# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 03:13:19 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: {2-[1-(3-fluoro-4-hydroxyphenyl)-1H-1,2,3-triazol-4-yl]-8-oxo-1,7-naphthyridin-7(8H)-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN1C=Cc2ccc(nc2C1=O)c3cn(nn3)c4ccc(O)c(F)c4
#
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
 C9Y  C9Y  '{2-[1-(3-fluoro-4-hydroxyphenyl)-1H-1,2,3-triazol-4-yl]-8-oxo-1,7-naphthyridin-7(8H)-yl}acetic acid'  ligand  39  28  .  2022-07-24  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_C9Y
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
 C9Y  O3   O  O      0  -0.478  -2.9187   1.5232   0.8646
 C9Y  C4   C  CR66   0   0.203  -3.3263  -1.9690  -0.0093
 C9Y  C5   C  CR16   0  -0.202  -2.5198  -3.0638  -0.3658
 C9Y  C6   C  CR16   0  -0.275  -1.1608  -2.9096  -0.4244
 C9Y  N1   N  NR5    0  -0.387   2.8166  -0.6314  -0.1394
 C9Y  C7   C  CR6    0   0.167  -0.6079  -1.6494  -0.1278
 C9Y  C8   C  CR5    0   0.125   0.8328  -1.4308  -0.1808
 C9Y  N2   N  N      0  -0.088   2.9120  -1.9269  -0.4238
 C9Y  C9   C  CR15   0  -0.059   1.5331  -0.2672   0.0226
 C9Y  C10  C  CR6    0   0.354   3.9745   0.1716  -0.0452
 C9Y  C11  C  CR16   0  -0.289   3.9662   1.4652  -0.5431
 C9Y  C12  C  CR16   0  -0.341   5.1007   2.2522  -0.4357
 C9Y  N3   N  N      0  -0.311   1.7257  -2.4113  -0.4473
 C9Y  C13  C  CR6    0   0.240   6.2593   1.7568   0.1516
 C9Y  C14  C  CR6    0   0.451   6.2319   0.4482   0.6296
 C9Y  C15  C  CR16   0  -0.433   5.1152  -0.3494   0.5507
 C9Y  N4   N  N      0  -0.432  -1.3498  -0.6140   0.2063
 C9Y  N    N  NR6    0  -0.501  -4.7983   0.2632   0.7451
 C9Y  C    C  C      0   0.419  -5.8419   2.3033  -0.2498
 C9Y  C1   C  CH2    0  -0.471  -5.6121   1.4355   1.0096
 C9Y  C16  C  CR66   0  -0.025  -2.6728  -0.7605   0.2696
 C9Y  C17  C  CR6    0   0.539  -3.4393   0.4420   0.6420
 C9Y  C2   C  CR16   0   0.048  -5.4180  -0.9137   0.4377
 C9Y  C3   C  CR16   0  -0.467  -4.7474  -2.0249   0.0768
 C9Y  F    F  F      0  -0.315   7.3469  -0.0350   1.2030
 C9Y  O4   O  OH1    0  -0.619   7.3411   2.5434   0.2324
 C9Y  H1   H  HCR6   0   0.274  -2.9759  -4.0187  -0.5939
 C9Y  H2   H  HCR6   0   0.276  -0.5202  -3.7371  -0.6964
 C9Y  H3   H  HCR5   0   0.322   1.2260   0.7318   0.2779
 C9Y  H4   H  HCR6   0   0.292   3.0855   1.8655  -1.0267
 C9Y  H5   H  HCR6   0   0.290   5.0965   3.2620  -0.8246
 C9Y  H6   H  HCR6   0   0.306   5.1373  -1.3531   0.9541
 C9Y  H10  H  HCH2   0   0.267  -6.5746   1.0968   1.3963
 C9Y  H11  H  HCH2   0   0.267  -5.1484   2.0290   1.7959
 C9Y  H12  H  HCR6   0   0.301  -6.4954  -0.9037   0.5184
 C9Y  H13  H  HCR6   0   0.271  -5.2842  -2.9363  -0.1428
 C9Y  H14  H  HOH1   0   0.481   8.0678   2.0996   0.6857
 C9Y  O1   O  OC    -1  -0.613  -6.4511   3.3669  -0.0344
 C9Y  O2   O  O      0  -0.589  -5.4281   1.8591  -1.3312

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
 C9Y  C    C1   single    1.547  0.020  1.547
 C9Y  C1   N    single    1.451  0.020  1.451
 C9Y  O3   C17  double    1.221  0.020  1.221
 C9Y  N    C17  single    1.375  0.020  1.375
 C9Y  N    C2   single    1.365  0.020  1.365
 C9Y  C17  C16  single    1.474  0.020  1.474
 C9Y  C2   C3   double    1.347  0.020  1.347
 C9Y  C3   C4   single    1.425  0.020  1.425
 C9Y  C16  N4   aromatic  1.333  0.020  1.333
 C9Y  C16  C4   aromatic  1.402  0.020  1.402
 C9Y  N4   C7   aromatic  1.317  0.020  1.317
 C9Y  C4   C5   aromatic  1.406  0.020  1.406
 C9Y  C7   C8   single    1.458  0.020  1.458
 C9Y  C7   C6   aromatic  1.408  0.020  1.408
 C9Y  N3   C8   aromatic  1.353  0.020  1.353
 C9Y  N3   N2   aromatic  1.282  0.020  1.282
 C9Y  C5   C6   aromatic  1.369  0.020  1.369
 C9Y  C8   C9   aromatic  1.373  0.020  1.373
 C9Y  N2   N1   aromatic  1.330  0.020  1.330
 C9Y  C9   N1   aromatic  1.344  0.020  1.344
 C9Y  N1   C10  single    1.412  0.020  1.412
 C9Y  C10  C15  aromatic  1.388  0.020  1.388
 C9Y  C10  C11  aromatic  1.386  0.020  1.386
 C9Y  C15  C14  aromatic  1.375  0.020  1.375
 C9Y  C11  C12  aromatic  1.385  0.020  1.385
 C9Y  C14  F    single    1.344  0.020  1.344
 C9Y  C14  C13  aromatic  1.393  0.020  1.393
 C9Y  C12  C13  aromatic  1.390  0.020  1.390
 C9Y  C13  O4   single    1.340  0.020  1.340
 C9Y  C5   H1   single    0.930  0.020  1.080
 C9Y  C6   H2   single    0.930  0.020  1.080
 C9Y  C9   H3   single    0.930  0.020  1.080
 C9Y  C11  H4   single    0.930  0.020  1.080
 C9Y  C12  H5   single    0.930  0.020  1.080
 C9Y  C15  H6   single    0.930  0.020  1.080
 C9Y  C1   H10  single    0.970  0.020  1.090
 C9Y  C1   H11  single    0.970  0.020  1.090
 C9Y  C2   H12  single    0.930  0.020  1.080
 C9Y  C3   H13  single    0.930  0.020  1.080
 C9Y  O4   H14  single    0.850  0.020  0.980
 C9Y  C    O1   deloc     1.244  0.020  1.244
 C9Y  C    O2   deloc     1.240  0.020  1.240

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
 C9Y  C3   C4   C16  119.13  3.000
 C9Y  C16  C4   C5   117.02  3.000
 C9Y  C3   C4   C5   123.85  3.000
 C9Y  H1   C5   C6   120.57  3.000
 C9Y  H1   C5   C4   119.91  3.000
 C9Y  C6   C5   C4   119.52  3.000
 C9Y  H2   C6   C7   120.36  3.000
 C9Y  H2   C6   C5   120.85  3.000
 C9Y  C7   C6   C5   118.80  3.000
 C9Y  C10  N1   C9   128.38  3.000
 C9Y  C10  N1   N2   120.62  3.000
 C9Y  C9   N1   N2   111.00  3.000
 C9Y  N4   C7   C8   116.61  3.000
 C9Y  C8   C7   C6   120.97  3.000
 C9Y  N4   C7   C6   122.42  3.000
 C9Y  N3   C8   C9   107.87  3.000
 C9Y  C9   C8   C7   128.72  3.000
 C9Y  N3   C8   C7   123.41  3.000
 C9Y  N3   N2   N1   107.80  3.000
 C9Y  H3   C9   C8   132.57  3.000
 C9Y  H3   C9   N1   123.56  3.000
 C9Y  C8   C9   N1   103.86  3.000
 C9Y  C15  C10  C11  120.62  3.000
 C9Y  C11  C10  N1   120.12  3.000
 C9Y  C15  C10  N1   119.27  3.000
 C9Y  H4   C11  C12  119.43  3.000
 C9Y  H4   C11  C10  120.73  3.000
 C9Y  C12  C11  C10  119.84  3.000
 C9Y  H5   C12  C13  119.18  3.000
 C9Y  H5   C12  C11  119.95  3.000
 C9Y  C13  C12  C11  120.86  3.000
 C9Y  N2   N3   C8   109.48  3.000
 C9Y  O4   C13  C14  123.12  3.000
 C9Y  O4   C13  C12  119.28  3.000
 C9Y  C14  C13  C12  117.60  3.000
 C9Y  F    C14  C15  119.34  3.000
 C9Y  F    C14  C13  117.89  3.000
 C9Y  C15  C14  C13  122.76  3.000
 C9Y  H6   C15  C14  120.02  3.000
 C9Y  H6   C15  C10  121.66  3.000
 C9Y  C14  C15  C10  118.32  3.000
 C9Y  C16  N4   C7   119.01  3.000
 C9Y  C2   N    C17  122.96  3.000
 C9Y  C2   N    C1   118.87  3.000
 C9Y  C17  N    C1   117.58  3.000
 C9Y  O2   C    O1   128.34  3.000
 C9Y  O2   C    C1   117.35  3.000
 C9Y  O1   C    C1   114.29  3.000
 C9Y  H11  C1   H10  106.79  3.000
 C9Y  H11  C1   C    110.21  3.000
 C9Y  H10  C1   C    109.37  3.000
 C9Y  H11  C1   N    109.46  3.000
 C9Y  H10  C1   N    107.97  3.000
 C9Y  C    C1   N    112.84  3.000
 C9Y  C17  C16  N4   116.02  3.000
 C9Y  N4   C16  C4   123.24  3.000
 C9Y  C17  C16  C4   120.74  3.000
 C9Y  C16  C17  N    115.28  3.000
 C9Y  C16  C17  O3   123.16  3.000
 C9Y  N    C17  O3   121.55  3.000
 C9Y  H12  C2   C3   121.60  3.000
 C9Y  H12  C2   N    115.33  3.000
 C9Y  C3   C2   N    123.06  3.000
 C9Y  H13  C3   C2   120.20  3.000
 C9Y  H13  C3   C4   121.09  3.000
 C9Y  C2   C3   C4   118.71  3.000
 C9Y  H14  O4   C13  111.50  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
 C9Y  CONST_01  C7   N4   C16  C4      0.00   0.0  0
 C9Y  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 C9Y  CONST_03  N4   C16  C4   C5      0.00   0.0  0
 C9Y  CONST_04  N4   C7   C6   C5      0.00   0.0  0
 C9Y  CONST_05  C8   C7   C6   C5    180.00   0.0  0
 C9Y  CONST_06  C16  N4   C7   C6      0.00   0.0  0
 C9Y  CONST_07  N3   C8   C7   C6      0.00   0.0  0
 C9Y  CONST_08  C9   C8   C7   C6    180.00   0.0  0
 C9Y  CONST_09  C16  C4   C5   C6      0.00   0.0  0
 C9Y  CONST_10  C8   N3   N2   N1      0.00   0.0  0
 C9Y  CONST_11  C7   C8   C9   N1    180.00   0.0  0
 C9Y  CONST_12  N3   C8   C9   N1      0.00   0.0  0
 C9Y  CONST_13  C14  C15  C10  N1    180.00   0.0  0
 C9Y  CONST_14  C12  C11  C10  N1    180.00   0.0  0
 C9Y  CONST_15  N2   N3   C8   C7    180.00   0.0  0
 C9Y  CONST_16  C16  N4   C7   C8    180.00   0.0  0
 C9Y  CONST_17  N2   N1   C9   C8      0.00   0.0  0
 C9Y  CONST_18  C10  N1   C9   C8    180.00   0.0  0
 C9Y  CONST_19  C9   C8   N3   N2      0.00   0.0  0
 C9Y  CONST_22  N4   C7   C8   C9      0.00   0.0  0
 C9Y  CONST_23  N3   N2   N1   C9      0.00   0.0  0
 C9Y  CONST_26  N3   N2   N1   C10   180.00   0.0  0
 C9Y  CONST_27  C13  C14  C15  C10     0.00   0.0  0
 C9Y  CONST_28  C13  C12  C11  C10     0.00   0.0  0
 C9Y  CONST_29  C14  C15  C10  C11     0.00   0.0  0
 C9Y  CONST_30  C14  C13  C12  C11     0.00   0.0  0
 C9Y  CONST_31  C15  C10  C11  C12     0.00   0.0  0
 C9Y  CONST_32  C15  C14  C13  C12     0.00   0.0  0
 C9Y  CONST_33  N4   C7   C8   N3    180.00   0.0  0
 C9Y  CONST_34  C2   N    C17  C16     0.00   0.0  0
 C9Y  CONST_35  F    C14  C15  C10   180.00   0.0  0
 C9Y  CONST_36  O4   C13  C12  C11   180.00   0.0  0
 C9Y  CONST_37  F    C14  C13  C12   180.00   0.0  0
 C9Y  CONST_38  O4   C13  C14  C15   180.00   0.0  0
 C9Y  CONST_39  C2   N    C17  O3    180.00   0.0  0
 C9Y  CONST_40  C16  C17  N    C1    180.00   0.0  0
 C9Y  CONST_41  H2   C6   C5   C4    180.00   0.0  0
 C9Y  CONST_42  H6   C15  C10  N1      0.00   0.0  0
 C9Y  CONST_43  H4   C11  C10  N1      0.00   0.0  0
 C9Y  CONST_44  H3   C9   C8   C7      0.00   0.0  0
 C9Y  CONST_45  H1   C5   C6   C7    180.00   0.0  0
 C9Y  CONST_46  H5   C12  C11  C10   180.00   0.0  0
 C9Y  CONST_47  C1   N    C17  O3      0.00   0.0  0
 C9Y  Var_01    C17  N    C1   C      78.22  30.0  3
 C9Y  Var_02    O1   C    C1   N    -174.87  30.0  2

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
 C9Y  plan-1  N1   0.020
 C9Y  plan-1  C7   0.020
 C9Y  plan-1  C8   0.020
 C9Y  plan-1  N2   0.020
 C9Y  plan-1  C9   0.020
 C9Y  plan-1  C10  0.020
 C9Y  plan-1  N3   0.020
 C9Y  plan-1  H3   0.020
 C9Y  plan-2  N1   0.020
 C9Y  plan-2  C10  0.020
 C9Y  plan-2  C11  0.020
 C9Y  plan-2  C12  0.020
 C9Y  plan-2  C13  0.020
 C9Y  plan-2  C14  0.020
 C9Y  plan-2  C15  0.020
 C9Y  plan-2  F    0.020
 C9Y  plan-2  O4   0.020
 C9Y  plan-2  H4   0.020
 C9Y  plan-2  H5   0.020
 C9Y  plan-2  H6   0.020
 C9Y  plan-3  O3   0.020
 C9Y  plan-3  C4   0.020
 C9Y  plan-3  C5   0.020
 C9Y  plan-3  C6   0.020
 C9Y  plan-3  C7   0.020
 C9Y  plan-3  C8   0.020
 C9Y  plan-3  N4   0.020
 C9Y  plan-3  N    0.020
 C9Y  plan-3  C1   0.020
 C9Y  plan-3  C16  0.020
 C9Y  plan-3  C17  0.020
 C9Y  plan-3  C2   0.020
 C9Y  plan-3  C3   0.020
 C9Y  plan-3  H1   0.020
 C9Y  plan-3  H2   0.020
 C9Y  plan-3  H12  0.020
 C9Y  plan-3  H13  0.020
 C9Y  plan-4  C    0.020
 C9Y  plan-4  C1   0.020
 C9Y  plan-4  O1   0.020
 C9Y  plan-4  O2   0.020

