# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 21:48:36 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (4R)-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC(=O)Nc2ccccc2N1
#
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
 98  98  (4R)-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one  ligand  25  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_98
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
 98  C1   C  CH3   0  -0.664   1.3239  -2.7114   0.6609
 98  C2   C  CH1   0  -0.086   1.5174  -1.4138  -0.1147
 98  C3   C  CH2   0  -0.618   1.7827  -0.2554   0.8434
 98  C4   C  C     0   0.502   1.7822   1.0909   0.1637
 98  O    O  O     0  -0.477   2.7996   1.7314  -0.0491
 98  N1   N  NH1   0  -0.704   0.5592   1.5728  -0.1647
 98  C5   C  CR6   0   0.318  -0.6560   0.8797  -0.0649
 98  C10  C  CR16  0  -0.315  -1.7941   1.5548   0.3604
 98  C9   C  CR16  0  -0.273  -3.0288   0.9237   0.3766
 98  C8   C  CR16  0  -0.257  -3.1225  -0.4038  -0.0173
 98  C7   C  CR16  0  -0.341  -1.9857  -1.0896  -0.4176
 98  C6   C  CR6   0   0.277  -0.7399  -0.4637  -0.4648
 98  N2   N  NH1   0  -0.671   0.3851  -1.1040  -0.9900
 98  H1   H  HCH3  0   0.238   1.1866  -3.5539  -0.0188
 98  H2   H  HCH3  0   0.234   2.1937  -2.9267   1.2835
 98  H3   H  HCH3  0   0.227   0.4495  -2.6510   1.3116
 98  H4   H  HCH1  0   0.249   2.3907  -1.5211  -0.7640
 98  H5   H  HCH2  0   0.269   1.0357  -0.2593   1.6441
 98  H6   H  HCH2  0   0.285   2.7549  -0.4054   1.3110
 98  H7   H  HNH1  0   0.400   0.5261   2.5204  -0.5148
 98  H8   H  HCR6  0   0.266  -1.7087   2.5917   0.6622
 98  H9   H  HCR6  0   0.255  -3.9084   1.4662   0.6964
 98  H10  H  HCR6  0   0.256  -4.0785  -0.9111  -0.0079
 98  H11  H  HCR6  0   0.258  -2.0616  -2.1272  -0.7215
 98  H12  H  HNH1  0   0.372   0.1197  -1.9280  -1.5134

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
 98  C9   C10  aromatic  1.387  0.020  1.387
 98  C9   C8   aromatic  1.388  0.020  1.388
 98  C3   C4   single    1.508  0.020  1.508
 98  C3   C2   single    1.527  0.020  1.527
 98  C10  C5   aromatic  1.390  0.020  1.390
 98  C8   C7   aromatic  1.387  0.020  1.387
 98  C4   O    double    1.221  0.020  1.221
 98  C4   N1   single    1.355  0.020  1.355
 98  C5   N1   single    1.402  0.020  1.402
 98  C5   C6   aromatic  1.404  0.020  1.404
 98  C7   C6   aromatic  1.395  0.020  1.395
 98  C6   N2   single    1.397  0.020  1.397
 98  C2   N2   single    1.464  0.020  1.464
 98  C2   C1   single    1.524  0.020  1.524
 98  C1   H1   single    0.970  0.020  1.090
 98  C1   H2   single    0.970  0.020  1.090
 98  C1   H3   single    0.970  0.020  1.090
 98  C2   H4   single    0.970  0.020  1.090
 98  C3   H5   single    0.970  0.020  1.090
 98  C3   H6   single    0.970  0.020  1.090
 98  N1   H7   single    0.860  0.020  1.020
 98  C10  H8   single    0.930  0.020  1.080
 98  C9   H9   single    0.930  0.020  1.080
 98  C8   H10  single    0.930  0.020  1.080
 98  C7   H11  single    0.930  0.020  1.080
 98  N2   H12  single    0.890  0.020  1.040

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
 98  H3   C1   H2   108.02  3.000
 98  H3   C1   H1   108.25  3.000
 98  H2   C1   H1   107.66  3.000
 98  H3   C1   C2   110.97  3.000
 98  H2   C1   C2   110.93  3.000
 98  H1   C1   C2   110.88  3.000
 98  H4   C2   N2   106.46  3.000
 98  H4   C2   C3   107.96  3.000
 98  N2   C2   C3   110.43  3.000
 98  H4   C2   C1   108.66  3.000
 98  N2   C2   C1   112.72  3.000
 98  C3   C2   C1   110.41  3.000
 98  H6   C3   H5   107.13  3.000
 98  H6   C3   C4   108.46  3.000
 98  H5   C3   C4   109.42  3.000
 98  H6   C3   C2   108.67  3.000
 98  H5   C3   C2   109.73  3.000
 98  C4   C3   C2   113.23  3.000
 98  N1   C4   O    121.56  3.000
 98  N1   C4   C3   115.28  3.000
 98  O    C4   C3   123.13  3.000
 98  H7   N1   C5   117.36  3.000
 98  H7   N1   C4   116.55  3.000
 98  C5   N1   C4   126.10  3.000
 98  C6   C5   C10  120.19  3.000
 98  C6   C5   N1   120.28  3.000
 98  C10  C5   N1   119.42  3.000
 98  H8   C10  C9   120.17  3.000
 98  H8   C10  C5   119.05  3.000
 98  C9   C10  C5   120.77  3.000
 98  H9   C9   C8   120.58  3.000
 98  H9   C9   C10  119.94  3.000
 98  C8   C9   C10  119.48  3.000
 98  H10  C8   C7   119.66  3.000
 98  H10  C8   C9   120.36  3.000
 98  C7   C8   C9   119.97  3.000
 98  H11  C7   C6   118.85  3.000
 98  H11  C7   C8   119.80  3.000
 98  C6   C7   C8   121.33  3.000
 98  N2   C6   C7   121.75  3.000
 98  N2   C6   C5   119.84  3.000
 98  C7   C6   C5   118.23  3.000
 98  H12  N2   C6   110.89  3.000
 98  H12  N2   C2   109.87  3.000
 98  C6   N2   C2   119.67  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
 98  CONST_01  C8   C9   C10  C5     0.00  0.0  0
 98  CONST_02  C7   C8   C9   C10    0.00  0.0  0
 98  CONST_03  C6   C7   C8   C9     0.00  0.0  0
 98  CONST_04  H9   C9   C10  C5   180.00  0.0  0
 98  CONST_05  H10  C8   C9   C10  180.00  0.0  0
 98  CONST_06  H11  C7   C8   C9   180.00  0.0  0
 98  CONST_07  H8   C10  C9   C8   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
 98  chir_01  C2  C3  N2  C1  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
 98  plan-1  C3   0.020
 98  plan-1  C4   0.020
 98  plan-1  O    0.020
 98  plan-1  N1   0.020
 98  plan-1  C5   0.020
 98  plan-1  H7   0.020
 98  plan-2  N1   0.020
 98  plan-2  C5   0.020
 98  plan-2  C10  0.020
 98  plan-2  C9   0.020
 98  plan-2  C8   0.020
 98  plan-2  C7   0.020
 98  plan-2  C6   0.020
 98  plan-2  N2   0.020
 98  plan-2  H8   0.020
 98  plan-2  H9   0.020
 98  plan-2  H10  0.020
 98  plan-2  H11  0.020

