# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:39:28 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=NC(=C/c2cc(F)c(O)c(F)c2)\C1=O)C
#
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
 38E  38E  (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one  ligand  28  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_38E
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
 38E  F1   F  F     0  -0.316  -2.8975   2.3767  -0.0232
 38E  C2   C  CR6   0   0.511  -2.5552   1.0772  -0.0246
 38E  C1   C  CR6   0   0.076  -3.5986   0.1534  -0.0331
 38E  O1   O  OH1   0  -0.605  -4.8952   0.4732  -0.0392
 38E  C3   C  CR16  0  -0.498  -1.2300   0.7203  -0.0180
 38E  C4   C  CR6   0   0.163  -0.8863  -0.6372  -0.0188
 38E  C5   C  CR16  0  -0.485  -1.9138  -1.5883  -0.0259
 38E  C    C  CR6   0   0.496  -3.2281  -1.1877  -0.0330
 38E  F    F  F     0  -0.306  -4.2059  -2.1012  -0.0395
 38E  C6   C  C1    0  -0.386   0.4791  -1.1198  -0.0136
 38E  C7   C  CR5   0   0.102   1.6267  -0.4168  -0.0167
 38E  C9   C  CR5   0   0.539   2.9613  -1.0662  -0.0171
 38E  O    O  O     0  -0.444   3.2671  -2.2405  -0.0088
 38E  N1   N  NR5   0  -0.548   3.8234   0.0060  -0.0307
 38E  C10  C  CH3   0  -0.531   5.2644  -0.0774  -0.0231
 38E  C8   C  CR5   0   0.515   3.0724   1.1631  -0.0301
 38E  N    N  N     0  -0.492   1.7975   0.9604  -0.0233
 38E  C11  C  CH3   0  -0.759   3.7230   2.4913  -0.0420
 38E  H1   H  HOH1  0   0.486  -5.0182   1.4304  -0.0409
 38E  H2   H  HCR6  0   0.301  -0.4675   1.4862  -0.0130
 38E  H3   H  HCR6  0   0.290  -1.6862  -2.6466  -0.0261
 38E  H4   H  H     0   0.273   0.5907  -2.1992  -0.0084
 38E  H5   H  HCH3  0   0.271   5.5526  -1.1196  -0.1296
 38E  H6   H  HCH3  0   0.261   5.6871   0.4832  -0.8546
 38E  H7   H  HCH3  0   0.262   5.6758   0.3039   0.9104
 38E  H8   H  HCH3  0   0.273   4.3380   2.6143  -0.9357
 38E  H9   H  HCH3  0   0.278   2.9698   3.2737  -0.0236
 38E  H10  H  HCH3  0   0.274   4.3815   2.6112   0.8201

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
 38E  O    C9   double    1.214  0.020  1.214
 38E  F    C    single    1.338  0.020  1.338
 38E  C5   C    aromatic  1.374  0.020  1.374
 38E  C5   C4   aromatic  1.400  0.020  1.400
 38E  C6   C4   single    1.448  0.020  1.448
 38E  C6   C7   double    1.346  0.020  1.346
 38E  C9   C7   single    1.484  0.020  1.484
 38E  C9   N1   single    1.376  0.020  1.376
 38E  C    C1   aromatic  1.391  0.020  1.391
 38E  C4   C3   aromatic  1.400  0.020  1.400
 38E  C7   N    single    1.388  0.020  1.388
 38E  C10  N1   single    1.443  0.020  1.443
 38E  N1   C8   single    1.379  0.020  1.379
 38E  C1   O1   single    1.335  0.020  1.335
 38E  C1   C2   aromatic  1.394  0.020  1.394
 38E  C3   C2   aromatic  1.372  0.020  1.372
 38E  N    C8   double    1.291  0.020  1.291
 38E  C8   C11  single    1.479  0.020  1.479
 38E  C2   F1   single    1.344  0.020  1.344
 38E  O1   H1   single    0.850  0.020  0.980
 38E  C3   H2   single    0.930  0.020  1.080
 38E  C5   H3   single    0.930  0.020  1.080
 38E  C6   H4   single    0.930  0.020  1.080
 38E  C10  H5   single    0.970  0.020  1.090
 38E  C10  H6   single    0.970  0.020  1.090
 38E  C10  H7   single    0.970  0.020  1.090
 38E  C11  H8   single    0.970  0.020  1.090
 38E  C11  H9   single    0.970  0.020  1.090
 38E  C11  H10  single    0.970  0.020  1.090

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
 38E  C3   C2   C1   123.41  3.000
 38E  C3   C2   F1   119.82  3.000
 38E  C1   C2   F1   116.76  3.000
 38E  C    C1   O1   119.30  3.000
 38E  O1   C1   C2   124.63  3.000
 38E  C    C1   C2   116.07  3.000
 38E  H1   O1   C1   111.18  3.000
 38E  H2   C3   C4   120.92  3.000
 38E  H2   C3   C2   119.80  3.000
 38E  C4   C3   C2   119.28  3.000
 38E  C6   C4   C5   117.74  3.000
 38E  C6   C4   C3   123.68  3.000
 38E  C5   C4   C3   118.58  3.000
 38E  H3   C5   C    119.09  3.000
 38E  H3   C5   C4   120.65  3.000
 38E  C    C5   C4   120.26  3.000
 38E  F    C    C5   120.00  3.000
 38E  C5   C    C1   122.40  3.000
 38E  F    C    C1   117.61  3.000
 38E  H4   C6   C7   115.59  3.000
 38E  H4   C6   C4   115.37  3.000
 38E  C7   C6   C4   129.04  3.000
 38E  N    C7   C9   108.87  3.000
 38E  N    C7   C6   128.56  3.000
 38E  C9   C7   C6   122.56  3.000
 38E  N1   C9   O    126.60  3.000
 38E  N1   C9   C7   102.86  3.000
 38E  O    C9   C7   130.54  3.000
 38E  C8   N1   C10  126.30  3.000
 38E  C8   N1   C9   108.21  3.000
 38E  C10  N1   C9   125.49  3.000
 38E  H7   C10  H6   109.14  3.000
 38E  H7   C10  H5   108.64  3.000
 38E  H6   C10  H5   108.43  3.000
 38E  H7   C10  N1   111.19  3.000
 38E  H6   C10  N1   110.73  3.000
 38E  H5   C10  N1   108.64  3.000
 38E  C11  C8   N    125.13  3.000
 38E  C11  C8   N1   120.91  3.000
 38E  N    C8   N1   113.95  3.000
 38E  C8   N    C7   106.11  3.000
 38E  H10  C11  H9   109.02  3.000
 38E  H10  C11  H8   107.12  3.000
 38E  H9   C11  H8   108.87  3.000
 38E  H10  C11  C8   110.96  3.000
 38E  H9   C11  C8   109.98  3.000
 38E  H8   C11  C8   110.82  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
 38E  CONST_01  C5   C    C1  C2      0.00   0.0  0
 38E  CONST_02  C5   C4   C3  C2      0.00   0.0  0
 38E  CONST_03  C4   C5   C   C1      0.00   0.0  0
 38E  CONST_04  C4   C3   C2  C1      0.00   0.0  0
 38E  CONST_05  C    C5   C4  C3      0.00   0.0  0
 38E  CONST_06  C    C1   C2  C3      0.00   0.0  0
 38E  CONST_07  C8   N1   C9  C7      0.00   0.0  0
 38E  CONST_08  N1   C8   N   C7      0.00   0.0  0
 38E  CONST_09  C8   N    C7  C9      0.00   0.0  0
 38E  CONST_10  N    C8   N1  C9      0.00   0.0  0
 38E  CONST_11  N    C7   C9  N1      0.00   0.0  0
 38E  CONST_12  C    C1   C2  F1    180.00   0.0  0
 38E  CONST_13  C4   C3   C2  F1    180.00   0.0  0
 38E  CONST_14  F    C    C1  C2    180.00   0.0  0
 38E  CONST_15  C6   C4   C3  C2    180.00   0.0  0
 38E  CONST_16  C5   C    C1  O1    180.00   0.0  0
 38E  CONST_17  C3   C2   C1  O1    180.00   0.0  0
 38E  CONST_18  F    C    C5  C4    180.00   0.0  0
 38E  CONST_19  C6   C4   C5  C     180.00   0.0  0
 38E  CONST_20  C10  N1   C9  C7    180.00   0.0  0
 38E  CONST_21  C11  C8   N   C7    180.00   0.0  0
 38E  CONST_22  C11  C8   N1  C9    180.00   0.0  0
 38E  CONST_23  C8   N1   C9  O     180.00   0.0  0
 38E  CONST_24  N    C8   N1  C10   180.00   0.0  0
 38E  CONST_25  H3   C5   C   C1    180.00   0.0  0
 38E  CONST_26  H2   C3   C2  C1    180.00   0.0  0
 38E  CONST_27  C10  N1   C9  O       0.00   0.0  0
 38E  CONST_28  C11  C8   N1  C10     0.00   0.0  0
 38E  Var_01    C7   C6   C4  C3     -0.51  30.0  1
 38E  Var_02    C9   C7   C6  C4   -179.70  30.0  2
 38E  Var_03    H5   C10  N1  C9      6.95  30.0  3
 38E  Var_04    H8   C11  C8  N1     60.48  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
 38E  plan-1  C6   0.020
 38E  plan-1  C7   0.020
 38E  plan-1  C9   0.020
 38E  plan-1  O    0.020
 38E  plan-1  N1   0.020
 38E  plan-1  C10  0.020
 38E  plan-1  C8   0.020
 38E  plan-1  N    0.020
 38E  plan-1  C11  0.020
 38E  plan-2  F1   0.020
 38E  plan-2  C2   0.020
 38E  plan-2  C1   0.020
 38E  plan-2  O1   0.020
 38E  plan-2  C3   0.020
 38E  plan-2  C4   0.020
 38E  plan-2  C5   0.020
 38E  plan-2  C    0.020
 38E  plan-2  F    0.020
 38E  plan-2  C6   0.020
 38E  plan-2  H2   0.020
 38E  plan-2  H3   0.020

