# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:55:24 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: 3-[(2~{R})-4-methyl-5-oxidanylidene-2,3-dihydro-1,4-benzoxazepin-2-yl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C[C@H](Oc2ccccc2C1=O)c3cccc(c3)C#N
#
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
 R9Q  R9Q  3-[(2~{R})-4-methyl-5-oxidanylidene-2,3-dihydro-1,4-benzoxazepin-2-yl]benzenecarbonitrile  ligand  35  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R9Q
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
 R9Q  C4   C  CR16  0  -0.252  63.9095  -39.5540  15.6470
 R9Q  C5   C  CR16  0  -0.251  63.2836  -40.5546  14.9141
 R9Q  C6   C  CR16  0  -0.329  62.0884  -41.1014  15.3559
 R9Q  C7   C  CR6   0   0.364  61.5135  -40.6482  16.5358
 R9Q  C8   C  CR6   0  -0.125  62.1349  -39.6451  17.2842
 R9Q  C13  C  CR6   0   0.089  58.7386  -41.8290  18.5235
 R9Q  C15  C  CR16  0  -0.273  58.1880  -42.9033  19.2170
 R9Q  C17  C  CR16  0  -0.250  56.1203  -41.7177  19.5094
 R9Q  C11  C  CH2   0  -0.391  61.1154  -41.3924  19.1649
 R9Q  C12  C  CH1   0   0.006  60.1744  -41.9040  18.0780
 R9Q  C16  C  CR16  0  -0.230  56.8920  -42.8493  19.7088
 R9Q  C18  C  CR6   0   0.027  56.6676  -40.6437  18.8099
 R9Q  C19  C  CR16  0  -0.299  57.9709  -40.6924  18.3162
 R9Q  C3   C  CR16  0  -0.291  63.3277  -39.0972  16.8180
 R9Q  C9   C  C     0   0.558  61.5332  -39.0860  18.5318
 R9Q  N2   N  NT    0  -0.446  60.9641  -39.9692  19.3768
 R9Q  N21  N  NS    0  -0.250  55.2422  -38.5292  18.4162
 R9Q  O10  O  O     0  -0.484  61.5753  -37.8864  18.7654
 R9Q  O14  O  O2    0  -0.502  60.2939  -41.1381  16.8870
 R9Q  H1   H  HCR6  0   0.263  64.8417  -39.1262  15.3041
 R9Q  H2   H  HCR6  0   0.268  63.7265  -40.9126  13.9940
 R9Q  H3   H  HCR6  0   0.272  61.5875  -41.8705  14.7819
 R9Q  H4   H  HCR6  0   0.273  58.7791  -43.7981  19.3731
 R9Q  H5   H  HCR6  0   0.284  55.1073  -41.6660  19.8842
 R9Q  H6   H  HCH3  0   0.248  59.7990  -40.2864  21.0676
 R9Q  H7   H  HCH3  0   0.250  61.0687  -39.0787  21.2917
 R9Q  H8   H  HCH3  0   0.249  59.6182  -38.6851  20.3602
 R9Q  H9   H  HCH2  0   0.300  60.8980  -41.9203  20.0921
 R9Q  H10  H  HCH2  0   0.295  62.1500  -41.6387  18.9155
 R9Q  H11  H  HCH1  0   0.268  60.4366  -42.9498  17.8736
 R9Q  H12  H  HCR6  0   0.277  56.4806  -43.6944  20.2427
 R9Q  H13  H  HCR6  0   0.283  58.3657  -39.8435  17.7749
 R9Q  H14  H  HCR6  0   0.265  63.8055  -38.3110  17.3883
 R9Q  C1   C  CH3   0  -0.523  60.3347  -39.4729  20.5866
 R9Q  C20  C  CSP   0   0.055  55.8806  -39.4721  18.5915

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
 R9Q  C5   C6   aromatic  1.387  0.020  1.387
 R9Q  C5   C4   aromatic  1.389  0.020  1.389
 R9Q  C6   C7   aromatic  1.389  0.020  1.389
 R9Q  C4   C3   aromatic  1.385  0.020  1.385
 R9Q  C7   O14  single    1.360  0.020  1.360
 R9Q  C7   C8   aromatic  1.397  0.020  1.397
 R9Q  O14  C12  single    1.421  0.020  1.421
 R9Q  C3   C8   aromatic  1.393  0.020  1.393
 R9Q  C8   C9   single    1.494  0.020  1.494
 R9Q  C12  C13  single    1.505  0.020  1.505
 R9Q  C12  C11  single    1.526  0.020  1.526
 R9Q  C19  C13  aromatic  1.387  0.020  1.387
 R9Q  C19  C18  aromatic  1.394  0.020  1.394
 R9Q  N21  C20  triple    1.152  0.020  1.152
 R9Q  C20  C18  single    1.428  0.020  1.428
 R9Q  C9   O10  double    1.223  0.020  1.223
 R9Q  C9   N2   single    1.348  0.020  1.348
 R9Q  C13  C15  aromatic  1.392  0.020  1.392
 R9Q  C18  C17  aromatic  1.394  0.020  1.394
 R9Q  C11  N2   single    1.447  0.020  1.447
 R9Q  C15  C16  aromatic  1.387  0.020  1.387
 R9Q  N2   C1   single    1.451  0.020  1.451
 R9Q  C17  C16  aromatic  1.384  0.020  1.384
 R9Q  C4   H1   single    0.930  0.020  1.080
 R9Q  C5   H2   single    0.930  0.020  1.080
 R9Q  C6   H3   single    0.930  0.020  1.080
 R9Q  C15  H4   single    0.930  0.020  1.080
 R9Q  C17  H5   single    0.930  0.020  1.080
 R9Q  C1   H6   single    0.970  0.020  1.090
 R9Q  C1   H7   single    0.970  0.020  1.090
 R9Q  C1   H8   single    0.970  0.020  1.090
 R9Q  C11  H9   single    0.970  0.020  1.090
 R9Q  C11  H10  single    0.970  0.020  1.090
 R9Q  C12  H11  single    0.970  0.020  1.090
 R9Q  C16  H12  single    0.930  0.020  1.080
 R9Q  C19  H13  single    0.930  0.020  1.080
 R9Q  C3   H14  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
 R9Q  H1   C4   C3   119.98  3.000
 R9Q  H1   C4   C5   120.39  3.000
 R9Q  C3   C4   C5   119.63  3.000
 R9Q  H2   C5   C6   119.55  3.000
 R9Q  H2   C5   C4   120.17  3.000
 R9Q  C6   C5   C4   120.28  3.000
 R9Q  H3   C6   C7   119.40  3.000
 R9Q  H3   C6   C5   120.67  3.000
 R9Q  C7   C6   C5   119.93  3.000
 R9Q  O14  C7   C8   121.26  3.000
 R9Q  C8   C7   C6   120.35  3.000
 R9Q  O14  C7   C6   118.23  3.000
 R9Q  C9   C8   C3   118.51  3.000
 R9Q  C9   C8   C7   122.47  3.000
 R9Q  C3   C8   C7   118.94  3.000
 R9Q  C19  C13  C12  121.63  3.000
 R9Q  C19  C13  C15  119.20  3.000
 R9Q  C12  C13  C15  119.10  3.000
 R9Q  H4   C15  C16  119.38  3.000
 R9Q  H4   C15  C13  119.56  3.000
 R9Q  C16  C15  C13  121.07  3.000
 R9Q  H5   C17  C18  120.33  3.000
 R9Q  H5   C17  C16  120.76  3.000
 R9Q  C18  C17  C16  118.91  3.000
 R9Q  H10  C11  H9   105.91  3.000
 R9Q  H10  C11  N2   110.75  3.000
 R9Q  H9   C11  N2   109.35  3.000
 R9Q  H10  C11  C12  110.23  3.000
 R9Q  H9   C11  C12  108.72  3.000
 R9Q  N2   C11  C12  111.69  3.000
 R9Q  H11  C12  O14  109.72  3.000
 R9Q  H11  C12  C11  107.74  3.000
 R9Q  O14  C12  C11  111.37  3.000
 R9Q  H11  C12  C13  109.30  3.000
 R9Q  C11  C12  C13  111.14  3.000
 R9Q  O14  C12  C13  107.55  3.000
 R9Q  H12  C16  C17  119.87  3.000
 R9Q  H12  C16  C15  120.02  3.000
 R9Q  C17  C16  C15  120.11  3.000
 R9Q  C19  C18  C20  119.31  3.000
 R9Q  C20  C18  C17  119.51  3.000
 R9Q  C19  C18  C17  121.18  3.000
 R9Q  H13  C19  C18  119.40  3.000
 R9Q  H13  C19  C13  121.06  3.000
 R9Q  C18  C19  C13  119.54  3.000
 R9Q  H14  C3   C8   119.16  3.000
 R9Q  H14  C3   C4   119.98  3.000
 R9Q  C8   C3   C4   120.86  3.000
 R9Q  O10  C9   N2   122.51  3.000
 R9Q  N2   C9   C8   116.63  3.000
 R9Q  O10  C9   C8   120.85  3.000
 R9Q  C9   N2   C11  120.56  3.000
 R9Q  C11  N2   C1   120.25  3.000
 R9Q  C9   N2   C1   118.78  3.000
 R9Q  C12  O14  C7   119.07  3.000
 R9Q  H8   C1   H7   108.39  3.000
 R9Q  H8   C1   H6   108.03  3.000
 R9Q  H7   C1   H6   108.43  3.000
 R9Q  H8   C1   N2   111.06  3.000
 R9Q  H7   C1   N2   111.74  3.000
 R9Q  H6   C1   N2   109.09  3.000
 R9Q  N21  C20  C18  180.00  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
 R9Q  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 R9Q  CONST_02  C7   C8   C3   C4     0.00   0.0  0
 R9Q  CONST_03  C8   C7   C6   C5     0.00   0.0  0
 R9Q  CONST_04  C8   C3   C4   C5     0.00   0.0  0
 R9Q  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 R9Q  CONST_06  C3   C8   C7   C6     0.00   0.0  0
 R9Q  CONST_07  C17  C18  C19  C13    0.00   0.0  0
 R9Q  CONST_08  C17  C16  C15  C13    0.00   0.0  0
 R9Q  CONST_09  C18  C19  C13  C15    0.00   0.0  0
 R9Q  CONST_10  C18  C17  C16  C15    0.00   0.0  0
 R9Q  CONST_11  C19  C13  C15  C16    0.00   0.0  0
 R9Q  CONST_12  C19  C18  C17  C16    0.00   0.0  0
 R9Q  CONST_13  C18  C19  C13  C12  180.00   0.0  0
 R9Q  CONST_14  C16  C15  C13  C12  180.00   0.0  0
 R9Q  CONST_15  C11  N2   C9   C8     0.00   0.0  0
 R9Q  CONST_16  C20  C18  C19  C13  180.00   0.0  0
 R9Q  CONST_17  C16  C17  C18  C20  180.00   0.0  0
 R9Q  CONST_18  C1   N2   C9   C8   180.00   0.0  0
 R9Q  CONST_19  O10  C9   N2   C11  180.00   0.0  0
 R9Q  CONST_20  H3   C6   C5   C4   180.00   0.0  0
 R9Q  CONST_21  H14  C3   C4   C5   180.00   0.0  0
 R9Q  CONST_22  H1   C4   C5   C6   180.00   0.0  0
 R9Q  CONST_23  H2   C5   C6   C7   180.00   0.0  0
 R9Q  CONST_24  H12  C16  C15  C13  180.00   0.0  0
 R9Q  CONST_25  H13  C19  C13  C15  180.00   0.0  0
 R9Q  CONST_26  H5   C17  C16  C15  180.00   0.0  0
 R9Q  CONST_27  H4   C15  C16  C17  180.00   0.0  0
 R9Q  CONST_28  O10  C9   N2   C1     0.00   0.0  0
 R9Q  Var_01    N2   C9   C8   C7    41.70  30.0  1
 R9Q  Var_02    C9   N2   C11  C12  -78.88  30.0  1
 R9Q  Var_03    H6   C1   N2   C11  -15.96  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
 R9Q  chir_01  C12  O14  C13  C11  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
 R9Q  plan-1  C13  0.020
 R9Q  plan-1  C15  0.020
 R9Q  plan-1  C17  0.020
 R9Q  plan-1  C12  0.020
 R9Q  plan-1  C16  0.020
 R9Q  plan-1  C18  0.020
 R9Q  plan-1  C19  0.020
 R9Q  plan-1  N21  0.020
 R9Q  plan-1  H4   0.020
 R9Q  plan-1  H5   0.020
 R9Q  plan-1  H12  0.020
 R9Q  plan-1  H13  0.020
 R9Q  plan-1  C20  0.020
 R9Q  plan-2  C4   0.020
 R9Q  plan-2  C5   0.020
 R9Q  plan-2  C6   0.020
 R9Q  plan-2  C7   0.020
 R9Q  plan-2  C8   0.020
 R9Q  plan-2  C3   0.020
 R9Q  plan-2  C9   0.020
 R9Q  plan-2  O14  0.020
 R9Q  plan-2  H1   0.020
 R9Q  plan-2  H2   0.020
 R9Q  plan-2  H3   0.020
 R9Q  plan-2  H14  0.020
 R9Q  plan-3  C8   0.020
 R9Q  plan-3  C11  0.020
 R9Q  plan-3  C9   0.020
 R9Q  plan-3  N2   0.020
 R9Q  plan-3  O10  0.020
 R9Q  plan-3  C1   0.020

