# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 05:47:06 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 8,11,11-trimethyl-9-oxo-6,7,9,10,11,12-hexahydroindolo[2,1-d][1,5]benzoxazepine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c2CCOc3cc(ccc3n2c4CC(C)(C)CC(=O)c14)C(N)=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
 40Y  40Y  8,11,11-trimethyl-9-oxo-6,7,9,10,11,12-hexahydroindolo[2,1-d][1,5]benzoxazepine-3-carboxamide  ligand  47  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_40Y
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
 40Y  N1   N  NH2   0  -0.814  -5.4587   2.1438  -0.4207
 40Y  C4   C  CR5   0  -0.157   2.5952  -0.5503  -0.3970
 40Y  C5   C  C     0   0.316   3.9300   0.0044  -0.3481
 40Y  C6   C  CH2   0  -0.540   3.9919   1.5180  -0.3103
 40Y  C7   C  CT    0  -0.134   2.8439   2.1907   0.4563
 40Y  C8   C  CH2   0  -0.487   1.5001   1.7387  -0.1415
 40Y  C10  C  CH3   0  -0.636   2.9143   1.8189   1.9395
 40Y  C13  C  CR16  0  -0.296  -2.7713   1.2662  -0.9982
 40Y  C15  C  CR16  0  -0.366  -3.1639  -0.4949   0.5872
 40Y  C17  C  CH2   0  -0.161  -1.0344  -3.0766   0.7457
 40Y  C19  C  C     0   0.498  -5.1005   0.9053  -0.0560
 40Y  C14  C  CR6   0  -0.033  -3.6433   0.5765  -0.1610
 40Y  C12  C  CR16  0  -0.278  -1.4390   0.8972  -1.0781
 40Y  C16  C  CR6   0   0.347  -1.8265  -0.8468   0.5397
 40Y  O1   O  O2    0  -0.494  -1.3497  -1.8212   1.3515
 40Y  C18  C  CH2   0  -0.625  -0.2559  -2.9235  -0.5570
 40Y  C2   C  CR5   0   0.324   0.7890  -1.8703  -0.4719
 40Y  C11  C  CR6   0   0.265  -0.9554  -0.1472  -0.3033
 40Y  N    N  NR5   0  -0.641   0.3927  -0.5389  -0.3589
 40Y  C3   C  CR5   0   0.383   1.4846   0.2629  -0.3090
 40Y  O    O  O     0  -0.432   4.9428  -0.6772  -0.3735
 40Y  C1   C  CR5   0  -0.030   2.1517  -1.9118  -0.4958
 40Y  C    C  CH3   0  -0.742   3.0119  -3.1243  -0.6128
 40Y  H1   H  HNH2  0   0.408  -6.4259   2.4192  -0.3640
 40Y  H2   H  HNH2  0   0.415  -4.7919   2.8658  -0.6312
 40Y  H3   H  HCH2  0   0.257   4.9555   1.8260   0.1027
 40Y  H4   H  HCH2  0   0.268   3.9759   1.8574  -1.3542
 40Y  H5   H  HCH2  0   0.267   0.6756   2.0754   0.4942
 40Y  H6   H  HCH2  0   0.267   1.3534   2.2254  -1.1132
 40Y  H7   H  HCH3  0   0.233   2.7926   0.7477   2.1061
 40Y  H8   H  HCH3  0   0.231   3.8762   2.1129   2.3647
 40Y  H9   H  HCH3  0   0.231   2.1312   2.3308   2.5022
 40Y  H10  H  HCR6  0   0.267  -3.1173   2.0759  -1.6263
 40Y  H11  H  HCR6  0   0.277  -3.8280  -1.0445   1.2416
 40Y  H12  H  HCH2  0   0.249  -0.4354  -3.6044   1.4866
 40Y  H13  H  HCH2  0   0.237  -1.9495  -3.6503   0.5690
 40Y  H14  H  HCR6  0   0.284  -0.7789   1.4151  -1.7603
 40Y  H15  H  HCH2  0   0.289   0.1965  -3.8864  -0.7954
 40Y  H16  H  HCH2  0   0.272  -0.9452  -2.7071  -1.3797
 40Y  H17  H  HCH3  0   0.232   2.1471   4.2115   0.8351
 40Y  H18  H  HCH3  0   0.233   3.9022   4.0629   0.7499
 40Y  H19  H  HCH3  0   0.228   2.9407   4.0166  -0.7288
 40Y  H20  H  HCH3  0   0.240   3.6805  -3.2233   0.2428
 40Y  H21  H  HCH3  0   0.232   2.4145  -4.0334  -0.6711
 40Y  H22  H  HCH3  0   0.239   3.6410  -3.0844  -1.5025
 40Y  C9   C  CH3   0  -0.643   2.9653   3.7061   0.3178
 40Y  O2   O  O     0  -0.479  -5.9029   0.0713   0.3421

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
 40Y  C10  C7   single    1.531  0.020  1.531
 40Y  O2   C19  double    1.224  0.020  1.224
 40Y  C9   C7   single    1.527  0.020  1.527
 40Y  O1   C16  single    1.355  0.020  1.355
 40Y  O1   C17  single    1.429  0.020  1.429
 40Y  C7   C8   single    1.539  0.020  1.539
 40Y  C7   C6   single    1.536  0.020  1.536
 40Y  C15  C16  aromatic  1.384  0.020  1.384
 40Y  C15  C14  aromatic  1.392  0.020  1.392
 40Y  C19  C14  single    1.498  0.020  1.498
 40Y  C19  N1   single    1.340  0.020  1.340
 40Y  C16  C11  aromatic  1.400  0.020  1.400
 40Y  C8   C3   single    1.485  0.020  1.485
 40Y  C14  C13  aromatic  1.392  0.020  1.392
 40Y  C6   C5   single    1.515  0.020  1.515
 40Y  C17  C18  single    1.525  0.020  1.525
 40Y  C3   N    aromatic  1.356  0.020  1.356
 40Y  C3   C4   aromatic  1.379  0.020  1.379
 40Y  C11  N    aromatic  1.405  0.020  1.405
 40Y  C11  C12  aromatic  1.387  0.020  1.387
 40Y  C5   O    double    1.221  0.020  1.221
 40Y  C5   C4   single    1.446  0.020  1.446
 40Y  N    C2   aromatic  1.394  0.020  1.394
 40Y  C4   C1   aromatic  1.435  0.020  1.435
 40Y  C13  C12  aromatic  1.385  0.020  1.385
 40Y  C2   C1   aromatic  1.364  0.020  1.364
 40Y  C2   C18  single    1.486  0.020  1.486
 40Y  C1   C    single    1.491  0.020  1.491
 40Y  N1   H1   single    0.860  0.020  1.020
 40Y  N1   H2   single    0.860  0.020  1.020
 40Y  C6   H3   single    0.970  0.020  1.090
 40Y  C6   H4   single    0.970  0.020  1.090
 40Y  C8   H5   single    0.970  0.020  1.090
 40Y  C8   H6   single    0.970  0.020  1.090
 40Y  C10  H7   single    0.970  0.020  1.090
 40Y  C10  H8   single    0.970  0.020  1.090
 40Y  C10  H9   single    0.970  0.020  1.090
 40Y  C13  H10  single    0.930  0.020  1.080
 40Y  C15  H11  single    0.930  0.020  1.080
 40Y  C17  H12  single    0.970  0.020  1.090
 40Y  C17  H13  single    0.970  0.020  1.090
 40Y  C12  H14  single    0.930  0.020  1.080
 40Y  C18  H15  single    0.970  0.020  1.090
 40Y  C18  H16  single    0.970  0.020  1.090
 40Y  C9   H17  single    0.970  0.020  1.090
 40Y  C9   H18  single    0.970  0.020  1.090
 40Y  C9   H19  single    0.970  0.020  1.090
 40Y  C    H20  single    0.970  0.020  1.090
 40Y  C    H21  single    0.970  0.020  1.090
 40Y  C    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
 40Y  H2   N1   H1   116.90  3.000
 40Y  H2   N1   C19  122.94  3.000
 40Y  H1   N1   C19  119.61  3.000
 40Y  C1   C4   C3   108.35  3.000
 40Y  C1   C4   C5   130.64  3.000
 40Y  C3   C4   C5   120.99  3.000
 40Y  O    C5   C6   121.62  3.000
 40Y  O    C5   C4   123.42  3.000
 40Y  C6   C5   C4   114.94  3.000
 40Y  H4   C6   H3   106.57  3.000
 40Y  H4   C6   C7   109.17  3.000
 40Y  H3   C6   C7   110.31  3.000
 40Y  H4   C6   C5   106.53  3.000
 40Y  H3   C6   C5   109.08  3.000
 40Y  C7   C6   C5   114.80  3.000
 40Y  C9   C7   C10  108.99  3.000
 40Y  C9   C7   C8   109.01  3.000
 40Y  C10  C7   C8   110.20  3.000
 40Y  C8   C7   C6   109.28  3.000
 40Y  C9   C7   C6   109.27  3.000
 40Y  C10  C7   C6   110.06  3.000
 40Y  H6   C8   H5   106.11  3.000
 40Y  H6   C8   C3   109.86  3.000
 40Y  H5   C8   C3   111.31  3.000
 40Y  H6   C8   C7   109.31  3.000
 40Y  H5   C8   C7   109.99  3.000
 40Y  C3   C8   C7   110.17  3.000
 40Y  H9   C10  H8   107.75  3.000
 40Y  H9   C10  H7   107.56  3.000
 40Y  H8   C10  H7   107.64  3.000
 40Y  H9   C10  C7   110.65  3.000
 40Y  H8   C10  C7   110.64  3.000
 40Y  H7   C10  C7   112.42  3.000
 40Y  H10  C13  C12  118.28  3.000
 40Y  H10  C13  C14  121.33  3.000
 40Y  C12  C13  C14  120.36  3.000
 40Y  H11  C15  C16  118.99  3.000
 40Y  H11  C15  C14  120.30  3.000
 40Y  C16  C15  C14  120.67  3.000
 40Y  H13  C17  H12  108.40  3.000
 40Y  H13  C17  C18  109.97  3.000
 40Y  H12  C17  C18  110.42  3.000
 40Y  H13  C17  O1   110.15  3.000
 40Y  H12  C17  O1   104.99  3.000
 40Y  C18  C17  O1   112.73  3.000
 40Y  C14  C19  O2   120.74  3.000
 40Y  C14  C19  N1   116.36  3.000
 40Y  O2   C19  N1   122.90  3.000
 40Y  C19  C14  C15  117.80  3.000
 40Y  C19  C14  C13  122.89  3.000
 40Y  C15  C14  C13  119.28  3.000
 40Y  H14  C12  C11  120.01  3.000
 40Y  H14  C12  C13  119.74  3.000
 40Y  C11  C12  C13  120.24  3.000
 40Y  C11  C16  O1   120.09  3.000
 40Y  C11  C16  C15  119.68  3.000
 40Y  O1   C16  C15  120.16  3.000
 40Y  C16  O1   C17  117.09  3.000
 40Y  H16  C18  H15  105.75  3.000
 40Y  H16  C18  C2   110.22  3.000
 40Y  H15  C18  C2   110.29  3.000
 40Y  H16  C18  C17  109.89  3.000
 40Y  H15  C18  C17  108.05  3.000
 40Y  C2   C18  C17  112.40  3.000
 40Y  C1   C2   N    108.34  3.000
 40Y  C1   C2   C18  132.85  3.000
 40Y  N    C2   C18  118.80  3.000
 40Y  N    C11  C16  118.79  3.000
 40Y  N    C11  C12  121.48  3.000
 40Y  C16  C11  C12  119.72  3.000
 40Y  C3   N    C11  127.34  3.000
 40Y  C11  N    C2   122.85  3.000
 40Y  C3   N    C2   109.81  3.000
 40Y  N    C3   C8   126.88  3.000
 40Y  N    C3   C4   107.31  3.000
 40Y  C8   C3   C4   125.77  3.000
 40Y  C    C1   C2   127.06  3.000
 40Y  C    C1   C4   126.76  3.000
 40Y  C2   C1   C4   106.18  3.000
 40Y  H22  C    H21  107.65  3.000
 40Y  H22  C    H20  106.84  3.000
 40Y  H21  C    H20  107.61  3.000
 40Y  H22  C    C1   111.54  3.000
 40Y  H21  C    C1   111.50  3.000
 40Y  H20  C    C1   111.47  3.000
 40Y  H19  C9   H18  107.81  3.000
 40Y  H19  C9   H17  107.79  3.000
 40Y  H18  C9   H17  107.71  3.000
 40Y  H19  C9   C7   111.56  3.000
 40Y  H18  C9   C7   110.90  3.000
 40Y  H17  C9   C7   110.91  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
 40Y  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 40Y  CONST_02  C12  C13  C14  C15    0.00   0.0  0
 40Y  CONST_03  C11  C12  C13  C14    0.00   0.0  0
 40Y  CONST_04  C3   C4   C1   C2     0.00   0.0  0
 40Y  CONST_05  C1   C4   C3   N      0.00   0.0  0
 40Y  CONST_06  C    C1   C4   C5     0.00   0.0  0
 40Y  CONST_07  C16  C15  C14  C19  180.00   0.0  0
 40Y  CONST_08  C12  C13  C14  C19  180.00   0.0  0
 40Y  CONST_09  C    C1   C4   C3   180.00   0.0  0
 40Y  CONST_10  H11  C15  C14  C13  180.00   0.0  0
 40Y  CONST_11  H10  C13  C14  C15  180.00   0.0  0
 40Y  CONST_12  H14  C12  C13  C14  180.00   0.0  0
 40Y  CONST_13  H1   N1   C19  C14  180.00   0.0  0
 40Y  CONST_14  H2   N1   C19  C14    0.00   0.0  0
 40Y  Var_01    C7   C8   C3   C4   -21.87  30.0  1
 40Y  Var_02    C7   C6   C5   C4    34.06  30.0  1
 40Y  Var_03    C8   C7   C6   C5   -56.15  30.0  1
 40Y  Var_04    C3   C8   C7   C6    47.59  30.0  1
 40Y  Var_05    C3   C4   C5   C6    -4.77  30.0  1
 40Y  Var_06    C15  C14  C19  N1   159.57  30.0  2
 40Y  Var_07    H20  C    C1   C4    59.68  30.0  2
 40Y  Var_08    H7   C10  C7   C6   -62.47  30.0  3
 40Y  Var_09    H17  C9   C7   C6   178.70  30.0  3

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
 40Y  plan-1  N1   0.020
 40Y  plan-1  C19  0.020
 40Y  plan-1  C14  0.020
 40Y  plan-1  H1   0.020
 40Y  plan-1  H2   0.020
 40Y  plan-1  O2   0.020
 40Y  plan-2  C4   0.020
 40Y  plan-2  C5   0.020
 40Y  plan-2  C8   0.020
 40Y  plan-2  C18  0.020
 40Y  plan-2  C2   0.020
 40Y  plan-2  C11  0.020
 40Y  plan-2  N    0.020
 40Y  plan-2  C3   0.020
 40Y  plan-2  C1   0.020
 40Y  plan-2  C    0.020
 40Y  plan-3  C13  0.020
 40Y  plan-3  C15  0.020
 40Y  plan-3  C19  0.020
 40Y  plan-3  C14  0.020
 40Y  plan-3  C12  0.020
 40Y  plan-3  C16  0.020
 40Y  plan-3  O1   0.020
 40Y  plan-3  C11  0.020
 40Y  plan-3  N    0.020
 40Y  plan-3  H10  0.020
 40Y  plan-3  H11  0.020
 40Y  plan-3  H14  0.020
 40Y  plan-4  C4   0.020
 40Y  plan-4  C5   0.020
 40Y  plan-4  C6   0.020
 40Y  plan-4  O    0.020

