# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 13:53:57 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: 2-{[3-({[4-bromo-5-(1-fluoroethenyl)-3-methylthiophen-2-yl]methyl}amino)propyl]amino}quinolin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Br)c(sc1CNCCCNC2=CC(=O)c3ccccc3N2)C(F)=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
 U7S  U7S  2-{[3-({[4-bromo-5-(1-fluoroethenyl)-3-methylthiophen-2-yl]methyl}amino)propyl]amino}quinolin-4(1H)-one  ligand  48  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U7S
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
 U7S  C4   C   CR5   0  -0.286  -16.8877  -20.9758  15.6590
 U7S  C14  C   CR6   0   0.438  -15.2841  -29.9494  12.8881
 U7S  C5   C   CR5   0  -0.134  -17.6952  -22.0580  15.8906
 U7S  C6   C   C     0   0.580  -16.0261  -20.1703  16.5054
 U7S  C11  C   CH2   0  -0.276  -16.0178  -26.1080  11.0270
 U7S  C7   C   C2    0  -0.699  -15.9241  -20.0805  17.8238
 U7S  C8   C   CH2   0  -0.386  -18.5394  -21.9795  12.2091
 U7S  C9   C   CH2   0  -0.250  -17.2609  -24.0076  11.7543
 U7S  C10  C   CH2   0  -0.490  -16.2993  -24.6397  10.7578
 U7S  C12  C   CR6   0   0.663  -15.1001  -27.4985  12.8324
 U7S  C13  C   CR16  0  -0.615  -15.5265  -28.6895  12.2726
 U7S  N1   N   NH1   0  -0.576  -17.5855  -22.6527  11.3488
 U7S  N2   N   NH1   0  -0.682  -15.3463  -26.2886  12.2969
 U7S  C3   C   CR5   0  -0.254  -18.1014  -21.7914  13.6380
 U7S  N3   N   NR16  0  -0.782  -14.4064  -27.5108  14.0007
 U7S  C1   C   CH3   0  -0.730  -19.3248  -23.7110  14.7752
 U7S  C2   C   CR5   0   0.231  -18.3978  -22.5397  14.7447
 U7S  S1   S   S2    0   0.262  -16.9862  -20.5354  13.9951
 U7S  BR1  BR  BR    0  -0.018  -17.8749  -22.9180  17.5428
 U7S  F1   F   F     0  -0.325  -15.2308  -19.3813  15.7439
 U7S  C15  C   CR66  0  -0.117  -14.5343  -29.8986  14.1590
 U7S  C16  C   CR16  0  -0.303  -14.2295  -31.0657  14.8658
 U7S  C17  C   CR16  0  -0.258  -13.5285  -31.0166  16.0519
 U7S  C18  C   CR16  0  -0.254  -13.1139  -29.7809  16.5559
 U7S  C19  C   CR16  0  -0.320  -13.3994  -28.6148  15.8792
 U7S  C20  C   CR66  0   0.371  -14.1129  -28.6694  14.6766
 U7S  H1   H   HCH2  0   0.241  -16.9602  -26.6616  11.0408
 U7S  H2   H   HCH2  0   0.247  -15.4182  -26.5215  10.2088
 U7S  H3   H   H     0   0.277  -15.2014  -19.4093  18.2662
 U7S  H4   H   H     0   0.276  -16.5519  -20.6503  18.4872
 U7S  H5   H   HCH2  0   0.267  -18.7650  -21.0058  11.7685
 U7S  H6   H   HCH2  0   0.256  -19.4752  -22.5416  12.1975
 U7S  H7   H   HCH2  0   0.221  -18.1885  -24.5891  11.7727
 U7S  H8   H   HCH2  0   0.204  -16.8409  -24.0628  12.7690
 U7S  H9   H   HCH2  0   0.236  -15.3568  -24.0815  10.7417
 U7S  H10  H   HCH2  0   0.249  -16.7222  -24.5618   9.7544
 U7S  H11  H   HCR6  0   0.262  -16.0553  -28.6743  11.3303
 U7S  H13  H   HNH1  0   0.345  -16.7362  -22.1029  11.2858
 U7S  H15  H   HNH1  0   0.401  -14.8237  -25.5004  12.6475
 U7S  H16  H   HCH3  0   0.254  -18.7979  -24.6281  15.0428
 U7S  H17  H   HCH3  0   0.256  -20.1219  -23.5665  15.5055
 U7S  H18  H   HCH3  0   0.257  -19.7924  -23.8741  13.8073
 U7S  H19  H   HCR6  0   0.255  -14.5562  -32.0158  14.4638
 U7S  H20  H   HCR6  0   0.254  -13.3000  -31.9269  16.5898
 U7S  H21  H   HCR6  0   0.262  -12.5631  -29.7335  17.4864
 U7S  H22  H   HCR6  0   0.272  -13.0779  -27.6575  16.2718
 U7S  H12  H   HNR6  0   0.419  -14.1230  -26.6360  14.4190
 U7S  O1   O   O     0  -0.499  -15.6553  -31.0299  12.4138

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
 U7S  C10  C11  single    1.519  0.020  1.519
 U7S  C10  C9   single    1.522  0.020  1.522
 U7S  C11  N2   single    1.448  0.020  1.448
 U7S  C9   N1   single    1.451  0.020  1.451
 U7S  N1   C8   single    1.450  0.020  1.450
 U7S  N2   C12  single    1.346  0.020  1.346
 U7S  C8   C3   single    1.506  0.020  1.506
 U7S  C13  C12  double    1.383  0.020  1.383
 U7S  C13  C14  single    1.423  0.020  1.423
 U7S  O1   C14  double    1.237  0.020  1.237
 U7S  C14  C15  single    1.476  0.020  1.476
 U7S  C3   S1   aromatic  1.717  0.020  1.717
 U7S  C3   C2   aromatic  1.368  0.020  1.368
 U7S  N3   C20  single    1.373  0.020  1.373
 U7S  S1   C4   aromatic  1.724  0.020  1.724
 U7S  C15  C20  aromatic  1.399  0.020  1.399
 U7S  C15  C16  aromatic  1.398  0.020  1.398
 U7S  C20  C19  aromatic  1.399  0.020  1.399
 U7S  C1   C2   single    1.494  0.020  1.494
 U7S  C2   C5   aromatic  1.428  0.020  1.428
 U7S  C16  C17  aromatic  1.379  0.020  1.379
 U7S  C19  C18  aromatic  1.378  0.020  1.378
 U7S  C4   C5   aromatic  1.370  0.020  1.370
 U7S  C4   C6   single    1.452  0.020  1.452
 U7S  C5   BR1  single    1.871  0.020  1.871
 U7S  C17  C18  aromatic  1.397  0.020  1.397
 U7S  F1   C6   single    1.355  0.020  1.355
 U7S  C6   C7   double    1.325  0.020  1.325
 U7S  C11  H1   single    0.970  0.020  1.090
 U7S  C11  H2   single    0.970  0.020  1.090
 U7S  C7   H3   single    0.930  0.020  1.080
 U7S  C7   H4   single    0.930  0.020  1.080
 U7S  C8   H5   single    0.970  0.020  1.090
 U7S  C8   H6   single    0.970  0.020  1.090
 U7S  C9   H7   single    0.970  0.020  1.090
 U7S  C9   H8   single    0.970  0.020  1.090
 U7S  C10  H9   single    0.970  0.020  1.090
 U7S  C10  H10  single    0.970  0.020  1.090
 U7S  C13  H11  single    0.930  0.020  1.080
 U7S  N1   H13  single    0.890  0.020  1.040
 U7S  N2   H15  single    0.860  0.020  1.020
 U7S  C1   H16  single    0.970  0.020  1.090
 U7S  C1   H17  single    0.970  0.020  1.090
 U7S  C1   H18  single    0.970  0.020  1.090
 U7S  C16  H19  single    0.930  0.020  1.080
 U7S  C17  H20  single    0.930  0.020  1.080
 U7S  C18  H21  single    0.930  0.020  1.080
 U7S  C19  H22  single    0.930  0.020  1.080
 U7S  C12  N3   single    1.359  0.020  1.359
 U7S  N3   H12  single    0.860  0.020  1.020

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
 U7S  S1   C4   C6   117.05  3.000
 U7S  C6   C4   C5   133.60  3.000
 U7S  S1   C4   C5   109.34  3.000
 U7S  C15  C14  O1   120.83  3.000
 U7S  C15  C14  C13  115.36  3.000
 U7S  O1   C14  C13  123.80  3.000
 U7S  BR1  C5   C2   120.42  3.000
 U7S  BR1  C5   C4   124.67  3.000
 U7S  C2   C5   C4   114.89  3.000
 U7S  F1   C6   C7   118.33  3.000
 U7S  C7   C6   C4   131.54  3.000
 U7S  F1   C6   C4   110.11  3.000
 U7S  H2   C11  H1   106.87  3.000
 U7S  H2   C11  N2   110.74  3.000
 U7S  H1   C11  N2   109.01  3.000
 U7S  H2   C11  C10  109.51  3.000
 U7S  H1   C11  C10  109.39  3.000
 U7S  N2   C11  C10  111.22  3.000
 U7S  H4   C7   H3   117.80  3.000
 U7S  H4   C7   C6   122.16  3.000
 U7S  H3   C7   C6   120.04  3.000
 U7S  H6   C8   H5   106.12  3.000
 U7S  H6   C8   C3   108.88  3.000
 U7S  H5   C8   C3   109.35  3.000
 U7S  H6   C8   N1   108.57  3.000
 U7S  H5   C8   N1   108.08  3.000
 U7S  C3   C8   N1   115.43  3.000
 U7S  H8   C9   H7   106.35  3.000
 U7S  H8   C9   N1   112.97  3.000
 U7S  H7   C9   N1   108.13  3.000
 U7S  H8   C9   C10  110.00  3.000
 U7S  H7   C9   C10  109.00  3.000
 U7S  N1   C9   C10  110.25  3.000
 U7S  H10  C10  H9   106.47  3.000
 U7S  H10  C10  C9   109.11  3.000
 U7S  H9   C10  C9   109.97  3.000
 U7S  H10  C10  C11  107.68  3.000
 U7S  H9   C10  C11  109.61  3.000
 U7S  C9   C10  C11  113.73  3.000
 U7S  N3   C12  N2   116.34  3.000
 U7S  N3   C12  C13  119.84  3.000
 U7S  N2   C12  C13  123.82  3.000
 U7S  H11  C13  C12  119.45  3.000
 U7S  H11  C13  C14  118.23  3.000
 U7S  C12  C13  C14  122.32  3.000
 U7S  H13  N1   C9   109.66  3.000
 U7S  H13  N1   C8   109.64  3.000
 U7S  C9   N1   C8   114.51  3.000
 U7S  H15  N2   C12  118.00  3.000
 U7S  H15  N2   C11  116.60  3.000
 U7S  C12  N2   C11  123.09  3.000
 U7S  S1   C3   C2   111.87  3.000
 U7S  C2   C3   C8   129.49  3.000
 U7S  S1   C3   C8   118.52  3.000
 U7S  H12  N3   C20  117.83  3.000
 U7S  H12  N3   C12  119.43  3.000
 U7S  C20  N3   C12  122.68  3.000
 U7S  H18  C1   H17  107.56  3.000
 U7S  H18  C1   H16  107.45  3.000
 U7S  H17  C1   H16  107.46  3.000
 U7S  H18  C1   C2   111.49  3.000
 U7S  H17  C1   C2   111.30  3.000
 U7S  H16  C1   C2   111.37  3.000
 U7S  C1   C2   C3   125.42  3.000
 U7S  C1   C2   C5   123.60  3.000
 U7S  C3   C2   C5   110.98  3.000
 U7S  C3   S1   C4    92.92  3.000
 U7S  C20  C15  C16  118.74  3.000
 U7S  C16  C15  C14  121.14  3.000
 U7S  C20  C15  C14  120.12  3.000
 U7S  H19  C16  C17  120.29  3.000
 U7S  H19  C16  C15  118.64  3.000
 U7S  C17  C16  C15  121.07  3.000
 U7S  H20  C17  C18  120.14  3.000
 U7S  H20  C17  C16  120.35  3.000
 U7S  C18  C17  C16  119.51  3.000
 U7S  H21  C18  C19  119.37  3.000
 U7S  H21  C18  C17  119.99  3.000
 U7S  C19  C18  C17  120.64  3.000
 U7S  H22  C19  C20  119.81  3.000
 U7S  H22  C19  C18  120.54  3.000
 U7S  C20  C19  C18  119.64  3.000
 U7S  C19  C20  C15  120.39  3.000
 U7S  C19  C20  N3   119.94  3.000
 U7S  C15  C20  N3   119.67  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
 U7S  CONST_01  C2   C3   S1   C4      0.00   0.0  0
 U7S  CONST_02  C3   C2   C5   C4      0.00   0.0  0
 U7S  CONST_03  S1   C3   C2   C5      0.00   0.0  0
 U7S  CONST_04  C3   S1   C4   C5      0.00   0.0  0
 U7S  CONST_05  S1   C4   C5   C2      0.00   0.0  0
 U7S  CONST_06  C18  C19  C20  C15     0.00   0.0  0
 U7S  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 U7S  CONST_08  C19  C20  C15  C16     0.00   0.0  0
 U7S  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 U7S  CONST_10  C20  C15  C16  C17     0.00   0.0  0
 U7S  CONST_11  C20  C19  C18  C17     0.00   0.0  0
 U7S  CONST_12  C20  N3   C12  C13     0.00   0.0  0
 U7S  CONST_13  C8   C3   S1   C4    180.00   0.0  0
 U7S  CONST_14  C1   C2   C5   C4    180.00   0.0  0
 U7S  CONST_15  C8   C3   C2   C5    180.00   0.0  0
 U7S  CONST_16  C3   S1   C4   C6    180.00   0.0  0
 U7S  CONST_17  C2   C5   C4   C6    180.00   0.0  0
 U7S  CONST_18  BR1  C5   C2   C3    180.00   0.0  0
 U7S  CONST_19  S1   C3   C2   C1    180.00   0.0  0
 U7S  CONST_20  BR1  C5   C4   S1    180.00   0.0  0
 U7S  CONST_21  C20  N3   C12  N2    180.00   0.0  0
 U7S  CONST_22  H19  C16  C15  C14     0.00   0.0  0
 U7S  CONST_23  H22  C19  C20  N3      0.00   0.0  0
 U7S  CONST_24  H20  C17  C16  C15   180.00   0.0  0
 U7S  CONST_25  H21  C18  C17  C16   180.00   0.0  0
 U7S  CONST_26  H12  N3   C12  C13   180.00   0.0  0
 U7S  CONST_27  C13  C12  N2   C11     0.00   0.0  0
 U7S  CONST_28  N3   C12  N2   C11   180.00   0.0  0
 U7S  CONST_29  H15  N2   C12  C13   180.00   0.0  0
 U7S  Var_01    F1   C6   C4   C5    167.55  30.0  2
 U7S  Var_02    S1   C3   C8   N1     77.68  30.0  2
 U7S  Var_03    H16  C1   C2   C5    -62.96  30.0  2
 U7S  Var_04    C3   C8   N1   C9     61.54  30.0  3
 U7S  Var_05    C12  N2   C11  C10   173.35  30.0  3
 U7S  Var_06    H3   C7   C6   C4    179.75   0.0  2
 U7S  Var_07    N1   C9   C10  C11  -174.03  30.0  3
 U7S  Var_08    C10  C9   N1   C8    177.74  30.0  2
 U7S  Var_09    N2   C11  C10  C9    -63.93  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
 U7S  plan-1  C4   0.020
 U7S  plan-1  C5   0.020
 U7S  plan-1  C6   0.020
 U7S  plan-1  C8   0.020
 U7S  plan-1  C3   0.020
 U7S  plan-1  C1   0.020
 U7S  plan-1  C2   0.020
 U7S  plan-1  S1   0.020
 U7S  plan-1  BR1  0.020
 U7S  plan-2  C14  0.020
 U7S  plan-2  C11  0.020
 U7S  plan-2  C12  0.020
 U7S  plan-2  C13  0.020
 U7S  plan-2  N2   0.020
 U7S  plan-2  N3   0.020
 U7S  plan-2  C15  0.020
 U7S  plan-2  C16  0.020
 U7S  plan-2  C17  0.020
 U7S  plan-2  C18  0.020
 U7S  plan-2  C19  0.020
 U7S  plan-2  C20  0.020
 U7S  plan-2  H11  0.020
 U7S  plan-2  H15  0.020
 U7S  plan-2  H19  0.020
 U7S  plan-2  H20  0.020
 U7S  plan-2  H21  0.020
 U7S  plan-2  H22  0.020
 U7S  plan-2  H12  0.020
 U7S  plan-2  O1   0.020
 U7S  plan-3  C4   0.020
 U7S  plan-3  C6   0.020
 U7S  plan-3  C7   0.020
 U7S  plan-3  F1   0.020
 U7S  plan-3  H3   0.020
 U7S  plan-3  H4   0.020

