# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 11:37:11 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [(1~{R})-2-[(4-fluorophenyl)amino]-2-oxidanylidene-1-phenyl-ethyl] 3-azanylpyrazine-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccnc1C(=O)O[C@@H](C(=O)Nc2ccc(F)cc2)c3ccccc3
#
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
 6UY  6UY  '[(1~{R})-2-[(4-fluorophenyl)amino]-2-oxidanylidene-1-phenyl-ethyl] 3-azanylpyrazine-2-carboxylate'  ligand  42  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6UY
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
 6UY  C1   C  C     0   0.519   1.0068  -0.2418  -0.1481
 6UY  C2   C  CR6   0   0.366   3.4351  -0.4796   0.2693
 6UY  C3   C  CR16  0  -0.287   3.8726  -0.7569  -1.0250
 6UY  C4   C  CR16  0  -0.403   5.1861  -1.1475  -1.2445
 6UY  C5   C  CR6   0   0.514   6.0526  -1.2520  -0.1761
 6UY  C6   C  CR16  0  -0.399   5.6467  -0.9743   1.1144
 6UY  C7   C  CR16  0  -0.323   4.3340  -0.5915   1.3300
 6UY  N1   N  NH1   0  -0.738   2.1328  -0.0586   0.5759
 6UY  N2   N  N     0  -0.337  -3.3094  -1.7619  -0.8200
 6UY  N3   N  N     0  -0.410  -5.8612  -1.6318   0.2166
 6UY  N4   N  NH2   0  -0.830  -5.2548  -0.0204   1.7023
 6UY  C8   C  CH1   0  -0.156  -0.2117   0.4359   0.4819
 6UY  O1   O  O     0  -0.442   0.9413  -0.8218  -1.2106
 6UY  F1   F  F     0  -0.316   7.3229  -1.6294  -0.3965
 6UY  O2   O  O2    0  -0.451  -1.3294  -0.3298   0.0675
 6UY  C9   C  C     0   0.639  -2.4810  -0.0905   0.6837
 6UY  C10  C  CR6   0  -0.056  -3.5834  -0.9237   0.1688
 6UY  C11  C  CR16  0  -0.168  -4.2676  -2.5260  -1.2985
 6UY  C12  C  CR16  0  -0.070  -5.5527  -2.4510  -0.7620
 6UY  C13  C  CR6   0   0.484  -4.8956  -0.8405   0.7133
 6UY  O3   O  O     0  -0.446  -2.5994   0.7198   1.5751
 6UY  C14  C  CR6   0   0.096  -0.2810   1.8602  -0.0100
 6UY  C15  C  CR16  0  -0.303   0.0350   2.9080   0.8458
 6UY  C16  C  CR16  0  -0.242   0.0131   4.2181   0.3870
 6UY  C17  C  CR16  0  -0.259  -0.3362   4.4874  -0.9292
 6UY  C18  C  CR16  0  -0.240  -0.6581   3.4418  -1.7857
 6UY  C19  C  CR16  0  -0.276  -0.6261   2.1315  -1.3316
 6UY  H1   H  HCR6  0   0.286   3.2097  -0.6684  -1.8702
 6UY  H2   H  HCR6  0   0.285   5.5263  -1.3622  -2.2487
 6UY  H3   H  HCR6  0   0.286   6.3375  -1.0588   1.9426
 6UY  H4   H  HCR6  0   0.284   4.0058  -0.3792   2.3402
 6UY  H5   H  HNH1  0   0.419   2.0240   0.3510   1.4919
 6UY  H6   H  HNH2  0   0.417  -4.5978   0.6026   2.1369
 6UY  H7   H  HNH2  0   0.401  -6.2060  -0.0408   2.0281
 6UY  H8   H  HCH1  0   0.303  -0.1284   0.4244   1.5735
 6UY  H9   H  HCR6  0   0.270  -4.0310  -3.2052  -2.1072
 6UY  H10  H  HCR6  0   0.281  -6.3462  -3.0826  -1.1457
 6UY  H11  H  HCR6  0   0.259   0.2912   2.7048   1.8788
 6UY  H12  H  HCR6  0   0.261   0.2580   5.0285   1.0611
 6UY  H13  H  HCR6  0   0.261  -0.3613   5.5088  -1.2862
 6UY  H14  H  HCR6  0   0.261  -0.9319   3.6470  -2.8124
 6UY  H15  H  HCR6  0   0.261  -0.8723   1.3248  -2.0108

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
 6UY  F1   C5   single    1.343  0.020  1.343
 6UY  C6   C5   aromatic  1.381  0.020  1.381
 6UY  C6   C7   aromatic  1.384  0.020  1.384
 6UY  C5   C4   aromatic  1.380  0.020  1.380
 6UY  C17  C18  aromatic  1.389  0.020  1.389
 6UY  C17  C16  aromatic  1.388  0.020  1.388
 6UY  C18  C19  aromatic  1.387  0.020  1.387
 6UY  C7   C2   aromatic  1.395  0.020  1.395
 6UY  C4   C3   aromatic  1.388  0.020  1.388
 6UY  C16  C15  aromatic  1.388  0.020  1.388
 6UY  C19  C14  aromatic  1.393  0.020  1.393
 6UY  C2   C3   aromatic  1.394  0.020  1.394
 6UY  C2   N1   single    1.403  0.020  1.403
 6UY  C15  C14  aromatic  1.389  0.020  1.389
 6UY  O1   C1   double    1.212  0.020  1.212
 6UY  C14  C8   single    1.508  0.020  1.508
 6UY  N1   C1   single    1.351  0.020  1.351
 6UY  C1   C8   single    1.530  0.020  1.530
 6UY  C8   O2   single    1.417  0.020  1.417
 6UY  O2   C9   single    1.328  0.020  1.328
 6UY  C9   O3   double    1.210  0.020  1.210
 6UY  C9   C10  single    1.475  0.020  1.475
 6UY  N2   C10  aromatic  1.325  0.020  1.325
 6UY  N2   C11  aromatic  1.316  0.020  1.316
 6UY  C10  C13  aromatic  1.423  0.020  1.423
 6UY  C11  C12  aromatic  1.395  0.020  1.395
 6UY  C13  N4   single    1.334  0.020  1.334
 6UY  C13  N3   aromatic  1.344  0.020  1.344
 6UY  C12  N3   aromatic  1.313  0.020  1.313
 6UY  C3   H1   single    0.930  0.020  1.080
 6UY  C4   H2   single    0.930  0.020  1.080
 6UY  C6   H3   single    0.930  0.020  1.080
 6UY  C7   H4   single    0.930  0.020  1.080
 6UY  N1   H5   single    0.860  0.020  1.020
 6UY  N4   H6   single    0.860  0.020  1.020
 6UY  N4   H7   single    0.860  0.020  1.020
 6UY  C8   H8   single    0.970  0.020  1.090
 6UY  C11  H9   single    0.930  0.020  1.080
 6UY  C12  H10  single    0.930  0.020  1.080
 6UY  C15  H11  single    0.930  0.020  1.080
 6UY  C16  H12  single    0.930  0.020  1.080
 6UY  C17  H13  single    0.930  0.020  1.080
 6UY  C18  H14  single    0.930  0.020  1.080
 6UY  C19  H15  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
 6UY  O1   C1   C8   121.99  3.000
 6UY  C8   C1   N1   112.52  3.000
 6UY  O1   C1   N1   125.42  3.000
 6UY  N1   C2   C7   117.14  3.000
 6UY  N1   C2   C3   123.64  3.000
 6UY  C7   C2   C3   119.20  3.000
 6UY  H1   C3   C4   118.76  3.000
 6UY  H1   C3   C2   121.24  3.000
 6UY  C4   C3   C2   119.99  3.000
 6UY  H2   C4   C5   120.42  3.000
 6UY  H2   C4   C3   120.02  3.000
 6UY  C5   C4   C3   119.56  3.000
 6UY  F1   C5   C6   119.19  3.000
 6UY  C6   C5   C4   121.59  3.000
 6UY  F1   C5   C4   119.22  3.000
 6UY  H3   C6   C7   120.52  3.000
 6UY  H3   C6   C5   120.80  3.000
 6UY  C7   C6   C5   118.68  3.000
 6UY  H4   C7   C6   119.13  3.000
 6UY  H4   C7   C2   119.88  3.000
 6UY  C6   C7   C2   120.99  3.000
 6UY  H5   N1   C2   114.85  3.000
 6UY  H5   N1   C1   116.84  3.000
 6UY  C2   N1   C1   128.02  3.000
 6UY  C11  N2   C10  119.23  3.000
 6UY  C13  N3   C12  118.31  3.000
 6UY  H7   N4   H6   119.41  3.000
 6UY  H7   N4   C13  118.84  3.000
 6UY  H6   N4   C13  121.74  3.000
 6UY  H8   C8   C14  109.79  3.000
 6UY  H8   C8   O2   110.24  3.000
 6UY  C14  C8   O2   112.25  3.000
 6UY  H8   C8   C1   110.20  3.000
 6UY  O2   C8   C1   105.58  3.000
 6UY  C14  C8   C1   108.70  3.000
 6UY  C9   O2   C8   116.81  3.000
 6UY  O3   C9   C10  124.21  3.000
 6UY  C10  C9   O2   112.61  3.000
 6UY  O3   C9   O2   123.18  3.000
 6UY  C13  C10  C9   121.51  3.000
 6UY  C13  C10  N2   120.88  3.000
 6UY  C9   C10  N2   117.61  3.000
 6UY  H9   C11  C12  121.51  3.000
 6UY  H9   C11  N2   118.49  3.000
 6UY  C12  C11  N2   120.00  3.000
 6UY  H10  C12  C11  120.46  3.000
 6UY  H10  C12  N3   117.08  3.000
 6UY  C11  C12  N3   122.46  3.000
 6UY  C10  C13  N4   124.60  3.000
 6UY  N4   C13  N3   116.27  3.000
 6UY  C10  C13  N3   119.13  3.000
 6UY  C19  C14  C15  119.60  3.000
 6UY  C15  C14  C8   120.05  3.000
 6UY  C19  C14  C8   120.32  3.000
 6UY  H11  C15  C16  119.72  3.000
 6UY  H11  C15  C14  119.97  3.000
 6UY  C16  C15  C14  120.30  3.000
 6UY  H12  C16  C17  120.15  3.000
 6UY  H12  C16  C15  119.82  3.000
 6UY  C17  C16  C15  120.03  3.000
 6UY  H13  C17  C18  120.10  3.000
 6UY  H13  C17  C16  120.11  3.000
 6UY  C18  C17  C16  119.79  3.000
 6UY  H14  C18  C19  119.71  3.000
 6UY  H14  C18  C17  120.05  3.000
 6UY  C19  C18  C17  120.24  3.000
 6UY  H15  C19  C18  119.54  3.000
 6UY  H15  C19  C14  120.43  3.000
 6UY  C18  C19  C14  120.03  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
 6UY  CONST_01  C5   C6   C7   C2     0.00   0.0  0
 6UY  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 6UY  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 6UY  CONST_04  C6   C7   C2   C3     0.00   0.0  0
 6UY  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 6UY  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 6UY  CONST_07  N3   C13  C10  N2     0.00   0.0  0
 6UY  CONST_08  N3   C12  C11  N2     0.00   0.0  0
 6UY  CONST_09  C12  C11  N2   C10    0.00   0.0  0
 6UY  CONST_10  C12  N3   C13  C10    0.00   0.0  0
 6UY  CONST_11  C13  C10  N2   C11    0.00   0.0  0
 6UY  CONST_12  C13  N3   C12  C11    0.00   0.0  0
 6UY  CONST_13  C17  C18  C19  C14    0.00   0.0  0
 6UY  CONST_14  C17  C16  C15  C14    0.00   0.0  0
 6UY  CONST_15  C18  C17  C16  C15    0.00   0.0  0
 6UY  CONST_16  C18  C19  C14  C15    0.00   0.0  0
 6UY  CONST_17  C19  C18  C17  C16    0.00   0.0  0
 6UY  CONST_18  C19  C14  C15  C16    0.00   0.0  0
 6UY  CONST_19  F1   C5   C4   C3   180.00   0.0  0
 6UY  CONST_20  N1   C2   C3   C4   180.00   0.0  0
 6UY  CONST_21  N1   C2   C7   C6   180.00   0.0  0
 6UY  CONST_22  F1   C5   C6   C7   180.00   0.0  0
 6UY  CONST_23  N4   C13  C10  N2   180.00   0.0  0
 6UY  CONST_24  C9   C10  C13  N3   180.00   0.0  0
 6UY  CONST_25  C12  N3   C13  N4   180.00   0.0  0
 6UY  CONST_26  C18  C19  C14  C8   180.00   0.0  0
 6UY  CONST_27  C16  C15  C14  C8   180.00   0.0  0
 6UY  CONST_28  C11  N2   C10  C9   180.00   0.0  0
 6UY  CONST_29  H3   C6   C7   C2   180.00   0.0  0
 6UY  CONST_30  H2   C4   C3   C2   180.00   0.0  0
 6UY  CONST_31  H4   C7   C2   C3   180.00   0.0  0
 6UY  CONST_32  H1   C3   C4   C5   180.00   0.0  0
 6UY  CONST_33  H10  C12  C11  N2   180.00   0.0  0
 6UY  CONST_34  H9   C11  C12  N3   180.00   0.0  0
 6UY  CONST_35  H14  C18  C19  C14  180.00   0.0  0
 6UY  CONST_36  H12  C16  C15  C14  180.00   0.0  0
 6UY  CONST_37  H13  C17  C16  C15  180.00   0.0  0
 6UY  CONST_38  H15  C19  C14  C15  180.00   0.0  0
 6UY  CONST_39  H11  C15  C16  C17  180.00   0.0  0
 6UY  CONST_43  H6   N4   C13  N3   180.00   0.0  0
 6UY  CONST_44  H7   N4   C13  N3     0.00   0.0  0
 6UY  CONST_45  O1   C1   N1   C2     0.00   0.0  0
 6UY  CONST_46  C8   C1   N1   C2   180.00   0.0  0
 6UY  Var_01    O2   C9   C10  N2    -0.98  30.0  3
 6UY  Var_02    C10  C9   O2   C8   179.22  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
 6UY  chir_01  C8  C14  C1  O2  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
 6UY  plan-1  C2   0.020
 6UY  plan-1  C3   0.020
 6UY  plan-1  C4   0.020
 6UY  plan-1  C5   0.020
 6UY  plan-1  C6   0.020
 6UY  plan-1  C7   0.020
 6UY  plan-1  N1   0.020
 6UY  plan-1  F1   0.020
 6UY  plan-1  H1   0.020
 6UY  plan-1  H2   0.020
 6UY  plan-1  H3   0.020
 6UY  plan-1  H4   0.020
 6UY  plan-2  O2   0.020
 6UY  plan-2  C9   0.020
 6UY  plan-2  C10  0.020
 6UY  plan-2  O3   0.020
 6UY  plan-3  N2   0.020
 6UY  plan-3  N3   0.020
 6UY  plan-3  N4   0.020
 6UY  plan-3  C9   0.020
 6UY  plan-3  C10  0.020
 6UY  plan-3  C11  0.020
 6UY  plan-3  C12  0.020
 6UY  plan-3  C13  0.020
 6UY  plan-3  H9   0.020
 6UY  plan-3  H10  0.020
 6UY  plan-4  C8   0.020
 6UY  plan-4  C14  0.020
 6UY  plan-4  C15  0.020
 6UY  plan-4  C16  0.020
 6UY  plan-4  C17  0.020
 6UY  plan-4  C18  0.020
 6UY  plan-4  C19  0.020
 6UY  plan-4  H11  0.020
 6UY  plan-4  H12  0.020
 6UY  plan-4  H13  0.020
 6UY  plan-4  H14  0.020
 6UY  plan-4  H15  0.020
 6UY  plan-5  C1   0.020
 6UY  plan-5  C2   0.020
 6UY  plan-5  N1   0.020
 6UY  plan-5  C8   0.020
 6UY  plan-5  O1   0.020
 6UY  plan-5  H5   0.020
 6UY  plan-6  N4   0.020
 6UY  plan-6  C13  0.020
 6UY  plan-6  H6   0.020
 6UY  plan-6  H7   0.020

