# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 02:01:48 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3S)-3-(4-methoxybenzyl)-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C[C@@H]2N(C)C(=O)c3ccccc3NC2=O)cc1
#
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
 58D  58D  (3S)-3-(4-methoxybenzyl)-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione  ligand  41  23  .  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_58D
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
 58D  C4   C  C     0   0.554  -1.1428   0.1714  -1.4597
 58D  C7   C  CH1   0  -0.263  -0.6342  -1.5346   0.2645
 58D  C8   C  CH2   0  -0.544  -0.0333  -0.6234   1.3516
 58D  C10  C  CR16  0  -0.286   2.4364  -1.0442   1.1217
 58D  C13  C  CR16  0  -0.331   2.8543   1.4430  -0.0023
 58D  C15  C  C     0   0.537  -2.0240  -2.0440   0.6005
 58D  C20  C  CR16  0  -0.246  -3.9076   2.3764   0.9490
 58D  C22  C  CH3   0  -0.436   6.2655   0.1984  -0.0757
 58D  C12  C  CR6   0   0.369   3.9337   0.5727   0.1576
 58D  C11  C  CR16  0  -0.367   3.7177  -0.6805   0.7263
 58D  C14  C  CR16  0  -0.292   1.5872   1.0611   0.3996
 58D  C9   C  CR6   0   0.128   1.3527  -0.1889   0.9694
 58D  O16  O  O     0  -0.446  -2.2211  -3.1982   0.9271
 58D  N17  N  NH1   0  -0.723  -3.0425  -1.1511   0.5162
 58D  C18  C  CR6   0   0.359  -2.9737   0.2320   0.3405
 58D  C19  C  CR16  0  -0.318  -3.8974   1.0000   1.0535
 58D  C1   C  CR16  0  -0.255  -2.9886   3.0179   0.1265
 58D  C2   C  CR16  0  -0.272  -2.0970   2.2609  -0.6067
 58D  C3   C  CR6   0  -0.098  -2.0720   0.8656  -0.5211
 58D  O5   O  O     0  -0.481  -0.9054   0.6827  -2.5466
 58D  N6   N  NT    0  -0.460  -0.5948  -1.0038  -1.0887
 58D  C23  C  CH3   0  -0.533   0.2729  -1.6982  -2.0258
 58D  H1   H  HCH1  0   0.311  -0.0122  -2.4282   0.2470
 58D  H2   H  HCH2  0   0.274  -0.6569   0.2484   1.5475
 58D  H3   H  HCH2  0   0.279  -0.0114  -1.2049   2.2764
 58D  H4   H  HCR6  0   0.254   2.2882  -2.0244   1.5612
 58D  H5   H  HCR6  0   0.261   3.0171   2.4209  -0.4388
 58D  H6   H  HCR6  0   0.271  -4.6283   2.9495   1.5170
 58D  H7   H  HCH3  0   0.228   6.4287  -0.0495   0.9765
 58D  H8   H  HCH3  0   0.227   6.1891  -0.7302  -0.6479
 58D  H9   H  HCH3  0   0.259   7.1213   0.7622  -0.4390
 58D  H10  H  HCR6  0   0.277   4.5272  -1.3831   0.8711
 58D  H11  H  HCR6  0   0.247   0.7678   1.7602   0.2756
 58D  H12  H  HNH1  0   0.414  -3.9359  -1.5055   0.8322
 58D  H13  H  HCR6  0   0.280  -4.6065   0.5029   1.7042
 58D  H14  H  HCR6  0   0.264  -2.9791   4.0963   0.0474
 58D  H15  H  HCR6  0   0.269  -1.4003   2.7544  -1.2708
 58D  H16  H  HCH3  0   0.262  -0.0082  -1.4697  -3.0486
 58D  H17  H  HCH3  0   0.247   1.3187  -1.4204  -1.8784
 58D  H18  H  HCH3  0   0.252   0.1766  -2.7713  -1.8756
 58D  O21  O  O2    0  -0.472   5.1337   1.0253  -0.2552

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
 58D  C19  C20  aromatic  1.380  0.020  1.380
 58D  C19  C18  aromatic  1.397  0.020  1.397
 58D  C20  C1   aromatic  1.390  0.020  1.390
 58D  N17  C18  single    1.396  0.020  1.396
 58D  N17  C15  single    1.357  0.020  1.357
 58D  C18  C3   aromatic  1.399  0.020  1.399
 58D  C1   C2   aromatic  1.380  0.020  1.380
 58D  O16  C15  double    1.216  0.020  1.216
 58D  C15  C7   single    1.518  0.020  1.518
 58D  C3   C2   aromatic  1.398  0.020  1.398
 58D  C3   C4   single    1.492  0.020  1.492
 58D  C7   C8   single    1.540  0.020  1.540
 58D  C7   N6   single    1.454  0.020  1.454
 58D  C4   N6   single    1.349  0.020  1.349
 58D  C4   O5   double    1.224  0.020  1.224
 58D  C8   C9   single    1.502  0.020  1.502
 58D  N6   C23  single    1.454  0.020  1.454
 58D  C9   C14  aromatic  1.394  0.020  1.394
 58D  C9   C10  aromatic  1.389  0.020  1.389
 58D  C14  C13  aromatic  1.383  0.020  1.383
 58D  C10  C11  aromatic  1.389  0.020  1.389
 58D  C13  C12  aromatic  1.396  0.020  1.396
 58D  C11  C12  aromatic  1.393  0.020  1.393
 58D  C12  O21  single    1.347  0.020  1.347
 58D  O21  C22  single    1.413  0.020  1.413
 58D  C7   H1   single    0.970  0.020  1.090
 58D  C8   H2   single    0.970  0.020  1.090
 58D  C8   H3   single    0.970  0.020  1.090
 58D  C10  H4   single    0.930  0.020  1.080
 58D  C13  H5   single    0.930  0.020  1.080
 58D  C20  H6   single    0.930  0.020  1.080
 58D  C22  H7   single    0.970  0.020  1.090
 58D  C22  H8   single    0.970  0.020  1.090
 58D  C22  H9   single    0.970  0.020  1.090
 58D  C11  H10  single    0.930  0.020  1.080
 58D  C14  H11  single    0.930  0.020  1.080
 58D  N17  H12  single    0.860  0.020  1.020
 58D  C19  H13  single    0.930  0.020  1.080
 58D  C1   H14  single    0.930  0.020  1.080
 58D  C2   H15  single    0.930  0.020  1.080
 58D  C23  H16  single    0.970  0.020  1.090
 58D  C23  H17  single    0.970  0.020  1.090
 58D  C23  H18  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
 58D  N6   C4   O5   121.95  3.000
 58D  O5   C4   C3   119.01  3.000
 58D  N6   C4   C3   119.04  3.000
 58D  H1   C7   N6   105.61  3.000
 58D  H1   C7   C15  104.55  3.000
 58D  N6   C7   C15  110.69  3.000
 58D  H1   C7   C8   105.90  3.000
 58D  N6   C7   C8   115.48  3.000
 58D  C15  C7   C8   113.54  3.000
 58D  H3   C8   H2   106.57  3.000
 58D  H3   C8   C9   110.53  3.000
 58D  H2   C8   C9   110.03  3.000
 58D  H3   C8   C7   106.87  3.000
 58D  H2   C8   C7   112.14  3.000
 58D  C9   C8   C7   110.58  3.000
 58D  H4   C10  C9   119.63  3.000
 58D  H4   C10  C11  118.55  3.000
 58D  C9   C10  C11  121.81  3.000
 58D  H5   C13  C14  120.27  3.000
 58D  H5   C13  C12  119.52  3.000
 58D  C14  C13  C12  120.21  3.000
 58D  N17  C15  O16  121.31  3.000
 58D  O16  C15  C7   121.78  3.000
 58D  N17  C15  C7   116.91  3.000
 58D  H6   C20  C1   120.44  3.000
 58D  H6   C20  C19  119.56  3.000
 58D  C1   C20  C19  120.00  3.000
 58D  H9   C22  H8   108.70  3.000
 58D  H9   C22  H7   108.76  3.000
 58D  H8   C22  H7   108.75  3.000
 58D  H9   C22  O21  106.53  3.000
 58D  H8   C22  O21  111.99  3.000
 58D  H7   C22  O21  111.99  3.000
 58D  C11  C12  O21  124.43  3.000
 58D  O21  C12  C13  116.38  3.000
 58D  C11  C12  C13  119.19  3.000
 58D  H10  C11  C12  121.53  3.000
 58D  H10  C11  C10  118.82  3.000
 58D  C12  C11  C10  119.65  3.000
 58D  H11  C14  C9   119.86  3.000
 58D  H11  C14  C13  118.76  3.000
 58D  C9   C14  C13  121.37  3.000
 58D  C14  C9   C10  117.77  3.000
 58D  C10  C9   C8   120.93  3.000
 58D  C14  C9   C8   121.25  3.000
 58D  H12  N17  C18  115.46  3.000
 58D  H12  N17  C15  114.39  3.000
 58D  C18  N17  C15  128.52  3.000
 58D  C3   C18  C19  119.44  3.000
 58D  C3   C18  N17  123.92  3.000
 58D  C19  C18  N17  116.61  3.000
 58D  H13  C19  C18  119.16  3.000
 58D  H13  C19  C20  119.88  3.000
 58D  C18  C19  C20  120.96  3.000
 58D  H14  C1   C2   120.15  3.000
 58D  H14  C1   C20  120.62  3.000
 58D  C2   C1   C20  119.22  3.000
 58D  H15  C2   C3   118.78  3.000
 58D  H15  C2   C1   119.47  3.000
 58D  C3   C2   C1   121.75  3.000
 58D  C2   C3   C18  118.57  3.000
 58D  C2   C3   C4   115.91  3.000
 58D  C18  C3   C4   125.32  3.000
 58D  C23  N6   C7   116.22  3.000
 58D  C23  N6   C4   118.77  3.000
 58D  C7   N6   C4   124.27  3.000
 58D  H18  C23  H17  108.48  3.000
 58D  H18  C23  H16  108.35  3.000
 58D  H17  C23  H16  108.77  3.000
 58D  H18  C23  N6   109.23  3.000
 58D  H17  C23  N6   111.29  3.000
 58D  H16  C23  N6   110.64  3.000
 58D  C12  O21  C22  118.54  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
 58D  CONST_01  C13  C14  C9   C10    0.00   0.0  0
 58D  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 58D  CONST_03  C3   C2   C1   C20    0.00   0.0  0
 58D  CONST_04  C9   C14  C13  C12    0.00   0.0  0
 58D  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 58D  CONST_06  C14  C9   C10  C11    0.00   0.0  0
 58D  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 58D  CONST_08  C1   C20  C19  C18    0.00   0.0  0
 58D  CONST_09  C2   C1   C20  C19    0.00   0.0  0
 58D  CONST_10  C13  C14  C9   C8   180.00   0.0  0
 58D  CONST_11  C11  C10  C9   C8   180.00   0.0  0
 58D  CONST_12  O21  C12  C11  C10  180.00   0.0  0
 58D  CONST_13  C14  C13  C12  O21  180.00   0.0  0
 58D  CONST_14  H11  C14  C9   C10  180.00   0.0  0
 58D  CONST_15  H10  C11  C12  C13  180.00   0.0  0
 58D  CONST_16  H15  C2   C1   C20  180.00   0.0  0
 58D  CONST_17  H4   C10  C11  C12  180.00   0.0  0
 58D  CONST_18  H5   C13  C12  C11  180.00   0.0  0
 58D  CONST_19  H6   C20  C19  C18  180.00   0.0  0
 58D  CONST_20  H14  C1   C20  C19  180.00   0.0  0
 58D  CONST_21  H13  C19  C20  C1   180.00   0.0  0
 58D  Var_01    C14  C9   C8   C7    99.01  30.0  2
 58D  Var_02    C11  C12  O21  C22   -1.67  30.0  2
 58D  Var_03    H7   C22  O21  C12  -59.20  30.0  3

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
 58D  chir_01  C7  C15  C8  N6  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
 58D  plan-1  C8   0.020
 58D  plan-1  C10  0.020
 58D  plan-1  C13  0.020
 58D  plan-1  C12  0.020
 58D  plan-1  C11  0.020
 58D  plan-1  C14  0.020
 58D  plan-1  C9   0.020
 58D  plan-1  H4   0.020
 58D  plan-1  H5   0.020
 58D  plan-1  H10  0.020
 58D  plan-1  H11  0.020
 58D  plan-1  O21  0.020
 58D  plan-2  C4   0.020
 58D  plan-2  C20  0.020
 58D  plan-2  N17  0.020
 58D  plan-2  C18  0.020
 58D  plan-2  C19  0.020
 58D  plan-2  C1   0.020
 58D  plan-2  C2   0.020
 58D  plan-2  C3   0.020
 58D  plan-2  H6   0.020
 58D  plan-2  H13  0.020
 58D  plan-2  H14  0.020
 58D  plan-2  H15  0.020
 58D  plan-3  C4   0.020
 58D  plan-3  C7   0.020
 58D  plan-3  C3   0.020
 58D  plan-3  O5   0.020
 58D  plan-3  N6   0.020
 58D  plan-3  C23  0.020
 58D  plan-4  C7   0.020
 58D  plan-4  C15  0.020
 58D  plan-4  O16  0.020
 58D  plan-4  N17  0.020
 58D  plan-4  C18  0.020
 58D  plan-4  H12  0.020

