# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 04:46:02 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (5R)-5-methyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-4,5,6,7-tetrahydro-2H-indazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCc2n[nH]c(C(=O)N[C@H]3COc4ccccc4N(C)C3=O)c2C1
#
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
 L4Y  L4Y  (5R)-5-methyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-4,5,6,7-tetrahydro-2H-indazole-3-carboxamide  ligand  48  26  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_L4Y
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
 L4Y  C4   C  C     0  -0.507   5.8849  -0.6627  -0.4480
 L4Y  C14  C  CH1   0  -0.291  -1.4684  -0.7034  -0.2423
 L4Y  C5   C  CR56  0   0.230   4.4261  -0.9216  -0.6239
 L4Y  C6   C  CR56  0  -0.107   3.4279   0.0326  -0.3638
 L4Y  C7   C  CR5   0   0.231   2.2470  -0.6314  -0.6286
 L4Y  C3   C  C     0  -0.432   6.1272   0.8438  -0.3456
 L4Y  C1   C  CH3   0  -0.660   5.5358   2.9676   0.8879
 L4Y  C2   C  CR16  0  -0.245   5.1546   1.5184   0.6253
 L4Y  N8   N  NR15  0  -0.506   2.5955  -1.8832  -1.0093
 L4Y  N10  N  N     0  -0.277   3.9038  -2.0697  -1.0259
 L4Y  O12  O  O     0  -0.463   0.6206   1.0567  -0.5887
 L4Y  N13  N  NH1   0  -0.657  -0.0947  -1.0823  -0.3966
 L4Y  C15  C  CH2   0  -0.150  -2.3487  -1.9164  -0.5601
 L4Y  O16  O  O2    0  -0.490  -3.6746  -1.7362  -0.1016
 L4Y  C17  C  CR6   0   0.319  -4.2424  -0.5388  -0.4163
 L4Y  C18  C  CR16  0  -0.334  -5.1978  -0.4583  -1.4177
 L4Y  C19  C  CR16  0  -0.256  -5.8224   0.7519  -1.6833
 L4Y  C20  C  CR16  0  -0.259  -5.4739   1.8850  -0.9606
 L4Y  C21  C  CR16  0  -0.300  -4.5015   1.8102   0.0250
 L4Y  C22  C  CR6   0   0.261  -3.8765   0.6000   0.3064
 L4Y  N23  N  NT    0  -0.538  -2.9155   0.4992   1.3328
 L4Y  C24  C  C     0   0.557  -1.7474  -0.1694   1.1665
 L4Y  O25  O  O     0  -0.463  -0.9492  -0.3139   2.0723
 L4Y  C26  C  CH3   0  -0.542  -3.1853   1.0942   2.6356
 L4Y  C27  C  C     0  -0.484   3.7168   1.4196   0.1024
 L4Y  H1   H  H     0   0.245   6.2399  -1.1536   0.4636
 L4Y  H2   H  H     0   0.252   6.4574  -1.0924  -1.2728
 L4Y  H3   H  HCH1  0   0.308  -1.6809   0.0903  -0.9633
 L4Y  H4   H  H     0   0.236   7.1565   1.0246  -0.0270
 L4Y  H5   H  H     0   0.222   6.0235   1.3014  -1.3356
 L4Y  H6   H  HCH3  0   0.216   5.5093   3.5549  -0.0327
 L4Y  H7   H  HCH3  0   0.227   4.8505   3.4347   1.5975
 L4Y  H8   H  HCH3  0   0.229   6.5427   3.0426   1.3013
 L4Y  H9   H  HCR6  0   0.224   5.2036   0.9738   1.5765
 L4Y  H10  H  HNR5  0   0.419   1.9911  -2.6124  -1.3553
 L4Y  H11  H  HNH1  0   0.407   0.1734  -1.9873  -0.0397
 L4Y  H12  H  HCH2  0   0.256  -2.3236  -2.1071  -1.6379
 L4Y  H13  H  HCH2  0   0.255  -1.9725  -2.8024  -0.0463
 L4Y  H14  H  HCR6  0   0.273  -5.4650  -1.3510  -1.9691
 L4Y  H15  H  HCR6  0   0.265  -6.5771   0.8079  -2.4559
 L4Y  H16  H  HCR6  0   0.264  -5.9547   2.8321  -1.1650
 L4Y  H17  H  HCR6  0   0.279  -4.2241   2.6982   0.5789
 L4Y  H18  H  HCH3  0   0.260  -3.0826   0.3500   3.4237
 L4Y  H19  H  HCH3  0   0.252  -2.5064   1.9202   2.8452
 L4Y  H20  H  HCH3  0   0.259  -4.2043   1.4679   2.6517
 L4Y  H21  H  H     0   0.233   3.5867   2.1248  -0.7260
 L4Y  H22  H  H     0   0.244   3.0114   1.7316   0.8758
 L4Y  C11  C  C     0   0.540   0.8664  -0.1363  -0.5293

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
 L4Y  C18  C19  aromatic  1.388  0.020  1.388
 L4Y  C18  C17  aromatic  1.386  0.020  1.386
 L4Y  C19  C20  aromatic  1.388  0.020  1.388
 L4Y  O16  C17  single    1.362  0.020  1.362
 L4Y  O16  C15  single    1.415  0.020  1.415
 L4Y  C17  C22  aromatic  1.397  0.020  1.397
 L4Y  C20  C21  aromatic  1.387  0.020  1.387
 L4Y  C15  C14  single    1.532  0.020  1.532
 L4Y  C22  C21  aromatic  1.391  0.020  1.391
 L4Y  C22  N23  single    1.410  0.020  1.410
 L4Y  N23  C26  single    1.457  0.020  1.457
 L4Y  N23  C24  single    1.356  0.020  1.356
 L4Y  C14  C24  single    1.532  0.020  1.532
 L4Y  C14  N13  single    1.433  0.020  1.433
 L4Y  C24  O25  double    1.216  0.020  1.216
 L4Y  N13  C11  single    1.355  0.020  1.355
 L4Y  O12  C11  double    1.220  0.020  1.220
 L4Y  C11  C7   single    1.470  0.020  1.470
 L4Y  C7   C6   aromatic  1.380  0.020  1.380
 L4Y  C7   N8   aromatic  1.354  0.020  1.354
 L4Y  C27  C6   single    1.491  0.020  1.491
 L4Y  C27  C2   single    1.533  0.020  1.533
 L4Y  C6   C5   aromatic  1.405  0.020  1.405
 L4Y  N8   N10  aromatic  1.322  0.020  1.322
 L4Y  C1   C2   single    1.521  0.020  1.521
 L4Y  N10  C5   aromatic  1.324  0.020  1.324
 L4Y  C5   C4   single    1.492  0.020  1.492
 L4Y  C2   C3   single    1.531  0.020  1.531
 L4Y  C3   C4   single    1.529  0.020  1.529
 L4Y  C4   H1   single    0.970  0.020  1.090
 L4Y  C4   H2   single    0.970  0.020  1.090
 L4Y  C14  H3   single    0.970  0.020  1.090
 L4Y  C3   H4   single    0.970  0.020  1.090
 L4Y  C3   H5   single    0.970  0.020  1.090
 L4Y  C1   H6   single    0.970  0.020  1.090
 L4Y  C1   H7   single    0.970  0.020  1.090
 L4Y  C1   H8   single    0.970  0.020  1.090
 L4Y  C2   H9   single    0.970  0.020  1.090
 L4Y  N8   H10  single    0.860  0.020  1.020
 L4Y  N13  H11  single    0.890  0.020  1.040
 L4Y  C15  H12  single    0.970  0.020  1.090
 L4Y  C15  H13  single    0.970  0.020  1.090
 L4Y  C18  H14  single    0.930  0.020  1.080
 L4Y  C19  H15  single    0.930  0.020  1.080
 L4Y  C20  H16  single    0.930  0.020  1.080
 L4Y  C21  H17  single    0.930  0.020  1.080
 L4Y  C26  H18  single    0.970  0.020  1.090
 L4Y  C26  H19  single    0.970  0.020  1.090
 L4Y  C26  H20  single    0.970  0.020  1.090
 L4Y  C27  H21  single    0.970  0.020  1.090
 L4Y  C27  H22  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
 L4Y  H2   C4   H1   106.41  3.000
 L4Y  H2   C4   C3   110.80  3.000
 L4Y  H1   C4   C3   109.55  3.000
 L4Y  H2   C4   C5   110.80  3.000
 L4Y  H1   C4   C5   109.72  3.000
 L4Y  C3   C4   C5   109.50  3.000
 L4Y  H3   C14  C24  108.55  3.000
 L4Y  H3   C14  C15  109.05  3.000
 L4Y  C24  C14  C15  111.22  3.000
 L4Y  H3   C14  N13  107.89  3.000
 L4Y  C24  C14  N13  111.45  3.000
 L4Y  C15  C14  N13  108.60  3.000
 L4Y  N10  C5   C6   111.40  3.000
 L4Y  N10  C5   C4   124.90  3.000
 L4Y  C6   C5   C4   123.70  3.000
 L4Y  C27  C6   C7   132.30  3.000
 L4Y  C27  C6   C5   123.49  3.000
 L4Y  C7   C6   C5   104.21  3.000
 L4Y  N8   C7   C11  124.90  3.000
 L4Y  N8   C7   C6   106.17  3.000
 L4Y  C11  C7   C6   128.93  3.000
 L4Y  H5   C3   H4   106.47  3.000
 L4Y  H5   C3   C2   109.20  3.000
 L4Y  H4   C3   C2   109.92  3.000
 L4Y  H5   C3   C4   109.63  3.000
 L4Y  H4   C3   C4   109.38  3.000
 L4Y  C2   C3   C4   112.08  3.000
 L4Y  H8   C1   H7   107.68  3.000
 L4Y  H8   C1   H6   107.74  3.000
 L4Y  H7   C1   H6   107.62  3.000
 L4Y  H8   C1   C2   111.23  3.000
 L4Y  H7   C1   C2   111.26  3.000
 L4Y  H6   C1   C2   111.14  3.000
 L4Y  H9   C2   C27  107.79  3.000
 L4Y  H9   C2   C1   108.18  3.000
 L4Y  C27  C2   C1   110.81  3.000
 L4Y  H9   C2   C3   107.62  3.000
 L4Y  C1   C2   C3   111.72  3.000
 L4Y  C27  C2   C3   110.55  3.000
 L4Y  H10  N8   N10  119.15  3.000
 L4Y  H10  N8   C7   127.64  3.000
 L4Y  N10  N8   C7   112.88  3.000
 L4Y  N8   N10  C5   105.33  3.000
 L4Y  H11  N13  C11  118.19  3.000
 L4Y  H11  N13  C14  116.97  3.000
 L4Y  C11  N13  C14  120.38  3.000
 L4Y  H13  C15  H12  108.32  3.000
 L4Y  H13  C15  O16  105.90  3.000
 L4Y  H12  C15  O16  111.26  3.000
 L4Y  H13  C15  C14  110.32  3.000
 L4Y  H12  C15  C14  109.20  3.000
 L4Y  O16  C15  C14  111.75  3.000
 L4Y  C17  O16  C15  115.33  3.000
 L4Y  C22  C17  C18  120.44  3.000
 L4Y  C22  C17  O16  119.19  3.000
 L4Y  C18  C17  O16  120.34  3.000
 L4Y  H14  C18  C19  120.70  3.000
 L4Y  H14  C18  C17  119.34  3.000
 L4Y  C19  C18  C17  119.94  3.000
 L4Y  H15  C19  C20  120.32  3.000
 L4Y  H15  C19  C18  119.74  3.000
 L4Y  C20  C19  C18  119.95  3.000
 L4Y  H16  C20  C21  119.55  3.000
 L4Y  H16  C20  C19  120.31  3.000
 L4Y  C21  C20  C19  120.14  3.000
 L4Y  H17  C21  C22  119.66  3.000
 L4Y  H17  C21  C20  119.95  3.000
 L4Y  C22  C21  C20  120.39  3.000
 L4Y  N23  C22  C21  121.06  3.000
 L4Y  N23  C22  C17  119.79  3.000
 L4Y  C21  C22  C17  119.13  3.000
 L4Y  C26  N23  C24  118.05  3.000
 L4Y  C24  N23  C22  122.22  3.000
 L4Y  C26  N23  C22  119.70  3.000
 L4Y  O25  C24  N23  122.19  3.000
 L4Y  O25  C24  C14  121.60  3.000
 L4Y  N23  C24  C14  116.19  3.000
 L4Y  H20  C26  H19  108.72  3.000
 L4Y  H20  C26  H18  108.25  3.000
 L4Y  H19  C26  H18  108.68  3.000
 L4Y  H20  C26  N23  109.12  3.000
 L4Y  H19  C26  N23  111.48  3.000
 L4Y  H18  C26  N23  110.52  3.000
 L4Y  H22  C27  H21  105.95  3.000
 L4Y  H22  C27  C2   110.23  3.000
 L4Y  H21  C27  C2   109.13  3.000
 L4Y  H22  C27  C6   111.21  3.000
 L4Y  H21  C27  C6   109.83  3.000
 L4Y  C2   C27  C6   110.38  3.000
 L4Y  N13  C11  O12  123.00  3.000
 L4Y  O12  C11  C7   121.03  3.000
 L4Y  N13  C11  C7   115.95  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
 L4Y  CONST_01  N8   C7   C6   C5      0.00   0.0  0
 L4Y  CONST_02  C7   N8   N10  C5      0.00   0.0  0
 L4Y  CONST_03  N10  N8   C7   C6      0.00   0.0  0
 L4Y  CONST_04  N8   N10  C5   C6      0.00   0.0  0
 L4Y  CONST_05  N10  C5   C6   C7      0.00   0.0  0
 L4Y  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 L4Y  CONST_07  C21  C20  C19  C18     0.00   0.0  0
 L4Y  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 L4Y  CONST_09  C11  C7   C6   C5    180.00   0.0  0
 L4Y  CONST_10  C27  C6   C7   C11     0.00   0.0  0
 L4Y  CONST_11  N10  N8   C7   C11   180.00   0.0  0
 L4Y  CONST_12  H10  N8   N10  C5    180.00   0.0  0
 L4Y  CONST_13  H15  C19  C18  C17   180.00   0.0  0
 L4Y  CONST_14  H16  C20  C19  C18   180.00   0.0  0
 L4Y  CONST_15  H17  C21  C20  C19   180.00   0.0  0
 L4Y  CONST_16  H14  C18  C19  C20   180.00   0.0  0
 L4Y  CONST_17  C7   C11  N13  C14   180.00   0.0  0
 L4Y  CONST_18  O12  C11  N13  C14     0.00   0.0  0
 L4Y  Var_01    C2   C27  C6   C5    -16.03  30.0  1
 L4Y  Var_02    C2   C3   C4   C5     47.03  30.0  1
 L4Y  Var_03    C3   C4   C5   C6    -15.96  30.0  1
 L4Y  Var_04    N13  C11  C7   C6   -158.06  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
 L4Y  chir_01  C14  C15  C24  N13  negativ
 L4Y  chir_02  C2   C27  C1   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
 L4Y  plan-1  C4   0.020
 L4Y  plan-1  C5   0.020
 L4Y  plan-1  C6   0.020
 L4Y  plan-1  C7   0.020
 L4Y  plan-1  N8   0.020
 L4Y  plan-1  N10  0.020
 L4Y  plan-1  C27  0.020
 L4Y  plan-1  H10  0.020
 L4Y  plan-1  C11  0.020
 L4Y  plan-2  O16  0.020
 L4Y  plan-2  C17  0.020
 L4Y  plan-2  C18  0.020
 L4Y  plan-2  C19  0.020
 L4Y  plan-2  C20  0.020
 L4Y  plan-2  C21  0.020
 L4Y  plan-2  C22  0.020
 L4Y  plan-2  N23  0.020
 L4Y  plan-2  H14  0.020
 L4Y  plan-2  H15  0.020
 L4Y  plan-2  H16  0.020
 L4Y  plan-2  H17  0.020
 L4Y  plan-3  C14  0.020
 L4Y  plan-3  C22  0.020
 L4Y  plan-3  N23  0.020
 L4Y  plan-3  C24  0.020
 L4Y  plan-3  O25  0.020
 L4Y  plan-3  C26  0.020
 L4Y  plan-4  C14  0.020
 L4Y  plan-4  C7   0.020
 L4Y  plan-4  O12  0.020
 L4Y  plan-4  N13  0.020
 L4Y  plan-4  H11  0.020
 L4Y  plan-4  C11  0.020

