# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:46:49 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: (5R)-4-(5-bromothiophene-2-carbonyl)-5-(3,5-dimethylphenyl)-7-methyl-1,3,4,5-tetrahydro-2H-1,4-benzodiazepin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2NC(=O)CN([C@H](c3cc(C)cc(C)c3)c2c1)C(=O)c4sc(Br)cc4
#
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
 T9A  T9A  (5R)-4-(5-bromothiophene-2-carbonyl)-5-(3,5-dimethylphenyl)-7-methyl-1,3,4,5-tetrahydro-2H-1,4-benzodiazepin-2-one  ligand  50  29  .  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_T9A
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
 T9A  C4   C   CR16  0  -0.362  23.3715  41.4851   2.3099
 T9A  C5   C   CR6   0   0.131  24.1714  41.8828   3.3715
 T9A  C6   C   CH3   0  -0.725  25.6121  41.4683   3.4527
 T9A  N1   N   NH1   0  -0.695  22.1947  43.8568  -0.0491
 T9A  C7   C   CR16  0  -0.366  23.6157  42.6972   4.3594
 T9A  C8   C   CR6   0   0.137  22.2889  43.0984   4.3035
 T9A  C9   C   CH3   0  -0.725  21.6897  43.9537   5.3818
 T9A  C10  C   CR16  0  -0.368  21.5060  42.6792   3.2270
 T9A  C11  C   CR6   0   0.198  21.9321  41.4530  -0.2549
 T9A  C12  C   CR16  0  -0.394  22.1701  40.2892  -0.9781
 T9A  C13  C   CR6   0   0.114  22.9309  40.2844  -2.1411
 T9A  C14  C   CH3   0  -0.724  23.2018  39.0135  -2.8913
 T9A  C15  C   CR16  0  -0.305  23.4551  41.4992  -2.5803
 T9A  O1   O   O     0  -0.475  17.6545  41.8619   0.7756
 T9A  C19  C   CR5   0  -0.321  18.6717  40.2301   2.0752
 T9A  S    S   S2    0   0.327  17.3038  39.2089   1.8267
 T9A  C22  C   CR5   0  -0.344  17.7911  38.1898   3.1108
 T9A  BR   BR  BR    0   0.037  16.7949  36.6840   3.5384
 T9A  C21  C   CR15  0  -0.141  18.9297  38.6169   3.7268
 T9A  C20  C   CR15  0  -0.189  19.4309  39.7967   3.1271
 T9A  N    N   NT    0  -0.467  19.8976  42.0447   0.9692
 T9A  C1   C   CH2   0  -0.429  19.8327  43.3007   0.2351
 T9A  C2   C   CH1   0  -0.276  21.1932  41.3823   1.0630
 T9A  C17  C   CR6   0   0.285  22.4345  42.6596  -0.7364
 T9A  C16  C   CR16  0  -0.283  23.2031  42.6744  -1.8955
 T9A  C    C   C     0   0.468  21.0143  44.2261   0.4966
 T9A  O    O   O     0  -0.450  20.8784  45.2756   1.0974
 T9A  C3   C   CR6   0   0.150  22.0394  41.8864   2.2241
 T9A  H1   H   HCR6  0   0.242  23.7977  40.8589   1.5341
 T9A  H2   H   HCH3  0   0.247  26.2748  42.3203   3.2900
 T9A  H3   H   HCH3  0   0.245  25.8532  41.0601   4.4348
 T9A  H4   H   HCH3  0   0.243  25.8553  40.7134   2.7061
 T9A  H5   H   HNH1  0   0.408  22.9530  44.5218   0.0214
 T9A  H6   H   HCR6  0   0.239  24.2344  43.0255   5.1884
 T9A  H7   H   HCH3  0   0.248  21.0844  43.3549   6.0653
 T9A  H8   H   HCH3  0   0.244  22.4575  44.4496   5.9744
 T9A  H9   H   HCH3  0   0.244  21.0375  44.7212   4.9643
 T9A  H10  H   HCR6  0   0.249  20.4695  42.9918   3.1841
 T9A  H11  H   HCR6  0   0.255  21.7734  39.3524  -0.6023
 T9A  H12  H   HCH3  0   0.249  24.2621  38.7571  -2.8600
 T9A  H13  H   HCH3  0   0.246  22.6457  38.1756  -2.4732
 T9A  H14  H   HCH3  0   0.248  22.9262  39.1076  -3.9423
 T9A  H15  H   HCR6  0   0.257  24.0597  41.5308  -3.4789
 T9A  H16  H   HCR5  0   0.296  19.3909  38.1206   4.5678
 T9A  H17  H   HCR5  0   0.294  20.3086  40.3086   3.4954
 T9A  H18  H   HCH2  0   0.299  18.9409  43.8390   0.5417
 T9A  H19  H   HCH2  0   0.284  19.7529  43.1183  -0.8431
 T9A  H20  H   HCH1  0   0.315  21.0018  40.3232   1.2408
 T9A  H21  H   HCR6  0   0.271  23.5986  43.6132  -2.2630
 T9A  C18  C   C     0   0.566  18.7109  41.4359   1.2223

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
 T9A  C14  C13  single    1.501  0.020  1.501
 T9A  C15  C13  aromatic  1.394  0.020  1.394
 T9A  C15  C16  aromatic  1.383  0.020  1.383
 T9A  C13  C12  aromatic  1.390  0.020  1.390
 T9A  C16  C17  aromatic  1.391  0.020  1.391
 T9A  C12  C11  aromatic  1.391  0.020  1.391
 T9A  C17  C11  aromatic  1.393  0.020  1.393
 T9A  C17  N1   single    1.401  0.020  1.401
 T9A  C11  C2   single    1.513  0.020  1.513
 T9A  N1   C    single    1.352  0.020  1.352
 T9A  C1   C    single    1.524  0.020  1.524
 T9A  C1   N    single    1.456  0.020  1.456
 T9A  C    O    double    1.217  0.020  1.217
 T9A  O1   C18  double    1.224  0.020  1.224
 T9A  N    C2   single    1.458  0.020  1.458
 T9A  N    C18  single    1.358  0.020  1.358
 T9A  C2   C3   single    1.523  0.020  1.523
 T9A  C18  C19  single    1.477  0.020  1.477
 T9A  S    C19  aromatic  1.725  0.020  1.725
 T9A  S    C22  aromatic  1.710  0.020  1.710
 T9A  C19  C20  aromatic  1.368  0.020  1.368
 T9A  C3   C4   aromatic  1.394  0.020  1.394
 T9A  C3   C10  aromatic  1.385  0.020  1.385
 T9A  C4   C5   aromatic  1.387  0.020  1.387
 T9A  C22  BR   single    1.855  0.020  1.855
 T9A  C22  C21  aromatic  1.363  0.020  1.363
 T9A  C20  C21  aromatic  1.415  0.020  1.415
 T9A  C10  C8   aromatic  1.396  0.020  1.396
 T9A  C5   C6   single    1.501  0.020  1.501
 T9A  C5   C7   aromatic  1.396  0.020  1.396
 T9A  C8   C7   aromatic  1.387  0.020  1.387
 T9A  C8   C9   single    1.501  0.020  1.501
 T9A  C4   H1   single    0.930  0.020  1.080
 T9A  C6   H2   single    0.970  0.020  1.090
 T9A  C6   H3   single    0.970  0.020  1.090
 T9A  C6   H4   single    0.970  0.020  1.090
 T9A  N1   H5   single    0.860  0.020  1.020
 T9A  C7   H6   single    0.930  0.020  1.080
 T9A  C9   H7   single    0.970  0.020  1.090
 T9A  C9   H8   single    0.970  0.020  1.090
 T9A  C9   H9   single    0.970  0.020  1.090
 T9A  C10  H10  single    0.930  0.020  1.080
 T9A  C12  H11  single    0.930  0.020  1.080
 T9A  C14  H12  single    0.970  0.020  1.090
 T9A  C14  H13  single    0.970  0.020  1.090
 T9A  C14  H14  single    0.970  0.020  1.090
 T9A  C15  H15  single    0.930  0.020  1.080
 T9A  C21  H16  single    0.930  0.020  1.080
 T9A  C20  H17  single    0.930  0.020  1.080
 T9A  C1   H18  single    0.970  0.020  1.090
 T9A  C1   H19  single    0.970  0.020  1.090
 T9A  C2   H20  single    0.970  0.020  1.090
 T9A  C16  H21  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
 T9A  H1   C4   C3   119.86  3.000
 T9A  H1   C4   C5   119.10  3.000
 T9A  C3   C4   C5   121.03  3.000
 T9A  C7   C5   C6   120.33  3.000
 T9A  C7   C5   C4   118.64  3.000
 T9A  C6   C5   C4   121.03  3.000
 T9A  H4   C6   H3   107.97  3.000
 T9A  H4   C6   H2   107.65  3.000
 T9A  H3   C6   H2   106.99  3.000
 T9A  H4   C6   C5   111.63  3.000
 T9A  H3   C6   C5   111.36  3.000
 T9A  H2   C6   C5   111.04  3.000
 T9A  H5   N1   C    116.55  3.000
 T9A  H5   N1   C17  117.90  3.000
 T9A  C    N1   C17  125.51  3.000
 T9A  H6   C7   C8   119.25  3.000
 T9A  H6   C7   C5   119.35  3.000
 T9A  C8   C7   C5   121.40  3.000
 T9A  C10  C8   C9   120.09  3.000
 T9A  C9   C8   C7   121.17  3.000
 T9A  C10  C8   C7   118.74  3.000
 T9A  H9   C9   H8   108.03  3.000
 T9A  H9   C9   H7   107.11  3.000
 T9A  H8   C9   H7   107.45  3.000
 T9A  H9   C9   C8   111.40  3.000
 T9A  H8   C9   C8   111.64  3.000
 T9A  H7   C9   C8   111.01  3.000
 T9A  H10  C10  C3   120.31  3.000
 T9A  H10  C10  C8   118.73  3.000
 T9A  C3   C10  C8   120.96  3.000
 T9A  C17  C11  C2   121.19  3.000
 T9A  C2   C11  C12  119.84  3.000
 T9A  C17  C11  C12  118.91  3.000
 T9A  H11  C12  C13  119.16  3.000
 T9A  H11  C12  C11  118.69  3.000
 T9A  C13  C12  C11  122.12  3.000
 T9A  C15  C13  C14  120.84  3.000
 T9A  C15  C13  C12  117.81  3.000
 T9A  C14  C13  C12  121.34  3.000
 T9A  H14  C14  H13  107.90  3.000
 T9A  H14  C14  H12  107.06  3.000
 T9A  H13  C14  H12  107.72  3.000
 T9A  H14  C14  C13  111.29  3.000
 T9A  H13  C14  C13  111.56  3.000
 T9A  H12  C14  C13  111.10  3.000
 T9A  H15  C15  C16  119.17  3.000
 T9A  H15  C15  C13  119.77  3.000
 T9A  C16  C15  C13  121.05  3.000
 T9A  C20  C19  S    111.30  3.000
 T9A  C20  C19  C18  133.46  3.000
 T9A  S    C19  C18  114.90  3.000
 T9A  C22  S    C19   91.07  3.000
 T9A  C21  C22  BR   126.77  3.000
 T9A  C21  C22  S    112.99  3.000
 T9A  BR   C22  S    120.24  3.000
 T9A  H16  C21  C20  124.19  3.000
 T9A  H16  C21  C22  124.37  3.000
 T9A  C20  C21  C22  111.44  3.000
 T9A  H17  C20  C21  122.55  3.000
 T9A  H17  C20  C19  124.25  3.000
 T9A  C21  C20  C19  113.18  3.000
 T9A  C2   N    C1   117.64  3.000
 T9A  C2   N    C18  124.12  3.000
 T9A  C1   N    C18  116.22  3.000
 T9A  H19  C1   H18  107.48  3.000
 T9A  H19  C1   C    109.05  3.000
 T9A  H18  C1   C    106.70  3.000
 T9A  H19  C1   N    110.82  3.000
 T9A  H18  C1   N    108.78  3.000
 T9A  C    C1   N    113.75  3.000
 T9A  H20  C2   C3   107.14  3.000
 T9A  H20  C2   N    107.20  3.000
 T9A  C3   C2   N    113.11  3.000
 T9A  H20  C2   C11  105.85  3.000
 T9A  C3   C2   C11  112.18  3.000
 T9A  N    C2   C11  110.90  3.000
 T9A  C16  C17  C11  119.78  3.000
 T9A  C11  C17  N1   120.59  3.000
 T9A  C16  C17  N1   119.62  3.000
 T9A  H21  C16  C17  119.59  3.000
 T9A  H21  C16  C15  120.13  3.000
 T9A  C17  C16  C15  120.28  3.000
 T9A  O    C    C1   121.46  3.000
 T9A  O    C    N1   122.17  3.000
 T9A  C1   C    N1   116.23  3.000
 T9A  C2   C3   C10  121.85  3.000
 T9A  C10  C3   C4   119.22  3.000
 T9A  C2   C3   C4   118.86  3.000
 T9A  N    C18  C19  119.79  3.000
 T9A  C19  C18  O1   118.17  3.000
 T9A  N    C18  O1   122.04  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
 T9A  CONST_01  C8   C10  C3   C4      0.00   0.0  0
 T9A  CONST_02  C8   C7   C5   C4      0.00   0.0  0
 T9A  CONST_03  C10  C3   C4   C5      0.00   0.0  0
 T9A  CONST_04  C10  C8   C7   C5      0.00   0.0  0
 T9A  CONST_05  C3   C4   C5   C7      0.00   0.0  0
 T9A  CONST_06  C3   C10  C8   C7      0.00   0.0  0
 T9A  CONST_07  C15  C13  C12  C11     0.00   0.0  0
 T9A  CONST_08  C15  C16  C17  C11     0.00   0.0  0
 T9A  CONST_09  C16  C15  C13  C12     0.00   0.0  0
 T9A  CONST_10  C16  C17  C11  C12     0.00   0.0  0
 T9A  CONST_11  C17  C16  C15  C13     0.00   0.0  0
 T9A  CONST_12  C17  C11  C12  C13     0.00   0.0  0
 T9A  CONST_13  C21  C22  S    C19     0.00   0.0  0
 T9A  CONST_14  C22  C21  C20  C19     0.00   0.0  0
 T9A  CONST_15  C21  C20  C19  S       0.00   0.0  0
 T9A  CONST_16  C20  C21  C22  S       0.00   0.0  0
 T9A  CONST_17  C20  C19  S    C22     0.00   0.0  0
 T9A  CONST_18  C2   C3   C4   C5    180.00   0.0  0
 T9A  CONST_19  C2   C3   C10  C8    180.00   0.0  0
 T9A  CONST_20  C17  N1   C    C1      0.00   0.0  0
 T9A  CONST_21  C9   C8   C7   C5    180.00   0.0  0
 T9A  CONST_22  C3   C4   C5   C6    180.00   0.0  0
 T9A  CONST_23  C8   C7   C5   C6    180.00   0.0  0
 T9A  CONST_24  C3   C10  C8   C9    180.00   0.0  0
 T9A  CONST_25  C14  C13  C12  C11   180.00   0.0  0
 T9A  CONST_26  C16  C15  C13  C14   180.00   0.0  0
 T9A  CONST_27  C22  S    C19  C18   180.00   0.0  0
 T9A  CONST_28  C21  C20  C19  C18   180.00   0.0  0
 T9A  CONST_29  BR   C22  S    C19   180.00   0.0  0
 T9A  CONST_30  C20  C21  C22  BR    180.00   0.0  0
 T9A  CONST_31  C1   N    C18  C19   180.00   0.0  0
 T9A  CONST_33  O    C    N1   C17   180.00   0.0  0
 T9A  CONST_34  H10  C10  C3   C4    180.00   0.0  0
 T9A  CONST_35  H6   C7   C5   C4    180.00   0.0  0
 T9A  CONST_36  H21  C16  C17  N1      0.00   0.0  0
 T9A  CONST_37  H1   C4   C5   C7    180.00   0.0  0
 T9A  CONST_38  H15  C15  C13  C12   180.00   0.0  0
 T9A  CONST_39  H11  C12  C13  C15   180.00   0.0  0
 T9A  CONST_40  H16  C21  C20  C19   180.00   0.0  0
 T9A  CONST_41  H17  C20  C19  S     180.00   0.0  0
 T9A  CONST_42  H5   N1   C    C1    180.00   0.0  0
 T9A  CONST_43  C1   N    C18  O1      0.00   0.0  0
 T9A  Var_01    N    C1   C    N1     72.34  30.0  1
 T9A  Var_02    C    N1   C17  C11   -42.89  30.0  1
 T9A  Var_03    C    C1   N    C2    -41.10  30.0  1
 T9A  Var_04    N    C18  C19  S    -156.63  30.0  2
 T9A  Var_05    H2   C6   C5   C4    110.08  30.0  2
 T9A  Var_06    H7   C9   C8   C7   -101.62  30.0  2
 T9A  Var_07    H12  C14  C13  C12  -113.79  30.0  2

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
 T9A  chir_01  C2  C11  N  C3  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
 T9A  plan-1  C19  0.020
 T9A  plan-1  S    0.020
 T9A  plan-1  C22  0.020
 T9A  plan-1  BR   0.020
 T9A  plan-1  C21  0.020
 T9A  plan-1  C20  0.020
 T9A  plan-1  H16  0.020
 T9A  plan-1  H17  0.020
 T9A  plan-1  C18  0.020
 T9A  plan-2  C4   0.020
 T9A  plan-2  C5   0.020
 T9A  plan-2  C6   0.020
 T9A  plan-2  C7   0.020
 T9A  plan-2  C8   0.020
 T9A  plan-2  C9   0.020
 T9A  plan-2  C10  0.020
 T9A  plan-2  C2   0.020
 T9A  plan-2  C3   0.020
 T9A  plan-2  H1   0.020
 T9A  plan-2  H6   0.020
 T9A  plan-2  H10  0.020
 T9A  plan-3  N1   0.020
 T9A  plan-3  C11  0.020
 T9A  plan-3  C12  0.020
 T9A  plan-3  C13  0.020
 T9A  plan-3  C14  0.020
 T9A  plan-3  C15  0.020
 T9A  plan-3  C2   0.020
 T9A  plan-3  C17  0.020
 T9A  plan-3  C16  0.020
 T9A  plan-3  H11  0.020
 T9A  plan-3  H15  0.020
 T9A  plan-3  H21  0.020
 T9A  plan-4  N1   0.020
 T9A  plan-4  C1   0.020
 T9A  plan-4  C17  0.020
 T9A  plan-4  C    0.020
 T9A  plan-4  O    0.020
 T9A  plan-4  H5   0.020
 T9A  plan-5  O1   0.020
 T9A  plan-5  C19  0.020
 T9A  plan-5  N    0.020
 T9A  plan-5  C1   0.020
 T9A  plan-5  C2   0.020
 T9A  plan-5  C18  0.020

