# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 00:08:10 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (4S)-1-methyl-4-phenyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C[C@H](Nc2ccccc12)c3ccccc3
#
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
 2NJ  2NJ  (4S)-1-methyl-4-phenyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one  ligand  35  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2NJ
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
 2NJ  O    O  O     0  -0.482  -1.9567  -2.9422  -0.6153
 2NJ  C9   C  C     0   0.527  -1.5863  -1.7819  -0.5250
 2NJ  N    N  NT    0  -0.532  -2.4240  -0.7873  -0.1355
 2NJ  C    C  CH3   0  -0.547  -3.8195  -1.1004   0.1331
 2NJ  C8   C  CH2   0  -0.621  -0.1693  -1.3708  -0.8500
 2NJ  C7   C  CH1   0  -0.179   0.6420  -1.0941   0.4138
 2NJ  C10  C  CR6   0   0.163   2.0471  -0.6382   0.0815
 2NJ  C15  C  CR16  0  -0.326   3.1389  -1.3513   0.5657
 2NJ  C14  C  CR16  0  -0.238   4.4377  -0.9358   0.2973
 2NJ  C13  C  CR16  0  -0.269   4.6583   0.2079  -0.4562
 2NJ  C12  C  CR16  0  -0.239   3.5743   0.9294  -0.9433
 2NJ  C11  C  CR16  0  -0.306   2.2795   0.5086  -0.6786
 2NJ  N1   N  NH1   0  -0.661  -0.0726  -0.1466   1.2727
 2NJ  C6   C  CR6   0   0.277  -0.8366   0.8711   0.6999
 2NJ  C1   C  CR6   0   0.297  -2.0045   0.5550  -0.0122
 2NJ  C5   C  CR16  0  -0.336  -0.5100   2.2157   0.8797
 2NJ  C4   C  CR16  0  -0.255  -1.3197   3.2251   0.3836
 2NJ  C3   C  CR16  0  -0.273  -2.4639   2.9051  -0.3339
 2NJ  C2   C  CR16  0  -0.300  -2.7952   1.5735  -0.5330
 2NJ  H1   H  HCH3  0   0.247  -4.4289  -1.0628  -0.7712
 2NJ  H2   H  HCH3  0   0.263  -3.9008  -2.0961   0.5600
 2NJ  H3   H  HCH3  0   0.254  -4.2156  -0.3861   0.8504
 2NJ  H4   H  HCH2  0   0.296   0.3061  -2.1828  -1.3981
 2NJ  H5   H  HCH2  0   0.279  -0.1685  -0.4942  -1.5017
 2NJ  H6   H  HCH1  0   0.268   0.7207  -2.0321   0.9713
 2NJ  H7   H  HCR6  0   0.253   2.9726  -2.2405   1.1631
 2NJ  H8   H  HCR6  0   0.256   5.2752  -1.5059   0.6788
 2NJ  H9   H  HCR6  0   0.257   5.6680   0.5379  -0.6632
 2NJ  H10  H  HCR6  0   0.257   3.7382   1.8223  -1.5327
 2NJ  H11  H  HCR6  0   0.251   1.4491   1.0829  -1.0717
 2NJ  H12  H  HNH1  0   0.376   0.5386   0.2130   1.9929
 2NJ  H13  H  HCR6  0   0.260   0.3922   2.4655   1.4259
 2NJ  H14  H  HCR6  0   0.257  -1.0469   4.2594   0.5465
 2NJ  H15  H  HCR6  0   0.256  -3.0972   3.6838  -0.7376
 2NJ  H16  H  HCR6  0   0.270  -3.6897   1.3210  -1.0887

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
 2NJ  C    N    single    1.455  0.020  1.455
 2NJ  C2   C3   aromatic  1.387  0.020  1.387
 2NJ  C2   C1   aromatic  1.391  0.020  1.391
 2NJ  C3   C4   aromatic  1.388  0.020  1.388
 2NJ  N    C1   single    1.412  0.020  1.412
 2NJ  N    C9   single    1.357  0.020  1.357
 2NJ  C1   C6   aromatic  1.404  0.020  1.404
 2NJ  O    C9   double    1.221  0.020  1.221
 2NJ  C9   C8   single    1.511  0.020  1.511
 2NJ  C4   C5   aromatic  1.386  0.020  1.386
 2NJ  C8   C7   single    1.527  0.020  1.527
 2NJ  C6   C5   aromatic  1.395  0.020  1.395
 2NJ  C6   N1   single    1.396  0.020  1.396
 2NJ  N1   C7   single    1.465  0.020  1.465
 2NJ  C7   C10  single    1.514  0.020  1.514
 2NJ  C15  C10  aromatic  1.391  0.020  1.391
 2NJ  C15  C14  aromatic  1.390  0.020  1.390
 2NJ  C10  C11  aromatic  1.395  0.020  1.395
 2NJ  C14  C13  aromatic  1.387  0.020  1.387
 2NJ  C11  C12  aromatic  1.387  0.020  1.387
 2NJ  C13  C12  aromatic  1.390  0.020  1.390
 2NJ  C    H1   single    0.970  0.020  1.090
 2NJ  C    H2   single    0.970  0.020  1.090
 2NJ  C    H3   single    0.970  0.020  1.090
 2NJ  C8   H4   single    0.970  0.020  1.090
 2NJ  C8   H5   single    0.970  0.020  1.090
 2NJ  C7   H6   single    0.970  0.020  1.090
 2NJ  C15  H7   single    0.930  0.020  1.080
 2NJ  C14  H8   single    0.930  0.020  1.080
 2NJ  C13  H9   single    0.930  0.020  1.080
 2NJ  C12  H10  single    0.930  0.020  1.080
 2NJ  C11  H11  single    0.930  0.020  1.080
 2NJ  N1   H12  single    0.890  0.020  1.040
 2NJ  C5   H13  single    0.930  0.020  1.080
 2NJ  C4   H14  single    0.930  0.020  1.080
 2NJ  C3   H15  single    0.930  0.020  1.080
 2NJ  C2   H16  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
 2NJ  C8   C9   N    116.18  3.000
 2NJ  C8   C9   O    121.80  3.000
 2NJ  N    C9   O    122.02  3.000
 2NJ  C1   N    C    118.26  3.000
 2NJ  C1   N    C9   122.57  3.000
 2NJ  C    N    C9   119.15  3.000
 2NJ  H3   C    H2   108.40  3.000
 2NJ  H3   C    H1   108.71  3.000
 2NJ  H2   C    H1   108.40  3.000
 2NJ  H3   C    N    109.26  3.000
 2NJ  H2   C    N    109.96  3.000
 2NJ  H1   C    N    112.03  3.000
 2NJ  H5   C8   H4   107.32  3.000
 2NJ  H5   C8   C7   110.36  3.000
 2NJ  H4   C8   C7   108.65  3.000
 2NJ  H5   C8   C9   110.33  3.000
 2NJ  H4   C8   C9   108.35  3.000
 2NJ  C7   C8   C9   111.69  3.000
 2NJ  H6   C7   N1   106.91  3.000
 2NJ  H6   C7   C10  107.66  3.000
 2NJ  N1   C7   C10  112.74  3.000
 2NJ  H6   C7   C8   107.73  3.000
 2NJ  C10  C7   C8   111.47  3.000
 2NJ  N1   C7   C8   110.07  3.000
 2NJ  C11  C10  C15  118.70  3.000
 2NJ  C11  C10  C7   121.44  3.000
 2NJ  C15  C10  C7   119.84  3.000
 2NJ  H7   C15  C14  119.67  3.000
 2NJ  H7   C15  C10  119.46  3.000
 2NJ  C14  C15  C10  120.86  3.000
 2NJ  H8   C14  C13  120.17  3.000
 2NJ  H8   C14  C15  119.83  3.000
 2NJ  C13  C14  C15  119.99  3.000
 2NJ  H9   C13  C12  120.15  3.000
 2NJ  H9   C13  C14  120.24  3.000
 2NJ  C12  C13  C14  119.62  3.000
 2NJ  H10  C12  C11  119.71  3.000
 2NJ  H10  C12  C13  120.06  3.000
 2NJ  C11  C12  C13  120.24  3.000
 2NJ  H11  C11  C12  119.04  3.000
 2NJ  H11  C11  C10  120.37  3.000
 2NJ  C12  C11  C10  120.59  3.000
 2NJ  H12  N1   C6   111.35  3.000
 2NJ  H12  N1   C7   110.67  3.000
 2NJ  C6   N1   C7   119.87  3.000
 2NJ  C5   C6   C1   118.50  3.000
 2NJ  C5   C6   N1   121.44  3.000
 2NJ  C1   C6   N1   119.96  3.000
 2NJ  C2   C1   C6   119.87  3.000
 2NJ  C6   C1   N    120.37  3.000
 2NJ  C2   C1   N    119.65  3.000
 2NJ  H13  C5   C4   119.93  3.000
 2NJ  H13  C5   C6   118.81  3.000
 2NJ  C4   C5   C6   121.26  3.000
 2NJ  H14  C4   C3   120.40  3.000
 2NJ  H14  C4   C5   119.67  3.000
 2NJ  C3   C4   C5   119.92  3.000
 2NJ  H15  C3   C2   119.85  3.000
 2NJ  H15  C3   C4   120.64  3.000
 2NJ  C2   C3   C4   119.51  3.000
 2NJ  H16  C2   C3   119.67  3.000
 2NJ  H16  C2   C1   119.41  3.000
 2NJ  C3   C2   C1   120.91  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
 2NJ  CONST_01  C13  C14  C15  C10    0.00  0.0  0
 2NJ  CONST_02  C13  C12  C11  C10    0.00  0.0  0
 2NJ  CONST_03  C12  C11  C10  C15    0.00  0.0  0
 2NJ  CONST_04  C12  C13  C14  C15    0.00  0.0  0
 2NJ  CONST_05  C11  C10  C15  C14    0.00  0.0  0
 2NJ  CONST_06  C11  C12  C13  C14    0.00  0.0  0
 2NJ  CONST_07  C3   C4   C5   C6     0.00  0.0  0
 2NJ  CONST_08  C4   C3   C2   C1     0.00  0.0  0
 2NJ  CONST_09  C2   C3   C4   C5     0.00  0.0  0
 2NJ  CONST_10  C14  C15  C10  C7   180.00  0.0  0
 2NJ  CONST_11  C12  C11  C10  C7   180.00  0.0  0
 2NJ  CONST_12  H7   C15  C10  C7     0.00  0.0  0
 2NJ  CONST_13  H11  C11  C10  C7     0.00  0.0  0
 2NJ  CONST_14  H8   C14  C15  C10  180.00  0.0  0
 2NJ  CONST_15  H10  C12  C11  C10  180.00  0.0  0
 2NJ  CONST_16  H9   C13  C14  C15  180.00  0.0  0
 2NJ  CONST_17  H14  C4   C5   C6   180.00  0.0  0
 2NJ  CONST_18  H15  C3   C2   C1   180.00  0.0  0
 2NJ  CONST_19  H16  C2   C3   C4   180.00  0.0  0
 2NJ  CONST_20  H13  C5   C4   C3   180.00  0.0  0

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
 2NJ  chir_01  C7  C8  N1  C10  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
 2NJ  plan-1  C7   0.020
 2NJ  plan-1  C10  0.020
 2NJ  plan-1  C15  0.020
 2NJ  plan-1  C14  0.020
 2NJ  plan-1  C13  0.020
 2NJ  plan-1  C12  0.020
 2NJ  plan-1  C11  0.020
 2NJ  plan-1  H7   0.020
 2NJ  plan-1  H8   0.020
 2NJ  plan-1  H9   0.020
 2NJ  plan-1  H10  0.020
 2NJ  plan-1  H11  0.020
 2NJ  plan-2  N    0.020
 2NJ  plan-2  N1   0.020
 2NJ  plan-2  C6   0.020
 2NJ  plan-2  C1   0.020
 2NJ  plan-2  C5   0.020
 2NJ  plan-2  C4   0.020
 2NJ  plan-2  C3   0.020
 2NJ  plan-2  C2   0.020
 2NJ  plan-2  H13  0.020
 2NJ  plan-2  H14  0.020
 2NJ  plan-2  H15  0.020
 2NJ  plan-2  H16  0.020
 2NJ  plan-3  O    0.020
 2NJ  plan-3  C9   0.020
 2NJ  plan-3  N    0.020
 2NJ  plan-3  C    0.020
 2NJ  plan-3  C8   0.020
 2NJ  plan-3  C1   0.020

