# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 14:45:30 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (3~{E})-3-[(5-methylfuran-2-yl)methylidene]-1~{H}-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(cc1)/C=C2/C(=O)Nc3ccccc23
#
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
 QYZ  QYZ  (3~{E})-3-[(5-methylfuran-2-yl)methylidene]-1~{H}-indol-2-one  ligand  28  17  .  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_QYZ
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
 QYZ  C1   C  CH3   0  -0.756  -24.0815  -23.0158  -10.6569
 QYZ  N1   N  NR15  0  -0.771  -18.3224  -27.7682   -9.9123
 QYZ  O1   O  O     0  -0.436  -22.7003  -24.8626   -9.9406
 QYZ  C2   C  CR5   0   0.373  -23.8735  -24.2185   -9.8229
 QYZ  O2   O  O     0  -0.451  -19.6659  -28.8550   -8.3978
 QYZ  C3   C  CR15  0  -0.368  -24.6546  -24.8514   -8.9014
 QYZ  C4   C  CR15  0  -0.311  -23.9026  -25.9504   -8.4293
 QYZ  C5   C  CR5   0   0.373  -22.7038  -25.9203   -9.0938
 QYZ  C6   C  C1    0  -0.432  -21.5985  -26.8014   -8.9811
 QYZ  C7   C  CR5   0  -0.002  -20.3845  -26.8405   -9.5763
 QYZ  C8   C  CR5   0   0.514  -19.4641  -27.9535   -9.1897
 QYZ  C9   C  CR56  0   0.370  -18.4068  -26.6534  -10.7272
 QYZ  C10  C  CR56  0   0.037  -19.6628  -26.0406  -10.5599
 QYZ  C11  C  CR16  0  -0.386  -19.9428  -24.8968  -11.2982
 QYZ  C12  C  CR16  0  -0.254  -18.9852  -24.3933  -12.1739
 QYZ  C13  C  CR16  0  -0.267  -17.7535  -25.0190  -12.3192
 QYZ  C14  C  CR16  0  -0.304  -17.4474  -26.1653  -11.5919
 QYZ  H1   H  HCH3  0   0.264  -23.3563  -22.2353  -10.4192
 QYZ  H2   H  HCH3  0   0.263  -23.9830  -23.2441  -11.7198
 QYZ  H3   H  HCH3  0   0.264  -25.0783  -22.6163  -10.4851
 QYZ  H4   H  HNR5  0   0.409  -17.5188  -28.3750   -9.8556
 QYZ  H5   H  HCR5  0   0.270  -25.6475  -24.5565   -8.6033
 QYZ  H6   H  HCR5  0   0.276  -24.1947  -26.6805   -7.6911
 QYZ  H7   H  H     0   0.285  -21.7855  -27.5958   -8.2643
 QYZ  H8   H  HCR6  0   0.264  -20.8897  -24.3901  -11.2071
 QYZ  H9   H  HCR6  0   0.252  -19.2070  -23.5027  -12.7468
 QYZ  H10  H  HCR6  0   0.257  -17.0202  -24.6136  -13.0042
 QYZ  H11  H  HCR6  0   0.265  -16.4893  -26.6572  -11.6995

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
 QYZ  C13  C12  aromatic  1.389  0.020  1.389
 QYZ  C13  C14  aromatic  1.392  0.020  1.392
 QYZ  C12  C11  aromatic  1.392  0.020  1.392
 QYZ  C14  C9   aromatic  1.381  0.020  1.381
 QYZ  C11  C10  aromatic  1.390  0.020  1.390
 QYZ  C1   C2   single    1.478  0.020  1.478
 QYZ  C9   C10  aromatic  1.408  0.020  1.408
 QYZ  C9   N1   single    1.383  0.020  1.383
 QYZ  C10  C7   single    1.459  0.020  1.459
 QYZ  O1   C2   aromatic  1.344  0.020  1.344
 QYZ  O1   C5   aromatic  1.355  0.020  1.355
 QYZ  N1   C8   single    1.364  0.020  1.364
 QYZ  C2   C3   aromatic  1.364  0.020  1.364
 QYZ  C7   C8   single    1.495  0.020  1.495
 QYZ  C7   C6   double    1.353  0.020  1.353
 QYZ  C8   O2   double    1.217  0.020  1.217
 QYZ  C5   C6   single    1.418  0.020  1.418
 QYZ  C5   C4   aromatic  1.371  0.020  1.371
 QYZ  C3   C4   aromatic  1.413  0.020  1.413
 QYZ  C1   H1   single    0.970  0.020  1.090
 QYZ  C1   H2   single    0.970  0.020  1.090
 QYZ  C1   H3   single    0.970  0.020  1.090
 QYZ  N1   H4   single    0.860  0.020  1.020
 QYZ  C3   H5   single    0.930  0.020  1.080
 QYZ  C4   H6   single    0.930  0.020  1.080
 QYZ  C6   H7   single    0.930  0.020  1.080
 QYZ  C11  H8   single    0.930  0.020  1.080
 QYZ  C12  H9   single    0.930  0.020  1.080
 QYZ  C13  H10  single    0.930  0.020  1.080
 QYZ  C14  H11  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
 QYZ  H3   C1   H2   108.26  3.000
 QYZ  H3   C1   H1   108.17  3.000
 QYZ  H2   C1   H1   107.56  3.000
 QYZ  H3   C1   C2   109.80  3.000
 QYZ  H2   C1   C2   111.50  3.000
 QYZ  H1   C1   C2   111.43  3.000
 QYZ  H4   N1   C9   124.51  3.000
 QYZ  H4   N1   C8   123.75  3.000
 QYZ  C9   N1   C8   111.74  3.000
 QYZ  C5   O1   C2   108.50  3.000
 QYZ  C3   C2   O1   109.68  3.000
 QYZ  C3   C2   C1   132.70  3.000
 QYZ  O1   C2   C1   117.62  3.000
 QYZ  H5   C3   C4   127.65  3.000
 QYZ  H5   C3   C2   125.98  3.000
 QYZ  C4   C3   C2   106.37  3.000
 QYZ  H6   C4   C5   125.69  3.000
 QYZ  H6   C4   C3   127.67  3.000
 QYZ  C5   C4   C3   106.64  3.000
 QYZ  C6   C5   C4   129.01  3.000
 QYZ  C4   C5   O1   108.80  3.000
 QYZ  C6   C5   O1   122.19  3.000
 QYZ  H7   C6   C7   115.07  3.000
 QYZ  H7   C6   C5   111.88  3.000
 QYZ  C7   C6   C5   133.04  3.000
 QYZ  C10  C7   C8   106.14  3.000
 QYZ  C8   C7   C6   117.40  3.000
 QYZ  C10  C7   C6   136.46  3.000
 QYZ  C7   C8   O2   128.15  3.000
 QYZ  O2   C8   N1   125.75  3.000
 QYZ  C7   C8   N1   106.10  3.000
 QYZ  C14  C9   C10  122.72  3.000
 QYZ  C10  C9   N1   109.59  3.000
 QYZ  C14  C9   N1   127.69  3.000
 QYZ  C11  C10  C9   118.36  3.000
 QYZ  C9   C10  C7   106.43  3.000
 QYZ  C11  C10  C7   135.21  3.000
 QYZ  H8   C11  C12  119.18  3.000
 QYZ  H8   C11  C10  121.26  3.000
 QYZ  C12  C11  C10  119.56  3.000
 QYZ  H9   C12  C13  119.81  3.000
 QYZ  H9   C12  C11  119.33  3.000
 QYZ  C13  C12  C11  120.86  3.000
 QYZ  H10  C13  C14  119.36  3.000
 QYZ  H10  C13  C12  119.89  3.000
 QYZ  C14  C13  C12  120.75  3.000
 QYZ  H11  C14  C13  121.14  3.000
 QYZ  H11  C14  C9   121.11  3.000
 QYZ  C13  C14  C9   117.75  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
 QYZ  CONST_01  C4   C3   C2   O1     0.00   0.0  0
 QYZ  CONST_02  C3   C4   C5   O1     0.00   0.0  0
 QYZ  CONST_03  C4   C5   O1   C2     0.00   0.0  0
 QYZ  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 QYZ  CONST_05  C5   O1   C2   C3     0.00   0.0  0
 QYZ  CONST_06  C12  C13  C14  C9     0.00   0.0  0
 QYZ  CONST_07  C12  C11  C10  C9     0.00   0.0  0
 QYZ  CONST_08  C13  C12  C11  C10    0.00   0.0  0
 QYZ  CONST_09  C13  C14  C9   C10    0.00   0.0  0
 QYZ  CONST_10  C14  C13  C12  C11    0.00   0.0  0
 QYZ  CONST_11  C14  C9   C10  C11    0.00   0.0  0
 QYZ  CONST_12  C9   N1   C8   C7     0.00   0.0  0
 QYZ  CONST_13  C5   O1   C2   C1   180.00   0.0  0
 QYZ  CONST_14  C4   C3   C2   C1   180.00   0.0  0
 QYZ  CONST_15  C6   C5   O1   C2   180.00   0.0  0
 QYZ  CONST_16  C6   C5   C4   C3   180.00   0.0  0
 QYZ  CONST_17  C9   N1   C8   O2   180.00   0.0  0
 QYZ  CONST_18  C10  C7   C6   C5     0.00   0.0  0
 QYZ  CONST_19  C8   C7   C6   C5   180.00   0.0  0
 QYZ  CONST_20  H11  C14  C9   N1     0.00   0.0  0
 QYZ  CONST_21  H5   C3   C2   O1   180.00   0.0  0
 QYZ  CONST_22  H6   C4   C5   O1   180.00   0.0  0
 QYZ  CONST_23  H8   C11  C10  C7     0.00   0.0  0
 QYZ  CONST_24  H10  C13  C14  C9   180.00   0.0  0
 QYZ  CONST_25  H9   C12  C11  C10  180.00   0.0  0
 QYZ  CONST_26  H4   N1   C8   C7   180.00   0.0  0
 QYZ  CONST_27  H7   C6   C7   C8     0.00   0.0  0
 QYZ  Var_01    C7   C6   C5   O1     0.95  30.0  2
 QYZ  Var_02    H1   C1   C2   O1   -61.97  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
 QYZ  plan-1  C1   0.020
 QYZ  plan-1  O1   0.020
 QYZ  plan-1  C2   0.020
 QYZ  plan-1  C3   0.020
 QYZ  plan-1  C4   0.020
 QYZ  plan-1  C5   0.020
 QYZ  plan-1  C6   0.020
 QYZ  plan-1  H5   0.020
 QYZ  plan-1  H6   0.020
 QYZ  plan-2  N1   0.020
 QYZ  plan-2  O2   0.020
 QYZ  plan-2  C5   0.020
 QYZ  plan-2  C6   0.020
 QYZ  plan-2  C7   0.020
 QYZ  plan-2  C8   0.020
 QYZ  plan-2  C9   0.020
 QYZ  plan-2  C10  0.020
 QYZ  plan-2  C11  0.020
 QYZ  plan-2  C12  0.020
 QYZ  plan-2  C13  0.020
 QYZ  plan-2  C14  0.020
 QYZ  plan-2  H4   0.020
 QYZ  plan-2  H7   0.020
 QYZ  plan-2  H8   0.020
 QYZ  plan-2  H9   0.020
 QYZ  plan-2  H10  0.020
 QYZ  plan-2  H11  0.020

