# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:01:06 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (11R)-10-acetyl-11-(2,4-dichlorophenyl)-6-hydroxy-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1[C@@H](c2ccc(Cl)cc2Cl)C3=C(CC(C)(C)CC3=O)Nc4c(O)cccc14
#
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
 XND  XND  (11R)-10-acetyl-11-(2,4-dichlorophenyl)-6-hydroxy-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one  ligand  52  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XND
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
 XND  CL29  CL  CL    0  -0.117  -4.9944   1.2144   2.3934
 XND  C22   C   CR6   0  -0.066  -3.5586   0.9927   1.4539
 XND  C21   C   CR16  0  -0.159  -3.6740   0.6088   0.1280
 XND  C20   C   CR6   0  -0.105  -2.5169   0.4356  -0.6133
 XND  CL28  CL  CL    0  -0.107  -2.6926  -0.0471  -2.2679
 XND  C23   C   CR16  0  -0.184  -2.3190   1.2026   2.0314
 XND  C24   C   CR16  0  -0.316  -1.1828   1.0187   1.2595
 XND  C16   C   CR6   0   0.234  -1.2474   0.6302  -0.0725
 XND  C11   C   CH1   0  -0.204  -0.0017   0.4062  -0.9006
 XND  C5    C   C     0  -0.140   1.2637   0.9683  -0.3149
 XND  C6    C   C     0   0.376   1.5442   2.3516  -0.6451
 XND  O25   O   O     0  -0.457   0.7372   3.0270  -1.2755
 XND  C1    C   CH2   0  -0.530   2.8338   2.9662  -0.1637
 XND  N10   N   NT    0  -0.513   0.1433  -1.0217  -1.1830
 XND  C17   C   C     0   0.507   0.7274  -1.4177  -2.3498
 XND  C19   C   CH3   0  -0.790   0.9788  -2.8954  -2.5092
 XND  O18   O   O     0  -0.476   1.0243  -0.6126  -3.2156
 XND  C9    C   CR6   0   0.220  -0.0598  -1.8933  -0.0936
 XND  C15   C   CR16  0  -0.284  -1.1637  -2.7321  -0.0321
 XND  C14   C   CR16  0  -0.266  -1.3248  -3.5655   1.0600
 XND  C13   C   CR16  0  -0.374  -0.4058  -3.5419   2.1010
 XND  C12   C   CR6   0   0.301   0.6769  -2.6768   2.0592
 XND  O30   O   OH1   0  -0.628   1.5997  -2.5957   3.0364
 XND  C8    C   CR6   0   0.296   0.8562  -1.8371   0.9492
 XND  N7    N   NH1   0  -0.762   1.9804  -1.0105   0.9154
 XND  C4    C   C     0   0.377   2.1499   0.2466   0.4354
 XND  C3    C   CH2   0  -0.525   3.4723   0.8292   0.8560
 XND  C2    C   CT    0  -0.137   3.9709   1.9578  -0.0403
 XND  C27   C   CH3   0  -0.641   4.3771   1.4255  -1.4168
 XND  C26   C   CH3   0  -0.641   5.1820   2.6185   0.6119
 XND  H21   H   HCR6  0   0.301  -4.6443   0.4485  -0.3210
 XND  H23   H   HCR6  0   0.284  -2.2331   1.5034   3.0661
 XND  H24   H   HCR6  0   0.267  -0.2150   1.1884   1.7133
 XND  H11   H   HCH1  0   0.285  -0.1583   0.9013  -1.8604
 XND  H1    H   HCH2  0   0.257   3.1027   3.7881  -0.8319
 XND  H1A   H   HCH2  0   0.266   2.6376   3.4144   0.8187
 XND  H19   H   HCH3  0   0.272   0.0413  -3.4469  -2.5868
 XND  H19A  H   HCH3  0   0.268   1.5533  -3.0643  -3.4164
 XND  H19B  H   HCH3  0   0.264   1.5257  -3.3081  -1.6613
 XND  H15   H   HCR6  0   0.258  -1.8793  -2.7268  -0.8428
 XND  H14   H   HCR6  0   0.266  -2.1729  -4.2343   1.1126
 XND  H13   H   HCR6  0   0.279  -0.5392  -4.1919   2.9579
 XND  HO30  H   HOH1  0   0.485   1.4236  -3.2463   3.7256
 XND  HN7   H   HNH1  0   0.414   2.7533  -1.3474   1.4701
 XND  H3    H   HCH2  0   0.283   3.3642   1.1965   1.8839
 XND  H3A   H   HCH2  0   0.269   4.2184   0.0291   0.8971
 XND  H27   H   HCH3  0   0.231   4.7458   2.2391  -2.0445
 XND  H27A  H   HCH3  0   0.230   5.1791   0.6914  -1.3212
 XND  H27B  H   HCH3  0   0.236   3.5517   0.9473  -1.9465
 XND  H26   H   HCH3  0   0.228   4.9398   3.0063   1.6034
 XND  H26A  H   HCH3  0   0.232   6.0061   1.9099   0.7192
 XND  H26B  H   HCH3  0   0.233   5.5395   3.4525   0.0052

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
 XND  CL29  C22   single    1.730  0.020  1.730
 XND  C22   C21   aromatic  1.385  0.020  1.385
 XND  C22   C23   aromatic  1.384  0.020  1.384
 XND  C21   C20   aromatic  1.385  0.020  1.385
 XND  C20   CL28  single    1.733  0.020  1.733
 XND  C20   C16   aromatic  1.394  0.020  1.394
 XND  C23   C24   aromatic  1.386  0.020  1.386
 XND  C24   C16   aromatic  1.389  0.020  1.389
 XND  C16   C11   single    1.513  0.020  1.513
 XND  C11   C5    single    1.503  0.020  1.503
 XND  C11   N10   single    1.463  0.020  1.463
 XND  C5    C6    single    1.450  0.020  1.450
 XND  C5    C4    double    1.367  0.020  1.367
 XND  C6    O25   double    1.227  0.020  1.227
 XND  C6    C1    single    1.507  0.020  1.507
 XND  C1    C2    single    1.525  0.020  1.525
 XND  N10   C17   single    1.364  0.020  1.364
 XND  N10   C9    single    1.410  0.020  1.410
 XND  C17   C19   single    1.507  0.020  1.507
 XND  C17   O18   double    1.219  0.020  1.219
 XND  C9    C15   aromatic  1.388  0.020  1.388
 XND  C9    C8    aromatic  1.389  0.020  1.389
 XND  C15   C14   aromatic  1.383  0.020  1.383
 XND  C14   C13   aromatic  1.389  0.020  1.389
 XND  C13   C12   aromatic  1.386  0.020  1.386
 XND  C12   O30   single    1.347  0.020  1.347
 XND  C12   C8    aromatic  1.403  0.020  1.403
 XND  C8    N7    single    1.396  0.020  1.396
 XND  N7    C4    single    1.356  0.020  1.356
 XND  C4    C3    single    1.505  0.020  1.505
 XND  C3    C2    single    1.525  0.020  1.525
 XND  C2    C27   single    1.531  0.020  1.531
 XND  C2    C26   single    1.526  0.020  1.526
 XND  C21   H21   single    0.930  0.020  1.080
 XND  C23   H23   single    0.930  0.020  1.080
 XND  C24   H24   single    0.930  0.020  1.080
 XND  C11   H11   single    0.970  0.020  1.090
 XND  C1    H1    single    0.970  0.020  1.090
 XND  C1    H1A   single    0.970  0.020  1.090
 XND  C19   H19   single    0.970  0.020  1.090
 XND  C19   H19A  single    0.970  0.020  1.090
 XND  C19   H19B  single    0.970  0.020  1.090
 XND  C15   H15   single    0.930  0.020  1.080
 XND  C14   H14   single    0.930  0.020  1.080
 XND  C13   H13   single    0.930  0.020  1.080
 XND  O30   HO30  single    0.850  0.020  0.980
 XND  N7    HN7   single    0.860  0.020  1.020
 XND  C3    H3    single    0.970  0.020  1.090
 XND  C3    H3A   single    0.970  0.020  1.090
 XND  C27   H27   single    0.970  0.020  1.090
 XND  C27   H27A  single    0.970  0.020  1.090
 XND  C27   H27B  single    0.970  0.020  1.090
 XND  C26   H26   single    0.970  0.020  1.090
 XND  C26   H26A  single    0.970  0.020  1.090
 XND  C26   H26B  single    0.970  0.020  1.090

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
 XND  C23   C22  C21   121.08  3.000
 XND  C23   C22  CL29  119.83  3.000
 XND  C21   C22  CL29  119.09  3.000
 XND  H21   C21  C20   120.59  3.000
 XND  H21   C21  C22   120.90  3.000
 XND  C20   C21  C22   118.51  3.000
 XND  C16   C20  CL28  120.13  3.000
 XND  C16   C20  C21   122.40  3.000
 XND  CL28  C20  C21   117.47  3.000
 XND  H23   C23  C24   120.33  3.000
 XND  H23   C23  C22   120.86  3.000
 XND  C24   C23  C22   118.82  3.000
 XND  H24   C24  C16   119.18  3.000
 XND  H24   C24  C23   118.61  3.000
 XND  C16   C24  C23   122.21  3.000
 XND  C11   C16  C24   121.88  3.000
 XND  C11   C16  C20   121.14  3.000
 XND  C24   C16  C20   116.97  3.000
 XND  H11   C11  N10   106.70  3.000
 XND  H11   C11  C5    107.08  3.000
 XND  N10   C11  C5    110.90  3.000
 XND  H11   C11  C16   107.23  3.000
 XND  N10   C11  C16   109.38  3.000
 XND  C5    C11  C16   115.12  3.000
 XND  C4    C5   C6    120.22  3.000
 XND  C4    C5   C11   124.20  3.000
 XND  C6    C5   C11   115.53  3.000
 XND  C1    C6   O25   120.16  3.000
 XND  C1    C6   C5    118.81  3.000
 XND  O25   C6   C5    121.01  3.000
 XND  H1A   C1   H1    106.51  3.000
 XND  H1A   C1   C2    109.33  3.000
 XND  H1    C1   C2    111.31  3.000
 XND  H1A   C1   C6    107.42  3.000
 XND  H1    C1   C6    108.78  3.000
 XND  C2    C1   C6    113.21  3.000
 XND  C9    N10  C17   122.92  3.000
 XND  C9    N10  C11   116.10  3.000
 XND  C17   N10  C11   119.41  3.000
 XND  O18   C17  C19   122.12  3.000
 XND  O18   C17  N10   121.36  3.000
 XND  C19   C17  N10   116.52  3.000
 XND  H19B  C19  H19A  108.98  3.000
 XND  H19B  C19  H19   107.17  3.000
 XND  H19A  C19  H19   108.44  3.000
 XND  H19B  C19  C17   111.87  3.000
 XND  H19A  C19  C17   109.19  3.000
 XND  H19   C19  C17   111.10  3.000
 XND  C8    C9   C15   121.05  3.000
 XND  C8    C9   N10   117.39  3.000
 XND  C15   C9   N10   121.50  3.000
 XND  H15   C15  C14   121.18  3.000
 XND  H15   C15  C9    119.35  3.000
 XND  C14   C15  C9    119.46  3.000
 XND  H14   C14  C13   119.54  3.000
 XND  H14   C14  C15   120.16  3.000
 XND  C13   C14  C15   120.30  3.000
 XND  H13   C13  C12   119.62  3.000
 XND  H13   C13  C14   120.07  3.000
 XND  C12   C13  C14   120.31  3.000
 XND  C8    C12  O30   116.77  3.000
 XND  C8    C12  C13   119.80  3.000
 XND  O30   C12  C13   123.43  3.000
 XND  HO30  O30  C12   110.67  3.000
 XND  N7    C8   C12   118.45  3.000
 XND  N7    C8   C9    122.47  3.000
 XND  C12   C8   C9    119.03  3.000
 XND  HN7   N7   C4    114.09  3.000
 XND  HN7   N7   C8    113.95  3.000
 XND  C4    N7   C8    131.16  3.000
 XND  C3    C4   N7    111.70  3.000
 XND  C3    C4   C5    121.24  3.000
 XND  N7    C4   C5    127.05  3.000
 XND  H3A   C3   H3    106.06  3.000
 XND  H3A   C3   C2    109.88  3.000
 XND  H3    C3   C2    109.59  3.000
 XND  H3A   C3   C4    109.05  3.000
 XND  H3    C3   C4    107.75  3.000
 XND  C2    C3   C4    114.17  3.000
 XND  C26   C2   C27   108.92  3.000
 XND  C26   C2   C3    109.19  3.000
 XND  C27   C2   C3    110.97  3.000
 XND  C26   C2   C1    109.89  3.000
 XND  C27   C2   C1    110.80  3.000
 XND  C3    C2   C1    107.05  3.000
 XND  H27B  C27  H27A  107.68  3.000
 XND  H27B  C27  H27   107.64  3.000
 XND  H27A  C27  H27   107.66  3.000
 XND  H27B  C27  C2    112.84  3.000
 XND  H27A  C27  C2    110.50  3.000
 XND  H27   C27  C2    110.33  3.000
 XND  H26B  C26  H26A  107.65  3.000
 XND  H26B  C26  H26   107.81  3.000
 XND  H26A  C26  H26   107.98  3.000
 XND  H26B  C26  C2    110.68  3.000
 XND  H26A  C26  C2    111.10  3.000
 XND  H26   C26  C2    111.46  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
 XND  CONST_01  C16   C20  C21  C22     0.00   0.0  0
 XND  CONST_02  C16   C24  C23  C22     0.00   0.0  0
 XND  CONST_03  C24   C23  C22  C21     0.00   0.0  0
 XND  CONST_04  C24   C16  C20  C21     0.00   0.0  0
 XND  CONST_05  C23   C22  C21  C20     0.00   0.0  0
 XND  CONST_06  C23   C24  C16  C20     0.00   0.0  0
 XND  CONST_07  C13   C14  C15  C9      0.00   0.0  0
 XND  CONST_08  C12   C13  C14  C15     0.00   0.0  0
 XND  CONST_09  C8    C12  C13  C14     0.00   0.0  0
 XND  CONST_10  C11   C16  C20  C21   180.00   0.0  0
 XND  CONST_11  C11   C16  C24  C23   180.00   0.0  0
 XND  CONST_12  C20   C21  C22  CL29  180.00   0.0  0
 XND  CONST_13  C24   C23  C22  CL29  180.00   0.0  0
 XND  CONST_14  CL28  C20  C21  C22   180.00   0.0  0
 XND  CONST_15  C24   C16  C20  CL28  180.00   0.0  0
 XND  CONST_16  C11   C16  C20  CL28    0.00   0.0  0
 XND  CONST_17  O30   C12  C13  C14   180.00   0.0  0
 XND  CONST_18  H24   C24  C23  C22   180.00   0.0  0
 XND  CONST_19  H23   C23  C22  C21   180.00   0.0  0
 XND  CONST_20  H21   C21  C22  C23   180.00   0.0  0
 XND  CONST_21  H14   C14  C15  C9    180.00   0.0  0
 XND  CONST_22  H13   C13  C14  C15   180.00   0.0  0
 XND  CONST_23  H15   C15  C14  C13   180.00   0.0  0
 XND  Var_01    C2    C1   C6   C5     30.32  30.0  1
 XND  Var_02    C3    C2   C1   C6    -54.57  30.0  1
 XND  Var_03    C4    C3   C2   C1     51.59  30.0  1
 XND  Var_04    H27   C27  C2   C1     62.05  30.0  3
 XND  Var_05    H26   C26  C2   C1     58.96  30.0  3
 XND  Var_06    H19   C19  C17  N10    67.37  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
 XND  chir_01  C11  C16  C5  N10  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
 XND  plan-1  CL29  0.020
 XND  plan-1  C22   0.020
 XND  plan-1  C21   0.020
 XND  plan-1  C20   0.020
 XND  plan-1  CL28  0.020
 XND  plan-1  C23   0.020
 XND  plan-1  C24   0.020
 XND  plan-1  C16   0.020
 XND  plan-1  C11   0.020
 XND  plan-1  H21   0.020
 XND  plan-1  H23   0.020
 XND  plan-1  H24   0.020
 XND  plan-2  N10   0.020
 XND  plan-2  C9    0.020
 XND  plan-2  C15   0.020
 XND  plan-2  C14   0.020
 XND  plan-2  C13   0.020
 XND  plan-2  C12   0.020
 XND  plan-2  O30   0.020
 XND  plan-2  C8    0.020
 XND  plan-2  N7    0.020
 XND  plan-2  H15   0.020
 XND  plan-2  H14   0.020
 XND  plan-2  H13   0.020
 XND  plan-3  C11   0.020
 XND  plan-3  N10   0.020
 XND  plan-3  C17   0.020
 XND  plan-3  C19   0.020
 XND  plan-3  O18   0.020
 XND  plan-3  C9    0.020
 XND  plan-4  C5    0.020
 XND  plan-4  C6    0.020
 XND  plan-4  O25   0.020
 XND  plan-4  C1    0.020
 XND  plan-5  C8    0.020
 XND  plan-5  N7    0.020
 XND  plan-5  C4    0.020
 XND  plan-5  HN7   0.020

