# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 10:08:04 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-(4-bromothiophen-3-yl)-N-(6-chloro-3,3-dimethyl-3,4-dihydroisoquinolin-1-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)Cc2cc(Cl)ccc2C(=N1)N[C@@H](Cc3cscc3Br)C(O)=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
 1B9  1B9  3-(4-bromothiophen-3-yl)-N-(6-chloro-3,3-dimethyl-3,4-dihydroisoquinolin-1-yl)-L-alanine  ligand  43  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1B9
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
 1B9  CL1  CL  CL    0  -0.122  -6.4011  -1.8074   0.0800
 1B9  C6   C   CR6   0  -0.032  -4.8265  -1.0898   0.0064
 1B9  C5   C   CR16  0  -0.217  -3.7575  -1.8452  -0.4482
 1B9  C4   C   CR16  0  -0.304  -2.5021  -1.2598  -0.4986
 1B9  C1   C   CR16  0  -0.286  -4.6634   0.2247   0.4181
 1B9  C2   C   CR66  0   0.118  -3.4055   0.8053   0.3635
 1B9  C3   C   CR66  0   0.005  -2.3219   0.0635  -0.1107
 1B9  C7   C   C     0  -0.494  -3.1419   2.2145   0.7934
 1B9  C8   C   CR6   0   0.029  -1.7541   2.3379   1.4354
 1B9  C11  C   CH3   0  -0.634  -1.4241   3.8130   1.6350
 1B9  C12  C   CH3   0  -0.635  -1.7100   1.6210   2.7882
 1B9  N9   N   N     0  -0.420  -0.7307   1.7759   0.5628
 1B9  C10  C   CR6   0   0.448  -1.0055   0.7356  -0.1197
 1B9  N13  N   NH1   0  -0.662  -0.0273   0.1469  -0.8775
 1B9  C14  C   CH1   0  -0.165   1.2580   0.7743  -0.9470
 1B9  C15  C   C     0   0.545   1.1797   2.1430  -1.6102
 1B9  O17  O   O     0  -0.441   0.3963   2.4272  -2.4788
 1B9  O16  O   OH1   0  -0.589   2.1256   2.9594  -1.1687
 1B9  C18  C   CH2   0  -0.570   2.2322  -0.1133  -1.7394
 1B9  C19  C   CR5   0   0.274   2.4308  -1.4442  -1.0880
 1B9  C23  C   CR5   0  -0.085   3.2689  -1.7021   0.0403
 1B9  BR2  BR  BR    0  -0.032   4.3349  -0.3868   0.8482
 1B9  C20  C   CR15  0  -0.542   1.7945  -2.5860  -1.4715
 1B9  S21  S   S2    0   0.246   2.1967  -3.9306  -0.4933
 1B9  C22  C   CR15  0  -0.454   3.2476  -2.9900   0.4737
 1B9  H1   H   HCR6  0   0.283  -3.8958  -2.8745  -0.7489
 1B9  H2   H   HCR6  0   0.259  -1.6639  -1.8609  -0.8274
 1B9  H3   H   HCR6  0   0.275  -5.5087   0.7918   0.7867
 1B9  H4   H   H     0   0.259  -3.1791   2.8673  -0.0870
 1B9  H5   H   H     0   0.255  -3.9184   2.5645   1.4764
 1B9  H6   H   HCH3  0   0.217  -2.1424   4.2878   2.3053
 1B9  H7   H   HCH3  0   0.227  -0.4291   3.9289   2.0668
 1B9  H8   H   HCH3  0   0.225  -1.4412   4.3485   0.6843
 1B9  H9   H   HCH3  0   0.229  -1.9788   0.5671   2.6987
 1B9  H10  H   HCH3  0   0.231  -0.7052   1.6751   3.2093
 1B9  H11  H   HCH3  0   0.224  -2.3974   2.0848   3.4980
 1B9  H12  H   HNH1  0   0.389  -0.3360  -0.3205  -1.7168
 1B9  H13  H   HCH1  0   0.280   1.6338   0.9131   0.0682
 1B9  H14  H   HOH1  0   0.481   2.0930   3.7989  -1.6516
 1B9  H15  H   HCH2  0   0.281   1.8456  -0.2577  -2.7513
 1B9  H16  H   HCH2  0   0.285   3.1865   0.4062  -1.8441
 1B9  H17  H   HCR5  0   0.303   1.1040  -2.6998  -2.2939
 1B9  H18  H   HCR5  0   0.317   3.7925  -3.4295   1.2946

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
 1B9  CL1  C6   single    1.732  0.020  1.732
 1B9  C5   C6   aromatic  1.386  0.020  1.386
 1B9  C5   C4   aromatic  1.386  0.020  1.386
 1B9  C6   C1   aromatic  1.387  0.020  1.387
 1B9  C4   C3   aromatic  1.391  0.020  1.391
 1B9  O17  C15  double    1.204  0.020  1.204
 1B9  C1   C2   aromatic  1.386  0.020  1.386
 1B9  C3   C2   aromatic  1.396  0.020  1.396
 1B9  C3   C10  single    1.478  0.020  1.478
 1B9  C2   C7   single    1.497  0.020  1.497
 1B9  C15  O16  single    1.325  0.020  1.325
 1B9  C15  C14  single    1.523  0.020  1.523
 1B9  N13  C10  single    1.370  0.020  1.370
 1B9  N13  C14  single    1.432  0.020  1.432
 1B9  C10  N9   double    1.274  0.020  1.274
 1B9  C14  C18  single    1.538  0.020  1.538
 1B9  C7   C8   single    1.534  0.020  1.534
 1B9  C18  C19  single    1.495  0.020  1.495
 1B9  C20  C19  aromatic  1.362  0.020  1.362
 1B9  C20  S21  aromatic  1.711  0.020  1.711
 1B9  N9   C8   single    1.458  0.020  1.458
 1B9  C19  C23  aromatic  1.429  0.020  1.429
 1B9  C8   C12  single    1.532  0.020  1.532
 1B9  C8   C11  single    1.525  0.020  1.525
 1B9  S21  C22  aromatic  1.710  0.020  1.710
 1B9  C23  C22  aromatic  1.359  0.020  1.359
 1B9  C23  BR2  single    1.876  0.020  1.876
 1B9  C5   H1   single    0.930  0.020  1.080
 1B9  C4   H2   single    0.930  0.020  1.080
 1B9  C1   H3   single    0.930  0.020  1.080
 1B9  C7   H4   single    0.970  0.020  1.090
 1B9  C7   H5   single    0.970  0.020  1.090
 1B9  C11  H6   single    0.970  0.020  1.090
 1B9  C11  H7   single    0.970  0.020  1.090
 1B9  C11  H8   single    0.970  0.020  1.090
 1B9  C12  H9   single    0.970  0.020  1.090
 1B9  C12  H10  single    0.970  0.020  1.090
 1B9  C12  H11  single    0.970  0.020  1.090
 1B9  N13  H12  single    0.890  0.020  1.040
 1B9  C14  H13  single    0.970  0.020  1.090
 1B9  O16  H14  single    0.850  0.020  0.980
 1B9  C18  H15  single    0.970  0.020  1.090
 1B9  C18  H16  single    0.970  0.020  1.090
 1B9  C20  H17  single    0.930  0.020  1.080
 1B9  C22  H18  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
 1B9  C1   C6   C5   121.55  3.000
 1B9  C1   C6   CL1  119.14  3.000
 1B9  C5   C6   CL1  119.31  3.000
 1B9  H1   C5   C4   120.52  3.000
 1B9  H1   C5   C6   120.77  3.000
 1B9  C4   C5   C6   118.71  3.000
 1B9  H2   C4   C3   120.85  3.000
 1B9  H2   C4   C5   118.53  3.000
 1B9  C3   C4   C5   120.61  3.000
 1B9  H3   C1   C2   120.16  3.000
 1B9  H3   C1   C6   120.37  3.000
 1B9  C2   C1   C6   119.46  3.000
 1B9  C7   C2   C3   117.46  3.000
 1B9  C7   C2   C1   122.87  3.000
 1B9  C3   C2   C1   119.67  3.000
 1B9  C10  C3   C2   116.85  3.000
 1B9  C10  C3   C4   123.12  3.000
 1B9  C2   C3   C4   119.98  3.000
 1B9  H5   C7   H4   106.70  3.000
 1B9  H5   C7   C8   110.84  3.000
 1B9  H4   C7   C8   108.59  3.000
 1B9  H5   C7   C2   110.87  3.000
 1B9  H4   C7   C2   108.90  3.000
 1B9  C8   C7   C2   110.81  3.000
 1B9  N9   C8   C12  109.15  3.000
 1B9  C12  C8   C11  109.33  3.000
 1B9  N9   C8   C11  107.43  3.000
 1B9  C11  C8   C7   109.17  3.000
 1B9  C12  C8   C7   110.98  3.000
 1B9  N9   C8   C7   110.71  3.000
 1B9  H8   C11  H7   107.88  3.000
 1B9  H8   C11  H6   108.14  3.000
 1B9  H7   C11  H6   108.12  3.000
 1B9  H8   C11  C8   110.94  3.000
 1B9  H7   C11  C8   110.61  3.000
 1B9  H6   C11  C8   111.03  3.000
 1B9  H11  C12  H10  107.94  3.000
 1B9  H11  C12  H9   107.97  3.000
 1B9  H10  C12  H9   107.84  3.000
 1B9  H11  C12  C8   110.94  3.000
 1B9  H10  C12  C8   110.14  3.000
 1B9  H9   C12  C8   111.87  3.000
 1B9  C10  N9   C8   118.95  3.000
 1B9  N13  C10  N9   119.54  3.000
 1B9  N9   C10  C3   124.06  3.000
 1B9  N13  C10  C3   116.34  3.000
 1B9  H12  N13  C14  115.92  3.000
 1B9  H12  N13  C10  116.14  3.000
 1B9  C14  N13  C10  118.64  3.000
 1B9  H13  C14  C18  109.55  3.000
 1B9  H13  C14  C15  107.97  3.000
 1B9  C18  C14  C15  109.08  3.000
 1B9  H13  C14  N13  108.64  3.000
 1B9  C18  C14  N13  109.92  3.000
 1B9  C15  C14  N13  111.64  3.000
 1B9  O16  C15  O17  124.02  3.000
 1B9  O16  C15  C14  111.83  3.000
 1B9  O17  C15  C14  124.05  3.000
 1B9  H14  O16  C15  110.10  3.000
 1B9  H16  C18  H15  106.46  3.000
 1B9  H16  C18  C19  110.45  3.000
 1B9  H15  C18  C19  109.44  3.000
 1B9  H16  C18  C14  109.18  3.000
 1B9  H15  C18  C14  109.22  3.000
 1B9  C19  C18  C14  111.93  3.000
 1B9  C20  C19  C23  110.18  3.000
 1B9  C23  C19  C18  125.63  3.000
 1B9  C20  C19  C18  124.16  3.000
 1B9  C22  C23  BR2  122.42  3.000
 1B9  BR2  C23  C19  123.15  3.000
 1B9  C22  C23  C19  114.43  3.000
 1B9  H17  C20  S21  120.20  3.000
 1B9  H17  C20  C19  126.97  3.000
 1B9  S21  C20  C19  112.83  3.000
 1B9  C22  S21  C20   92.03  3.000
 1B9  H18  C22  S21  121.11  3.000
 1B9  H18  C22  C23  128.37  3.000
 1B9  S21  C22  C23  110.52  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
 1B9  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 1B9  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 1B9  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 1B9  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 1B9  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 1B9  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 1B9  CONST_07  C22  S21  C20  C19     0.00   0.0  0
 1B9  CONST_08  S21  C22  C23  C19     0.00   0.0  0
 1B9  CONST_09  S21  C20  C19  C23     0.00   0.0  0
 1B9  CONST_10  C20  S21  C22  C23     0.00   0.0  0
 1B9  CONST_11  C22  C23  C19  C20     0.00   0.0  0
 1B9  CONST_12  C8   N9   C10  C3      0.00   0.0  0
 1B9  CONST_13  C4   C5   C6   CL1   180.00   0.0  0
 1B9  CONST_14  C2   C1   C6   CL1   180.00   0.0  0
 1B9  CONST_15  S21  C20  C19  C18   180.00   0.0  0
 1B9  CONST_16  C22  C23  C19  C18   180.00   0.0  0
 1B9  CONST_17  C20  C19  C23  BR2   180.00   0.0  0
 1B9  CONST_18  S21  C22  C23  BR2   180.00   0.0  0
 1B9  CONST_19  N13  C10  N9   C8    180.00   0.0  0
 1B9  CONST_20  H2   C4   C5   C6    180.00   0.0  0
 1B9  CONST_21  H3   C1   C6   C5    180.00   0.0  0
 1B9  CONST_22  H1   C5   C6   C1    180.00   0.0  0
 1B9  CONST_23  H18  C22  C23  C19   180.00   0.0  0
 1B9  CONST_24  H17  C20  C19  C23   180.00   0.0  0
 1B9  CONST_25  C14  N13  C10  C3    180.00   0.0  0
 1B9  CONST_26  C14  N13  C10  N9      0.00   0.0  0
 1B9  CONST_28  H14  O16  C15  C14   180.00   0.0  0
 1B9  Var_01    N9   C10  C3   C4   -159.10  30.0  1
 1B9  Var_02    C8   C7   C2   C1    145.26  30.0  1
 1B9  Var_03    N9   C8   C7   C2     52.11  30.0  1
 1B9  Var_04    C20  C19  C18  C14    99.24  30.0  2
 1B9  Var_05    H9   C12  C8   C7     57.30  30.0  3
 1B9  Var_06    H6   C11  C8   C7     61.46  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
 1B9  chir_01  C14  C15  N13  C18  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
 1B9  plan-1  C18  0.020
 1B9  plan-1  C19  0.020
 1B9  plan-1  C23  0.020
 1B9  plan-1  BR2  0.020
 1B9  plan-1  C20  0.020
 1B9  plan-1  S21  0.020
 1B9  plan-1  C22  0.020
 1B9  plan-1  H17  0.020
 1B9  plan-1  H18  0.020
 1B9  plan-2  CL1  0.020
 1B9  plan-2  C6   0.020
 1B9  plan-2  C5   0.020
 1B9  plan-2  C4   0.020
 1B9  plan-2  C1   0.020
 1B9  plan-2  C2   0.020
 1B9  plan-2  C3   0.020
 1B9  plan-2  C7   0.020
 1B9  plan-2  C10  0.020
 1B9  plan-2  H1   0.020
 1B9  plan-2  H2   0.020
 1B9  plan-2  H3   0.020
 1B9  plan-3  C3   0.020
 1B9  plan-3  C8   0.020
 1B9  plan-3  N9   0.020
 1B9  plan-3  C10  0.020
 1B9  plan-3  N13  0.020
 1B9  plan-3  C14  0.020
 1B9  plan-3  H12  0.020
 1B9  plan-4  C14  0.020
 1B9  plan-4  C15  0.020
 1B9  plan-4  O17  0.020
 1B9  plan-4  O16  0.020
 1B9  plan-4  H14  0.020

