# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 17:24:36 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 1-ethyl-3-{5'-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)-4-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridin-6-yl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1cc(c2scc(n2)C(F)(F)F)c(cn1)c3cncc(c3)C4=NNC(=O)O4
#
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
 1YP  1YP  1-ethyl-3-{5'-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)-4-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridin-6-yl}urea  ligand  47  33  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1YP
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
 1YP  C1   C  CH3   0  -0.691   8.4407  -3.3381   0.7742
 1YP  C2   C  CH2   0  -0.261   7.0898  -3.7872   0.2489
 1YP  C3   C  C     0   0.729   4.8371  -2.8350   0.0923
 1YP  N6   N  NR15  0  -0.507  -5.7477  -3.0037   1.5782
 1YP  C7   C  CR6   0  -0.035   0.1455  -0.9210  -0.6293
 1YP  C8   C  CR16  0  -0.069   0.7438  -2.1641  -0.7751
 1YP  C9   C  CR6   0  -0.145  -1.2870  -0.7711  -0.9458
 1YP  C10  C  CR16  0  -0.170  -2.2628  -1.4143  -0.2050
 1YP  C11  C  CR6   0  -0.086  -3.5991  -1.2588  -0.5668
 1YP  C12  C  CR16  0  -0.059  -3.8987  -0.4610  -1.6667
 1YP  C13  C  CR16  0  -0.054  -1.7011  -0.0037  -2.0376
 1YP  C14  C  CR5   0   0.507  -4.6407  -1.9152   0.1995
 1YP  C15  C  CR5   0   0.657  -6.6705  -2.5287   0.7173
 1YP  C16  C  CR5   0  -0.046   0.4943   1.4976   0.0368
 1YP  N1   N  NH1   0  -0.677   6.1743  -2.6659   0.1905
 1YP  O1   O  O     0  -0.499   4.2936  -3.9234   0.1144
 1YP  N2   N  NH1   0  -0.779   4.1562  -1.6278  -0.0025
 1YP  C4   C  CR6   0   0.573   2.8086  -1.4198  -0.1999
 1YP  C5   C  CR16  0  -0.465   2.3176  -0.1230  -0.0063
 1YP  C6   C  CR6   0   0.233   0.9750   0.1338  -0.2182
 1YP  N3   N  N     0  -0.422   2.0272  -2.4194  -0.5753
 1YP  N4   N  N     0  -0.384  -2.9665   0.1487  -2.3865
 1YP  N5   N  N     0  -0.242  -4.4908  -2.6199   1.2554
 1YP  O2   O  O     0  -0.444  -7.8638  -2.6458   0.6689
 1YP  O3   O  O     0  -0.459  -5.9290  -1.8145  -0.1872
 1YP  N7   N  N     0  -0.385   1.2658   2.5363  -0.0441
 1YP  C17  C  CR5   0   0.070   0.6097   3.6644   0.3190
 1YP  C18  C  CR15  0  -0.522  -0.6847   3.5085   0.7001
 1YP  S1   S  S2    0   0.307  -1.1087   1.8648   0.5823
 1YP  F1   F  F     0  -0.301   0.5926   5.9700   0.6880
 1YP  F2   F  F     0  -0.310   2.4442   4.9207   1.0396
 1YP  F3   F  F     0  -0.310   1.7611   5.2405  -0.9708
 1YP  H1   H  HCH3  0   0.242   9.1318  -4.1794   0.7929
 1YP  H2   H  HCH3  0   0.231   8.8785  -2.5655   0.1399
 1YP  H3   H  HCH3  0   0.234   8.3598  -2.9423   1.7867
 1YP  H4   H  HCH2  0   0.230   7.2076  -4.2452  -0.7384
 1YP  H5   H  HCH2  0   0.240   6.6711  -4.5501   0.9046
 1YP  H6   H  HNR5  0   0.448  -5.9222  -3.5699   2.3939
 1YP  H7   H  HCR6  0   0.272   0.1390  -3.0055  -1.0972
 1YP  H8   H  HCR6  0   0.284  -1.9902  -2.0180   0.6515
 1YP  H9   H  HCR6  0   0.283  -4.9237  -0.3097  -1.9836
 1YP  H10  H  HCR6  0   0.280  -0.9626   0.5044  -2.6495
 1YP  H11  H  HNH1  0   0.397   6.5742  -1.7634  -0.0138
 1YP  H12  H  HNH1  0   0.418   4.6918  -0.7911   0.1722
 1YP  H13  H  HCR6  0   0.286   2.9750   0.6672   0.3313
 1YP  H14  H  HCR5  0   0.332  -1.3976   4.2506   1.0237
 1YP  C19  C  CT    0   1.071   1.3513   4.9556   0.2700

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
 1YP  C1   C2   single    1.517  0.020  1.517
 1YP  C2   N1   single    1.449  0.020  1.449
 1YP  N1   C3   single    1.351  0.020  1.351
 1YP  C3   O1   double    1.217  0.020  1.217
 1YP  C3   N2   single    1.389  0.020  1.389
 1YP  N2   C4   single    1.378  0.020  1.378
 1YP  C4   N3   aromatic  1.323  0.020  1.323
 1YP  C4   C5   aromatic  1.400  0.020  1.400
 1YP  N3   C8   aromatic  1.324  0.020  1.324
 1YP  C5   C6   aromatic  1.383  0.020  1.383
 1YP  S1   C16  aromatic  1.733  0.020  1.733
 1YP  S1   C18  aromatic  1.702  0.020  1.702
 1YP  C8   C7   aromatic  1.387  0.020  1.387
 1YP  C6   C7   aromatic  1.403  0.020  1.403
 1YP  C6   C16  single    1.468  0.020  1.468
 1YP  C7   C9   single    1.475  0.020  1.475
 1YP  C16  N7   aromatic  1.296  0.020  1.296
 1YP  C18  C17  aromatic  1.358  0.020  1.358
 1YP  C13  C9   aromatic  1.397  0.020  1.397
 1YP  C13  N4   aromatic  1.322  0.020  1.322
 1YP  C9   C10  aromatic  1.384  0.020  1.384
 1YP  N7   C17  aromatic  1.355  0.020  1.355
 1YP  N4   C12  aromatic  1.326  0.020  1.326
 1YP  C17  C19  single    1.490  0.020  1.490
 1YP  C10  C11  aromatic  1.393  0.020  1.393
 1YP  C12  C11  aromatic  1.391  0.020  1.391
 1YP  F1   C19  single    1.334  0.020  1.334
 1YP  C19  F3   single    1.337  0.020  1.337
 1YP  C19  F2   single    1.337  0.020  1.337
 1YP  C11  C14  single    1.450  0.020  1.450
 1YP  C14  O3   single    1.349  0.020  1.349
 1YP  C14  N5   double    1.278  0.020  1.278
 1YP  O3   C15  single    1.370  0.020  1.370
 1YP  N5   N6   single    1.353  0.020  1.353
 1YP  C15  N6   single    1.348  0.020  1.348
 1YP  C15  O2   double    1.200  0.020  1.200
 1YP  C1   H1   single    0.970  0.020  1.090
 1YP  C1   H2   single    0.970  0.020  1.090
 1YP  C1   H3   single    0.970  0.020  1.090
 1YP  C2   H4   single    0.970  0.020  1.090
 1YP  C2   H5   single    0.970  0.020  1.090
 1YP  N6   H6   single    0.860  0.020  1.020
 1YP  C8   H7   single    0.930  0.020  1.080
 1YP  C10  H8   single    0.930  0.020  1.080
 1YP  C12  H9   single    0.930  0.020  1.080
 1YP  C13  H10  single    0.930  0.020  1.080
 1YP  N1   H11  single    0.860  0.020  1.020
 1YP  N2   H12  single    0.860  0.020  1.020
 1YP  C5   H13  single    0.930  0.020  1.080
 1YP  C18  H14  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
 1YP  H3   C1   H2   108.21  3.000
 1YP  H3   C1   H1   108.15  3.000
 1YP  H2   C1   H1   107.60  3.000
 1YP  H3   C1   C2   111.28  3.000
 1YP  H2   C1   C2   111.44  3.000
 1YP  H1   C1   C2   110.02  3.000
 1YP  H5   C2   H4   106.92  3.000
 1YP  H5   C2   N1   108.86  3.000
 1YP  H4   C2   N1   110.82  3.000
 1YP  H5   C2   C1   109.94  3.000
 1YP  H4   C2   C1   109.89  3.000
 1YP  N1   C2   C1   110.34  3.000
 1YP  N2   C3   O1   124.03  3.000
 1YP  N2   C3   N1   112.41  3.000
 1YP  O1   C3   N1   123.54  3.000
 1YP  H6   N6   N5   120.86  3.000
 1YP  H6   N6   C15  126.58  3.000
 1YP  N5   N6   C15  112.55  3.000
 1YP  C6   C7   C9   124.09  3.000
 1YP  C9   C7   C8   119.18  3.000
 1YP  C6   C7   C8   116.70  3.000
 1YP  H7   C8   N3   115.83  3.000
 1YP  H7   C8   C7   119.05  3.000
 1YP  N3   C8   C7   125.10  3.000
 1YP  C13  C9   C10  117.69  3.000
 1YP  C10  C9   C7   121.52  3.000
 1YP  C13  C9   C7   120.76  3.000
 1YP  H8   C10  C11  120.61  3.000
 1YP  H8   C10  C9   120.34  3.000
 1YP  C11  C10  C9   119.04  3.000
 1YP  C14  C11  C12  121.51  3.000
 1YP  C14  C11  C10  120.07  3.000
 1YP  C12  C11  C10  118.41  3.000
 1YP  H9   C12  N4   116.23  3.000
 1YP  H9   C12  C11  120.99  3.000
 1YP  N4   C12  C11  122.77  3.000
 1YP  H10  C13  N4   116.66  3.000
 1YP  H10  C13  C9   119.74  3.000
 1YP  N4   C13  C9   123.60  3.000
 1YP  O3   C14  N5   112.95  3.000
 1YP  N5   C14  C11  127.01  3.000
 1YP  O3   C14  C11  120.04  3.000
 1YP  O3   C15  O2   124.21  3.000
 1YP  O2   C15  N6   132.22  3.000
 1YP  O3   C15  N6   103.57  3.000
 1YP  S1   C16  N7   113.61  3.000
 1YP  N7   C16  C6   122.58  3.000
 1YP  S1   C16  C6   123.67  3.000
 1YP  H11  N1   C3   119.33  3.000
 1YP  H11  N1   C2   116.77  3.000
 1YP  C3   N1   C2   122.10  3.000
 1YP  H12  N2   C4   114.77  3.000
 1YP  H12  N2   C3   116.66  3.000
 1YP  C4   N2   C3   128.35  3.000
 1YP  N3   C4   C5   122.13  3.000
 1YP  C5   C4   N2   117.58  3.000
 1YP  N3   C4   N2   120.28  3.000
 1YP  H13  C5   C6   120.13  3.000
 1YP  H13  C5   C4   120.43  3.000
 1YP  C6   C5   C4   119.42  3.000
 1YP  C5   C6   C16  117.62  3.000
 1YP  C16  C6   C7   123.74  3.000
 1YP  C5   C6   C7   118.62  3.000
 1YP  C4   N3   C8   118.02  3.000
 1YP  C13  N4   C12  118.48  3.000
 1YP  C14  N5   N6   104.15  3.000
 1YP  C15  O3   C14  106.77  3.000
 1YP  C17  N7   C16  111.24  3.000
 1YP  C18  C17  N7   116.17  3.000
 1YP  N7   C17  C19  118.16  3.000
 1YP  C18  C17  C19  125.67  3.000
 1YP  H14  C18  S1   121.38  3.000
 1YP  H14  C18  C17  129.41  3.000
 1YP  S1   C18  C17  109.20  3.000
 1YP  C18  S1   C16   89.77  3.000
 1YP  F3   C19  F2   106.80  3.000
 1YP  F2   C19  F1   107.72  3.000
 1YP  F3   C19  F1   107.64  3.000
 1YP  F2   C19  C17  111.42  3.000
 1YP  F3   C19  C17  111.57  3.000
 1YP  F1   C19  C17  111.45  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
 1YP  CONST_01  C4   N3   C8   C7      0.00   0.0  0
 1YP  CONST_02  C4   C5   C6   C7      0.00   0.0  0
 1YP  CONST_05  N4   C13  C9   C7    180.00   0.0  0
 1YP  CONST_06  C11  C10  C9   C7    180.00   0.0  0
 1YP  CONST_07  C5   C4   N3   C8      0.00   0.0  0
 1YP  CONST_08  C5   C6   C7   C8      0.00   0.0  0
 1YP  CONST_09  C16  C6   C7   C8    180.00   0.0  0
 1YP  CONST_12  N3   C8   C7   C9    180.00   0.0  0
 1YP  CONST_13  C5   C6   C7   C9    180.00   0.0  0
 1YP  CONST_14  C16  C6   C7   C9      0.00   0.0  0
 1YP  CONST_15  C12  N4   C13  C9      0.00   0.0  0
 1YP  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 1YP  CONST_18  N4   C13  C9   C10     0.00   0.0  0
 1YP  CONST_19  N4   C12  C11  C10     0.00   0.0  0
 1YP  CONST_20  C13  C9   C10  C11     0.00   0.0  0
 1YP  CONST_21  C13  N4   C12  C11     0.00   0.0  0
 1YP  CONST_23  C17  C18  S1   C16     0.00   0.0  0
 1YP  CONST_24  C4   C5   C6   C16   180.00   0.0  0
 1YP  CONST_25  C18  C17  N7   C16     0.00   0.0  0
 1YP  CONST_28  N3   C4   C5   C6      0.00   0.0  0
 1YP  CONST_29  N3   C8   C7   C6      0.00   0.0  0
 1YP  CONST_30  C18  S1   C16  C6    180.00   0.0  0
 1YP  CONST_31  C17  N7   C16  C6    180.00   0.0  0
 1YP  CONST_32  C18  S1   C16  N7      0.00   0.0  0
 1YP  CONST_33  S1   C18  C17  N7      0.00   0.0  0
 1YP  CONST_34  S1   C16  N7   C17     0.00   0.0  0
 1YP  CONST_35  C14  C11  C10  C9    180.00   0.0  0
 1YP  CONST_36  N4   C12  C11  C14   180.00   0.0  0
 1YP  CONST_37  N2   C4   N3   C8    180.00   0.0  0
 1YP  CONST_38  C19  C17  N7   C16   180.00   0.0  0
 1YP  CONST_39  S1   C18  C17  C19   180.00   0.0  0
 1YP  CONST_40  C6   C5   C4   N2    180.00   0.0  0
 1YP  CONST_41  H13  C5   C6   C7    180.00   0.0  0
 1YP  CONST_42  H10  C13  C9   C7      0.00   0.0  0
 1YP  CONST_43  H8   C10  C9   C7      0.00   0.0  0
 1YP  CONST_44  H7   C8   C7   C9      0.00   0.0  0
 1YP  CONST_45  H9   C12  C11  C10   180.00   0.0  0
 1YP  CONST_46  H14  C18  S1   C16   180.00   0.0  0
 1YP  CONST_47  N3   C4   N2   C3      0.00   0.0  0
 1YP  CONST_48  C5   C4   N2   C3    180.00   0.0  0
 1YP  CONST_49  H12  N2   C4   C5      0.00   0.0  0
 1YP  CONST_50  C4   N2   C3   O1      0.00   0.0  0
 1YP  CONST_51  C4   N2   C3   N1    180.00   0.0  0
 1YP  CONST_52  O1   C3   N1   C2      0.00   0.0  0
 1YP  CONST_53  N2   C3   N1   C2    180.00   0.0  0
 1YP  CONST_54  H11  N1   C3   O1    180.00   0.0  0
 1YP  Var_01    O3   C14  C11  C10  -176.96  30.0  2
 1YP  Var_02    F1   C19  C17  N7   -178.30  30.0  2
 1YP  Var_03    C3   N1   C2   C1   -162.71  30.0  3
 1YP  Var_04    H1   C1   C2   N1   -178.62  30.0  3

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
 1YP  plan-1  N6   0.020
 1YP  plan-1  C11  0.020
 1YP  plan-1  C14  0.020
 1YP  plan-1  C15  0.020
 1YP  plan-1  N5   0.020
 1YP  plan-1  O2   0.020
 1YP  plan-1  O3   0.020
 1YP  plan-1  H6   0.020
 1YP  plan-2  C16  0.020
 1YP  plan-2  C6   0.020
 1YP  plan-2  N7   0.020
 1YP  plan-2  C17  0.020
 1YP  plan-2  C18  0.020
 1YP  plan-2  S1   0.020
 1YP  plan-2  H14  0.020
 1YP  plan-2  C19  0.020
 1YP  plan-3  C7   0.020
 1YP  plan-3  C9   0.020
 1YP  plan-3  C10  0.020
 1YP  plan-3  C11  0.020
 1YP  plan-3  C12  0.020
 1YP  plan-3  C13  0.020
 1YP  plan-3  C14  0.020
 1YP  plan-3  N4   0.020
 1YP  plan-3  H8   0.020
 1YP  plan-3  H9   0.020
 1YP  plan-3  H10  0.020
 1YP  plan-4  C7   0.020
 1YP  plan-4  C8   0.020
 1YP  plan-4  C9   0.020
 1YP  plan-4  C16  0.020
 1YP  plan-4  N2   0.020
 1YP  plan-4  C4   0.020
 1YP  plan-4  C5   0.020
 1YP  plan-4  C6   0.020
 1YP  plan-4  N3   0.020
 1YP  plan-4  H7   0.020
 1YP  plan-4  H13  0.020
 1YP  plan-5  C2   0.020
 1YP  plan-5  C3   0.020
 1YP  plan-5  N1   0.020
 1YP  plan-5  O1   0.020
 1YP  plan-5  N2   0.020
 1YP  plan-5  C4   0.020
 1YP  plan-5  H11  0.020
 1YP  plan-5  H12  0.020

