# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:04:38 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (2R)-5-[(2-chlorophenyl)sulfanyl]-6'-(4-fluorophenoxy)-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(Oc5ccc(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
 D3J  D3J  (2R)-5-[(2-chlorophenyl)sulfanyl]-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro[2,2'-bipyridin]-6(1H)-one  ligand  53  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_D3J
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
 D3J  C4    C   CR16  0  -0.276  -0.3540   3.0238   0.7098
 D3J  C14   C   C     0   0.579   0.0758  -0.2752  -0.8780
 D3J  C5    C   CR16  0  -0.413  -1.3811   4.1158  -1.6337
 D3J  C6    C   CR16  0  -0.304  -2.2406   3.6048  -0.6704
 D3J  C11   C   CR6   0   0.289  -2.2957  -0.8352   1.0637
 D3J  C7    C   CR6   0   0.357  -1.7221   3.0672   0.4946
 D3J  C9    C   CR6   0   0.501  -2.7173   1.3061   1.6930
 D3J  C12   C   CT    0  -0.083  -1.6269  -1.7838   0.0547
 D3J  C3    C   CR16  0  -0.368   0.5093   3.5251  -0.2487
 D3J  C2    C   CR6   0   0.524  -0.0211   4.0616  -1.4045
 D3J  O8    O   O2    0  -0.521  -2.5921   2.6329   1.4702
 D3J  N10   N   N     0  -0.432  -2.1668   0.4657   0.8488
 D3J  N13   N   NH1   0  -0.634  -1.0284  -1.0589  -1.0475
 D3J  C15   C   C     0  -0.484   0.8882  -0.5766   0.3121
 D3J  S16   S   S2    0   0.102   2.1851   0.5126   0.7452
 D3J  C17   C   CR6   0  -0.021   3.4727   0.0979  -0.3933
 D3J  C18   C   CR6   0  -0.070   4.5703   0.9507  -0.4806
 D3J  C19   C   CR16  0  -0.200   5.6258   0.6883  -1.3389
 D3J  C20   C   CR16  0  -0.276   5.5918  -0.4465  -2.1343
 D3J  C21   C   CR16  0  -0.234   4.5040  -1.3063  -2.0607
 D3J  C22   C   CR16  0  -0.248   3.4547  -1.0379  -1.1963
 D3J  CL23  CL  CL    0  -0.116   4.6205   2.3757   0.5066
 D3J  C24   C   C     0   0.494   0.6307  -1.6614   1.0773
 D3J  O25   O   OH1   0  -0.571   1.3551  -2.0463   2.1101
 D3J  C26   C   CH2   0  -0.543  -0.5137  -2.5622   0.7571
 D3J  C28   C   CR5   0   0.234  -2.6924  -2.7004  -0.4984
 D3J  C29   C   CR15  0  -0.566  -2.6900  -4.0611  -0.4403
 D3J  S30   S   S2    0   0.236  -4.0824  -4.7327  -1.1769
 D3J  C31   C   CR15  0  -0.463  -4.6904  -3.1816  -1.5768
 D3J  C32   C   CR15  0  -0.204  -3.8571  -2.1960  -1.1534
 D3J  C33   C   CR16  0  -0.325  -3.0022  -1.3432   2.1423
 D3J  C34   C   CR16  0  -0.147  -3.5813  -0.4420   3.0275
 D3J  C35   C   CR16  0  -0.389  -3.4441   0.9159   2.8145
 D3J  H1    H   HCR6  0   0.269   0.0429   2.5966   1.6211
 D3J  H2    H   HCR6  0   0.281  -1.7697   4.5422  -2.5489
 D3J  H3    H   HCR6  0   0.275  -3.3106   3.6329  -0.8296
 D3J  H4    H   HCR6  0   0.255   1.5795   3.4785  -0.1004
 D3J  H5    H   HNH1  0   0.395  -1.6550  -0.7378  -1.7722
 D3J  H6    H   HCR6  0   0.283   6.4653   1.3685  -1.3837
 D3J  H7    H   HCR6  0   0.269   6.4127  -0.6539  -2.8071
 D3J  H8    H   HCR6  0   0.267   4.4695  -2.1946  -2.6772
 D3J  H9    H   HCR6  0   0.267   2.6162  -1.7192  -1.1418
 D3J  H10   H   HOH1  0   0.482   2.1029  -1.4353   2.2334
 D3J  H11   H   HCH2  0   0.296  -0.8823  -3.0366   1.6672
 D3J  H12   H   HCH2  0   0.307  -0.1429  -3.3608   0.1052
 D3J  H13   H   HCR5  0   0.301  -1.9507  -4.7139  -0.0015
 D3J  H14   H   HCR5  0   0.300  -5.6298  -3.0773  -2.0971
 D3J  H15   H   HCR5  0   0.272  -4.0680  -1.1441  -1.2947
 D3J  H16   H   HCR6  0   0.268  -3.1109  -2.4092   2.2906
 D3J  H17   H   HCR6  0   0.279  -4.1372  -0.8011   3.8832
 D3J  H18   H   HCR6  0   0.279  -3.8777   1.6461   3.4838
 D3J  F1    F   F     0  -0.321   0.8170   4.5471  -2.3379
 D3J  O27   O   O     0  -0.452   0.4143   0.5585  -1.6976

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
 D3J  C3   C4    aromatic  1.384  0.020  1.384
 D3J  C3   C2    aromatic  1.380  0.020  1.380
 D3J  F1   C2    single    1.345  0.020  1.345
 D3J  C4   C7    aromatic  1.386  0.020  1.386
 D3J  C2   C5    aromatic  1.380  0.020  1.380
 D3J  S30  C29   aromatic  1.712  0.020  1.712
 D3J  S30  C31   aromatic  1.713  0.020  1.713
 D3J  C7   O8    single    1.377  0.020  1.377
 D3J  C7   C6    aromatic  1.384  0.020  1.384
 D3J  C5   C6    aromatic  1.389  0.020  1.389
 D3J  O8   C9    single    1.351  0.020  1.351
 D3J  C29  C28   aromatic  1.362  0.020  1.362
 D3J  C9   C35   aromatic  1.392  0.020  1.392
 D3J  C9   N10   aromatic  1.312  0.020  1.312
 D3J  C35  C34   aromatic  1.381  0.020  1.381
 D3J  C31  C32   aromatic  1.358  0.020  1.358
 D3J  N10  C11   aromatic  1.325  0.020  1.325
 D3J  C34  C33   aromatic  1.390  0.020  1.390
 D3J  C28  C32   aromatic  1.428  0.020  1.428
 D3J  C28  C12   single    1.510  0.020  1.510
 D3J  C11  C33   aromatic  1.386  0.020  1.386
 D3J  C11  C12   single    1.538  0.020  1.538
 D3J  C12  C26   single    1.529  0.020  1.529
 D3J  C12  N13   single    1.449  0.020  1.449
 D3J  C26  C24   single    1.491  0.020  1.491
 D3J  N13  C14   single    1.365  0.020  1.365
 D3J  C24  O25   single    1.319  0.020  1.319
 D3J  C24  C15   double    1.352  0.020  1.352
 D3J  C21  C22   aromatic  1.386  0.020  1.386
 D3J  C21  C20   aromatic  1.388  0.020  1.388
 D3J  C22  C17   aromatic  1.391  0.020  1.391
 D3J  C14  C15   single    1.472  0.020  1.472
 D3J  C14  O27   double    1.217  0.020  1.217
 D3J  C15  S16   single    1.748  0.020  1.748
 D3J  C20  C19   aromatic  1.386  0.020  1.386
 D3J  C17  S16   single    1.768  0.020  1.768
 D3J  C17  C18   aromatic  1.393  0.020  1.393
 D3J  C19  C18   aromatic  1.386  0.020  1.386
 D3J  C18  CL23  single    1.734  0.020  1.734
 D3J  C4   H1    single    0.930  0.020  1.080
 D3J  C5   H2    single    0.930  0.020  1.080
 D3J  C6   H3    single    0.930  0.020  1.080
 D3J  C3   H4    single    0.930  0.020  1.080
 D3J  N13  H5    single    0.890  0.020  1.040
 D3J  C19  H6    single    0.930  0.020  1.080
 D3J  C20  H7    single    0.930  0.020  1.080
 D3J  C21  H8    single    0.930  0.020  1.080
 D3J  C22  H9    single    0.930  0.020  1.080
 D3J  O25  H10   single    0.850  0.020  0.980
 D3J  C26  H11   single    0.970  0.020  1.090
 D3J  C26  H12   single    0.970  0.020  1.090
 D3J  C29  H13   single    0.930  0.020  1.080
 D3J  C31  H14   single    0.930  0.020  1.080
 D3J  C32  H15   single    0.930  0.020  1.080
 D3J  C33  H16   single    0.930  0.020  1.080
 D3J  C34  H17   single    0.930  0.020  1.080
 D3J  C35  H18   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
 D3J  H1    C4   C3   119.84  3.000
 D3J  H1    C4   C7   120.36  3.000
 D3J  C3    C4   C7   119.80  3.000
 D3J  O27   C14  C15  122.08  3.000
 D3J  O27   C14  N13  122.33  3.000
 D3J  C15   C14  N13  115.43  3.000
 D3J  H2    C5   C2   120.66  3.000
 D3J  H2    C5   C6   120.63  3.000
 D3J  C2    C5   C6   118.70  3.000
 D3J  H3    C6   C7   120.29  3.000
 D3J  H3    C6   C5   120.03  3.000
 D3J  C7    C6   C5   119.68  3.000
 D3J  C33   C11  N10  122.39  3.000
 D3J  C33   C11  C12  120.42  3.000
 D3J  N10   C11  C12  117.19  3.000
 D3J  O8    C7   C6   118.83  3.000
 D3J  C6    C7   C4   120.86  3.000
 D3J  O8    C7   C4   120.24  3.000
 D3J  C35   C9   N10  123.90  3.000
 D3J  N10   C9   O8   118.94  3.000
 D3J  C35   C9   O8   117.16  3.000
 D3J  C28   C12  C26  111.89  3.000
 D3J  C26   C12  N13  107.66  3.000
 D3J  C28   C12  N13  108.45  3.000
 D3J  N13   C12  C11  111.73  3.000
 D3J  C26   C12  C11  109.22  3.000
 D3J  C28   C12  C11  107.93  3.000
 D3J  H4    C3   C2   120.79  3.000
 D3J  H4    C3   C4   120.45  3.000
 D3J  C2    C3   C4   118.76  3.000
 D3J  F1    C2   C3   118.81  3.000
 D3J  F1    C2   C5   118.98  3.000
 D3J  C3    C2   C5   122.21  3.000
 D3J  C9    O8   C7   119.01  3.000
 D3J  C9    N10  C11  118.93  3.000
 D3J  H5    N13  C12  116.65  3.000
 D3J  H5    N13  C14  114.10  3.000
 D3J  C12   N13  C14  121.81  3.000
 D3J  C24   C15  S16  120.06  3.000
 D3J  S16   C15  C14  118.82  3.000
 D3J  C24   C15  C14  121.10  3.000
 D3J  C17   S16  C15  103.57  3.000
 D3J  C22   C17  C18  118.29  3.000
 D3J  C18   C17  S16  118.08  3.000
 D3J  C22   C17  S16  123.63  3.000
 D3J  CL23  C18  C19  119.09  3.000
 D3J  CL23  C18  C17  119.36  3.000
 D3J  C19   C18  C17  121.55  3.000
 D3J  H6    C19  C20  120.68  3.000
 D3J  H6    C19  C18  119.86  3.000
 D3J  C20   C19  C18  119.46  3.000
 D3J  H7    C20  C21  120.60  3.000
 D3J  H7    C20  C19  119.69  3.000
 D3J  C21   C20  C19  119.72  3.000
 D3J  H8    C21  C22  119.37  3.000
 D3J  H8    C21  C20  120.21  3.000
 D3J  C22   C21  C20  120.42  3.000
 D3J  H9    C22  C21  119.76  3.000
 D3J  H9    C22  C17  119.68  3.000
 D3J  C21   C22  C17  120.56  3.000
 D3J  C26   C24  O25  114.41  3.000
 D3J  O25   C24  C15  124.93  3.000
 D3J  C26   C24  C15  120.62  3.000
 D3J  H10   O25  C24  109.75  3.000
 D3J  H12   C26  H11  107.09  3.000
 D3J  H12   C26  C24  107.96  3.000
 D3J  H11   C26  C24  110.06  3.000
 D3J  H12   C26  C12  110.13  3.000
 D3J  H11   C26  C12  111.02  3.000
 D3J  C24   C26  C12  110.47  3.000
 D3J  C32   C28  C29  111.95  3.000
 D3J  C32   C28  C12  121.93  3.000
 D3J  C29   C28  C12  126.12  3.000
 D3J  H13   C29  S30  119.64  3.000
 D3J  H13   C29  C28  128.52  3.000
 D3J  S30   C29  C28  111.84  3.000
 D3J  C31   S30  C29   91.94  3.000
 D3J  H14   C31  C32  127.90  3.000
 D3J  H14   C31  S30  120.60  3.000
 D3J  C32   C31  S30  111.49  3.000
 D3J  H15   C32  C31  123.03  3.000
 D3J  H15   C32  C28  124.20  3.000
 D3J  C31   C32  C28  112.77  3.000
 D3J  H16   C33  C34  120.66  3.000
 D3J  H16   C33  C11  121.27  3.000
 D3J  C34   C33  C11  118.07  3.000
 D3J  H17   C34  C35  119.95  3.000
 D3J  H17   C34  C33  120.18  3.000
 D3J  C35   C34  C33  119.86  3.000
 D3J  H18   C35  C34  121.91  3.000
 D3J  H18   C35  C9   121.25  3.000
 D3J  C34   C35  C9   116.84  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
 D3J  CONST_01  C5    C2   C3   C4     0.00   0.0  0
 D3J  CONST_02  C5    C6   C7   C4     0.00   0.0  0
 D3J  CONST_03  C3    C4   C7   C6     0.00   0.0  0
 D3J  CONST_04  C3    C2   C5   C6     0.00   0.0  0
 D3J  CONST_05  C35   C9   N10  C11    0.00   0.0  0
 D3J  CONST_06  C35   C34  C33  C11    0.00   0.0  0
 D3J  CONST_07  C2    C3   C4   C7     0.00   0.0  0
 D3J  CONST_08  C2    C5   C6   C7     0.00   0.0  0
 D3J  CONST_09  C33   C34  C35  C9     0.00   0.0  0
 D3J  CONST_10  C33   C11  N10  C9     0.00   0.0  0
 D3J  CONST_11  C34   C35  C9   N10    0.00   0.0  0
 D3J  CONST_12  C34   C33  C11  N10    0.00   0.0  0
 D3J  CONST_13  C20   C21  C22  C17    0.00   0.0  0
 D3J  CONST_14  C20   C19  C18  C17    0.00   0.0  0
 D3J  CONST_15  C21   C22  C17  C18    0.00   0.0  0
 D3J  CONST_16  C21   C20  C19  C18    0.00   0.0  0
 D3J  CONST_17  C22   C21  C20  C19    0.00   0.0  0
 D3J  CONST_18  C22   C17  C18  C19    0.00   0.0  0
 D3J  CONST_19  C31   S30  C29  C28    0.00   0.0  0
 D3J  CONST_20  S30   C31  C32  C28    0.00   0.0  0
 D3J  CONST_21  C32   C31  S30  C29    0.00   0.0  0
 D3J  CONST_22  C31   C32  C28  C29    0.00   0.0  0
 D3J  CONST_23  C32   C28  C29  S30    0.00   0.0  0
 D3J  CONST_24  C12   C11  N10  C9   180.00   0.0  0
 D3J  CONST_25  S30   C29  C28  C12  180.00   0.0  0
 D3J  CONST_26  C31   C32  C28  C12  180.00   0.0  0
 D3J  CONST_27  C34   C33  C11  C12  180.00   0.0  0
 D3J  CONST_29  F1    C2   C3   C4   180.00   0.0  0
 D3J  CONST_30  O8    C7   C6   C5   180.00   0.0  0
 D3J  CONST_31  F1    C2   C5   C6   180.00   0.0  0
 D3J  CONST_32  O8    C9   N10  C11  180.00   0.0  0
 D3J  CONST_33  O8    C7   C4   C3   180.00   0.0  0
 D3J  CONST_34  C34   C35  C9   O8   180.00   0.0  0
 D3J  CONST_35  C21   C22  C17  S16  180.00   0.0  0
 D3J  CONST_36  C19   C18  C17  S16  180.00   0.0  0
 D3J  CONST_37  CL23  C18  C19  C20  180.00   0.0  0
 D3J  CONST_38  CL23  C18  C17  C22  180.00   0.0  0
 D3J  CONST_40  H3    C6   C7   C4   180.00   0.0  0
 D3J  CONST_41  H4    C3   C2   C5   180.00   0.0  0
 D3J  CONST_42  H1    C4   C7   C6   180.00   0.0  0
 D3J  CONST_43  H17   C34  C33  C11  180.00   0.0  0
 D3J  CONST_44  H2    C5   C6   C7   180.00   0.0  0
 D3J  CONST_45  H13   C29  C28  C12    0.00   0.0  0
 D3J  CONST_46  H15   C32  C28  C12    0.00   0.0  0
 D3J  CONST_47  H16   C33  C11  C12    0.00   0.0  0
 D3J  CONST_48  H18   C35  C9   N10  180.00   0.0  0
 D3J  CONST_49  H8    C21  C22  C17  180.00   0.0  0
 D3J  CONST_50  H6    C19  C18  C17  180.00   0.0  0
 D3J  CONST_51  H9    C22  C17  C18  180.00   0.0  0
 D3J  CONST_52  H7    C20  C19  C18  180.00   0.0  0
 D3J  CONST_53  H14   C31  C32  C28  180.00   0.0  0
 D3J  CONST_54  H5    N13  C14  C15  180.00   0.0  0
 D3J  Var_01    C26   C24  C15  C14   -1.85  30.0  1
 D3J  Var_02    C15   C24  C26  C12  -28.62  30.0  1
 D3J  Var_03    C24   C15  C14  N13    7.69  30.0  1
 D3J  Var_04    C35   C9   O8   C7   170.44  30.0  2
 D3J  Var_05    C22   C17  S16  C15  -12.16  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
 D3J  chir_01  C12  C11  C26  N13  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
 D3J  plan-1  C12   0.020
 D3J  plan-1  C28   0.020
 D3J  plan-1  C29   0.020
 D3J  plan-1  S30   0.020
 D3J  plan-1  C31   0.020
 D3J  plan-1  C32   0.020
 D3J  plan-1  H13   0.020
 D3J  plan-1  H14   0.020
 D3J  plan-1  H15   0.020
 D3J  plan-2  C11   0.020
 D3J  plan-2  C9    0.020
 D3J  plan-2  C12   0.020
 D3J  plan-2  O8    0.020
 D3J  plan-2  N10   0.020
 D3J  plan-2  C33   0.020
 D3J  plan-2  C34   0.020
 D3J  plan-2  C35   0.020
 D3J  plan-2  H16   0.020
 D3J  plan-2  H17   0.020
 D3J  plan-2  H18   0.020
 D3J  plan-3  C4    0.020
 D3J  plan-3  C5    0.020
 D3J  plan-3  C6    0.020
 D3J  plan-3  C7    0.020
 D3J  plan-3  C3    0.020
 D3J  plan-3  C2    0.020
 D3J  plan-3  O8    0.020
 D3J  plan-3  H1    0.020
 D3J  plan-3  H2    0.020
 D3J  plan-3  H3    0.020
 D3J  plan-3  H4    0.020
 D3J  plan-3  F1    0.020
 D3J  plan-4  S16   0.020
 D3J  plan-4  C17   0.020
 D3J  plan-4  C18   0.020
 D3J  plan-4  C19   0.020
 D3J  plan-4  C20   0.020
 D3J  plan-4  C21   0.020
 D3J  plan-4  C22   0.020
 D3J  plan-4  CL23  0.020
 D3J  plan-4  H6    0.020
 D3J  plan-4  H7    0.020
 D3J  plan-4  H8    0.020
 D3J  plan-4  H9    0.020
 D3J  plan-5  C14   0.020
 D3J  plan-5  C12   0.020
 D3J  plan-5  N13   0.020
 D3J  plan-5  C15   0.020
 D3J  plan-5  H5    0.020
 D3J  plan-5  O27   0.020

