# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 16:41:29 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 5-[(3-{[(4R)-6,8-dibromo-3,4-dihydro-2H-1-benzopyran-4-yl]amino}propyl)amino]thieno[3,2-b]pyridin-7(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cc(Br)c2OCC[C@@H](NCCCNC3=CC(=O)c4sccc4N3)c2c1
#
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
 U81  U81  5-[(3-{[(4R)-6,8-dibromo-3,4-dihydro-2H-1-benzopyran-4-yl]amino}propyl)amino]thieno[3,2-b]pyridin-7(4H)-one  ligand  46  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U81
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
 U81  C4   C   CR6   0  -0.245  -16.8437  -21.1073  14.8505
 U81  C14  C   CR16  0  -0.617  -15.8179  -29.1245  11.6197
 U81  C5   C   CR16  0  -0.212  -17.1825  -22.1380  15.7109
 U81  C6   C   CR6   0  -0.129  -17.9755  -23.1687  15.2310
 U81  C11  C   CH2   0  -0.489  -16.7244  -25.1314  10.0173
 U81  C7   C   CR16  0  -0.277  -18.4128  -23.1735  13.9183
 U81  C8   C   CR6   0   0.026  -18.0518  -22.1521  13.0488
 U81  C9   C   CH1   0  -0.176  -18.4823  -22.1831  11.5960
 U81  C12  C   CH2   0  -0.279  -16.4899  -26.5935  10.3579
 U81  C13  C   CR6   0   0.660  -15.3023  -27.9154  12.0527
 U81  N1   N   NH1   0  -0.581  -17.6182  -22.9789  10.7369
 U81  N2   N   NH1   0  -0.684  -15.6455  -26.7187  11.5280
 U81  C3   C   CR6   0   0.451  -17.2715  -21.0911  13.5196
 U81  N3   N   NR16  0  -0.769  -14.4084  -27.8813  13.0809
 U81  C1   C   CH2   0  -0.501  -18.5504  -20.7477  11.0907
 U81  C2   C   CH2   0  -0.197  -17.2576  -20.0203  11.3871
 U81  O1   O   O2    0  -0.459  -16.9300  -20.0335  12.7767
 U81  C15  C   CR6   0   0.469  -15.4645  -30.3791  12.2120
 U81  O2   O   O     0  -0.504  -15.8968  -31.4824  11.8545
 U81  C16  C   CR56  0  -0.423  -14.5160  -30.2394  13.2950
 U81  C17  C   CR56  0   0.397  -14.0127  -29.0290  13.7029
 U81  C18  C   CR15  0  -0.196  -13.0915  -29.1386  14.7825
 U81  C19  C   CR15  0  -0.458  -12.9273  -30.4359  15.1554
 U81  S1   S   S2    0   0.225  -13.8650  -31.5319  14.2252
 U81  BR1  BR  BR    0  -0.044  -18.4677  -24.5769  16.3886
 U81  BR2  BR  BR    0  -0.024  -15.7873  -19.6855  15.4905
 U81  H3   H   HCR6  0   0.297  -16.8372  -22.1290  16.7361
 U81  H4   H   HCH2  0   0.234  -15.7581  -24.6396   9.8584
 U81  H5   H   HCH2  0   0.251  -17.2545  -25.0833   9.0646
 U81  H6   H   HCR6  0   0.289  -19.0478  -23.9706  13.5512
 U81  H7   H   HCH1  0   0.268  -19.4814  -22.6263  11.5469
 U81  H10  H   HCH2  0   0.239  -17.4483  -27.0821  10.5538
 U81  H11  H   HCH2  0   0.245  -16.0424  -27.1030   9.4973
 U81  H12  H   HNH1  0   0.347  -16.6845  -22.5843  10.7208
 U81  H14  H   HNH1  0   0.398  -15.0280  -25.9422  11.7127
 U81  H15  H   HCH2  0   0.259  -19.3865  -20.2292  11.5659
 U81  H16  H   HCH2  0   0.264  -18.7259  -20.7327  10.0141
 U81  H17  H   HCH2  0   0.234  -16.4214  -20.4499  10.8261
 U81  H18  H   HCH2  0   0.260  -17.3250  -18.9691  11.1106
 U81  H19  H   HCR5  0   0.285  -12.5873  -28.3029  15.2465
 U81  H20  H   HCR5  0   0.303  -12.2901  -30.8050  15.9445
 U81  H2   H   HNR6  0   0.423  -14.0553  -26.9963  13.4150
 U81  C10  C   CH2   0  -0.260  -17.5180  -24.3850  11.0807
 U81  H1   H   HCR6  0   0.267  -16.5103  -29.1340  10.7900
 U81  H8   H   HCH2  0   0.225  -18.5291  -24.8006  11.1360
 U81  H9   H   HCH2  0   0.208  -17.0635  -24.5539  12.0668

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
 U81  C11  C12  single    1.519  0.020  1.519
 U81  C11  C10  single    1.522  0.020  1.522
 U81  C12  N2   single    1.448  0.020  1.448
 U81  N1   C10  single    1.451  0.020  1.451
 U81  N1   C9   single    1.455  0.020  1.455
 U81  C1   C2   single    1.513  0.020  1.513
 U81  C1   C9   single    1.523  0.020  1.523
 U81  N2   C13  single    1.351  0.020  1.351
 U81  C2   O1   single    1.428  0.020  1.428
 U81  C14  C13  double    1.384  0.020  1.384
 U81  C14  C15  single    1.432  0.020  1.432
 U81  C9   C8   single    1.516  0.020  1.516
 U81  O2   C15  double    1.238  0.020  1.238
 U81  C15  C16  single    1.446  0.020  1.446
 U81  O1   C3   single    1.337  0.020  1.337
 U81  N3   C17  single    1.364  0.020  1.364
 U81  C8   C3   aromatic  1.399  0.020  1.399
 U81  C8   C7   aromatic  1.389  0.020  1.389
 U81  C16  C17  aromatic  1.373  0.020  1.373
 U81  C16  S1   aromatic  1.720  0.020  1.720
 U81  C3   C4   aromatic  1.398  0.020  1.398
 U81  C17  C18  aromatic  1.423  0.020  1.423
 U81  C7   C6   aromatic  1.384  0.020  1.384
 U81  S1   C19  aromatic  1.716  0.020  1.716
 U81  C18  C19  aromatic  1.360  0.020  1.360
 U81  C4   BR2  single    1.883  0.020  1.883
 U81  C4   C5   aromatic  1.385  0.020  1.385
 U81  C6   C5   aromatic  1.386  0.020  1.386
 U81  C6   BR1  single    1.888  0.020  1.888
 U81  C14  H1   single    0.930  0.020  1.080
 U81  C5   H3   single    0.930  0.020  1.080
 U81  C11  H4   single    0.970  0.020  1.090
 U81  C11  H5   single    0.970  0.020  1.090
 U81  C7   H6   single    0.930  0.020  1.080
 U81  C9   H7   single    0.970  0.020  1.090
 U81  C10  H8   single    0.970  0.020  1.090
 U81  C10  H9   single    0.970  0.020  1.090
 U81  C12  H10  single    0.970  0.020  1.090
 U81  C12  H11  single    0.970  0.020  1.090
 U81  N1   H12  single    0.890  0.020  1.040
 U81  N2   H14  single    0.890  0.020  1.040
 U81  C1   H15  single    0.970  0.020  1.090
 U81  C1   H16  single    0.970  0.020  1.090
 U81  C2   H17  single    0.970  0.020  1.090
 U81  C2   H18  single    0.970  0.020  1.090
 U81  C18  H19  single    0.930  0.020  1.080
 U81  C19  H20  single    0.930  0.020  1.080
 U81  N3   C13  single    1.363  0.020  1.363
 U81  N3   H2   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
 U81  BR2  C4   C3   119.11  3.000
 U81  BR2  C4   C5   119.21  3.000
 U81  C3   C4   C5   121.68  3.000
 U81  H1   C14  C15  117.90  3.000
 U81  H1   C14  C13  119.12  3.000
 U81  C15  C14  C13  122.97  3.000
 U81  H3   C5   C6   121.12  3.000
 U81  H3   C5   C4   120.30  3.000
 U81  C6   C5   C4   118.58  3.000
 U81  BR1  C6   C7   119.78  3.000
 U81  BR1  C6   C5   119.43  3.000
 U81  C7   C6   C5   120.79  3.000
 U81  H5   C11  H4   106.37  3.000
 U81  H5   C11  C12  108.25  3.000
 U81  H4   C11  C12  109.16  3.000
 U81  H5   C11  C10  109.57  3.000
 U81  H4   C11  C10  109.93  3.000
 U81  C12  C11  C10  113.31  3.000
 U81  H6   C7   C8   118.77  3.000
 U81  H6   C7   C6   120.62  3.000
 U81  C8   C7   C6   120.60  3.000
 U81  C3   C8   C9   119.78  3.000
 U81  C3   C8   C7   119.48  3.000
 U81  C9   C8   C7   120.74  3.000
 U81  H7   C9   C1   109.03  3.000
 U81  H7   C9   N1   107.11  3.000
 U81  C1   C9   N1   110.25  3.000
 U81  H7   C9   C8   108.10  3.000
 U81  C1   C9   C8   108.14  3.000
 U81  N1   C9   C8   114.10  3.000
 U81  H11  C12  H10  106.92  3.000
 U81  H11  C12  N2   110.87  3.000
 U81  H10  C12  N2   109.12  3.000
 U81  H11  C12  C11  109.54  3.000
 U81  H10  C12  C11  109.56  3.000
 U81  N2   C12  C11  110.75  3.000
 U81  N3   C13  N2   115.94  3.000
 U81  N3   C13  C14  120.15  3.000
 U81  N2   C13  C14  123.90  3.000
 U81  H12  N1   C10  108.51  3.000
 U81  H12  N1   C9   110.08  3.000
 U81  C10  N1   C9   115.54  3.000
 U81  H14  N2   C13  117.07  3.000
 U81  H14  N2   C12  115.98  3.000
 U81  C13  N2   C12  122.58  3.000
 U81  O1   C3   C8   123.75  3.000
 U81  C8   C3   C4   118.84  3.000
 U81  O1   C3   C4   117.39  3.000
 U81  H2   N3   C17  119.02  3.000
 U81  H2   N3   C13  120.06  3.000
 U81  C17  N3   C13  120.88  3.000
 U81  H16  C1   H15  107.43  3.000
 U81  H16  C1   C2   108.92  3.000
 U81  H15  C1   C2   109.91  3.000
 U81  H16  C1   C9   110.33  3.000
 U81  H15  C1   C9   109.70  3.000
 U81  C2   C1   C9   110.49  3.000
 U81  H18  C2   H17  107.21  3.000
 U81  H18  C2   O1   105.68  3.000
 U81  H17  C2   O1   108.65  3.000
 U81  H18  C2   C1   111.20  3.000
 U81  H17  C2   C1   111.33  3.000
 U81  O1   C2   C1   112.48  3.000
 U81  C2   O1   C3   119.31  3.000
 U81  C16  C15  O2   122.10  3.000
 U81  C16  C15  C14  112.76  3.000
 U81  O2   C15  C14  125.14  3.000
 U81  S1   C16  C17  111.28  3.000
 U81  S1   C16  C15  125.48  3.000
 U81  C17  C16  C15  123.23  3.000
 U81  C18  C17  C16  113.25  3.000
 U81  C18  C17  N3   126.75  3.000
 U81  C16  C17  N3   120.00  3.000
 U81  H19  C18  C19  124.31  3.000
 U81  H19  C18  C17  124.62  3.000
 U81  C19  C18  C17  111.07  3.000
 U81  H20  C19  S1   120.03  3.000
 U81  H20  C19  C18  126.73  3.000
 U81  S1   C19  C18  113.24  3.000
 U81  C19  S1   C16   91.15  3.000
 U81  H9   C10  H8   106.16  3.000
 U81  H9   C10  N1   112.96  3.000
 U81  H8   C10  N1   108.43  3.000
 U81  H9   C10  C11  109.63  3.000
 U81  H8   C10  C11  109.31  3.000
 U81  N1   C10  C11  110.22  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
 U81  CONST_01  C7   C8   C3   C4     0.00   0.0  0
 U81  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 U81  CONST_03  C8   C3   C4   C5     0.00   0.0  0
 U81  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 U81  CONST_05  C3   C8   C7   C6     0.00   0.0  0
 U81  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 U81  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 U81  CONST_08  C18  C19  S1   C16    0.00   0.0  0
 U81  CONST_09  C19  S1   C16  C17    0.00   0.0  0
 U81  CONST_10  S1   C19  C18  C17    0.00   0.0  0
 U81  CONST_11  S1   C16  C17  C18    0.00   0.0  0
 U81  CONST_12  C17  N3   C13  C14    0.00   0.0  0
 U81  CONST_13  BR1  C6   C5   C4   180.00   0.0  0
 U81  CONST_14  BR2  C4   C5   C6   180.00   0.0  0
 U81  CONST_15  BR2  C4   C3   C8   180.00   0.0  0
 U81  CONST_16  BR1  C6   C7   C8   180.00   0.0  0
 U81  CONST_17  BR2  C4   C3   O1     0.00   0.0  0
 U81  CONST_18  C17  N3   C13  N2   180.00   0.0  0
 U81  CONST_19  H6   C7   C6   C5   180.00   0.0  0
 U81  CONST_20  H3   C5   C6   C7   180.00   0.0  0
 U81  CONST_21  H19  C18  C17  N3     0.00   0.0  0
 U81  CONST_22  H20  C19  S1   C16  180.00   0.0  0
 U81  CONST_23  H2   N3   C13  C14  180.00   0.0  0
 U81  CONST_24  C12  N2   C13  C14    0.00   0.0  0
 U81  CONST_25  N3   C13  N2   C12  180.00   0.0  0
 U81  Var_01    O1   C2   C1   C9   -56.67  30.0  1
 U81  Var_02    C1   C2   O1   C3    32.82  30.0  1
 U81  Var_03    C13  N2   C12  C11  178.92  30.0  3
 U81  Var_04    C9   N1   C10  C11  173.30  30.0  2
 U81  Var_05    N2   C12  C11  C10  -65.35  30.0  3
 U81  Var_06    N1   C10  C11  C12  175.82  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
 U81  chir_01  C9  N1  C1  C8  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
 U81  plan-1  C14  0.020
 U81  plan-1  C12  0.020
 U81  plan-1  C13  0.020
 U81  plan-1  N2   0.020
 U81  plan-1  N3   0.020
 U81  plan-1  C15  0.020
 U81  plan-1  O2   0.020
 U81  plan-1  C16  0.020
 U81  plan-1  C17  0.020
 U81  plan-1  C18  0.020
 U81  plan-1  C19  0.020
 U81  plan-1  S1   0.020
 U81  plan-1  H14  0.020
 U81  plan-1  H19  0.020
 U81  plan-1  H20  0.020
 U81  plan-1  H2   0.020
 U81  plan-1  H1   0.020
 U81  plan-2  C4   0.020
 U81  plan-2  C5   0.020
 U81  plan-2  C6   0.020
 U81  plan-2  C7   0.020
 U81  plan-2  C8   0.020
 U81  plan-2  C9   0.020
 U81  plan-2  C3   0.020
 U81  plan-2  O1   0.020
 U81  plan-2  BR1  0.020
 U81  plan-2  BR2  0.020
 U81  plan-2  H3   0.020
 U81  plan-2  H6   0.020

