# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:30:17 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: (5~{Z})-5-[(2-methoxy-4-oxidanyl-phenyl)methylidene]-3-methyl-2-[(~{E})-2-pyridin-4-ylethenyl]imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)ccc1\C=C2/N=C(/C=C/c3ccncc3)N(C)C2=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
 S1Q  S1Q  (5~{Z})-5-[(2-methoxy-4-oxidanyl-phenyl)methylidene]-3-methyl-2-[(~{E})-2-pyridin-4-ylethenyl]imidazol-4-one  ligand  42  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S1Q
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
 S1Q  O1    O  OH1   0  -0.615  -25.1257  -3.2477   0.4008
 S1Q  C2    C  CR16  0  -0.529  -26.0227  -5.4635   0.4790
 S1Q  O3    O  O     0  -0.450  -31.8554  -8.5783   0.2598
 S1Q  C4    C  CR6   0  -0.002  -28.4430  -5.7401   0.3224
 S1Q  C6    C  CR16  0  -0.348  -27.4426  -3.5183   0.2519
 S1Q  C7    C  C1    0  -0.357  -29.5819  -6.6177   0.2974
 S1Q  C8    C  CR5   0   0.095  -30.9013  -6.3197   0.2103
 S1Q  C10   C  CR5   0   0.588  -32.7823  -5.3015   0.0642
 S1Q  C13   C  C1    0  -0.373  -33.8020  -4.2786  -0.0345
 S1Q  C14   C  C1    0  -0.242  -33.5016  -2.9733  -0.0761
 S1Q  C15   C  CR6   0   0.239  -34.4596  -1.8794  -0.1821
 S1Q  C16   C  CR16  0  -0.375  -33.9882  -0.5668  -0.1915
 S1Q  C17   C  CR16  0  -0.056  -34.8902   0.4802  -0.2940
 S1Q  C18   C  CR16  0  -0.060  -36.6555  -0.9421  -0.3778
 S1Q  C19   C  CR16  0  -0.383  -35.8419  -2.0562  -0.2800
 S1Q  C1    C  CR6   0   0.401  -26.1712  -4.0821   0.3792
 S1Q  C5    C  CR16  0  -0.294  -28.5437  -4.3427   0.2260
 S1Q  C3    C  CR6   0   0.403  -27.1412  -6.2877   0.4504
 S1Q  O2    O  O2    0  -0.461  -27.0603  -7.6187   0.5426
 S1Q  C11   C  CH3   0  -0.439  -25.7956  -8.2385   0.6835
 S1Q  N2    N  N     0  -0.498  -31.5065  -5.0816   0.1237
 S1Q  N1    N  NR5   0  -0.584  -33.1129  -6.6413   0.1030
 S1Q  C9    C  CR5   0   0.519  -31.9445  -7.3673   0.2000
 S1Q  N3    N  N     0  -0.400  -36.2026   0.3087  -0.3860
 S1Q  H1    H  HOH1  0   0.479  -24.2948  -3.7301   0.4916
 S1Q  H21   H  HCR6  0   0.299  -25.0280  -5.8804   0.5777
 S1Q  H22   H  HCR6  0   0.265  -27.5535  -2.4447   0.1748
 S1Q  H45   H  H     0   0.266  -29.3736  -7.6791   0.3597
 S1Q  H83   H  HCH3  0   0.274  -34.3486  -8.2923   0.0834
 S1Q  H81   H  HCH3  0   0.261  -35.0359  -6.8892   0.9060
 S1Q  H82   H  HCH3  0   0.261  -34.9497  -6.9313  -0.8669
 S1Q  H10   H  H     0   0.296  -34.8307  -4.6147  -0.0746
 S1Q  H11   H  H     0   0.273  -32.4582  -2.6785  -0.0288
 S1Q  H131  H  HCR6  0   0.273  -32.9277  -0.3619  -0.1196
 S1Q  H141  H  HCR6  0   0.266  -34.5309   1.5033  -0.3021
 S1Q  H142  H  HCR6  0   0.267  -37.7299  -1.0672  -0.4543
 S1Q  H132  H  HCR6  0   0.271  -36.2939  -3.0387  -0.2837
 S1Q  H32   H  HCR6  0   0.279  -29.5250  -3.9024   0.1283
 S1Q  H332  H  HCH3  0   0.266  -25.9856  -9.3068   0.7432
 S1Q  H333  H  HCH3  0   0.235  -25.1484  -8.0419  -0.1744
 S1Q  H331  H  HCH3  0   0.235  -25.2875  -7.9179   1.5958
 S1Q  C12   C  CH3   0  -0.547  -34.4389  -7.2102   0.0535

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
 S1Q  N3   C18   aromatic  1.330  0.020  1.330
 S1Q  N3   C17   aromatic  1.327  0.020  1.327
 S1Q  C18  C19   aromatic  1.383  0.020  1.383
 S1Q  C17  C16   aromatic  1.386  0.020  1.386
 S1Q  C19  C15   aromatic  1.397  0.020  1.397
 S1Q  C16  C15   aromatic  1.395  0.020  1.395
 S1Q  C15  C14   single    1.458  0.020  1.458
 S1Q  C14  C13   double    1.340  0.020  1.340
 S1Q  C13  C10   single    1.448  0.020  1.448
 S1Q  C12  N1    single    1.444  0.020  1.444
 S1Q  C10  N1    single    1.381  0.020  1.381
 S1Q  C10  N2    double    1.296  0.020  1.296
 S1Q  N1   C9    single    1.379  0.020  1.379
 S1Q  N2   C8    single    1.381  0.020  1.381
 S1Q  C9   C8    single    1.479  0.020  1.479
 S1Q  C9   O3    double    1.216  0.020  1.216
 S1Q  C8   C7    double    1.355  0.020  1.355
 S1Q  C5   C6    aromatic  1.376  0.020  1.376
 S1Q  C5   C4    aromatic  1.404  0.020  1.404
 S1Q  C6   C1    aromatic  1.397  0.020  1.397
 S1Q  C7   C4    single    1.438  0.020  1.438
 S1Q  C4   C3    aromatic  1.418  0.020  1.418
 S1Q  C1   O1    single    1.338  0.020  1.338
 S1Q  C1   C2    aromatic  1.393  0.020  1.393
 S1Q  C3   C2    aromatic  1.390  0.020  1.390
 S1Q  C3   O2    single    1.337  0.020  1.337
 S1Q  O2   C11   single    1.415  0.020  1.415
 S1Q  O1   H1    single    0.850  0.020  0.980
 S1Q  C2   H21   single    0.930  0.020  1.080
 S1Q  C6   H22   single    0.930  0.020  1.080
 S1Q  C7   H45   single    0.930  0.020  1.080
 S1Q  C12  H83   single    0.970  0.020  1.090
 S1Q  C12  H81   single    0.970  0.020  1.090
 S1Q  C12  H82   single    0.970  0.020  1.090
 S1Q  C13  H10   single    0.930  0.020  1.080
 S1Q  C14  H11   single    0.930  0.020  1.080
 S1Q  C16  H131  single    0.930  0.020  1.080
 S1Q  C17  H141  single    0.930  0.020  1.080
 S1Q  C18  H142  single    0.930  0.020  1.080
 S1Q  C19  H132  single    0.930  0.020  1.080
 S1Q  C5   H32   single    0.930  0.020  1.080
 S1Q  C11  H332  single    0.970  0.020  1.090
 S1Q  C11  H333  single    0.970  0.020  1.090
 S1Q  C11  H331  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
 S1Q  H1    O1   C1    111.26  3.000
 S1Q  H21   C2   C3    120.85  3.000
 S1Q  H21   C2   C1    119.09  3.000
 S1Q  C3    C2   C1    120.06  3.000
 S1Q  C3    C4   C5    117.14  3.000
 S1Q  C3    C4   C7    119.54  3.000
 S1Q  C5    C4   C7    123.32  3.000
 S1Q  H22   C6   C5    120.74  3.000
 S1Q  H22   C6   C1    120.02  3.000
 S1Q  C5    C6   C1    119.23  3.000
 S1Q  H45   C7   C8    113.97  3.000
 S1Q  H45   C7   C4    116.39  3.000
 S1Q  C8    C7   C4    129.64  3.000
 S1Q  C9    C8   N2    109.00  3.000
 S1Q  C9    C8   C7    122.11  3.000
 S1Q  N2    C8   C7    128.89  3.000
 S1Q  N1    C10  N2    113.52  3.000
 S1Q  N2    C10  C13   125.21  3.000
 S1Q  N1    C10  C13   121.26  3.000
 S1Q  H10   C13  C14   120.94  3.000
 S1Q  H10   C13  C10   116.89  3.000
 S1Q  C14   C13  C10   122.17  3.000
 S1Q  H11   C14  C15   115.54  3.000
 S1Q  H11   C14  C13   118.61  3.000
 S1Q  C15   C14  C13   125.85  3.000
 S1Q  C19   C15  C16   116.94  3.000
 S1Q  C16   C15  C14   118.98  3.000
 S1Q  C19   C15  C14   124.08  3.000
 S1Q  H131  C16  C17   119.97  3.000
 S1Q  H131  C16  C15   120.59  3.000
 S1Q  C17   C16  C15   119.44  3.000
 S1Q  H141  C17  N3    116.69  3.000
 S1Q  H141  C17  C16   119.85  3.000
 S1Q  N3    C17  C16   123.46  3.000
 S1Q  H142  C18  N3    116.45  3.000
 S1Q  H142  C18  C19   119.67  3.000
 S1Q  N3    C18  C19   123.88  3.000
 S1Q  H132  C19  C18   119.06  3.000
 S1Q  H132  C19  C15   121.92  3.000
 S1Q  C18   C19  C15   119.02  3.000
 S1Q  C6    C1   C2    120.26  3.000
 S1Q  C2    C1   O1    122.28  3.000
 S1Q  C6    C1   O1    117.46  3.000
 S1Q  H32   C5   C6    118.98  3.000
 S1Q  H32   C5   C4    118.49  3.000
 S1Q  C6    C5   C4    122.52  3.000
 S1Q  O2    C3   C4    116.51  3.000
 S1Q  O2    C3   C2    122.72  3.000
 S1Q  C4    C3   C2    120.78  3.000
 S1Q  C11   O2   C3    119.80  3.000
 S1Q  H331  C11  H333  109.12  3.000
 S1Q  H331  C11  H332  108.91  3.000
 S1Q  H333  C11  H332  108.88  3.000
 S1Q  H331  C11  O2    111.73  3.000
 S1Q  H333  C11  O2    111.86  3.000
 S1Q  H332  C11  O2    106.24  3.000
 S1Q  C10   N2   C8    106.39  3.000
 S1Q  C9    N1   C12   124.97  3.000
 S1Q  C9    N1   C10   108.06  3.000
 S1Q  C12   N1   C10   126.97  3.000
 S1Q  N1    C9   C8    103.02  3.000
 S1Q  C8    C9   O3    130.83  3.000
 S1Q  N1    C9   O3    126.15  3.000
 S1Q  C18   N3   C17   117.25  3.000
 S1Q  H82   C12  H81   109.21  3.000
 S1Q  H82   C12  H83   108.51  3.000
 S1Q  H81   C12  H83   108.52  3.000
 S1Q  H82   C12  N1    111.03  3.000
 S1Q  H81   C12  N1    111.12  3.000
 S1Q  H83   C12  N1    108.38  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
 S1Q  CONST_01  C5    C6   C1   C2      0.00   0.0  0
 S1Q  CONST_02  C5    C4   C3   C2      0.00   0.0  0
 S1Q  CONST_03  C1    C6   C5   C4      0.00   0.0  0
 S1Q  CONST_04  C1    C2   C3   C4      0.00   0.0  0
 S1Q  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 S1Q  CONST_06  C3    C2   C1   C6      0.00   0.0  0
 S1Q  CONST_07  N3    C18  C19  C15     0.00   0.0  0
 S1Q  CONST_08  N3    C17  C16  C15     0.00   0.0  0
 S1Q  CONST_09  C18   N3   C17  C16     0.00   0.0  0
 S1Q  CONST_10  C18   C19  C15  C16     0.00   0.0  0
 S1Q  CONST_11  C19   C18  N3   C17     0.00   0.0  0
 S1Q  CONST_12  C19   C15  C16  C17     0.00   0.0  0
 S1Q  CONST_13  N1    C10  N2   C8      0.00   0.0  0
 S1Q  CONST_14  C10   N1   C9   C8      0.00   0.0  0
 S1Q  CONST_15  C9    C8   N2   C10     0.00   0.0  0
 S1Q  CONST_16  C9    N1   C10  N2      0.00   0.0  0
 S1Q  CONST_17  N1    C9   C8   N2      0.00   0.0  0
 S1Q  CONST_18  C5    C6   C1   O1    180.00   0.0  0
 S1Q  CONST_19  C3    C2   C1   O1    180.00   0.0  0
 S1Q  CONST_20  C7    C4   C3   C2    180.00   0.0  0
 S1Q  CONST_21  C7    C4   C5   C6    180.00   0.0  0
 S1Q  CONST_22  C18   C19  C15  C14   180.00   0.0  0
 S1Q  CONST_23  C17   C16  C15  C14   180.00   0.0  0
 S1Q  CONST_24  O2    C3   C2   C1    180.00   0.0  0
 S1Q  CONST_25  O2    C3   C4   C5    180.00   0.0  0
 S1Q  CONST_26  C10   N1   C9   O3    180.00   0.0  0
 S1Q  CONST_27  C13   C10  N2   C8    180.00   0.0  0
 S1Q  CONST_28  C12   N1   C9   C8    180.00   0.0  0
 S1Q  CONST_29  N2    C10  N1   C12   180.00   0.0  0
 S1Q  CONST_30  C9    N1   C10  C13   180.00   0.0  0
 S1Q  CONST_31  H22   C6   C1   C2    180.00   0.0  0
 S1Q  CONST_32  H21   C2   C3   C4    180.00   0.0  0
 S1Q  CONST_33  H142  C18  C19  C15   180.00   0.0  0
 S1Q  CONST_34  H141  C17  C16  C15   180.00   0.0  0
 S1Q  CONST_35  H132  C19  C15  C16   180.00   0.0  0
 S1Q  CONST_36  H131  C16  C15  C19   180.00   0.0  0
 S1Q  CONST_37  H32   C5   C6   C1    180.00   0.0  0
 S1Q  CONST_38  C12   N1   C9   O3      0.00   0.0  0
 S1Q  CONST_39  C15   C14  C13  C10   180.00   0.0  0
 S1Q  CONST_40  C13   C10  N1   C12     0.00   0.0  0
 S1Q  CONST_41  H11   C14  C13  C10     0.00   0.0  0
 S1Q  CONST_42  H10   C13  C14  C15     0.00   0.0  0
 S1Q  Var_01    N2    C8   C7   C4     -0.10   0.0  2
 S1Q  Var_02    C5    C4   C7   C8     -1.42  30.0  2
 S1Q  Var_03    C19   C15  C14  C13    -1.22  30.0  2
 S1Q  Var_04    N1    C10  C13  C14  -179.87  30.0  2
 S1Q  Var_05    H83   C12  N1   C10   178.82  30.0  3
 S1Q  Var_06    H332  C11  O2   C3    179.67  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
 S1Q  plan-1  O3    0.020
 S1Q  plan-1  C4    0.020
 S1Q  plan-1  C7    0.020
 S1Q  plan-1  C8    0.020
 S1Q  plan-1  C10   0.020
 S1Q  plan-1  C13   0.020
 S1Q  plan-1  N2    0.020
 S1Q  plan-1  N1    0.020
 S1Q  plan-1  C9    0.020
 S1Q  plan-1  H45   0.020
 S1Q  plan-1  C12   0.020
 S1Q  plan-2  O1    0.020
 S1Q  plan-2  C2    0.020
 S1Q  plan-2  C4    0.020
 S1Q  plan-2  C6    0.020
 S1Q  plan-2  C7    0.020
 S1Q  plan-2  C1    0.020
 S1Q  plan-2  C5    0.020
 S1Q  plan-2  C3    0.020
 S1Q  plan-2  O2    0.020
 S1Q  plan-2  H21   0.020
 S1Q  plan-2  H22   0.020
 S1Q  plan-2  H32   0.020
 S1Q  plan-3  C14   0.020
 S1Q  plan-3  C15   0.020
 S1Q  plan-3  C16   0.020
 S1Q  plan-3  C17   0.020
 S1Q  plan-3  C18   0.020
 S1Q  plan-3  C19   0.020
 S1Q  plan-3  N3    0.020
 S1Q  plan-3  H131  0.020
 S1Q  plan-3  H141  0.020
 S1Q  plan-3  H142  0.020
 S1Q  plan-3  H132  0.020
 S1Q  plan-4  C10   0.020
 S1Q  plan-4  C13   0.020
 S1Q  plan-4  C14   0.020
 S1Q  plan-4  C15   0.020
 S1Q  plan-4  H10   0.020
 S1Q  plan-4  H11   0.020

