# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:44:51 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-{2-[(4-{N-[(7S)-4-fluorobicyclo[4.2.0]octa-1,3,5-trien-7-yl]-N'-hydroxycarbamimidoyl}-1,2,5-oxadiazol-3-yl)sulfanyl]ethyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCSc1nonc1/C(N[C@H]2Cc3ccc(F)cc23)=N/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
 OY4  OY4  N-{2-[(4-{N-[(7S)-4-fluorobicyclo[4.2.0]octa-1,3,5-trien-7-yl]-N'-hydroxycarbamimidoyl}-1,2,5-oxadiazol-3-yl)sulfanyl]ethyl}acetamide  ligand  41  25  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OY4
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
 OY4  C2   C  CR6   0   0.527  -5.1327  -1.6684  -0.9952
 OY4  C3   C  CR16  0  -0.415  -6.3440  -1.0383  -0.7407
 OY4  C4   C  CR16  0  -0.337  -6.3875   0.1209   0.0348
 OY4  C5   C  C     0   0.093  -5.1761   0.5837   0.5078
 OY4  C6   C  C     0  -0.492  -4.5143   1.6799   1.3081
 OY4  C7   C  C     0  -0.178  -3.1710   0.9093   1.0699
 OY4  N10  N  N     0  -0.226  -0.0869   1.9959  -0.6375
 OY4  C12  C  CR5   0   0.156  -0.2957   0.0830   0.5763
 OY4  N13  N  N     0  -0.126  -0.9243  -0.8871   1.1559
 OY4  O14  O  O     0  -0.203  -0.0215  -1.8251   1.4315
 OY4  C16  C  CR5   0   0.072   1.0879  -0.2926   0.4851
 OY4  C18  C  CH2   0  -0.617   3.7793  -0.4881   0.2290
 OY4  C19  C  CH2   0  -0.240   5.0447   0.1334  -0.3416
 OY4  C21  C  C     0   0.527   7.4323  -0.3757  -0.3572
 OY4  C24  C  C     0   0.188  -3.9879  -0.0752   0.2482
 OY4  F1   F  F     0  -0.321  -5.1519  -2.7812  -1.7522
 OY4  N8   N  NH1   0  -0.670  -2.1641   1.6985   0.4096
 OY4  C9   C  C     0   0.445  -0.9020   1.3199   0.0899
 OY4  O11  O  OH1   0  -0.560  -0.6468   3.1606  -1.0873
 OY4  N15  N  N     0  -0.129   1.2108  -1.4645   1.0220
 OY4  S17  S  S2    0   0.120   2.3957   0.6130  -0.1956
 OY4  N20  N  NH1   0  -0.635   6.1782  -0.6955   0.0016
 OY4  C22  C  CH3   0  -0.776   8.5031  -1.3448   0.0745
 OY4  O23  O  O     0  -0.507   7.6881   0.6368  -0.9956
 OY4  C25  C  CR16  0  -0.501  -3.9090  -1.2247  -0.5113
 OY4  H1   H  HCR6  0   0.279  -7.2525  -1.4569  -1.1544
 OY4  H2   H  HCR6  0   0.263  -7.3317   0.6126   0.2293
 OY4  H3   H  H     0   0.264  -4.5469   2.6704   0.8501
 OY4  H4   H  H     0   0.268  -4.8080   1.7718   2.3538
 OY4  H5   H  H     0   0.287  -2.7772   0.4796   1.9895
 OY4  H6   H  HCH2  0   0.295   3.6069  -1.4751  -0.2018
 OY4  H7   H  HCH2  0   0.294   3.8488  -0.5844   1.3134
 OY4  H8   H  HCH2  0   0.253   4.9574   0.2246  -1.4274
 OY4  H9   H  HCH2  0   0.252   5.1834   1.1416   0.0580
 OY4  H10  H  HNH1  0   0.403  -2.5156   2.4696  -0.1382
 OY4  H11  H  HOH1  0   0.483   0.0234   3.5395  -1.6650
 OY4  H12  H  HNH1  0   0.407   6.0168  -1.5412   0.5236
 OY4  H13  H  HCH3  0   0.249   8.1248  -2.1866   0.6516
 OY4  H14  H  HCH3  0   0.267   9.0142  -1.7334  -0.8063
 OY4  H15  H  HCH3  0   0.266   9.2455  -0.8198   0.6751
 OY4  H16  H  HCR6  0   0.272  -2.9905  -1.7558  -0.7245

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
 OY4  O23  C21  double    1.224  0.020  1.224
 OY4  C19  C18  single    1.521  0.020  1.521
 OY4  C19  N20  single    1.446  0.020  1.446
 OY4  C21  N20  single    1.343  0.020  1.343
 OY4  C21  C22  single    1.507  0.020  1.507
 OY4  C18  S17  single    1.819  0.020  1.819
 OY4  S17  C16  single    1.730  0.020  1.730
 OY4  N15  C16  aromatic  1.295  0.020  1.295
 OY4  N15  O14  aromatic  1.348  0.020  1.348
 OY4  C16  C12  aromatic  1.437  0.020  1.437
 OY4  O14  N13  aromatic  1.331  0.020  1.331
 OY4  N13  C12  aromatic  1.293  0.020  1.293
 OY4  C12  C9   single    1.461  0.020  1.461
 OY4  N10  C9   double    1.285  0.020  1.285
 OY4  N10  O11  single    1.368  0.020  1.368
 OY4  C9   N8   single    1.356  0.020  1.356
 OY4  F1   C2   single    1.346  0.020  1.346
 OY4  C25  C2   aromatic  1.389  0.020  1.389
 OY4  C25  C24  aromatic  1.380  0.020  1.380
 OY4  N8   C7   single    1.440  0.020  1.440
 OY4  C2   C3   aromatic  1.389  0.020  1.389
 OY4  C24  C7   single    1.520  0.020  1.520
 OY4  C24  C5   aromatic  1.383  0.020  1.383
 OY4  C7   C6   single    1.567  0.020  1.567
 OY4  C3   C4   aromatic  1.395  0.020  1.395
 OY4  C5   C6   single    1.510  0.020  1.510
 OY4  C5   C4   aromatic  1.380  0.020  1.380
 OY4  C3   H1   single    0.930  0.020  1.080
 OY4  C4   H2   single    0.930  0.020  1.080
 OY4  C6   H3   single    0.970  0.020  1.090
 OY4  C6   H4   single    0.970  0.020  1.090
 OY4  C7   H5   single    0.970  0.020  1.090
 OY4  C18  H6   single    0.970  0.020  1.090
 OY4  C18  H7   single    0.970  0.020  1.090
 OY4  C19  H8   single    0.970  0.020  1.090
 OY4  C19  H9   single    0.970  0.020  1.090
 OY4  N8   H10  single    0.890  0.020  1.040
 OY4  O11  H11  single    0.850  0.020  0.980
 OY4  N20  H12  single    0.860  0.020  1.020
 OY4  C22  H13  single    0.970  0.020  1.090
 OY4  C22  H14  single    0.970  0.020  1.090
 OY4  C22  H15  single    0.970  0.020  1.090
 OY4  C25  H16  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
 OY4  C25  C2   F1   118.21  3.000
 OY4  C25  C2   C3   124.04  3.000
 OY4  F1   C2   C3   117.75  3.000
 OY4  H1   C3   C4   120.50  3.000
 OY4  H1   C3   C2   119.11  3.000
 OY4  C4   C3   C2   120.39  3.000
 OY4  H2   C4   C5   123.49  3.000
 OY4  H2   C4   C3   120.31  3.000
 OY4  C5   C4   C3   116.21  3.000
 OY4  C24  C5   C6    93.95  3.000
 OY4  C6   C5   C4   144.06  3.000
 OY4  C24  C5   C4   121.99  3.000
 OY4  H4   C6   H3   108.53  3.000
 OY4  H4   C6   C7   114.73  3.000
 OY4  H3   C6   C7   114.08  3.000
 OY4  H4   C6   C5   116.84  3.000
 OY4  H3   C6   C5   115.04  3.000
 OY4  C7   C6   C5    86.45  3.000
 OY4  H5   C7   N8   110.54  3.000
 OY4  H5   C7   C24  113.28  3.000
 OY4  N8   C7   C24  118.87  3.000
 OY4  H5   C7   C6   112.07  3.000
 OY4  C24  C7   C6    86.56  3.000
 OY4  N8   C7   C6   113.56  3.000
 OY4  O11  N10  C9   111.99  3.000
 OY4  C9   C12  C16  126.87  3.000
 OY4  C9   C12  N13  125.63  3.000
 OY4  C16  C12  N13  107.49  3.000
 OY4  O14  N13  C12  106.96  3.000
 OY4  N15  O14  N13  111.64  3.000
 OY4  S17  C16  N15  124.41  3.000
 OY4  N15  C16  C12  107.56  3.000
 OY4  S17  C16  C12  128.03  3.000
 OY4  H7   C18  H6   108.84  3.000
 OY4  H7   C18  S17  109.51  3.000
 OY4  H6   C18  S17  109.60  3.000
 OY4  H7   C18  C19  110.85  3.000
 OY4  H6   C18  C19  110.68  3.000
 OY4  S17  C18  C19  107.34  3.000
 OY4  H9   C19  H8   107.24  3.000
 OY4  H9   C19  N20  110.03  3.000
 OY4  H8   C19  N20  110.26  3.000
 OY4  H9   C19  C18  110.20  3.000
 OY4  H8   C19  C18  109.89  3.000
 OY4  N20  C19  C18  109.21  3.000
 OY4  O23  C21  C22  122.19  3.000
 OY4  C22  C21  N20  115.70  3.000
 OY4  O23  C21  N20  122.11  3.000
 OY4  C25  C24  C7   143.71  3.000
 OY4  C7   C24  C5    92.96  3.000
 OY4  C25  C24  C5   123.31  3.000
 OY4  H10  N8   C9   114.18  3.000
 OY4  H10  N8   C7   115.10  3.000
 OY4  C9   N8   C7   127.31  3.000
 OY4  N8   C9   C12  122.98  3.000
 OY4  N8   C9   N10  125.25  3.000
 OY4  C12  C9   N10  111.76  3.000
 OY4  H11  O11  N10  104.33  3.000
 OY4  C16  N15  O14  106.34  3.000
 OY4  C18  S17  C16   99.57  3.000
 OY4  H12  N20  C21  119.22  3.000
 OY4  H12  N20  C19  118.62  3.000
 OY4  C21  N20  C19  122.16  3.000
 OY4  H15  C22  H14  107.32  3.000
 OY4  H15  C22  H13  108.49  3.000
 OY4  H14  C22  H13  108.40  3.000
 OY4  H15  C22  C21  109.40  3.000
 OY4  H14  C22  C21  109.32  3.000
 OY4  H13  C22  C21  113.71  3.000
 OY4  H16  C25  C24  124.45  3.000
 OY4  H16  C25  C2   121.50  3.000
 OY4  C24  C25  C2   114.05  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
 OY4  CONST_01  C5   C24  C25  C2      0.00   0.0  0
 OY4  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 OY4  CONST_03  C24  C25  C2   C3      0.00   0.0  0
 OY4  CONST_04  C24  C5   C4   C3      0.00   0.0  0
 OY4  CONST_05  C25  C2   C3   C4      0.00   0.0  0
 OY4  CONST_06  C25  C24  C5   C4      0.00   0.0  0
 OY4  CONST_07  O14  N15  C16  C12     0.00   0.0  0
 OY4  CONST_08  N15  O14  N13  C12     0.00   0.0  0
 OY4  CONST_09  C16  N15  O14  N13     0.00   0.0  0
 OY4  CONST_10  N15  C16  C12  N13     0.00   0.0  0
 OY4  CONST_11  C16  C12  N13  O14     0.00   0.0  0
 OY4  CONST_12  F1   C2   C3   C4    180.00   0.0  0
 OY4  CONST_13  S17  C16  C12  N13   180.00   0.0  0
 OY4  CONST_14  S17  C16  N15  O14   180.00   0.0  0
 OY4  CONST_15  C9   C12  N13  O14   180.00   0.0  0
 OY4  CONST_16  F1   C2   C25  C24   180.00   0.0  0
 OY4  CONST_17  N15  C16  C12  C9    180.00   0.0  0
 OY4  CONST_18  H2   C4   C3   C2    180.00   0.0  0
 OY4  CONST_19  H16  C25  C2   C3    180.00   0.0  0
 OY4  CONST_20  H1   C3   C4   C5    180.00   0.0  0
 OY4  CONST_21  C12  C9   N8   C7      0.00   0.0  0
 OY4  CONST_22  N10  C9   N8   C7    180.00   0.0  0
 OY4  CONST_23  O11  N10  C9   C12   180.00   0.0  0
 OY4  CONST_24  H10  N8   C9   C12   180.00   0.0  0
 OY4  CONST_25  O23  C21  N20  C19     0.00   0.0  0
 OY4  CONST_26  C22  C21  N20  C19   180.00   0.0  0
 OY4  CONST_27  O11  N10  C9   N8      0.00   0.0  0
 OY4  CONST_28  H12  N20  C21  C22     0.00   0.0  0
 OY4  Var_01    H3   C6   C5   C4    -66.92  30.0  1
 OY4  Var_02    C16  C12  C9   N10     9.95  30.0  2
 OY4  Var_03    N15  C16  S17  C18    -4.56  30.0  2
 OY4  Var_04    C19  C18  S17  C16   178.17  30.0  1
 OY4  Var_05    C21  N20  C19  C18  -178.98  30.0  3
 OY4  Var_06    N20  C19  C18  S17   178.62  30.0  1
 OY4  Var_07    H13  C22  C21  N20    -1.27  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
 OY4  chir_01  C7  N8  C24  C6  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
 OY4  plan-1  C12  0.020
 OY4  plan-1  N13  0.020
 OY4  plan-1  O14  0.020
 OY4  plan-1  C16  0.020
 OY4  plan-1  C9   0.020
 OY4  plan-1  N15  0.020
 OY4  plan-1  S17  0.020
 OY4  plan-2  C2   0.020
 OY4  plan-2  C3   0.020
 OY4  plan-2  C4   0.020
 OY4  plan-2  C5   0.020
 OY4  plan-2  C6   0.020
 OY4  plan-2  C7   0.020
 OY4  plan-2  C24  0.020
 OY4  plan-2  F1   0.020
 OY4  plan-2  C25  0.020
 OY4  plan-2  H1   0.020
 OY4  plan-2  H2   0.020
 OY4  plan-2  H16  0.020
 OY4  plan-3  C19  0.020
 OY4  plan-3  C21  0.020
 OY4  plan-3  N20  0.020
 OY4  plan-3  C22  0.020
 OY4  plan-3  O23  0.020
 OY4  plan-3  H12  0.020
 OY4  plan-4  C7   0.020
 OY4  plan-4  N10  0.020
 OY4  plan-4  C12  0.020
 OY4  plan-4  N8   0.020
 OY4  plan-4  C9   0.020
 OY4  plan-4  O11  0.020
 OY4  plan-4  H10  0.020

