# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 09:19:29 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (2R)-5-[(2-chlorophenyl)sulfanyl]-6'-[(4-fluorophenyl)amino]-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro[2,2'-bipyridin]-6(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(Sc2ccccc2Cl)C(=O)N[C@](C1)(c3cscc3)c4cccc(Nc5ccc(F)cc5)n4
#
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
 D0V  D0V  (2R)-5-[(2-chlorophenyl)sulfanyl]-6'-[(4-fluorophenyl)amino]-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro[2,2'-bipyridin]-6(1H)-one  ligand  54  35  .  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_D0V
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
 D0V  C4   C   C     0  -0.485  -0.3087  -1.4141  -1.3208
 D0V  C6   C   CR6   0  -0.034  -2.8471  -0.9464  -0.3322
 D0V  C11  C   CR16  0  -0.226  -2.9486   0.1105   1.8326
 D0V  C7   C   CR6   0  -0.069  -4.2131  -1.2023  -0.2371
 D0V  C9   C   CR16  0  -0.202  -4.9437  -0.8179   0.8760
 D0V  C10  C   CR16  0  -0.275  -4.3066  -0.1625   1.9185
 D0V  C12  C   CR16  0  -0.246  -2.2265  -0.2717   0.7137
 D0V  C13  C   C     0   0.552   0.2823  -2.6322  -0.7509
 D0V  C3   C   CH2   0  -0.540   1.9300  -0.3592  -1.3823
 D0V  C2   C   C     0   0.523   0.4642  -0.3462  -1.6363
 D0V  S5   S   S2    0   0.078  -1.9915  -1.4541  -1.8000
 D0V  CL8  CL  CL    0  -0.119  -5.0236  -2.0117  -1.5379
 D0V  N14  N   NH1   0  -0.653   1.6123  -2.5756  -0.4645
 D0V  C15  C   CT    0  -0.055   2.3310  -1.3226  -0.2642
 D0V  C16  C   CR5   0   0.189   3.8143  -1.5867  -0.4036
 D0V  C17  C   CR15  0  -0.547   4.7909  -0.9339   0.2876
 D0V  S18  S   S2    0   0.233   6.3551  -1.4126  -0.2146
 D0V  C19  C   CR15  0  -0.464   5.7148  -2.5034  -1.3693
 D0V  C20  C   CR15  0  -0.199   4.3555  -2.4917  -1.3661
 D0V  C21  C   CR6   0   0.330   1.9958  -0.7848   1.1307
 D0V  N22  N   N     0  -0.501   1.3223   0.3572   1.2121
 D0V  C23  C   CR6   0   0.532   0.9761   0.8221   2.4077
 D0V  N24  N   NH1   0  -0.791   0.2499   1.9800   2.5070
 D0V  C25  C   CR6   0   0.350  -0.3458   2.7534   1.5120
 D0V  C26  C   CR16  0  -0.324  -1.5044   3.4567   1.8548
 D0V  C27  C   CR16  0  -0.401  -2.1485   4.2679   0.9378
 D0V  C28  C   CR6   0   0.502  -1.6327   4.3653  -0.3399
 D0V  F29  F   F     0  -0.322  -2.2610   5.1408  -1.2437
 D0V  C30  C   CR16  0  -0.404  -0.4883   3.6900  -0.7076
 D0V  C31  C   CR16  0  -0.273   0.1634   2.8914   0.2216
 D0V  C32  C   CR16  0  -0.403   1.3180   0.1538   3.5943
 D0V  C33  C   CR16  0  -0.144   2.0108  -1.0301   3.4961
 D0V  C34  C   CR16  0  -0.354   2.3590  -1.5249   2.2438
 D0V  O35  O   O     0  -0.469  -0.3646  -3.6544  -0.5851
 D0V  H1   H   HCR6  0   0.253  -2.4462   0.6291   2.6378
 D0V  H2   H   HCR6  0   0.283  -6.0025  -1.0333   0.9261
 D0V  H3   H   HCR6  0   0.269  -4.8739   0.1354   2.7897
 D0V  H4   H   HCR6  0   0.284  -1.1722  -0.0396   0.6483
 D0V  H5   H   HCH2  0   0.313   2.4155  -0.6715  -2.3133
 D0V  H6   H   HCH2  0   0.306   2.2901   0.6448  -1.1620
 D0V  H7   H   HOH1  0   0.478  -0.9181   0.6541  -2.4406
 D0V  H8   H   HNH1  0   0.397   1.9767  -3.3855   0.0185
 D0V  H9   H   HCR5  0   0.295   4.6784  -0.1955   1.0663
 D0V  H10  H   HCR5  0   0.298   6.3707  -3.0976  -1.9862
 D0V  H11  H   HCR5  0   0.272   3.7540  -3.1045  -2.0224
 D0V  H12  H   HNH1  0   0.409  -0.0399   2.2095   3.4448
 D0V  H13  H   HCR6  0   0.274  -1.9133   3.3647   2.8537
 D0V  H14  H   HCR6  0   0.278  -3.0459   4.8046   1.2160
 D0V  H15  H   HCR6  0   0.273  -0.0931   3.7873  -1.7101
 D0V  H16  H   HCR6  0   0.283   1.0677   2.3821  -0.0655
 D0V  H17  H   HCR6  0   0.277   1.0319   0.5572   4.5569
 D0V  H18  H   HCR6  0   0.273   2.2809  -1.5730   4.3922
 D0V  H19  H   HCR6  0   0.264   2.9064  -2.4532   2.1521
 D0V  O1   O   OH1   0  -0.565   0.0315   0.7362  -2.2429

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
 D0V  C27  C26  aromatic  1.383  0.020  1.383
 D0V  C27  C28  aromatic  1.381  0.020  1.381
 D0V  F29  C28  single    1.347  0.020  1.347
 D0V  C26  C25  aromatic  1.398  0.020  1.398
 D0V  C28  C30  aromatic  1.379  0.020  1.379
 D0V  C9   C10  aromatic  1.386  0.020  1.386
 D0V  C9   C7   aromatic  1.386  0.020  1.386
 D0V  C10  C11  aromatic  1.388  0.020  1.388
 D0V  C25  N24  single    1.394  0.020  1.394
 D0V  C25  C31  aromatic  1.394  0.020  1.394
 D0V  C30  C31  aromatic  1.388  0.020  1.388
 D0V  CL8  C7   single    1.733  0.020  1.733
 D0V  C7   C6   aromatic  1.393  0.020  1.393
 D0V  O1   C2   single    1.314  0.020  1.314
 D0V  C11  C12  aromatic  1.385  0.020  1.385
 D0V  N24  C23  single    1.370  0.020  1.370
 D0V  C6   C12  aromatic  1.391  0.020  1.391
 D0V  C6   S5   single    1.773  0.020  1.773
 D0V  S5   C4   single    1.750  0.020  1.750
 D0V  C2   C4   double    1.355  0.020  1.355
 D0V  C2   C3   single    1.488  0.020  1.488
 D0V  C23  C32  aromatic  1.404  0.020  1.404
 D0V  C23  N22  aromatic  1.329  0.020  1.329
 D0V  C32  C33  aromatic  1.375  0.020  1.375
 D0V  N22  C21  aromatic  1.328  0.020  1.328
 D0V  C4   C13  single    1.469  0.020  1.469
 D0V  C3   C15  single    1.529  0.020  1.529
 D0V  C33  C34  aromatic  1.391  0.020  1.391
 D0V  C21  C15  single    1.532  0.020  1.532
 D0V  C21  C34  aromatic  1.385  0.020  1.385
 D0V  C15  N14  single    1.458  0.020  1.458
 D0V  C15  C16  single    1.513  0.020  1.513
 D0V  C13  O35  double    1.221  0.020  1.221
 D0V  C13  N14  single    1.362  0.020  1.362
 D0V  C16  C20  aromatic  1.428  0.020  1.428
 D0V  C16  C17  aromatic  1.363  0.020  1.363
 D0V  C20  C19  aromatic  1.359  0.020  1.359
 D0V  C17  S18  aromatic  1.711  0.020  1.711
 D0V  C19  S18  aromatic  1.713  0.020  1.713
 D0V  C11  H1   single    0.930  0.020  1.080
 D0V  C9   H2   single    0.930  0.020  1.080
 D0V  C10  H3   single    0.930  0.020  1.080
 D0V  C12  H4   single    0.930  0.020  1.080
 D0V  C3   H5   single    0.970  0.020  1.090
 D0V  C3   H6   single    0.970  0.020  1.090
 D0V  O1   H7   single    0.850  0.020  0.980
 D0V  N14  H8   single    0.890  0.020  1.040
 D0V  C17  H9   single    0.930  0.020  1.080
 D0V  C19  H10  single    0.930  0.020  1.080
 D0V  C20  H11  single    0.930  0.020  1.080
 D0V  N24  H12  single    0.860  0.020  1.020
 D0V  C26  H13  single    0.930  0.020  1.080
 D0V  C27  H14  single    0.930  0.020  1.080
 D0V  C30  H15  single    0.930  0.020  1.080
 D0V  C31  H16  single    0.930  0.020  1.080
 D0V  C32  H17  single    0.930  0.020  1.080
 D0V  C33  H18  single    0.930  0.020  1.080
 D0V  C34  H19  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
 D0V  S5   C4   C2   120.17  3.000
 D0V  C2   C4   C13  120.94  3.000
 D0V  S5   C4   C13  118.30  3.000
 D0V  S5   C6   C12  123.10  3.000
 D0V  S5   C6   C7   118.50  3.000
 D0V  C12  C6   C7   118.38  3.000
 D0V  H1   C11  C12  119.43  3.000
 D0V  H1   C11  C10  120.19  3.000
 D0V  C12  C11  C10  120.38  3.000
 D0V  CL8  C7   C9   119.06  3.000
 D0V  CL8  C7   C6   119.55  3.000
 D0V  C9   C7   C6   121.39  3.000
 D0V  H2   C9   C10  120.60  3.000
 D0V  H2   C9   C7   119.87  3.000
 D0V  C10  C9   C7   119.52  3.000
 D0V  H3   C10  C9   119.66  3.000
 D0V  H3   C10  C11  120.60  3.000
 D0V  C9   C10  C11  119.74  3.000
 D0V  H4   C12  C11  119.85  3.000
 D0V  H4   C12  C6   119.58  3.000
 D0V  C11  C12  C6   120.57  3.000
 D0V  O35  C13  N14  121.58  3.000
 D0V  N14  C13  C4   116.11  3.000
 D0V  O35  C13  C4   122.26  3.000
 D0V  H6   C3   H5   106.75  3.000
 D0V  H6   C3   C15  110.25  3.000
 D0V  H5   C3   C15  109.00  3.000
 D0V  H6   C3   C2   110.62  3.000
 D0V  H5   C3   C2   107.10  3.000
 D0V  C15  C3   C2   112.87  3.000
 D0V  O1   C2   C3   114.23  3.000
 D0V  C3   C2   C4   121.01  3.000
 D0V  O1   C2   C4   124.66  3.000
 D0V  C6   S5   C4   103.34  3.000
 D0V  H8   N14  C15  116.43  3.000
 D0V  H8   N14  C13  114.79  3.000
 D0V  C15  N14  C13  123.09  3.000
 D0V  C21  C15  C16  111.08  3.000
 D0V  C16  C15  N14  108.69  3.000
 D0V  C21  C15  N14  108.59  3.000
 D0V  C16  C15  C3   107.43  3.000
 D0V  N14  C15  C3   108.16  3.000
 D0V  C21  C15  C3   112.78  3.000
 D0V  C20  C16  C17  111.95  3.000
 D0V  C17  C16  C15  124.90  3.000
 D0V  C20  C16  C15  122.99  3.000
 D0V  H9   C17  S18  119.91  3.000
 D0V  H9   C17  C16  128.24  3.000
 D0V  S18  C17  C16  111.85  3.000
 D0V  C19  S18  C17   91.97  3.000
 D0V  H10  C19  C20  127.88  3.000
 D0V  H10  C19  S18  120.60  3.000
 D0V  C20  C19  S18  111.52  3.000
 D0V  H11  C20  C19  123.38  3.000
 D0V  H11  C20  C16  123.90  3.000
 D0V  C19  C20  C16  112.71  3.000
 D0V  C34  C21  N22  122.89  3.000
 D0V  C34  C21  C15  119.12  3.000
 D0V  N22  C21  C15  117.94  3.000
 D0V  C23  N22  C21  119.21  3.000
 D0V  C32  C23  N24  118.04  3.000
 D0V  C32  C23  N22  122.04  3.000
 D0V  N24  C23  N22  119.92  3.000
 D0V  H12  N24  C25  114.51  3.000
 D0V  H12  N24  C23  114.34  3.000
 D0V  C25  N24  C23  130.06  3.000
 D0V  C31  C25  C26  118.68  3.000
 D0V  C31  C25  N24  124.02  3.000
 D0V  C26  C25  N24  117.28  3.000
 D0V  H13  C26  C27  119.03  3.000
 D0V  H13  C26  C25  119.75  3.000
 D0V  C27  C26  C25  121.22  3.000
 D0V  H14  C27  C28  120.84  3.000
 D0V  H14  C27  C26  120.44  3.000
 D0V  C28  C27  C26  118.72  3.000
 D0V  C30  C28  F29  119.36  3.000
 D0V  C30  C28  C27  121.48  3.000
 D0V  F29  C28  C27  119.16  3.000
 D0V  H15  C30  C31  120.04  3.000
 D0V  H15  C30  C28  120.42  3.000
 D0V  C31  C30  C28  119.54  3.000
 D0V  H16  C31  C30  119.21  3.000
 D0V  H16  C31  C25  120.44  3.000
 D0V  C30  C31  C25  120.35  3.000
 D0V  H17  C32  C33  121.17  3.000
 D0V  H17  C32  C23  120.66  3.000
 D0V  C33  C32  C23  118.17  3.000
 D0V  H18  C33  C34  120.31  3.000
 D0V  H18  C33  C32  119.90  3.000
 D0V  C34  C33  C32  119.79  3.000
 D0V  H19  C34  C33  120.56  3.000
 D0V  H19  C34  C21  121.55  3.000
 D0V  C33  C34  C21  117.89  3.000
 D0V  H7   O1   C2   110.21  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
 D0V  CONST_01  C10  C9   C7   C6      0.00   0.0  0
 D0V  CONST_02  C10  C11  C12  C6      0.00   0.0  0
 D0V  CONST_03  C7   C9   C10  C11     0.00   0.0  0
 D0V  CONST_04  C7   C6   C12  C11     0.00   0.0  0
 D0V  CONST_05  C12  C11  C10  C9      0.00   0.0  0
 D0V  CONST_06  C12  C6   C7   C9      0.00   0.0  0
 D0V  CONST_07  S18  C19  C20  C16     0.00   0.0  0
 D0V  CONST_08  C19  S18  C17  C16     0.00   0.0  0
 D0V  CONST_09  C19  C20  C16  C17     0.00   0.0  0
 D0V  CONST_10  C20  C19  S18  C17     0.00   0.0  0
 D0V  CONST_11  C20  C16  C17  S18     0.00   0.0  0
 D0V  CONST_12  C32  C23  N22  C21     0.00   0.0  0
 D0V  CONST_13  C32  C33  C34  C21     0.00   0.0  0
 D0V  CONST_14  C33  C32  C23  N22     0.00   0.0  0
 D0V  CONST_15  C33  C34  C21  N22     0.00   0.0  0
 D0V  CONST_16  C34  C33  C32  C23     0.00   0.0  0
 D0V  CONST_17  C34  C21  N22  C23     0.00   0.0  0
 D0V  CONST_18  C28  C27  C26  C25     0.00   0.0  0
 D0V  CONST_19  C28  C30  C31  C25     0.00   0.0  0
 D0V  CONST_20  C30  C28  C27  C26     0.00   0.0  0
 D0V  CONST_21  C30  C31  C25  C26     0.00   0.0  0
 D0V  CONST_22  C31  C25  C26  C27     0.00   0.0  0
 D0V  CONST_23  C31  C30  C28  C27     0.00   0.0  0
 D0V  CONST_24  C23  N22  C21  C15   180.00   0.0  0
 D0V  CONST_25  C33  C34  C21  C15   180.00   0.0  0
 D0V  CONST_26  C19  C20  C16  C15   180.00   0.0  0
 D0V  CONST_27  S18  C17  C16  C15   180.00   0.0  0
 D0V  CONST_29  S5   C6   C12  C11   180.00   0.0  0
 D0V  CONST_30  S5   C6   C7   C9    180.00   0.0  0
 D0V  CONST_31  CL8  C7   C9   C10   180.00   0.0  0
 D0V  CONST_32  CL8  C7   C6   C12   180.00   0.0  0
 D0V  CONST_33  N24  C23  N22  C21   180.00   0.0  0
 D0V  CONST_34  C27  C26  C25  N24   180.00   0.0  0
 D0V  CONST_35  C30  C31  C25  N24   180.00   0.0  0
 D0V  CONST_36  C33  C32  C23  N24   180.00   0.0  0
 D0V  CONST_37  F29  C28  C27  C26   180.00   0.0  0
 D0V  CONST_38  C31  C30  C28  F29   180.00   0.0  0
 D0V  CONST_40  H2   C9   C7   C6    180.00   0.0  0
 D0V  CONST_41  H1   C11  C12  C6    180.00   0.0  0
 D0V  CONST_42  H3   C10  C9   C7    180.00   0.0  0
 D0V  CONST_43  H4   C12  C6   C7    180.00   0.0  0
 D0V  CONST_44  H19  C34  C21  C15     0.00   0.0  0
 D0V  CONST_45  H11  C20  C16  C15     0.00   0.0  0
 D0V  CONST_46  H9   C17  C16  C15     0.00   0.0  0
 D0V  CONST_47  H10  C19  C20  C16   180.00   0.0  0
 D0V  CONST_48  H18  C33  C34  C21   180.00   0.0  0
 D0V  CONST_49  H17  C32  C23  N22   180.00   0.0  0
 D0V  CONST_50  H14  C27  C26  C25   180.00   0.0  0
 D0V  CONST_51  H15  C30  C31  C25   180.00   0.0  0
 D0V  CONST_52  H16  C31  C25  C26   180.00   0.0  0
 D0V  CONST_53  H13  C26  C27  C28   180.00   0.0  0
 D0V  CONST_54  H8   N14  C13  C4    180.00   0.0  0
 D0V  Var_01    C15  C3   C2   C4    -24.75  30.0  1
 D0V  Var_02    C3   C2   C4   C13    -1.65  30.0  1
 D0V  Var_03    N14  C13  C4   C2      5.16  30.0  1
 D0V  Var_04    C7   C6   S5   C4   -163.12  30.0  3
 D0V  Var_05    C2   C4   S5   C6    -98.63  30.0  3
 D0V  Var_06    C25  N24  C23  N22     7.34  30.0  1
 D0V  Var_07    C26  C25  N24  C23   149.65  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
 D0V  chir_01  C15  C21  N14  C16  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
 D0V  plan-1  C15  0.020
 D0V  plan-1  C16  0.020
 D0V  plan-1  C17  0.020
 D0V  plan-1  S18  0.020
 D0V  plan-1  C19  0.020
 D0V  plan-1  C20  0.020
 D0V  plan-1  H9   0.020
 D0V  plan-1  H10  0.020
 D0V  plan-1  H11  0.020
 D0V  plan-2  C6   0.020
 D0V  plan-2  C11  0.020
 D0V  plan-2  C7   0.020
 D0V  plan-2  C9   0.020
 D0V  plan-2  C10  0.020
 D0V  plan-2  C12  0.020
 D0V  plan-2  S5   0.020
 D0V  plan-2  CL8  0.020
 D0V  plan-2  H1   0.020
 D0V  plan-2  H2   0.020
 D0V  plan-2  H3   0.020
 D0V  plan-2  H4   0.020
 D0V  plan-3  C15  0.020
 D0V  plan-3  C21  0.020
 D0V  plan-3  N22  0.020
 D0V  plan-3  C23  0.020
 D0V  plan-3  N24  0.020
 D0V  plan-3  C32  0.020
 D0V  plan-3  C33  0.020
 D0V  plan-3  C34  0.020
 D0V  plan-3  H17  0.020
 D0V  plan-3  H18  0.020
 D0V  plan-3  H19  0.020
 D0V  plan-4  N24  0.020
 D0V  plan-4  C25  0.020
 D0V  plan-4  C26  0.020
 D0V  plan-4  C27  0.020
 D0V  plan-4  C28  0.020
 D0V  plan-4  F29  0.020
 D0V  plan-4  C30  0.020
 D0V  plan-4  C31  0.020
 D0V  plan-4  H13  0.020
 D0V  plan-4  H14  0.020
 D0V  plan-4  H15  0.020
 D0V  plan-4  H16  0.020
 D0V  plan-5  C4   0.020
 D0V  plan-5  C13  0.020
 D0V  plan-5  N14  0.020
 D0V  plan-5  C15  0.020
 D0V  plan-5  O35  0.020
 D0V  plan-5  H8   0.020

