# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:31:25 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: 6-[(1R)-2-amino-1-phenylethyl]-3-(pyridin-3-yl)-5,6-dihydrothieno[2,3-c]pyridin-7(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H](N1CCc2c(scc2c3cccnc3)C1=O)c4ccccc4
#
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
 8Y1  8Y1  6-[(1R)-2-amino-1-phenylethyl]-3-(pyridin-3-yl)-5,6-dihydrothieno[2,3-c]pyridin-7(4H)-one  ligand  44  25  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8Y1
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
 8Y1  N1   N  NH2   0  -0.787  52.8990  -13.7837  45.7892
 8Y1  C6   C  CH2   0  -0.303  51.0904  -17.0490  45.6857
 8Y1  C7   C  CH2   0  -0.532  50.1255  -16.7243  46.8145
 8Y1  C8   C  CR5   0   0.184  48.8693  -16.1719  46.2242
 8Y1  C10  C  CR15  0  -0.551  46.6646  -15.5979  45.8509
 8Y1  C13  C  C     0   0.578  50.2050  -15.2369  44.3124
 8Y1  C15  C  CR6   0  -0.025  47.1078  -16.8559  47.9675
 8Y1  C17  C  CR16  0  -0.315  45.5921  -18.2002  49.2484
 8Y1  C20  C  CR16  0  -0.104  47.8440  -16.7027  49.1430
 8Y1  C21  C  CR6   0   0.144  53.1881  -16.9112  43.6204
 8Y1  C22  C  CR16  0  -0.292  52.6645  -17.3490  42.4040
 8Y1  C24  C  CR16  0  -0.267  54.1551  -19.2363  42.3964
 8Y1  C26  C  CR16  0  -0.320  54.2016  -17.6560  44.2132
 8Y1  C2   C  CH2   0  -0.268  53.4855  -15.0260  45.3275
 8Y1  C3   C  CH1   0  -0.210  52.6057  -15.6629  44.2520
 8Y1  N5   N  NT    0  -0.461  51.2685  -15.9329  44.7634
 8Y1  C9   C  CR5   0   0.159  47.5306  -16.2166  46.7154
 8Y1  S11  S  S2    0   0.282  47.4394  -14.9489  44.4773
 8Y1  C12  C  CR5   0  -0.392  48.9562  -15.5263  45.0259
 8Y1  C16  C  CR16  0  -0.193  45.9508  -17.6287  48.0397
 8Y1  C18  C  CR16  0  -0.069  46.4077  -17.9893  50.3502
 8Y1  N19  N  N     0  -0.397  47.5117  -17.2530  50.3018
 8Y1  C23  C  CR16  0  -0.243  53.1408  -18.4993  41.7951
 8Y1  C25  C  CR16  0  -0.240  54.6833  -18.8106  43.6056
 8Y1  H1   H  HNH2  0   0.351  53.4432  -13.4275  46.5638
 8Y1  H2   H  HNH2  0   0.341  52.9669  -13.0844  45.0603
 8Y1  H4   H  HCH2  0   0.255  50.7278  -17.9267  45.1412
 8Y1  H5   H  HCH2  0   0.270  52.0611  -17.3166  46.0986
 8Y1  H6   H  HCH2  0   0.269  49.9320  -17.6339  47.3851
 8Y1  H7   H  HCH2  0   0.268  50.5736  -16.0003  47.5022
 8Y1  H8   H  HCR5  0   0.302  45.5975  -15.4837  45.9726
 8Y1  H9   H  HCR6  0   0.275  44.7022  -18.8082  49.3355
 8Y1  H10  H  HCR6  0   0.262  48.7387  -16.0885  49.1462
 8Y1  H11  H  HCR6  0   0.250  51.8781  -16.7753  41.9267
 8Y1  H12  H  HCR6  0   0.256  54.5304  -20.1343  41.9229
 8Y1  H13  H  HCR6  0   0.257  54.6312  -17.3486  45.1585
 8Y1  H14  H  HCH2  0   0.221  53.5834  -15.6938  46.1871
 8Y1  H15  H  HCH2  0   0.215  54.4945  -14.9161  44.9064
 8Y1  H16  H  HCH1  0   0.277  52.4860  -14.9243  43.4574
 8Y1  H17  H  HCR6  0   0.270  45.3464  -17.7924  47.1561
 8Y1  H18  H  HCR6  0   0.268  46.1599  -18.4320  51.3082
 8Y1  H19  H  HCR6  0   0.256  52.7238  -18.8195  40.8489
 8Y1  H20  H  HCR6  0   0.256  55.4729  -19.3767  44.0828
 8Y1  O14  O  O     0  -0.499  50.2357  -14.4096  43.4076

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
 8Y1  C23  C24  aromatic  1.391  0.020  1.391
 8Y1  C23  C22  aromatic  1.386  0.020  1.386
 8Y1  C24  C25  aromatic  1.387  0.020  1.387
 8Y1  C22  C21  aromatic  1.395  0.020  1.395
 8Y1  O14  C13  double    1.226  0.020  1.226
 8Y1  C25  C26  aromatic  1.391  0.020  1.391
 8Y1  C21  C26  aromatic  1.390  0.020  1.390
 8Y1  C21  C3   single    1.515  0.020  1.515
 8Y1  S11  C12  aromatic  1.713  0.020  1.713
 8Y1  S11  C10  aromatic  1.705  0.020  1.705
 8Y1  C3   N5   single    1.457  0.020  1.457
 8Y1  C3   C2   single    1.529  0.020  1.529
 8Y1  C13  N5   single    1.349  0.020  1.349
 8Y1  C13  C12  single    1.467  0.020  1.467
 8Y1  N5   C6   single    1.459  0.020  1.459
 8Y1  C12  C8   aromatic  1.364  0.020  1.364
 8Y1  C2   N1   single    1.449  0.020  1.449
 8Y1  C10  C9   aromatic  1.371  0.020  1.371
 8Y1  C6   C7   single    1.520  0.020  1.520
 8Y1  C8   C9   aromatic  1.427  0.020  1.427
 8Y1  C8   C7   single    1.494  0.020  1.494
 8Y1  C9   C15  single    1.468  0.020  1.468
 8Y1  C16  C15  aromatic  1.393  0.020  1.393
 8Y1  C16  C17  aromatic  1.384  0.020  1.384
 8Y1  C15  C20  aromatic  1.396  0.020  1.396
 8Y1  C17  C18  aromatic  1.387  0.020  1.387
 8Y1  C20  N19  aromatic  1.325  0.020  1.325
 8Y1  C18  N19  aromatic  1.328  0.020  1.328
 8Y1  N1   H1   single    0.890  0.020  1.040
 8Y1  N1   H2   single    0.890  0.020  1.040
 8Y1  C6   H4   single    0.970  0.020  1.090
 8Y1  C6   H5   single    0.970  0.020  1.090
 8Y1  C7   H6   single    0.970  0.020  1.090
 8Y1  C7   H7   single    0.970  0.020  1.090
 8Y1  C10  H8   single    0.930  0.020  1.080
 8Y1  C17  H9   single    0.930  0.020  1.080
 8Y1  C20  H10  single    0.930  0.020  1.080
 8Y1  C22  H11  single    0.930  0.020  1.080
 8Y1  C24  H12  single    0.930  0.020  1.080
 8Y1  C26  H13  single    0.930  0.020  1.080
 8Y1  C2   H14  single    0.970  0.020  1.090
 8Y1  C2   H15  single    0.970  0.020  1.090
 8Y1  C3   H16  single    0.970  0.020  1.090
 8Y1  C16  H17  single    0.930  0.020  1.080
 8Y1  C18  H18  single    0.930  0.020  1.080
 8Y1  C23  H19  single    0.930  0.020  1.080
 8Y1  C25  H20  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
 8Y1  H2   N1   H1   105.78  3.000
 8Y1  H2   N1   C2   109.60  3.000
 8Y1  H1   N1   C2   109.16  3.000
 8Y1  H5   C6   H4   106.67  3.000
 8Y1  H5   C6   N5   108.61  3.000
 8Y1  H4   C6   N5   109.84  3.000
 8Y1  H5   C6   C7   109.69  3.000
 8Y1  H4   C6   C7   109.30  3.000
 8Y1  N5   C6   C7   112.56  3.000
 8Y1  H7   C7   H6   107.19  3.000
 8Y1  H7   C7   C8   110.36  3.000
 8Y1  H6   C7   C8   111.45  3.000
 8Y1  H7   C7   C6   110.37  3.000
 8Y1  H6   C7   C6   108.83  3.000
 8Y1  C8   C7   C6   108.62  3.000
 8Y1  C12  C8   C9   112.15  3.000
 8Y1  C9   C8   C7   129.90  3.000
 8Y1  C12  C8   C7   117.95  3.000
 8Y1  H8   C10  S11  119.96  3.000
 8Y1  H8   C10  C9   126.92  3.000
 8Y1  S11  C10  C9   113.11  3.000
 8Y1  O14  C13  C12  120.88  3.000
 8Y1  C12  C13  N5   114.00  3.000
 8Y1  O14  C13  N5   125.11  3.000
 8Y1  C16  C15  C9   121.67  3.000
 8Y1  C16  C15  C20  117.09  3.000
 8Y1  C9   C15  C20  121.24  3.000
 8Y1  H9   C17  C18  120.36  3.000
 8Y1  H9   C17  C16  121.05  3.000
 8Y1  C18  C17  C16  118.58  3.000
 8Y1  H10  C20  N19  116.06  3.000
 8Y1  H10  C20  C15  119.97  3.000
 8Y1  N19  C20  C15  123.97  3.000
 8Y1  C3   C21  C26  122.93  3.000
 8Y1  C3   C21  C22  118.54  3.000
 8Y1  C26  C21  C22  118.51  3.000
 8Y1  H11  C22  C23  119.67  3.000
 8Y1  H11  C22  C21  119.35  3.000
 8Y1  C23  C22  C21  120.98  3.000
 8Y1  H12  C24  C25  120.28  3.000
 8Y1  H12  C24  C23  120.23  3.000
 8Y1  C25  C24  C23  119.49  3.000
 8Y1  H13  C26  C25  118.66  3.000
 8Y1  H13  C26  C21  120.61  3.000
 8Y1  C25  C26  C21  120.72  3.000
 8Y1  H15  C2   H14  106.27  3.000
 8Y1  H15  C2   C3   107.49  3.000
 8Y1  H14  C2   C3   110.51  3.000
 8Y1  H15  C2   N1   114.08  3.000
 8Y1  H14  C2   N1   108.03  3.000
 8Y1  C3   C2   N1   110.39  3.000
 8Y1  H16  C3   N5   106.28  3.000
 8Y1  H16  C3   C2   107.06  3.000
 8Y1  N5   C3   C2   111.01  3.000
 8Y1  H16  C3   C21  107.23  3.000
 8Y1  C2   C3   C21  114.54  3.000
 8Y1  N5   C3   C21  110.27  3.000
 8Y1  C3   N5   C13  120.71  3.000
 8Y1  C13  N5   C6   120.66  3.000
 8Y1  C3   N5   C6   118.41  3.000
 8Y1  C15  C9   C10  123.52  3.000
 8Y1  C15  C9   C8   125.28  3.000
 8Y1  C10  C9   C8   111.19  3.000
 8Y1  C12  S11  C10   90.92  3.000
 8Y1  S11  C12  C13  122.10  3.000
 8Y1  C13  C12  C8   125.09  3.000
 8Y1  S11  C12  C8   112.61  3.000
 8Y1  H17  C16  C17  120.36  3.000
 8Y1  H17  C16  C15  120.33  3.000
 8Y1  C17  C16  C15  119.31  3.000
 8Y1  H18  C18  N19  116.66  3.000
 8Y1  H18  C18  C17  120.36  3.000
 8Y1  N19  C18  C17  122.98  3.000
 8Y1  C18  N19  C20  118.08  3.000
 8Y1  H19  C23  C24  120.15  3.000
 8Y1  H19  C23  C22  119.81  3.000
 8Y1  C24  C23  C22  120.04  3.000
 8Y1  H20  C25  C26  119.62  3.000
 8Y1  H20  C25  C24  120.12  3.000
 8Y1  C26  C25  C24  120.26  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
 8Y1  CONST_01  C10  S11  C12  C8     0.00   0.0  0
 8Y1  CONST_02  S11  C10  C9   C8     0.00   0.0  0
 8Y1  CONST_05  C12  C8   C9   C10    0.00   0.0  0
 8Y1  CONST_08  S11  C10  C9   C15  180.00   0.0  0
 8Y1  CONST_09  C12  C8   C9   C15  180.00   0.0  0
 8Y1  CONST_10  C18  C17  C16  C15    0.00   0.0  0
 8Y1  CONST_11  C18  N19  C20  C15    0.00   0.0  0
 8Y1  CONST_12  C9   C15  C16  C17  180.00   0.0  0
 8Y1  CONST_13  C20  C15  C16  C17    0.00   0.0  0
 8Y1  CONST_14  C20  N19  C18  C17    0.00   0.0  0
 8Y1  CONST_15  C24  C23  C22  C21    0.00   0.0  0
 8Y1  CONST_16  C24  C25  C26  C21    0.00   0.0  0
 8Y1  CONST_17  C25  C24  C23  C22    0.00   0.0  0
 8Y1  CONST_18  C25  C26  C21  C22    0.00   0.0  0
 8Y1  CONST_19  C23  C24  C25  C26    0.00   0.0  0
 8Y1  CONST_20  C23  C22  C21  C26    0.00   0.0  0
 8Y1  CONST_21  C12  S11  C10  C9     0.00   0.0  0
 8Y1  CONST_22  S11  C12  C8   C9     0.00   0.0  0
 8Y1  CONST_23  N19  C20  C15  C9   180.00   0.0  0
 8Y1  CONST_24  N19  C20  C15  C16    0.00   0.0  0
 8Y1  CONST_25  N19  C18  C17  C16    0.00   0.0  0
 8Y1  CONST_26  C15  C9   C8   C7     0.00   0.0  0
 8Y1  CONST_27  C12  C13  N5   C6     0.00   0.0  0
 8Y1  CONST_28  C23  C22  C21  C3   180.00   0.0  0
 8Y1  CONST_29  C25  C26  C21  C3   180.00   0.0  0
 8Y1  CONST_30  O14  C13  N5   C6   180.00   0.0  0
 8Y1  CONST_31  C12  C13  N5   C3   180.00   0.0  0
 8Y1  CONST_32  H8   C10  C9   C8   180.00   0.0  0
 8Y1  CONST_33  H9   C17  C16  C15  180.00   0.0  0
 8Y1  CONST_34  H17  C16  C15  C20  180.00   0.0  0
 8Y1  CONST_35  H18  C18  N19  C20  180.00   0.0  0
 8Y1  CONST_36  H19  C23  C22  C21  180.00   0.0  0
 8Y1  CONST_37  H20  C25  C26  C21  180.00   0.0  0
 8Y1  CONST_38  H12  C24  C23  C22  180.00   0.0  0
 8Y1  CONST_39  H13  C26  C21  C22  180.00   0.0  0
 8Y1  CONST_40  H11  C22  C23  C24  180.00   0.0  0
 8Y1  CONST_41  H10  C20  C15  C9     0.00   0.0  0
 8Y1  CONST_42  O14  C13  N5   C3     0.00   0.0  0
 8Y1  Var_01    C12  C8   C7   C6   -27.68  30.0  1
 8Y1  Var_02    C13  N5   C6   C7   -45.37  30.0  1
 8Y1  Var_03    N5   C13  C12  C8    15.08  30.0  1
 8Y1  Var_04    N5   C6   C7   C8    50.85  30.0  1
 8Y1  Var_05    H1   N1   C2   C3   174.23  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
 8Y1  chir_01  C3  C21  N5  C2  negativ

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
 8Y1  plan-1  C15  0.020
 8Y1  plan-1  C17  0.020
 8Y1  plan-1  C20  0.020
 8Y1  plan-1  C9   0.020
 8Y1  plan-1  C16  0.020
 8Y1  plan-1  C18  0.020
 8Y1  plan-1  N19  0.020
 8Y1  plan-1  H9   0.020
 8Y1  plan-1  H10  0.020
 8Y1  plan-1  H17  0.020
 8Y1  plan-1  H18  0.020
 8Y1  plan-2  C21  0.020
 8Y1  plan-2  C22  0.020
 8Y1  plan-2  C24  0.020
 8Y1  plan-2  C26  0.020
 8Y1  plan-2  C3   0.020
 8Y1  plan-2  C23  0.020
 8Y1  plan-2  C25  0.020
 8Y1  plan-2  H11  0.020
 8Y1  plan-2  H12  0.020
 8Y1  plan-2  H13  0.020
 8Y1  plan-2  H19  0.020
 8Y1  plan-2  H20  0.020
 8Y1  plan-3  C7   0.020
 8Y1  plan-3  C8   0.020
 8Y1  plan-3  C10  0.020
 8Y1  plan-3  C13  0.020
 8Y1  plan-3  C15  0.020
 8Y1  plan-3  C9   0.020
 8Y1  plan-3  S11  0.020
 8Y1  plan-3  C12  0.020
 8Y1  plan-3  H8   0.020
 8Y1  plan-4  C6   0.020
 8Y1  plan-4  C13  0.020
 8Y1  plan-4  C3   0.020
 8Y1  plan-4  N5   0.020
 8Y1  plan-4  C12  0.020
 8Y1  plan-4  O14  0.020

