# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 21:32:14 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (3~{R})-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H](Cc2ccccc2)C(=O)Nc3ccccc3C1=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
 8R0  8R0  (3~{R})-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione  ligand  37  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8R0
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
 8R0  C4   C  C     0   0.550   0.6232   0.1468  -1.4990
 8R0  C7   C  CH1   0  -0.268  -0.1947  -1.4578   0.2070
 8R0  C8   C  CH2   0  -0.543  -0.6938  -0.4686   1.2780
 8R0  C10  C  CR16  0  -0.307  -2.0848   1.3637   0.2602
 8R0  C13  C  CR16  0  -0.239  -4.4119  -0.0934   0.6296
 8R0  C15  C  C     0   0.537   1.0991  -2.1575   0.5870
 8R0  C20  C  CR16  0  -0.247   3.5243   1.9719   1.0642
 8R0  C12  C  CR16  0  -0.268  -4.4680   1.1504   0.0128
 8R0  C11  C  CR16  0  -0.242  -3.3008   1.8796  -0.1686
 8R0  C14  C  CR16  0  -0.300  -3.1946  -0.6057   1.0548
 8R0  C9   C  CR6   0   0.153  -2.0166   0.1159   0.8728
 8R0  O16  O  O     0  -0.445   1.1212  -3.3304   0.9047
 8R0  N17  N  NH1   0  -0.723   2.2331  -1.4134   0.5504
 8R0  C18  C  CR6   0   0.357   2.3565  -0.0321   0.3882
 8R0  C19  C  CR16  0  -0.316   3.3292   0.6082   1.1585
 8R0  C1   C  CR16  0  -0.255   2.7475   2.7263   0.1927
 8R0  C2   C  CR16  0  -0.273   1.8071   2.0922  -0.5944
 8R0  C3   C  CR6   0  -0.097   1.5934   0.7130  -0.5166
 8R0  O5   O  O     0  -0.481   0.5213   0.6713  -2.6007
 8R0  N6   N  NT    0  -0.459  -0.1157  -0.9252  -1.1437
 8R0  C23  C  CH3   0  -0.536  -1.0393  -1.5039  -2.1051
 8R0  H1   H  HCH1  0   0.316  -0.9337  -2.2571   0.1650
 8R0  H2   H  HCH2  0   0.281  -0.7894  -1.0275   2.2116
 8R0  H3   H  HCH2  0   0.276   0.0286   0.3263   1.4594
 8R0  H5   H  HCR6  0   0.255  -5.3191  -0.6639   0.7823
 8R0  H6   H  HCR6  0   0.271   4.2779   2.4472   1.6779
 8R0  H7   H  HCR6  0   0.256  -5.4173   1.5513  -0.3173
 8R0  H8   H  HCR6  0   0.255  -3.3354   2.8522  -0.6428
 8R0  H9   H  HCR6  0   0.251  -3.1593  -1.5771   1.5355
 8R0  H10  H  HNH1  0   0.414   3.0572  -1.8897   0.8935
 8R0  H11  H  HCR6  0   0.280   3.9256   0.0229   1.8473
 8R0  H12  H  HCR6  0   0.265   2.8853   3.7964   0.1192
 8R0  H13  H  HCR6  0   0.270   1.2215   2.6719  -1.2950
 8R0  H16  H  HCH3  0   0.265  -0.7626  -1.2230  -3.1151
 8R0  H14  H  HCH3  0   0.253  -1.0116  -2.5896  -2.0269
 8R0  H15  H  HCH3  0   0.248  -2.0608  -1.1693  -1.9147
 8R0  H4   H  HCR6  0   0.245  -1.1794   1.9444   0.1258

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
 8R0  C20  C19  aromatic  1.381  0.020  1.381
 8R0  C20  C1   aromatic  1.390  0.020  1.390
 8R0  C19  C18  aromatic  1.396  0.020  1.396
 8R0  N17  C18  single    1.396  0.020  1.396
 8R0  N17  C15  single    1.357  0.020  1.357
 8R0  C18  C3   aromatic  1.399  0.020  1.399
 8R0  C1   C2   aromatic  1.381  0.020  1.381
 8R0  O16  C15  double    1.215  0.020  1.215
 8R0  C15  C7   single    1.519  0.020  1.519
 8R0  C2   C3   aromatic  1.398  0.020  1.398
 8R0  C3   C4   single    1.492  0.020  1.492
 8R0  C7   C8   single    1.541  0.020  1.541
 8R0  C7   N6   single    1.454  0.020  1.454
 8R0  C8   C9   single    1.502  0.020  1.502
 8R0  C4   N6   single    1.350  0.020  1.350
 8R0  C4   O5   double    1.224  0.020  1.224
 8R0  N6   C23  single    1.453  0.020  1.453
 8R0  C9   C14  aromatic  1.393  0.020  1.393
 8R0  C9   C10  aromatic  1.392  0.020  1.392
 8R0  C14  C13  aromatic  1.388  0.020  1.388
 8R0  C10  C11  aromatic  1.389  0.020  1.389
 8R0  C13  C12  aromatic  1.389  0.020  1.389
 8R0  C11  C12  aromatic  1.388  0.020  1.388
 8R0  C7   H1   single    0.970  0.020  1.090
 8R0  C8   H2   single    0.970  0.020  1.090
 8R0  C8   H3   single    0.970  0.020  1.090
 8R0  C10  H4   single    0.930  0.020  1.080
 8R0  C13  H5   single    0.930  0.020  1.080
 8R0  C20  H6   single    0.930  0.020  1.080
 8R0  C12  H7   single    0.930  0.020  1.080
 8R0  C11  H8   single    0.930  0.020  1.080
 8R0  C14  H9   single    0.930  0.020  1.080
 8R0  N17  H10  single    0.860  0.020  1.020
 8R0  C19  H11  single    0.930  0.020  1.080
 8R0  C1   H12  single    0.930  0.020  1.080
 8R0  C2   H13  single    0.930  0.020  1.080
 8R0  C23  H16  single    0.970  0.020  1.090
 8R0  C23  H14  single    0.970  0.020  1.090
 8R0  C23  H15  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
 8R0  N6   C4   O5   122.11  3.000
 8R0  O5   C4   C3   118.94  3.000
 8R0  N6   C4   C3   118.95  3.000
 8R0  H1   C7   N6   105.65  3.000
 8R0  H1   C7   C15  104.44  3.000
 8R0  N6   C7   C15  110.78  3.000
 8R0  H1   C7   C8   106.14  3.000
 8R0  N6   C7   C8   115.35  3.000
 8R0  C15  C7   C8   113.43  3.000
 8R0  H3   C8   H2   106.80  3.000
 8R0  H3   C8   C9   110.19  3.000
 8R0  H2   C8   C9   110.65  3.000
 8R0  H3   C8   C7   111.68  3.000
 8R0  H2   C8   C7   107.09  3.000
 8R0  C9   C8   C7   110.34  3.000
 8R0  H4   C10  C9   119.60  3.000
 8R0  H4   C10  C11  119.61  3.000
 8R0  C9   C10  C11  120.79  3.000
 8R0  H5   C13  C14  119.83  3.000
 8R0  H5   C13  C12  120.04  3.000
 8R0  C14  C13  C12  120.13  3.000
 8R0  N17  C15  O16  121.41  3.000
 8R0  O16  C15  C7   121.70  3.000
 8R0  N17  C15  C7   116.90  3.000
 8R0  H6   C20  C1   120.43  3.000
 8R0  H6   C20  C19  119.58  3.000
 8R0  C1   C20  C19  119.99  3.000
 8R0  H7   C12  C11  120.21  3.000
 8R0  H7   C12  C13  120.16  3.000
 8R0  C11  C12  C13  119.63  3.000
 8R0  H8   C11  C12  120.16  3.000
 8R0  H8   C11  C10  119.80  3.000
 8R0  C12  C11  C10  120.04  3.000
 8R0  H9   C14  C9   119.62  3.000
 8R0  H9   C14  C13  119.68  3.000
 8R0  C9   C14  C13  120.70  3.000
 8R0  C14  C9   C10  118.71  3.000
 8R0  C10  C9   C8   120.72  3.000
 8R0  C14  C9   C8   120.52  3.000
 8R0  H10  N17  C18  115.67  3.000
 8R0  H10  N17  C15  114.42  3.000
 8R0  C18  N17  C15  128.28  3.000
 8R0  C3   C18  C19  119.52  3.000
 8R0  C3   C18  N17  123.64  3.000
 8R0  C19  C18  N17  116.81  3.000
 8R0  H11  C19  C18  119.13  3.000
 8R0  H11  C19  C20  119.96  3.000
 8R0  C18  C19  C20  120.91  3.000
 8R0  H12  C1   C2   120.17  3.000
 8R0  H12  C1   C20  120.56  3.000
 8R0  C2   C1   C20  119.26  3.000
 8R0  H13  C2   C3   118.83  3.000
 8R0  H13  C2   C1   119.46  3.000
 8R0  C3   C2   C1   121.71  3.000
 8R0  C2   C3   C18  118.57  3.000
 8R0  C2   C3   C4   115.92  3.000
 8R0  C18  C3   C4   125.34  3.000
 8R0  C23  N6   C7   115.73  3.000
 8R0  C23  N6   C4   119.35  3.000
 8R0  C7   N6   C4   124.42  3.000
 8R0  H15  C23  H14  108.48  3.000
 8R0  H15  C23  H16  108.78  3.000
 8R0  H14  C23  H16  108.59  3.000
 8R0  H15  C23  N6   110.93  3.000
 8R0  H14  C23  N6   109.47  3.000
 8R0  H16  C23  N6   110.54  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
 8R0  CONST_01  C13  C14  C9   C10    0.00   0.0  0
 8R0  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 8R0  CONST_03  C3   C2   C1   C20    0.00   0.0  0
 8R0  CONST_04  C9   C14  C13  C12    0.00   0.0  0
 8R0  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 8R0  CONST_06  C14  C9   C10  C11    0.00   0.0  0
 8R0  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 8R0  CONST_08  C1   C20  C19  C18    0.00   0.0  0
 8R0  CONST_09  C2   C1   C20  C19    0.00   0.0  0
 8R0  CONST_10  C13  C14  C9   C8   180.00   0.0  0
 8R0  CONST_11  C11  C10  C9   C8   180.00   0.0  0
 8R0  CONST_12  H9   C14  C9   C10  180.00   0.0  0
 8R0  CONST_13  H7   C12  C11  C10  180.00   0.0  0
 8R0  CONST_14  H8   C11  C12  C13  180.00   0.0  0
 8R0  CONST_15  H13  C2   C1   C20  180.00   0.0  0
 8R0  CONST_16  H4   C10  C11  C12  180.00   0.0  0
 8R0  CONST_17  H5   C13  C12  C11  180.00   0.0  0
 8R0  CONST_18  H6   C20  C19  C18  180.00   0.0  0
 8R0  CONST_19  H12  C1   C20  C19  180.00   0.0  0
 8R0  CONST_20  H11  C19  C20  C1   180.00   0.0  0
 8R0  Var_01    C14  C9   C8   C7    79.71  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
 8R0  chir_01  C7  C15  C8  N6  negativ

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
 8R0  plan-1  C8   0.020
 8R0  plan-1  C10  0.020
 8R0  plan-1  C13  0.020
 8R0  plan-1  C12  0.020
 8R0  plan-1  C11  0.020
 8R0  plan-1  C14  0.020
 8R0  plan-1  C9   0.020
 8R0  plan-1  H5   0.020
 8R0  plan-1  H7   0.020
 8R0  plan-1  H8   0.020
 8R0  plan-1  H9   0.020
 8R0  plan-1  H4   0.020
 8R0  plan-2  C4   0.020
 8R0  plan-2  C20  0.020
 8R0  plan-2  N17  0.020
 8R0  plan-2  C18  0.020
 8R0  plan-2  C19  0.020
 8R0  plan-2  C1   0.020
 8R0  plan-2  C2   0.020
 8R0  plan-2  C3   0.020
 8R0  plan-2  H6   0.020
 8R0  plan-2  H11  0.020
 8R0  plan-2  H12  0.020
 8R0  plan-2  H13  0.020
 8R0  plan-3  C4   0.020
 8R0  plan-3  C7   0.020
 8R0  plan-3  C3   0.020
 8R0  plan-3  O5   0.020
 8R0  plan-3  N6   0.020
 8R0  plan-3  C23  0.020
 8R0  plan-4  C7   0.020
 8R0  plan-4  C15  0.020
 8R0  plan-4  O16  0.020
 8R0  plan-4  N17  0.020
 8R0  plan-4  C18  0.020
 8R0  plan-4  H10  0.020

