0667   3.9017   0.4227
 W13  H2    H   HCH2  0   0.240   8.3179  -0.3300  -2.2248

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
 W13  CL1  C2    single    1.741  0.020  1.741
 W13  C3   C4    aromatic  1.377  0.020  1.377
 W13  C3   C2    aromatic  1.384  0.020  1.384
 W13  C4   C5    aromatic  1.400  0.020  1.400
 W13  C2   C15   aromatic  1.397  0.020  1.397
 W13  C9   C8    single    1.521  0.020  1.521
 W13  C9   O10   single    1.410  0.020  1.410
 W13  C8   C7    single    1.525  0.020  1.525
 W13  O10  C11   single    1.411  0.020  1.411
 W13  C11  C12   single    1.521  0.020  1.521
 W13  C5   C13   aromatic  1.410  0.020  1.410
 W13  C5   N6    single    1.363  0.020  1.363
 W13  C12  C7    single    1.531  0.020  1.531
 W13  C15  C13   aromatic  1.399  0.020  1.399
 W13  C15  C16   single    1.513  0.020  1.513
 W13  C17  C16   single    1.528  0.020  1.528
 W13  C17  C18   single    1.509  0.020  1.509
 W13  C7   N6    single    1.448  0.020  1.448
 W13  C13  CL14  single    1.744  0.020  1.744
 W13  C16  C30   single    1.527  0.020  1.527
 W13  O31  C18   double    1.216  0.020  1.216
 W13  C18  C19   single    1.459  0.020  1.459
 W13  C30  C28   single    1.491  0.020  1.491
 W13  C19  C28   double    1.365  0.020  1.365
 W13  C19  S20   single    1.756  0.020  1.756
 W13  C28  O29   single    1.313  0.020  1.313
 W13  S20  C21   single    1.772  0.020  1.772
 W13  C27  C21   aromatic  1.391  0.020  1.391
 W13  C27  C26   aromatic  1.386  0.020  1.386
 W13  C21  C22   aromatic  1.393  0.020  1.393
 W13  C26  C25   aromatic  1.388  0.020  1.388
 W13  C22  CL23  single    1.733  0.020  1.733
 W13  C22  C24   aromatic  1.385  0.020  1.385
 W13  C25  C24   aromatic  1.386  0.020  1.386
 W13  C4   H1    single    0.930  0.020  1.080
 W13  C11  H2    single    0.970  0.020  1.090
 W13  C11  H3    single    0.970  0.020  1.090
 W13  C7   H4    single    0.970  0.020  1.090
 W13  C8   H5    single    0.970  0.020  1.090
 W13  C8   H6    single    0.970  0.020  1.090
 W13  C9   H7    single    0.970  0.020  1.090
 W13  C9   H8    single    0.970  0.020  1.090
 W13  C12  H9    single    0.970  0.020  1.090
 W13  C12  H10   single    0.970  0.020  1.090
 W13  C3   H11   single    0.930  0.020  1.080
 W13  N6   H12   single    0.890  0.020  1.040
 W13  C16  H13   single    0.970  0.020  1.090
 W13  C17  H14   single    0.970  0.020  1.090
 W13  C17  H15   single    0.970  0.020  1.090
 W13  C24  H16   single    0.930  0.020  1.080
 W13  C25  H17   single    0.930  0.020  1.080
 W13  C26  H18   single    0.930  0.020  1.080
 W13  C27  H19   single    0.930  0.020  1.080
 W13  O29  H20   single    0.850  0.020  0.980
 W13  C30  H21   single    0.970  0.020  1.090
 W13  C30  H22   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
 W13  H1    C4   C3    118.63  3.000
 W13  H1    C4   C5    120.46  3.000
 W13  C3    C4   C5    120.91  3.000
 W13  N6    C5   C13   121.29  3.000
 W13  N6    C5   C4    122.14  3.000
 W13  C13   C5   C4    116.53  3.000
 W13  H3    C11  H2    107.30  3.000
 W13  H3    C11  O10   110.39  3.000
 W13  H2    C11  O10   107.05  3.000
 W13  H3    C11  C12   109.44  3.000
 W13  H2    C11  C12   110.59  3.000
 W13  O10   C11  C12   111.95  3.000
 W13  H4    C7   N6    108.50  3.000
 W13  H4    C7   C12   108.82  3.000
 W13  N6    C7   C12   113.63  3.000
 W13  H4    C7   C8    107.30  3.000
 W13  N6    C7   C8    109.25  3.000
 W13  C12   C7   C8    109.15  3.000
 W13  H6    C8   H5    107.40  3.000
 W13  H6    C8   C9    109.70  3.000
 W13  H5    C8   C9    109.31  3.000
 W13  H6    C8   C7    109.70  3.000
 W13  H5    C8   C7    110.47  3.000
 W13  C9    C8   C7    110.21  3.000
 W13  H8    C9   H7    107.34  3.000
 W13  H8    C9   O10   107.13  3.000
 W13  H7    C9   O10   110.39  3.000
 W13  H8    C9   C8    110.42  3.000
 W13  H7    C9   C8    109.26  3.000
 W13  O10   C9   C8    112.17  3.000
 W13  H10   C12  H9    107.14  3.000
 W13  H10   C12  C7    109.12  3.000
 W13  H9    C12  C7    111.25  3.000
 W13  H10   C12  C11   110.03  3.000
 W13  H9    C12  C11   109.14  3.000
 W13  C7    C12  C11   110.11  3.000
 W13  C15   C13  CL14  120.10  3.000
 W13  CL14  C13  C5    115.80  3.000
 W13  C15   C13  C5    124.10  3.000
 W13  H11   C3   C2    119.90  3.000
 W13  H11   C3   C4    119.30  3.000
 W13  C2    C3   C4    120.80  3.000
 W13  C15   C2   CL1   122.17  3.000
 W13  C15   C2   C3    121.55  3.000
 W13  CL1   C2   C3    116.28  3.000
 W13  H12   N6   C7    114.31  3.000
 W13  H12   N6   C5    116.11  3.000
 W13  C7    N6   C5    123.69  3.000
 W13  C9    O10  C11   112.11  3.000
 W13  C16   C15  C2    123.51  3.000
 W13  C16   C15  C13   120.39  3.000
 W13  C2    C15  C13   116.10  3.000
 W13  H13   C16  C30   104.99  3.000
 W13  H13   C16  C17   105.48  3.000
 W13  C30   C16  C17   111.71  3.000
 W13  H13   C16  C15   106.88  3.000
 W13  C30   C16  C15   113.36  3.000
 W13  C17   C16  C15   113.58  3.000
 W13  H15   C17  H14   107.08  3.000
 W13  H15   C17  C18   106.76  3.000
 W13  H14   C17  C18   108.75  3.000
 W13  H15   C17  C16   111.86  3.000
 W13  H14   C17  C16   110.52  3.000
 W13  C18   C17  C16   111.66  3.000
 W13  O31   C18  C19   121.59  3.000
 W13  C19   C18  C17   116.98  3.000
 W13  O31   C18  C17   121.41  3.000
 W13  C28   C19  S20   119.22  3.000
 W13  S20   C19  C18   118.27  3.000
 W13  C28   C19  C18   122.31  3.000
 W13  C21   S20  C19   103.23  3.000
 W13  C27   C21  C22   118.26  3.000
 W13  C22   C21  S20   117.86  3.000
 W13  C27   C21  S20   123.87  3.000
 W13  C24   C22  CL23  119.15  3.000
 W13  C24   C22  C21   121.55  3.000
 W13  CL23  C22  C21   119.30  3.000
 W13  H16   C24  C25   120.69  3.000
 W13  H16   C24  C22   119.82  3.000
 W13  C25   C24  C22   119.48  3.000
 W13  H17   C25  C26   120.56  3.000
 W13  H17   C25  C24   119.74  3.000
 W13  C26   C25  C24   119.69  3.000
 W13  H18   C26  C27   119.34  3.000
 W13  H18   C26  C25   120.21  3.000
 W13  C27   C26  C25   120.45  3.000
 W13  H19   C27  C26   119.55  3.000
 W13  H19   C27  C21   119.89  3.000
 W13  C26   C27  C21   120.56  3.000
 W13  C30   C28  O29   113.66  3.000
 W13  O29   C28  C19   123.60  3.000
 W13  C30   C28  C19   122.74  3.000
 W13  H20   O29  C28   110.21  3.000
 W13  H22   C30  H21   106.69  3.000
 W13  H22   C30  C28   108.83  3.000
 W13  H21   C30  C28   107.64  3.000
 W13  H22   C30  C16   110.15  3.000
 W13  H21   C30  C16   112.74  3.000
 W13  C28   C30  C16   110.63  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
 W13  CONST_01  C15   C2   C3   C4      0.00   0.0  0
 W13  CONST_02  C15   C13  C5   C4      0.00   0.0  0
 W13  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 W13  CONST_04  C2    C15  C13  C5      0.00   0.0  0
 W13  CONST_05  C3    C4   C5   C13     0.00   0.0  0
 W13  CONST_06  C3    C2   C15  C13     0.00   0.0  0
 W13  CONST_07  C25   C26  C27  C21     0.00   0.0  0
 W13  CONST_08  C25   C24  C22  C21     0.00   0.0  0
 W13  CONST_09  C26   C27  C21  C22     0.00   0.0  0
 W13  CONST_10  C26   C25  C24  C22     0.00   0.0  0
 W13  CONST_11  C27   C21  C22  C24     0.00   0.0  0
 W13  CONST_12  C27   C26  C25  C24     0.00   0.0  0
 W13  CONST_13  C16   C15  C13  C5    180.00   0.0  0
 W13  CONST_14  C16   C15  C2   C3    180.00   0.0  0
 W13  CONST_15  CL1   C2   C3   C4    180.00   0.0  0
 W13  CONST_16  CL14  C13  C5   C4    180.00   0.0  0
 W13  CONST_17  CL1   C2   C15  C13   180.00   0.0  0
 W13  CONST_18  N6    C5   C4   C3    180.00   0.0  0
 W13  CONST_19  C16   C15  C2   CL1     0.00   0.0  0
 W13  CONST_20  CL14  C13  C15  C2    180.00   0.0  0
 W13  CONST_21  C15   C13  C5   N6    180.00   0.0  0
 W13  CONST_22  C16   C15  C13  CL14    0.00   0.0  0
 W13  CONST_23  C26   C27  C21  S20   180.00   0.0  0
 W13  CONST_24  C24   C22  C21  S20   180.00   0.0  0
 W13  CONST_25  C27   C21  C22  CL23  180.00   0.0  0
 W13  CONST_26  C25   C24  C22  CL23  180.00   0.0  0
 W13  CONST_27  C7    N6   C5   C4      0.00   0.0  0
 W13  CONST_28  C13   C5   N6   C7    180.00   0.0  0
 W13  CONST_29  H11   C3   C4   C5    180.00   0.0  0
 W13  CONST_30  H1    C4   C5   C13   180.00   0.0  0
 W13  CONST_31  H18   C26  C27  C21   180.00   0.0  0
 W13  CONST_32  H16   C24  C22  C21   180.00   0.0  0
 W13  CONST_33  H19   C27  C21  C22   180.00   0.0  0
 W13  CONST_34  H17   C25  C24  C22   180.00   0.0  0
 W13  CONST_35  H12   N6   C5   C4    180.00   0.0  0
 W13  Var_01    C8    C9   O10  C11    59.46  30.0  1
 W13  Var_02    O10   C9   C8   C7    -56.16  30.0  1
 W13  Var_03    O10   C11  C12  C7     56.42  30.0  1
 W13  Var_04    C12   C11  O10  C9    -59.61  30.0  1
 W13  Var_05    C19   C18  C17  C16   -30.27  30.0  1
 W13  Var_06    C19   C28  C30  C16    23.00  30.0  1
 W13  Var_07    C28   C19  C18  C17     2.26  30.0  1
 W13  Var_08    C30   C28  C19  C18     1.48  30.0  1
 W13  Var_09    C27   C21  S20  C19    -4.60  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
 W13  chir_01  C7   C8   C12  N6   negativ
 W13  chir_02  C16  C15  C17  C30  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
 W13  plan-1  C4    0.020
 W13  plan-1  C5    0.020
 W13  plan-1  C13   0.020
 W13  plan-1  C3    0.020
 W13  plan-1  C2    0.020
 W13  plan-1  N6    0.020
 W13  plan-1  CL14  0.020
 W13  plan-1  C15   0.020
 W13  plan-1  C16   0.020
 W13  plan-1  H1    0.020
 W13  plan-1  H11   0.020
 W13  plan-1  CL1   0.020
 W13  plan-2  C5    0.020
 W13  plan-2  C7    0.020
 W13  plan-2  N6    0.020
 W13  plan-2  H12   0.020
 W13  plan-3  S20   0.020
 W13  plan-3  C21   0.020
 W13  plan-3  C22   0.020
 W13  plan-3  CL23  0.020
 W13  plan-3  C24   0.020
 W13  plan-3  C25   0.020
 W13  plan-3  C26   0.020
 W13  plan-3  C27   0.020
 W13  plan-3  H16   0.020
 W13  plan-3  H17   0.020
 W13  plan-3  H18   0.020
 W13  plan-3  H19   0.020
 W13  plan-4  C17   0.020
 W13  plan-4  C18   0.020
 W13  plan-4  C19   0.020
 W13  plan-4  O31   0.020

