# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:29:19 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-(2,6-difluorophenyl)-N-{4-[(3S)-pyrrolidin-3-yloxy]pyridin-3-yl}-1,3-thiazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(F)c1c2scc(n2)C(=O)Nc3cnccc3O[C@H]4CCNC4
#
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
 3YR  3YR  2-(2,6-difluorophenyl)-N-{4-[(3S)-pyrrolidin-3-yloxy]pyridin-3-yl}-1,3-thiazole-4-carboxamide  ligand  44  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3YR
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
 3YR  O2   O  O     0  -0.456  -0.5685   3.8089   0.5186
 3YR  C9   C  CR5   0   0.230   1.0006   2.0597   0.2890
 3YR  C8   C  CR15  0  -0.515   2.1333   2.7961   0.4550
 3YR  C10  C  C     0   0.510  -0.3723   2.6210   0.3308
 3YR  C11  C  CR6   0   0.211  -2.7093   1.8445   0.0803
 3YR  C12  C  CR16  0  -0.131  -3.3912   3.0455   0.2352
 3YR  C7   C  CR5   0   0.082   2.4528   0.4217   0.0513
 3YR  C3   C  CR16  0  -0.225   3.9085  -3.5500  -0.5602
 3YR  C2   C  CR16  0  -0.417   2.6000  -3.3522  -0.1488
 3YR  C4   C  CR16  0  -0.411   4.7558  -2.4711  -0.7599
 3YR  C5   C  CR6   0   0.556   4.2623  -1.2042  -0.5434
 3YR  C6   C  CR6   0  -0.348   2.9532  -0.9373  -0.1417
 3YR  O1   O  O2    0  -0.482  -2.7774  -0.4461  -0.3095
 3YR  C1   C  CR6   0   0.561   2.1485  -2.0645   0.0529
 3YR  S    S  S2    0   0.300   3.4953   1.7901   0.3150
 3YR  N4   N  N     0  -0.420   1.1951   0.7345   0.0659
 3YR  F1   F  F     0  -0.283   0.8937  -1.9042   0.4672
 3YR  N1   N  NH1   0  -0.756  -1.3271   1.6835   0.1404
 3YR  C15  C  CR6   0   0.410  -3.4718   0.6836  -0.1647
 3YR  C14  C  CR16  0  -0.421  -4.8501   0.8002  -0.2441
 3YR  C13  C  CR16  0  -0.081  -5.4176   2.0555  -0.0757
 3YR  N2   N  N     0  -0.409  -4.7169   3.1507   0.1594
 3YR  C16  C  CH1   0  -0.035  -3.4563  -1.6743  -0.5922
 3YR  C19  C  CH2   0  -0.292  -4.2198  -2.2052   0.6412
 3YR  N3   N  NH1   0  -0.618  -3.6467  -3.5206   0.8903
 3YR  C18  C  CH2   0  -0.289  -2.2598  -3.4584   0.4645
 3YR  C17  C  CH2   0  -0.466  -2.3885  -2.7319  -0.8662
 3YR  H1   H  HCR5  0   0.324   2.2269   3.8559   0.6325
 3YR  H2   H  HCR6  0   0.283  -2.8481   3.9582   0.4275
 3YR  H3   H  HCR6  0   0.290   4.2732  -4.5544  -0.7223
 3YR  H4   H  HCR6  0   0.292   1.9334  -4.1867   0.0210
 3YR  H5   H  HCR6  0   0.295   5.7803  -2.6074  -1.0775
 3YR  H6   H  HNH1  0   0.424  -0.9820   0.7408   0.0038
 3YR  H7   H  HCR6  0   0.292  -5.4901  -0.0508  -0.4298
 3YR  H8   H  HCR6  0   0.265  -6.4949   2.1638  -0.1335
 3YR  H9   H  HCH1  0   0.269  -4.1109  -1.5200  -1.4538
 3YR  H10  H  HCH2  0   0.229  -4.0834  -1.5068   1.4776
 3YR  H11  H  HCH2  0   0.236  -5.2939  -2.2803   0.4570
 3YR  H12  H  HNH1  0   0.355  -3.7429  -3.7891   1.8600
 3YR  H14  H  HCH2  0   0.203  -1.6123  -2.8919   1.1488
 3YR  H15  H  HCH2  0   0.234  -1.8352  -4.4582   0.3587
 3YR  H16  H  HCH2  0   0.250  -2.7536  -3.4183  -1.6310
 3YR  H17  H  HCH2  0   0.254  -1.4566  -2.2963  -1.2245
 3YR  F2   F  F     0  -0.299   5.0814  -0.1617  -0.7294

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
 3YR  O2   C10  double    1.219  0.020  1.219
 3YR  C8   S    aromatic  1.699  0.020  1.699
 3YR  C8   C9   aromatic  1.361  0.020  1.361
 3YR  S    C7   aromatic  1.740  0.020  1.740
 3YR  C10  C9   single    1.484  0.020  1.484
 3YR  C10  N1   single    1.352  0.020  1.352
 3YR  C12  N2   aromatic  1.332  0.020  1.332
 3YR  C12  C11  aromatic  1.390  0.020  1.390
 3YR  C9   N4   aromatic  1.358  0.020  1.358
 3YR  N2   C13  aromatic  1.321  0.020  1.321
 3YR  N1   C11  single    1.393  0.020  1.393
 3YR  C11  C15  aromatic  1.410  0.020  1.410
 3YR  F1   C1   single    1.331  0.020  1.331
 3YR  N4   C7   aromatic  1.296  0.020  1.296
 3YR  C7   C6   single    1.461  0.020  1.461
 3YR  C13  C14  aromatic  1.388  0.020  1.388
 3YR  C15  C14  aromatic  1.386  0.020  1.386
 3YR  C15  O1   single    1.334  0.020  1.334
 3YR  C1   C6   aromatic  1.399  0.020  1.399
 3YR  C1   C2   aromatic  1.379  0.020  1.379
 3YR  C6   C5   aromatic  1.395  0.020  1.395
 3YR  O1   C16  single    1.432  0.020  1.432
 3YR  C2   C3   aromatic  1.386  0.020  1.386
 3YR  C5   F2   single    1.339  0.020  1.339
 3YR  C5   C4   aromatic  1.377  0.020  1.377
 3YR  C19  N3   single    1.456  0.020  1.456
 3YR  C19  C16  single    1.545  0.020  1.545
 3YR  N3   C18  single    1.452  0.020  1.452
 3YR  C16  C17  single    1.528  0.020  1.528
 3YR  C3   C4   aromatic  1.386  0.020  1.386
 3YR  C18  C17  single    1.522  0.020  1.522
 3YR  C8   H1   single    0.930  0.020  1.080
 3YR  C12  H2   single    0.930  0.020  1.080
 3YR  C3   H3   single    0.930  0.020  1.080
 3YR  C2   H4   single    0.930  0.020  1.080
 3YR  C4   H5   single    0.930  0.020  1.080
 3YR  N1   H6   single    0.860  0.020  1.020
 3YR  C14  H7   single    0.930  0.020  1.080
 3YR  C13  H8   single    0.930  0.020  1.080
 3YR  C16  H9   single    0.970  0.020  1.090
 3YR  C19  H10  single    0.970  0.020  1.090
 3YR  C19  H11  single    0.970  0.020  1.090
 3YR  N3   H12  single    0.890  0.020  1.040
 3YR  C18  H14  single    0.970  0.020  1.090
 3YR  C18  H15  single    0.970  0.020  1.090
 3YR  C17  H16  single    0.970  0.020  1.090
 3YR  C17  H17  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
 3YR  N4   C9   C10  120.42  3.000
 3YR  N4   C9   C8   115.39  3.000
 3YR  C10  C9   C8   124.19  3.000
 3YR  H1   C8   S    121.72  3.000
 3YR  H1   C8   C9   128.60  3.000
 3YR  S    C8   C9   109.68  3.000
 3YR  N1   C10  C9   112.79  3.000
 3YR  N1   C10  O2   125.74  3.000
 3YR  C9   C10  O2   121.47  3.000
 3YR  C15  C11  N1   116.67  3.000
 3YR  C15  C11  C12  117.74  3.000
 3YR  N1   C11  C12  125.59  3.000
 3YR  H2   C12  N2   116.37  3.000
 3YR  H2   C12  C11  120.25  3.000
 3YR  N2   C12  C11  123.38  3.000
 3YR  N4   C7   S    112.94  3.000
 3YR  N4   C7   C6   123.95  3.000
 3YR  S    C7   C6   123.10  3.000
 3YR  H3   C3   C4   119.69  3.000
 3YR  H3   C3   C2   119.72  3.000
 3YR  C4   C3   C2   120.58  3.000
 3YR  H4   C2   C1   119.71  3.000
 3YR  H4   C2   C3   121.23  3.000
 3YR  C1   C2   C3   119.06  3.000
 3YR  H5   C4   C5   120.12  3.000
 3YR  H5   C4   C3   121.56  3.000
 3YR  C5   C4   C3   118.32  3.000
 3YR  F2   C5   C6   117.72  3.000
 3YR  F2   C5   C4   118.38  3.000
 3YR  C6   C5   C4   123.90  3.000
 3YR  C1   C6   C5   115.20  3.000
 3YR  C5   C6   C7   122.51  3.000
 3YR  C1   C6   C7   122.29  3.000
 3YR  C16  O1   C15  120.08  3.000
 3YR  F1   C1   C6   119.25  3.000
 3YR  C6   C1   C2   122.94  3.000
 3YR  F1   C1   C2   117.81  3.000
 3YR  C7   S    C8    89.88  3.000
 3YR  C7   N4   C9   112.11  3.000
 3YR  H6   N1   C11  116.09  3.000
 3YR  H6   N1   C10  115.07  3.000
 3YR  C11  N1   C10  128.82  3.000
 3YR  C14  C15  O1   125.65  3.000
 3YR  O1   C15  C11  115.76  3.000
 3YR  C14  C15  C11  118.59  3.000
 3YR  H7   C14  C13  119.39  3.000
 3YR  H7   C14  C15  122.19  3.000
 3YR  C13  C14  C15  118.42  3.000
 3YR  H8   C13  N2   116.97  3.000
 3YR  H8   C13  C14  119.35  3.000
 3YR  N2   C13  C14  123.67  3.000
 3YR  C13  N2   C12  118.19  3.000
 3YR  H9   C16  C17  112.03  3.000
 3YR  H9   C16  C19  112.45  3.000
 3YR  C17  C16  C19  104.52  3.000
 3YR  H9   C16  O1   108.58  3.000
 3YR  C17  C16  O1   107.33  3.000
 3YR  C19  C16  O1   111.81  3.000
 3YR  H11  C19  H10  107.11  3.000
 3YR  H11  C19  N3   110.71  3.000
 3YR  H10  C19  N3   113.28  3.000
 3YR  H11  C19  C16  112.03  3.000
 3YR  H10  C19  C16  109.16  3.000
 3YR  N3   C19  C16  104.63  3.000
 3YR  H12  N3   C18  112.56  3.000
 3YR  H12  N3   C19  111.50  3.000
 3YR  C18  N3   C19  106.68  3.000
 3YR  H15  C18  H14  107.65  3.000
 3YR  H15  C18  C17  112.68  3.000
 3YR  H14  C18  C17  110.38  3.000
 3YR  H15  C18  N3   111.14  3.000
 3YR  H14  C18  N3   113.71  3.000
 3YR  C17  C18  N3   101.31  3.000
 3YR  H17  C17  H16  107.91  3.000
 3YR  H17  C17  C18  113.97  3.000
 3YR  H16  C17  C18  109.95  3.000
 3YR  H17  C17  C16  112.34  3.000
 3YR  H16  C17  C16  109.11  3.000
 3YR  C18  C17  C16  103.46  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
 3YR  CONST_01  C7   S    C8   C9     0.00   0.0  0
 3YR  CONST_02  S    C7   N4   C9     0.00   0.0  0
 3YR  CONST_03  C6   C7   N4   C9   180.00   0.0  0
 3YR  CONST_04  N4   C7   S    C8     0.00   0.0  0
 3YR  CONST_05  C6   C7   S    C8   180.00   0.0  0
 3YR  CONST_06  C7   N4   C9   C8     0.00   0.0  0
 3YR  CONST_07  C13  N2   C12  C11    0.00   0.0  0
 3YR  CONST_08  C13  C14  C15  C11    0.00   0.0  0
 3YR  CONST_09  C14  C13  N2   C12    0.00   0.0  0
 3YR  CONST_10  C14  C15  C11  C12    0.00   0.0  0
 3YR  CONST_11  C2   C1   C6   C7   180.00   0.0  0
 3YR  CONST_12  C4   C5   C6   C7   180.00   0.0  0
 3YR  CONST_13  C6   C1   C2   C3     0.00   0.0  0
 3YR  CONST_14  C6   C5   C4   C3     0.00   0.0  0
 3YR  CONST_15  C5   C6   C1   C2     0.00   0.0  0
 3YR  CONST_16  C5   C4   C3   C2     0.00   0.0  0
 3YR  CONST_17  C1   C6   C5   C4     0.00   0.0  0
 3YR  CONST_18  C1   C2   C3   C4     0.00   0.0  0
 3YR  CONST_23  N4   C9   C8   S      0.00   0.0  0
 3YR  CONST_24  N2   C12  C11  C15    0.00   0.0  0
 3YR  CONST_25  N2   C13  C14  C15    0.00   0.0  0
 3YR  CONST_26  S    C8   C9   C10  180.00   0.0  0
 3YR  CONST_27  C7   N4   C9   C10  180.00   0.0  0
 3YR  CONST_28  O1   C15  C11  C12  180.00   0.0  0
 3YR  CONST_29  F1   C1   C6   C7     0.00   0.0  0
 3YR  CONST_30  F2   C5   C6   C7     0.00   0.0  0
 3YR  CONST_31  F1   C1   C2   C3   180.00   0.0  0
 3YR  CONST_32  F2   C5   C4   C3   180.00   0.0  0
 3YR  CONST_33  F1   C1   C6   C5   180.00   0.0  0
 3YR  CONST_34  C13  C14  C15  O1   180.00   0.0  0
 3YR  CONST_35  F2   C5   C6   C1   180.00   0.0  0
 3YR  CONST_36  N2   C12  C11  N1   180.00   0.0  0
 3YR  CONST_37  C14  C15  C11  N1   180.00   0.0  0
 3YR  CONST_38  H7   C14  C15  C11  180.00   0.0  0
 3YR  CONST_39  H8   C13  N2   C12  180.00   0.0  0
 3YR  CONST_40  H1   C8   S    C7   180.00   0.0  0
 3YR  CONST_41  H5   C4   C3   C2   180.00   0.0  0
 3YR  CONST_42  H4   C2   C3   C4   180.00   0.0  0
 3YR  CONST_43  H3   C3   C4   C5   180.00   0.0  0
 3YR  CONST_44  H2   C12  C11  C15  180.00   0.0  0
 3YR  CONST_45  C11  N1   C10  C9   180.00   0.0  0
 3YR  CONST_46  C12  C11  N1   C10    0.00   0.0  0
 3YR  CONST_47  C15  C11  N1   C10  180.00   0.0  0
 3YR  CONST_48  H6   N1   C11  C12  180.00   0.0  0
 3YR  CONST_49  C11  N1   C10  O2     0.00   0.0  0
 3YR  Var_01    C18  N3   C19  C16   31.13  30.0  1
 3YR  Var_02    N3   C18  C17  C16   39.47  30.0  1
 3YR  Var_03    C17  C18  N3   C19  -44.46  30.0  1
 3YR  Var_04    C8   C9   C10  O2     0.19  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
 3YR  chir_01  C16  O1  C19  C17  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
 3YR  plan-1  C9   0.020
 3YR  plan-1  C8   0.020
 3YR  plan-1  C10  0.020
 3YR  plan-1  C7   0.020
 3YR  plan-1  C6   0.020
 3YR  plan-1  S    0.020
 3YR  plan-1  N4   0.020
 3YR  plan-1  H1   0.020
 3YR  plan-2  C11  0.020
 3YR  plan-2  C12  0.020
 3YR  plan-2  O1   0.020
 3YR  plan-2  N1   0.020
 3YR  plan-2  C15  0.020
 3YR  plan-2  C14  0.020
 3YR  plan-2  C13  0.020
 3YR  plan-2  N2   0.020
 3YR  plan-2  H2   0.020
 3YR  plan-2  H7   0.020
 3YR  plan-2  H8   0.020
 3YR  plan-3  C7   0.020
 3YR  plan-3  C3   0.020
 3YR  plan-3  C2   0.020
 3YR  plan-3  C4   0.020
 3YR  plan-3  C5   0.020
 3YR  plan-3  C6   0.020
 3YR  plan-3  C1   0.020
 3YR  plan-3  F1   0.020
 3YR  plan-3  H3   0.020
 3YR  plan-3  H4   0.020
 3YR  plan-3  H5   0.020
 3YR  plan-3  F2   0.020
 3YR  plan-4  O2   0.020
 3YR  plan-4  C9   0.020
 3YR  plan-4  C10  0.020
 3YR  plan-4  C11  0.020
 3YR  plan-4  N1   0.020
 3YR  plan-4  H6   0.020

