# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 03:59:07 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 6'-[(ethylcarbamoyl)amino]-4'-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1cc(c2scc(n2)C(F)(F)F)c(cn1)c3cncc(c3)C(O)=O
#
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
 1YM  1YM  '6'-[(ethylcarbamoyl)amino]-4'-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridine-5-carboxylic acid'  ligand  44  30  .  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_1YM
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
 1YM  C1   C  CH3   0  -0.704   8.5863  -1.0943  -0.2897
 1YM  C2   C  CH2   0  -0.252   7.5902   0.0488  -0.3094
 1YM  O5   O  O     0  -0.502   5.2758   1.5847  -0.1668
 1YM  N6   N  NH1   0  -0.779   3.9793  -0.2976   0.1105
 1YM  C7   C  CR6   0   0.566   2.7175   0.2437   0.2331
 1YM  C8   C  CR16  0  -0.461   1.6222  -0.5964   0.0017
 1YM  C9   C  CR6   0   0.225   0.3411  -0.0907   0.1290
 1YM  C10  C  CR6   0  -0.024   0.1804   1.2524   0.5016
 1YM  C11  C  CR16  0  -0.072   1.3412   1.9866   0.7007
 1YM  C13  C  CR6   0  -0.142  -1.1277   1.8986   0.7125
 1YM  C14  C  CR16  0  -0.163  -1.5308   2.9838  -0.0494
 1YM  C15  C  CR6   0  -0.160  -2.7700   3.5649   0.1956
 1YM  C16  C  CR16  0  -0.044  -3.5598   3.0297   1.2085
 1YM  C19  C  C     0   0.538  -3.1981   4.7175  -0.6355
 1YM  C22  C  CR5   0  -0.047  -0.7779  -0.9887  -0.1838
 1YM  N23  N  N     0  -0.381  -0.7120  -2.2732  -0.0239
 1YM  C24  C  CR5   0   0.068  -1.8352  -2.8812  -0.4768
 1YM  C27  C  CT    0   1.070  -1.9327  -4.3628  -0.3546
 1YM  N3   N  NH1   0  -0.681   6.2469  -0.4515  -0.0951
 1YM  C4   C  C     0   0.733   5.1828   0.3756  -0.0562
 1YM  N12  N  N     0  -0.420   2.5711   1.5124   0.5798
 1YM  N17  N  N     0  -0.388  -3.1759   2.0030   1.9558
 1YM  C18  C  CR16  0  -0.053  -1.9946   1.4592   1.7145
 1YM  O20  O  O     0  -0.429  -2.5233   5.1823  -1.5206
 1YM  O21  O  OH1   0  -0.591  -4.3932   5.1747  -0.3008
 1YM  C25  C  CR15  0  -0.522  -2.7843  -2.0680  -1.0085
 1YM  S26  S  S2    0   0.307  -2.2502  -0.4545  -0.9239
 1YM  F28  F  F     0  -0.301  -3.0640  -4.8226  -0.8912
 1YM  F29  F  F     0  -0.310  -0.9136  -4.9710  -0.9703
 1YM  F30  F  F     0  -0.310  -1.9017  -4.7553   0.9235
 1YM  H1   H  HCH3  0   0.235   8.3799  -1.8181  -1.0791
 1YM  H2   H  HCH3  0   0.247   9.5931  -0.7099  -0.4453
 1YM  H3   H  HCH3  0   0.234   8.5745  -1.6180   0.6672
 1YM  H4   H  HCH2  0   0.233   7.8456   0.7762   0.4647
 1YM  H5   H  HCH2  0   0.232   7.6459   0.5729  -1.2667
 1YM  H6   H  HNH1  0   0.417   4.0020  -1.3004   0.0085
 1YM  H7   H  HCR6  0   0.288   1.7730  -1.6222  -0.3080
 1YM  H8   H  HCR6  0   0.272   1.2610   3.0269   0.9993
 1YM  H9   H  HCR6  0   0.283  -0.8928   3.3652  -0.8366
 1YM  H10  H  HCR6  0   0.285  -4.5355   3.4420   1.4332
 1YM  H11  H  HNH1  0   0.401   6.1266  -1.4448   0.0216
 1YM  H12  H  HCR6  0   0.279  -1.7075   0.6251   2.3471
 1YM  H13  H  HOH1  0   0.493  -4.6366   5.9224  -0.8674
 1YM  H14  H  HCR5  0   0.332  -3.7461  -2.3213  -1.4250

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
 1YM  C1   C2   single    1.516  0.020  1.516
 1YM  C2   N3   single    1.449  0.020  1.449
 1YM  N3   C4   single    1.348  0.020  1.348
 1YM  C4   O5   double    1.218  0.020  1.218
 1YM  C4   N6   single    1.389  0.020  1.389
 1YM  N6   C7   single    1.378  0.020  1.378
 1YM  C7   C8   aromatic  1.400  0.020  1.400
 1YM  C7   N12  aromatic  1.323  0.020  1.323
 1YM  C8   C9   aromatic  1.383  0.020  1.383
 1YM  N12  C11  aromatic  1.324  0.020  1.324
 1YM  S26  C22  aromatic  1.732  0.020  1.732
 1YM  S26  C25  aromatic  1.702  0.020  1.702
 1YM  C9   C22  single    1.468  0.020  1.468
 1YM  C9   C10  aromatic  1.403  0.020  1.403
 1YM  C11  C10  aromatic  1.388  0.020  1.388
 1YM  C22  N23  aromatic  1.296  0.020  1.296
 1YM  C10  C13  single    1.474  0.020  1.474
 1YM  C25  C24  aromatic  1.358  0.020  1.358
 1YM  O20  C19  double    1.206  0.020  1.206
 1YM  C14  C13  aromatic  1.386  0.020  1.386
 1YM  C14  C15  aromatic  1.390  0.020  1.390
 1YM  C13  C18  aromatic  1.396  0.020  1.396
 1YM  N23  C24  aromatic  1.355  0.020  1.355
 1YM  C24  C27  single    1.490  0.020  1.490
 1YM  C19  C15  single    1.484  0.020  1.484
 1YM  C19  O21  single    1.323  0.020  1.323
 1YM  C15  C16  aromatic  1.391  0.020  1.391
 1YM  C18  N17  aromatic  1.323  0.020  1.323
 1YM  F29  C27  single    1.337  0.020  1.337
 1YM  C27  F30  single    1.337  0.020  1.337
 1YM  C27  F28  single    1.334  0.020  1.334
 1YM  C16  N17  aromatic  1.327  0.020  1.327
 1YM  C1   H1   single    0.970  0.020  1.090
 1YM  C1   H2   single    0.970  0.020  1.090
 1YM  C1   H3   single    0.970  0.020  1.090
 1YM  C2   H4   single    0.970  0.020  1.090
 1YM  C2   H5   single    0.970  0.020  1.090
 1YM  N6   H6   single    0.860  0.020  1.020
 1YM  C8   H7   single    0.930  0.020  1.080
 1YM  C11  H8   single    0.930  0.020  1.080
 1YM  C14  H9   single    0.930  0.020  1.080
 1YM  C16  H10  single    0.930  0.020  1.080
 1YM  N3   H11  single    0.860  0.020  1.020
 1YM  C18  H12  single    0.930  0.020  1.080
 1YM  O21  H13  single    0.850  0.020  0.980
 1YM  C25  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
 1YM  H3   C1   H2   107.75  3.000
 1YM  H3   C1   H1   108.31  3.000
 1YM  H2   C1   H1   107.81  3.000
 1YM  H3   C1   C2   111.48  3.000
 1YM  H2   C1   C2   109.84  3.000
 1YM  H1   C1   C2   111.50  3.000
 1YM  H5   C2   H4   106.82  3.000
 1YM  H5   C2   N3   110.02  3.000
 1YM  H4   C2   N3   109.98  3.000
 1YM  H5   C2   C1   109.84  3.000
 1YM  H4   C2   C1   109.82  3.000
 1YM  N3   C2   C1   110.29  3.000
 1YM  H6   N6   C4   116.77  3.000
 1YM  H6   N6   C7   114.85  3.000
 1YM  C4   N6   C7   127.84  3.000
 1YM  N12  C7   C8   122.15  3.000
 1YM  N12  C7   N6   120.07  3.000
 1YM  C8   C7   N6   117.77  3.000
 1YM  H7   C8   C9   120.13  3.000
 1YM  H7   C8   C7   120.49  3.000
 1YM  C9   C8   C7   119.35  3.000
 1YM  C22  C9   C10  123.69  3.000
 1YM  C10  C9   C8   118.72  3.000
 1YM  C22  C9   C8   117.55  3.000
 1YM  C13  C10  C11  119.32  3.000
 1YM  C13  C10  C9   124.00  3.000
 1YM  C11  C10  C9   116.66  3.000
 1YM  H8   C11  N12  115.93  3.000
 1YM  H8   C11  C10  119.00  3.000
 1YM  N12  C11  C10  125.07  3.000
 1YM  C18  C13  C14  117.42  3.000
 1YM  C18  C13  C10  121.05  3.000
 1YM  C14  C13  C10  121.51  3.000
 1YM  H9   C14  C15  120.40  3.000
 1YM  H9   C14  C13  120.28  3.000
 1YM  C15  C14  C13  119.32  3.000
 1YM  C19  C15  C16  122.87  3.000
 1YM  C16  C15  C14  118.25  3.000
 1YM  C19  C15  C14  118.88  3.000
 1YM  H10  C16  N17  116.01  3.000
 1YM  H10  C16  C15  121.07  3.000
 1YM  N17  C16  C15  122.92  3.000
 1YM  O21  C19  O20  123.92  3.000
 1YM  O21  C19  C15  112.79  3.000
 1YM  O20  C19  C15  123.29  3.000
 1YM  S26  C22  N23  113.68  3.000
 1YM  N23  C22  C9   122.75  3.000
 1YM  S26  C22  C9   123.37  3.000
 1YM  C24  N23  C22  111.18  3.000
 1YM  C25  C24  C27  125.58  3.000
 1YM  C27  C24  N23  118.23  3.000
 1YM  C25  C24  N23  116.19  3.000
 1YM  F30  C27  F29  106.79  3.000
 1YM  F30  C27  F28  107.64  3.000
 1YM  F29  C27  F28  107.72  3.000
 1YM  F28  C27  C24  111.43  3.000
 1YM  F30  C27  C24  111.64  3.000
 1YM  F29  C27  C24  111.39  3.000
 1YM  H11  N3   C4   120.49  3.000
 1YM  H11  N3   C2   117.92  3.000
 1YM  C4   N3   C2   121.60  3.000
 1YM  N3   C4   N6   112.95  3.000
 1YM  N6   C4   O5   123.94  3.000
 1YM  N3   C4   O5   123.11  3.000
 1YM  C11  N12  C7   118.05  3.000
 1YM  C18  N17  C16  118.28  3.000
 1YM  H12  C18  N17  116.48  3.000
 1YM  H12  C18  C13  119.73  3.000
 1YM  N17  C18  C13  123.79  3.000
 1YM  H13  O21  C19  110.23  3.000
 1YM  H14  C25  S26  121.46  3.000
 1YM  H14  C25  C24  129.33  3.000
 1YM  S26  C25  C24  109.20  3.000
 1YM  C25  S26  C22   89.75  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
 1YM  CONST_01  C22  C9   C8   C7   180.00   0.0  0
 1YM  CONST_02  C10  C9   C8   C7     0.00   0.0  0
 1YM  CONST_03  C10  C11  N12  C7     0.00   0.0  0
 1YM  CONST_04  C11  N12  C7   C8     0.00   0.0  0
 1YM  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 1YM  CONST_08  C13  C10  C9   C8   180.00   0.0  0
 1YM  CONST_09  N12  C7   C8   C9     0.00   0.0  0
 1YM  CONST_10  C25  S26  C22  C9   180.00   0.0  0
 1YM  CONST_11  C24  N23  C22  C9   180.00   0.0  0
 1YM  CONST_12  N12  C11  C10  C9     0.00   0.0  0
 1YM  CONST_17  C15  C14  C13  C10  180.00   0.0  0
 1YM  CONST_18  N17  C18  C13  C10  180.00   0.0  0
 1YM  CONST_19  C22  C9   C10  C11  180.00   0.0  0
 1YM  CONST_22  C22  C9   C10  C13    0.00   0.0  0
 1YM  CONST_23  N12  C11  C10  C13  180.00   0.0  0
 1YM  CONST_24  C16  C15  C14  C13    0.00   0.0  0
 1YM  CONST_25  C16  N17  C18  C13    0.00   0.0  0
 1YM  CONST_26  N17  C18  C13  C14    0.00   0.0  0
 1YM  CONST_27  N17  C16  C15  C14    0.00   0.0  0
 1YM  CONST_28  C18  C13  C14  C15    0.00   0.0  0
 1YM  CONST_29  C18  N17  C16  C15    0.00   0.0  0
 1YM  CONST_30  C24  C25  S26  C22    0.00   0.0  0
 1YM  CONST_31  C25  C24  N23  C22    0.00   0.0  0
 1YM  CONST_32  C25  S26  C22  N23    0.00   0.0  0
 1YM  CONST_33  S26  C25  C24  N23    0.00   0.0  0
 1YM  CONST_34  S26  C22  N23  C24    0.00   0.0  0
 1YM  CONST_35  C9   C8   C7   N6   180.00   0.0  0
 1YM  CONST_36  C11  N12  C7   N6   180.00   0.0  0
 1YM  CONST_37  C19  C15  C14  C13  180.00   0.0  0
 1YM  CONST_38  N17  C16  C15  C19  180.00   0.0  0
 1YM  CONST_39  C27  C24  N23  C22  180.00   0.0  0
 1YM  CONST_40  S26  C25  C24  C27  180.00   0.0  0
 1YM  CONST_41  H8   C11  N12  C7   180.00   0.0  0
 1YM  CONST_42  H7   C8   C9   C10  180.00   0.0  0
 1YM  CONST_43  H9   C14  C13  C10    0.00   0.0  0
 1YM  CONST_44  H12  C18  C13  C10    0.00   0.0  0
 1YM  CONST_45  H10  C16  C15  C14  180.00   0.0  0
 1YM  CONST_46  H14  C25  S26  C22  180.00   0.0  0
 1YM  CONST_49  H6   N6   C7   C8     0.00   0.0  0
 1YM  CONST_50  C7   N6   C4   O5     0.00   0.0  0
 1YM  CONST_51  N3   C4   N6   C7   180.00   0.0  0
 1YM  CONST_52  H13  O21  C19  C15  180.00   0.0  0
 1YM  CONST_53  O5   C4   N3   C2     0.00   0.0  0
 1YM  CONST_54  N6   C4   N3   C2   180.00   0.0  0
 1YM  CONST_55  H11  N3   C4   O5   180.00   0.0  0
 1YM  Var_01    O20  C19  C15  C14    0.01  30.0  3
 1YM  Var_02    F29  C27  C24  N23  -57.04  30.0  2
 1YM  Var_03    C4   N3   C2   C1   179.34  30.0  3
 1YM  Var_04    H1   C1   C2   N3    60.89  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
 1YM  plan-1  C9   0.020
 1YM  plan-1  C22  0.020
 1YM  plan-1  N23  0.020
 1YM  plan-1  C24  0.020
 1YM  plan-1  C27  0.020
 1YM  plan-1  C25  0.020
 1YM  plan-1  S26  0.020
 1YM  plan-1  H14  0.020
 1YM  plan-2  C15  0.020
 1YM  plan-2  C19  0.020
 1YM  plan-2  O20  0.020
 1YM  plan-2  O21  0.020
 1YM  plan-2  H13  0.020
 1YM  plan-3  N6   0.020
 1YM  plan-3  C7   0.020
 1YM  plan-3  C8   0.020
 1YM  plan-3  C9   0.020
 1YM  plan-3  C10  0.020
 1YM  plan-3  C11  0.020
 1YM  plan-3  C13  0.020
 1YM  plan-3  C22  0.020
 1YM  plan-3  N12  0.020
 1YM  plan-3  H7   0.020
 1YM  plan-3  H8   0.020
 1YM  plan-4  C10  0.020
 1YM  plan-4  C13  0.020
 1YM  plan-4  C14  0.020
 1YM  plan-4  C15  0.020
 1YM  plan-4  C16  0.020
 1YM  plan-4  C19  0.020
 1YM  plan-4  N17  0.020
 1YM  plan-4  C18  0.020
 1YM  plan-4  H9   0.020
 1YM  plan-4  H10  0.020
 1YM  plan-4  H12  0.020
 1YM  plan-5  C2   0.020
 1YM  plan-5  O5   0.020
 1YM  plan-5  N6   0.020
 1YM  plan-5  C7   0.020
 1YM  plan-5  N3   0.020
 1YM  plan-5  C4   0.020
 1YM  plan-5  H6   0.020
 1YM  plan-5  H11  0.020

