# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 03:27:01 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (6R)-6-(3-aminophenyl)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(c1)[C@]2(CC(=C(Sc3ccccc3Cl)C(=O)O2)O)c4cscc4
#
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
 D4S  D4S  (6R)-6-(3-aminophenyl)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one  ligand  44  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D4S
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
 D4S  C4   C   CR16  0  -0.274   5.1399  -2.9370  -0.1783
 D4S  C14  C   CT    0   0.114  -1.8634   0.0734   0.1647
 D4S  C5   C   CR16  0  -0.232   3.7810  -3.0651   0.0716
 D4S  C6   C   CR16  0  -0.245   2.9723  -1.9417   0.1464
 D4S  C7   C   CR6   0  -0.030   3.5100  -0.6716  -0.0286
 D4S  C9   C   C     0  -0.525   0.9117   0.2399   0.1776
 D4S  C10  C   C     0   0.525   0.2881   0.1969   1.3822
 D4S  C13  C   CH2   0  -0.583  -1.1294  -0.2494   1.4624
 D4S  C3   C   CR16  0  -0.199   5.6918  -1.6767  -0.3485
 D4S  C2   C   CR6   0  -0.062   4.8766  -0.5593  -0.2729
 D4S  S8   S   S2    0   0.101   2.5558   0.8206   0.0484
 D4S  O11  O   OH1   0  -0.553   0.8490   0.4845   2.5301
 D4S  C15  C   CR5   0   0.188  -2.0602   1.5555  -0.0435
 D4S  C16  C   CR15  0  -0.550  -1.8414   2.5314   0.8814
 D4S  S17  S   S2    0   0.234  -2.2030   4.0862   0.2640
 D4S  C18  C   CR15  0  -0.462  -2.6564   3.4391  -1.2570
 D4S  C19  C   CR15  0  -0.185  -2.5355   2.0865  -1.2802
 D4S  C20  C   CR6   0   0.086  -3.1934  -0.6629   0.1587
 D4S  C21  C   CR16  0  -0.380  -3.3069  -1.9193  -0.4197
 D4S  C22  C   CR6   0   0.334  -4.5094  -2.6347  -0.3540
 D4S  N23  N   NH2   0  -0.862  -4.5955  -3.9012  -0.8859
 D4S  C24  C   CR16  0  -0.333  -5.5974  -2.0578   0.3105
 D4S  C25  C   CR16  0  -0.239  -5.4722  -0.8080   0.8914
 D4S  C26  C   CR16  0  -0.317  -4.2801  -0.1005   0.8226
 D4S  O27  O   O2    0  -0.469  -1.1023  -0.4220  -0.9463
 D4S  C28  C   C     0   0.585   0.2136  -0.1712  -1.0344
 D4S  O29  O   O     0  -0.423   0.7573  -0.3387  -2.0967
 D4S  H1   H   HCR6  0   0.271   5.7736  -3.8110  -0.2402
 D4S  H2   H   HCR6  0   0.269   3.3425  -4.0438   0.2119
 D4S  H3   H   HCR6  0   0.265   1.9161  -2.0590   0.3482
 D4S  H4   H   HCH2  0   0.312  -1.6382   0.2027   2.3141
 D4S  H5   H   HCH2  0   0.332  -1.1423  -1.3308   1.6341
 D4S  H6   H   HCR6  0   0.285   6.7500  -1.5591  -0.5385
 D4S  H12  H   HOH1  0   0.489   1.7792   0.7446   2.4018
 D4S  H7   H   HCR5  0   0.297  -1.4955   2.4332   1.8994
 D4S  H8   H   HCR5  0   0.299  -2.9902   4.0884  -2.0515
 D4S  H9   H   HCR5  0   0.272  -2.7792   1.4849  -2.1446
 D4S  H10  H   HCR6  0   0.259  -2.4661  -2.3704  -0.9313
 D4S  H11  H   HNH2  0   0.380  -3.9373  -4.1200  -1.6159
 D4S  H13  H   HNH2  0   0.380  -5.5228  -4.2298  -1.1009
 D4S  H14  H   HCR6  0   0.257  -6.5388  -2.5918   0.3665
 D4S  H15  H   HCR6  0   0.255  -6.3218  -0.3738   1.4029
 D4S  H16  H   HCR6  0   0.252  -4.2056   0.8782   1.2780
 D4S  CL1  CL  CL    0  -0.115   5.5750   1.0129  -0.4793

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
 D4S  C3   C4   aromatic  1.386  0.020  1.386
 D4S  C3   C2   aromatic  1.385  0.020  1.385
 D4S  C4   C5   aromatic  1.388  0.020  1.388
 D4S  CL1  C2   single    1.733  0.020  1.733
 D4S  C2   C7   aromatic  1.393  0.020  1.393
 D4S  O11  C10  single    1.310  0.020  1.310
 D4S  C5   C6   aromatic  1.386  0.020  1.386
 D4S  C7   C6   aromatic  1.390  0.020  1.390
 D4S  C7   S8   single    1.773  0.020  1.773
 D4S  S8   C9   single    1.748  0.020  1.748
 D4S  C10  C9   double    1.357  0.020  1.357
 D4S  C10  C13  single    1.488  0.020  1.488
 D4S  C9   C28  single    1.458  0.020  1.458
 D4S  C13  C14  single    1.525  0.020  1.525
 D4S  C18  C19  aromatic  1.358  0.020  1.358
 D4S  C18  S17  aromatic  1.714  0.020  1.714
 D4S  C19  C15  aromatic  1.427  0.020  1.427
 D4S  C15  C14  single    1.510  0.020  1.510
 D4S  C15  C16  aromatic  1.362  0.020  1.362
 D4S  C28  O29  double    1.205  0.020  1.205
 D4S  C28  O27  single    1.342  0.020  1.342
 D4S  S17  C16  aromatic  1.712  0.020  1.712
 D4S  C14  O27  single    1.435  0.020  1.435
 D4S  C14  C20  single    1.520  0.020  1.520
 D4S  C20  C26  aromatic  1.392  0.020  1.392
 D4S  C20  C21  aromatic  1.388  0.020  1.388
 D4S  C26  C25  aromatic  1.388  0.020  1.388
 D4S  C21  C22  aromatic  1.401  0.020  1.401
 D4S  C25  C24  aromatic  1.384  0.020  1.384
 D4S  C22  C24  aromatic  1.399  0.020  1.399
 D4S  C22  N23  single    1.376  0.020  1.376
 D4S  C4   H1   single    0.930  0.020  1.080
 D4S  C5   H2   single    0.930  0.020  1.080
 D4S  C6   H3   single    0.930  0.020  1.080
 D4S  C13  H4   single    0.970  0.020  1.090
 D4S  C13  H5   single    0.970  0.020  1.090
 D4S  C3   H6   single    0.930  0.020  1.080
 D4S  O11  H12  single    0.850  0.020  0.980
 D4S  C16  H7   single    0.930  0.020  1.080
 D4S  C18  H8   single    0.930  0.020  1.080
 D4S  C19  H9   single    0.930  0.020  1.080
 D4S  C21  H10  single    0.930  0.020  1.080
 D4S  N23  H11  single    0.890  0.020  1.040
 D4S  N23  H13  single    0.890  0.020  1.040
 D4S  C24  H14  single    0.930  0.020  1.080
 D4S  C25  H15  single    0.930  0.020  1.080
 D4S  C26  H16  single    0.930  0.020  1.080

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
 D4S  H1   C4   C3   119.64  3.000
 D4S  H1   C4   C5   120.64  3.000
 D4S  C3   C4   C5   119.73  3.000
 D4S  O27  C14  C20  107.08  3.000
 D4S  C20  C14  C15  111.16  3.000
 D4S  O27  C14  C15  107.54  3.000
 D4S  C20  C14  C13  108.77  3.000
 D4S  O27  C14  C13  109.29  3.000
 D4S  C15  C14  C13  112.82  3.000
 D4S  H2   C5   C6   119.33  3.000
 D4S  H2   C5   C4   120.26  3.000
 D4S  C6   C5   C4   120.41  3.000
 D4S  H3   C6   C7   120.01  3.000
 D4S  H3   C6   C5   119.46  3.000
 D4S  C7   C6   C5   120.53  3.000
 D4S  S8   C7   C2   117.89  3.000
 D4S  S8   C7   C6   123.73  3.000
 D4S  C2   C7   C6   118.38  3.000
 D4S  C28  C9   S8   118.85  3.000
 D4S  C28  C9   C10  120.59  3.000
 D4S  S8   C9   C10  120.55  3.000
 D4S  O11  C10  C13  115.25  3.000
 D4S  C13  C10  C9   119.67  3.000
 D4S  O11  C10  C9   125.05  3.000
 D4S  H5   C13  H4   106.35  3.000
 D4S  H5   C13  C10  108.41  3.000
 D4S  H4   C13  C10  111.24  3.000
 D4S  H5   C13  C14  109.68  3.000
 D4S  H4   C13  C14  110.63  3.000
 D4S  C10  C13  C14  110.43  3.000
 D4S  H6   C3   C2   119.85  3.000
 D4S  H6   C3   C4   120.66  3.000
 D4S  C2   C3   C4   119.50  3.000
 D4S  CL1  C2   C3   119.23  3.000
 D4S  CL1  C2   C7   119.31  3.000
 D4S  C3   C2   C7   121.46  3.000
 D4S  C9   S8   C7   103.29  3.000
 D4S  H12  O11  C10  110.61  3.000
 D4S  C19  C15  C16  112.04  3.000
 D4S  C16  C15  C14  126.07  3.000
 D4S  C19  C15  C14  121.88  3.000
 D4S  H7   C16  S17  119.37  3.000
 D4S  H7   C16  C15  128.79  3.000
 D4S  S17  C16  C15  111.84  3.000
 D4S  C18  S17  C16   91.89  3.000
 D4S  H8   C18  C19  127.89  3.000
 D4S  H8   C18  S17  120.54  3.000
 D4S  C19  C18  S17  111.57  3.000
 D4S  H9   C19  C18  123.22  3.000
 D4S  H9   C19  C15  124.12  3.000
 D4S  C18  C19  C15  112.66  3.000
 D4S  C26  C20  C21  120.04  3.000
 D4S  C21  C20  C14  120.77  3.000
 D4S  C26  C20  C14  119.04  3.000
 D4S  H10  C21  C22  118.43  3.000
 D4S  H10  C21  C20  120.71  3.000
 D4S  C22  C21  C20  120.86  3.000
 D4S  C24  C22  N23  120.94  3.000
 D4S  N23  C22  C21  120.37  3.000
 D4S  C24  C22  C21  118.64  3.000
 D4S  H13  N23  H11  112.10  3.000
 D4S  H13  N23  C22  116.13  3.000
 D4S  H11  N23  C22  116.05  3.000
 D4S  H14  C24  C25  120.12  3.000
 D4S  H14  C24  C22  119.79  3.000
 D4S  C25  C24  C22  120.08  3.000
 D4S  H15  C25  C26  119.54  3.000
 D4S  H15  C25  C24  119.31  3.000
 D4S  C26  C25  C24  121.15  3.000
 D4S  H16  C26  C25  119.96  3.000
 D4S  H16  C26  C20  120.82  3.000
 D4S  C25  C26  C20  119.22  3.000
 D4S  C28  O27  C14  120.41  3.000
 D4S  O29  C28  O27  118.30  3.000
 D4S  O27  C28  C9   117.87  3.000
 D4S  O29  C28  C9   123.79  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
 D4S  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 D4S  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 D4S  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 D4S  CONST_04  C2   C7   C6   C5     0.00   0.0  0
 D4S  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 D4S  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 D4S  CONST_07  S17  C18  C19  C15    0.00   0.0  0
 D4S  CONST_08  C18  S17  C16  C15    0.00   0.0  0
 D4S  CONST_09  C18  C19  C15  C16    0.00   0.0  0
 D4S  CONST_10  C19  C18  S17  C16    0.00   0.0  0
 D4S  CONST_11  C19  C15  C16  S17    0.00   0.0  0
 D4S  CONST_12  C24  C25  C26  C20    0.00   0.0  0
 D4S  CONST_13  C24  C22  C21  C20    0.00   0.0  0
 D4S  CONST_14  C25  C26  C20  C21    0.00   0.0  0
 D4S  CONST_15  C25  C24  C22  C21    0.00   0.0  0
 D4S  CONST_16  C26  C20  C21  C22    0.00   0.0  0
 D4S  CONST_17  C26  C25  C24  C22    0.00   0.0  0
 D4S  CONST_18  C18  C19  C15  C14  180.00   0.0  0
 D4S  CONST_19  S17  C16  C15  C14  180.00   0.0  0
 D4S  CONST_20  C25  C26  C20  C14  180.00   0.0  0
 D4S  CONST_21  C22  C21  C20  C14  180.00   0.0  0
 D4S  CONST_22  CL1  C2   C3   C4   180.00   0.0  0
 D4S  CONST_23  S8   C7   C6   C5   180.00   0.0  0
 D4S  CONST_24  CL1  C2   C7   C6   180.00   0.0  0
 D4S  CONST_25  S8   C7   C2   C3   180.00   0.0  0
 D4S  CONST_26  N23  C22  C21  C20  180.00   0.0  0
 D4S  CONST_27  C25  C24  C22  N23  180.00   0.0  0
 D4S  CONST_28  H3   C6   C5   C4   180.00   0.0  0
 D4S  CONST_29  H9   C19  C15  C14    0.00   0.0  0
 D4S  CONST_30  H7   C16  C15  C14    0.00   0.0  0
 D4S  CONST_31  H16  C26  C20  C14    0.00   0.0  0
 D4S  CONST_32  H10  C21  C20  C14    0.00   0.0  0
 D4S  CONST_33  H6   C3   C4   C5   180.00   0.0  0
 D4S  CONST_34  H1   C4   C5   C6   180.00   0.0  0
 D4S  CONST_35  H2   C5   C6   C7   180.00   0.0  0
 D4S  CONST_36  H8   C18  C19  C15  180.00   0.0  0
 D4S  CONST_37  H15  C25  C26  C20  180.00   0.0  0
 D4S  CONST_38  H14  C24  C22  C21  180.00   0.0  0
 D4S  Var_01    C9   C10  C13  C14  -28.81  30.0  1
 D4S  Var_02    C9   C28  O27  C14   18.33  30.0  1
 D4S  Var_03    O27  C28  C9   C10    8.53  30.0  1
 D4S  Var_04    C28  C9   C10  C13   -1.18  30.0  1
 D4S  Var_05    C10  C9   S8   C7    99.78  30.0  3
 D4S  Var_06    C2   C7   S8   C9   173.66  30.0  1

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
 D4S  chir_01  C14  C15  O27  C20  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
 D4S  plan-1  C14  0.020
 D4S  plan-1  C15  0.020
 D4S  plan-1  C16  0.020
 D4S  plan-1  S17  0.020
 D4S  plan-1  C18  0.020
 D4S  plan-1  C19  0.020
 D4S  plan-1  H7   0.020
 D4S  plan-1  H8   0.020
 D4S  plan-1  H9   0.020
 D4S  plan-2  C4   0.020
 D4S  plan-2  C5   0.020
 D4S  plan-2  C6   0.020
 D4S  plan-2  C7   0.020
 D4S  plan-2  C3   0.020
 D4S  plan-2  C2   0.020
 D4S  plan-2  S8   0.020
 D4S  plan-2  H1   0.020
 D4S  plan-2  H2   0.020
 D4S  plan-2  H3   0.020
 D4S  plan-2  H6   0.020
 D4S  plan-2  CL1  0.020
 D4S  plan-3  C14  0.020
 D4S  plan-3  C20  0.020
 D4S  plan-3  C21  0.020
 D4S  plan-3  C22  0.020
 D4S  plan-3  N23  0.020
 D4S  plan-3  C24  0.020
 D4S  plan-3  C25  0.020
 D4S  plan-3  C26  0.020
 D4S  plan-3  H10  0.020
 D4S  plan-3  H14  0.020
 D4S  plan-3  H15  0.020
 D4S  plan-3  H16  0.020
 D4S  plan-4  C22  0.020
 D4S  plan-4  N23  0.020
 D4S  plan-4  H11  0.020
 D4S  plan-4  H13  0.020
 D4S  plan-5  C9   0.020
 D4S  plan-5  O27  0.020
 D4S  plan-5  C28  0.020
 D4S  plan-5  O29  0.020

