# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 12:16:41 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (4R)-4-methyl-6-[1-methyl-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-5-yl]-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)Nc2cccc(c3ccc4n(C)nc(c5cnn(C)c5)c4c3)c2N1
#
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
 69E  69E  (4R)-4-methyl-6-[1-methyl-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-5-yl]-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one  ligand  51  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_69E
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
 69E  C4   C  CH2   0  -0.617   3.9522  -0.7794   1.8946
 69E  C5   C  C     0   0.488   5.2543  -0.6817   1.1383
 69E  C11  C  CR16  0  -0.329   1.5376  -1.1877  -2.2598
 69E  C8   C  CR6   0   0.350   3.9445  -0.8745  -0.9324
 69E  C9   C  CR16  0  -0.328   3.8341  -1.8201  -1.9444
 69E  C10  C  CR16  0  -0.245   2.6285  -1.9679  -2.6105
 69E  C12  C  CR6   0   0.026   1.6424  -0.2137  -1.2664
 69E  C13  C  CR6   0   0.170   2.8677  -0.0359  -0.6158
 69E  C1   C  CH3   0  -0.676   3.5240   1.6058   2.6507
 69E  C2   C  CH1   0  -0.098   3.0673   0.4788   1.7409
 69E  O6   O  O     0  -0.469   6.3414  -0.5703   1.6799
 69E  N7   N  NH1   0  -0.714   5.1478  -0.7447  -0.2188
 69E  N14  N  NH1   0  -0.645   3.0180   0.9703   0.3677
 69E  C15  C  CR6   0   0.085   0.4613   0.6104  -0.9261
 69E  C16  C  CR16  0  -0.268   0.5353   2.0254  -0.9530
 69E  C17  C  CR16  0  -0.311  -0.5484   2.8220  -0.6772
 69E  C18  C  CR56  0   0.440  -1.7499   2.1786  -0.3542
 69E  C19  C  CR56  0  -0.105  -1.8590   0.7791  -0.3374
 69E  C20  C  CR16  0  -0.412  -0.7351  -0.0073  -0.6217
 69E  C21  C  CR5   0   0.224  -3.2195   0.5382   0.0190
 69E  N22  N  N     0  -0.281  -3.8458   1.6813   0.1947
 69E  N23  N  NR5   0  -0.388  -2.9650   2.6647  -0.0130
 69E  C24  C  CH3   0  -0.524  -3.3873   4.0410   0.0120
 69E  C25  C  CR5   0  -0.172  -3.9051  -0.7260   0.2024
 69E  C26  C  CR15  0  -0.133  -3.5302  -2.0148  -0.2253
 69E  N27  N  N     0  -0.276  -4.4287  -2.9181   0.1184
 69E  N28  N  NR5   0  -0.265  -5.3790  -2.2461   0.7584
 69E  C29  C  CR15  0   0.045  -5.1161  -0.9338   0.8372
 69E  C30  C  CH3   0  -0.506  -6.5225  -2.9436   1.2956
 69E  H1   H  HCH2  0   0.281   3.4026  -1.6539   1.5356
 69E  H2   H  HCH2  0   0.277   4.1711  -0.9521   2.9480
 69E  H3   H  HCR6  0   0.254   0.5972  -1.3139  -2.7815
 69E  H4   H  HCR6  0   0.269   4.6808  -2.4478  -2.1933
 69E  H5   H  HCR6  0   0.261   2.5370  -2.7035  -3.3985
 69E  H6   H  HCH3  0   0.226   4.5423   1.9253   2.4144
 69E  H7   H  HCH3  0   0.243   2.8676   2.4703   2.5502
 69E  H8   H  HCH3  0   0.240   3.5089   1.2882   3.6927
 69E  H9   H  HCH1  0   0.253   2.0530   0.1875   2.0296
 69E  H10  H  HNH1  0   0.402   6.0135  -0.8155  -0.7357
 69E  H11  H  HNH1  0   0.355   3.8575   1.5074   0.1747
 69E  H12  H  HCR6  0   0.249   1.4744   2.4923  -1.2127
 69E  H13  H  HCR6  0   0.271  -0.4686   3.9004  -0.7143
 69E  H14  H  HCR6  0   0.250  -0.7898  -1.0879  -0.5881
 69E  H15  H  HCH3  0   0.254  -3.7555   4.3643  -0.9623
 69E  H16  H  HCH3  0   0.266  -4.1773   4.1587   0.7486
 69E  H17  H  HCH3  0   0.257  -2.5508   4.6748   0.2985
 69E  H18  H  HCR5  0   0.253  -2.6540  -2.3139  -0.7798
 69E  H19  H  HCR5  0   0.291  -5.7834  -0.2463   1.3309
 69E  H20  H  HCH3  0   0.262  -6.2135  -3.6399   2.0729
 69E  H21  H  HCH3  0   0.260  -7.2084  -2.2191   1.7241
 69E  H22  H  HCH3  0   0.262  -7.0336  -3.4909   0.5067

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
 69E  C30  N28  single    1.443  0.020  1.443
 69E  N28  N27  aromatic  1.328  0.020  1.328
 69E  N28  C29  aromatic  1.341  0.020  1.341
 69E  N7   C8   single    1.405  0.020  1.405
 69E  N7   C5   single    1.363  0.020  1.363
 69E  C9   C10  aromatic  1.385  0.020  1.385
 69E  C9   C8   aromatic  1.389  0.020  1.389
 69E  N27  C26  aromatic  1.320  0.020  1.320
 69E  O6   C5   double    1.220  0.020  1.220
 69E  C29  C25  aromatic  1.383  0.020  1.383
 69E  C10  C11  aromatic  1.386  0.020  1.386
 69E  C8   C13  aromatic  1.401  0.020  1.401
 69E  C5   C4   single    1.509  0.020  1.509
 69E  C11  C12  aromatic  1.395  0.020  1.395
 69E  C26  C25  aromatic  1.409  0.020  1.409
 69E  C13  C12  aromatic  1.399  0.020  1.399
 69E  C13  N14  single    1.415  0.020  1.415
 69E  C25  C21  single    1.450  0.020  1.450
 69E  C12  C15  single    1.480  0.020  1.480
 69E  N14  C2   single    1.459  0.020  1.459
 69E  C20  C15  aromatic  1.380  0.020  1.380
 69E  C20  C19  aromatic  1.401  0.020  1.401
 69E  C1   C2   single    1.519  0.020  1.519
 69E  C4   C2   single    1.546  0.020  1.546
 69E  C15  C16  aromatic  1.417  0.020  1.417
 69E  C21  C19  aromatic  1.427  0.020  1.427
 69E  C21  N22  aromatic  1.315  0.020  1.315
 69E  C19  C18  aromatic  1.404  0.020  1.404
 69E  N22  N23  aromatic  1.336  0.020  1.336
 69E  C16  C17  aromatic  1.373  0.020  1.373
 69E  C18  C17  aromatic  1.401  0.020  1.401
 69E  C18  N23  aromatic  1.353  0.020  1.353
 69E  N23  C24  single    1.440  0.020  1.440
 69E  C4   H1   single    0.970  0.020  1.090
 69E  C4   H2   single    0.970  0.020  1.090
 69E  C11  H3   single    0.930  0.020  1.080
 69E  C9   H4   single    0.930  0.020  1.080
 69E  C10  H5   single    0.930  0.020  1.080
 69E  C1   H6   single    0.970  0.020  1.090
 69E  C1   H7   single    0.970  0.020  1.090
 69E  C1   H8   single    0.970  0.020  1.090
 69E  C2   H9   single    0.970  0.020  1.090
 69E  N7   H10  single    0.860  0.020  1.020
 69E  N14  H11  single    0.890  0.020  1.040
 69E  C16  H12  single    0.930  0.020  1.080
 69E  C17  H13  single    0.930  0.020  1.080
 69E  C20  H14  single    0.930  0.020  1.080
 69E  C24  H15  single    0.970  0.020  1.090
 69E  C24  H16  single    0.970  0.020  1.090
 69E  C24  H17  single    0.970  0.020  1.090
 69E  C26  H18  single    0.930  0.020  1.080
 69E  C29  H19  single    0.930  0.020  1.080
 69E  C30  H20  single    0.970  0.020  1.090
 69E  C30  H21  single    0.970  0.020  1.090
 69E  C30  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
 69E  H2   C4   H1   106.95  3.000
 69E  H2   C4   C2   109.88  3.000
 69E  H1   C4   C2   109.30  3.000
 69E  H2   C4   C5   108.75  3.000
 69E  H1   C4   C5   108.72  3.000
 69E  C2   C4   C5   113.04  3.000
 69E  N7   C5   O6   121.07  3.000
 69E  O6   C5   C4   123.53  3.000
 69E  N7   C5   C4   115.39  3.000
 69E  H3   C11  C12  119.31  3.000
 69E  H3   C11  C10  119.74  3.000
 69E  C12  C11  C10  120.92  3.000
 69E  N7   C8   C13  119.22  3.000
 69E  C13  C8   C9   120.72  3.000
 69E  N7   C8   C9   120.06  3.000
 69E  H4   C9   C10  120.54  3.000
 69E  H4   C9   C8   119.98  3.000
 69E  C10  C9   C8   119.47  3.000
 69E  H5   C10  C9   119.76  3.000
 69E  H5   C10  C11  120.02  3.000
 69E  C9   C10  C11  120.21  3.000
 69E  C15  C12  C13  121.43  3.000
 69E  C15  C12  C11  119.51  3.000
 69E  C13  C12  C11  119.06  3.000
 69E  N14  C13  C12  120.45  3.000
 69E  N14  C13  C8   120.07  3.000
 69E  C12  C13  C8   119.48  3.000
 69E  H8   C1   H7   108.12  3.000
 69E  H8   C1   H6   107.76  3.000
 69E  H7   C1   H6   108.01  3.000
 69E  H8   C1   C2   110.64  3.000
 69E  H7   C1   C2   110.62  3.000
 69E  H6   C1   C2   111.56  3.000
 69E  H9   C2   N14  107.86  3.000
 69E  H9   C2   C1   108.56  3.000
 69E  N14  C2   C1   108.90  3.000
 69E  H9   C2   C4   106.73  3.000
 69E  C1   C2   C4   111.85  3.000
 69E  N14  C2   C4   112.77  3.000
 69E  H10  N7   C8   117.85  3.000
 69E  H10  N7   C5   116.47  3.000
 69E  C8   N7   C5   125.24  3.000
 69E  H11  N14  C2   109.22  3.000
 69E  H11  N14  C13  109.38  3.000
 69E  C2   N14  C13  114.72  3.000
 69E  C20  C15  C16  119.75  3.000
 69E  C16  C15  C12  120.66  3.000
 69E  C20  C15  C12  119.56  3.000
 69E  H12  C16  C17  118.92  3.000
 69E  H12  C16  C15  118.78  3.000
 69E  C17  C16  C15  122.30  3.000
 69E  H13  C17  C18  121.94  3.000
 69E  H13  C17  C16  120.88  3.000
 69E  C18  C17  C16  117.18  3.000
 69E  N23  C18  C19  106.58  3.000
 69E  N23  C18  C17  131.59  3.000
 69E  C19  C18  C17  121.83  3.000
 69E  C21  C19  C20  136.13  3.000
 69E  C21  C19  C18  104.21  3.000
 69E  C20  C19  C18  119.66  3.000
 69E  H14  C20  C19  120.90  3.000
 69E  H14  C20  C15  119.82  3.000
 69E  C19  C20  C15  119.27  3.000
 69E  C25  C21  N22  121.05  3.000
 69E  N22  C21  C19  109.92  3.000
 69E  C25  C21  C19  129.03  3.000
 69E  N23  N22  C21  107.75  3.000
 69E  C24  N23  N22  120.49  3.000
 69E  C24  N23  C18  127.69  3.000
 69E  N22  N23  C18  111.53  3.000
 69E  H17  C24  H16  108.51  3.000
 69E  H17  C24  H15  108.80  3.000
 69E  H16  C24  H15  109.15  3.000
 69E  H17  C24  N23  109.63  3.000
 69E  H16  C24  N23  109.18  3.000
 69E  H15  C24  N23  111.52  3.000
 69E  C29  C25  C26  103.58  3.000
 69E  C26  C25  C21  129.31  3.000
 69E  C29  C25  C21  127.10  3.000
 69E  H18  C26  N27  119.79  3.000
 69E  H18  C26  C25  128.73  3.000
 69E  N27  C26  C25  111.47  3.000
 69E  N28  N27  C26  105.44  3.000
 69E  C30  N28  C29  127.34  3.000
 69E  C29  N28  N27  112.53  3.000
 69E  C30  N28  N27  120.12  3.000
 69E  H19  C29  N28  121.99  3.000
 69E  H19  C29  C25  131.03  3.000
 69E  N28  C29  C25  106.97  3.000
 69E  H22  C30  H21  108.98  3.000
 69E  H22  C30  H20  109.24  3.000
 69E  H21  C30  H20  108.93  3.000
 69E  H22  C30  N28  110.21  3.000
 69E  H21  C30  N28  108.96  3.000
 69E  H20  C30  N28  110.49  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
 69E  CONST_01  C8   C9   C10  C11    0.00   0.0  0
 69E  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 69E  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 69E  CONST_06  C15  C12  C11  C10  180.00   0.0  0
 69E  CONST_07  C19  C20  C15  C12  180.00   0.0  0
 69E  CONST_08  C17  C16  C15  C12  180.00   0.0  0
 69E  CONST_11  C21  C19  C20  C15  180.00   0.0  0
 69E  CONST_12  C18  C19  C20  C15    0.00   0.0  0
 69E  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 69E  CONST_14  C19  C20  C15  C16    0.00   0.0  0
 69E  CONST_15  C19  C18  C17  C16    0.00   0.0  0
 69E  CONST_16  N23  C18  C17  C16  180.00   0.0  0
 69E  CONST_17  C20  C15  C16  C17    0.00   0.0  0
 69E  CONST_18  C20  C19  C18  C17    0.00   0.0  0
 69E  CONST_19  C21  C19  C18  C17  180.00   0.0  0
 69E  CONST_20  N22  N23  C18  C17  180.00   0.0  0
 69E  CONST_21  C25  C21  C19  C18  180.00   0.0  0
 69E  CONST_22  N22  C21  C19  C18    0.00   0.0  0
 69E  CONST_23  C21  N22  N23  C18    0.00   0.0  0
 69E  CONST_26  N23  N22  C21  C19    0.00   0.0  0
 69E  CONST_27  N22  N23  C18  C19    0.00   0.0  0
 69E  CONST_28  C25  C21  C19  C20    0.00   0.0  0
 69E  CONST_29  N22  C21  C19  C20  180.00   0.0  0
 69E  CONST_30  N23  C18  C19  C20  180.00   0.0  0
 69E  CONST_31  N28  C29  C25  C21  180.00   0.0  0
 69E  CONST_32  N27  C26  C25  C21  180.00   0.0  0
 69E  CONST_33  N23  C18  C19  C21    0.00   0.0  0
 69E  CONST_36  C25  C21  N22  N23  180.00   0.0  0
 69E  CONST_37  N27  N28  C29  C25    0.00   0.0  0
 69E  CONST_38  N28  N27  C26  C25    0.00   0.0  0
 69E  CONST_39  C29  N28  N27  C26    0.00   0.0  0
 69E  CONST_40  N28  C29  C25  C26    0.00   0.0  0
 69E  CONST_41  C29  C25  C26  N27    0.00   0.0  0
 69E  CONST_42  C24  N23  C18  C17    0.00   0.0  0
 69E  CONST_43  C24  N23  C18  C19  180.00   0.0  0
 69E  CONST_44  C24  N23  N22  C21  180.00   0.0  0
 69E  CONST_45  C30  N28  C29  C25  180.00   0.0  0
 69E  CONST_46  C30  N28  N27  C26  180.00   0.0  0
 69E  CONST_47  H4   C9   C10  C11  180.00   0.0  0
 69E  CONST_48  H5   C10  C9   C8   180.00   0.0  0
 69E  CONST_49  H3   C11  C10  C9   180.00   0.0  0
 69E  CONST_50  H14  C20  C15  C12    0.00   0.0  0
 69E  CONST_51  H12  C16  C15  C12    0.00   0.0  0
 69E  CONST_52  H13  C17  C16  C15  180.00   0.0  0
 69E  CONST_53  H19  C29  C25  C21    0.00   0.0  0
 69E  CONST_54  H18  C26  C25  C21    0.00   0.0  0
 69E  Var_01    H15  C24  N23  C18   86.91  30.0  2
 69E  Var_02    H20  C30  N28  N27   63.75  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
 69E  chir_01  C2  N14  C1  C4  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
 69E  plan-1  C21  0.020
 69E  plan-1  C25  0.020
 69E  plan-1  C26  0.020
 69E  plan-1  N27  0.020
 69E  plan-1  N28  0.020
 69E  plan-1  C29  0.020
 69E  plan-1  C30  0.020
 69E  plan-1  H18  0.020
 69E  plan-1  H19  0.020
 69E  plan-2  C12  0.020
 69E  plan-2  C15  0.020
 69E  plan-2  C16  0.020
 69E  plan-2  C17  0.020
 69E  plan-2  C18  0.020
 69E  plan-2  C19  0.020
 69E  plan-2  C20  0.020
 69E  plan-2  C21  0.020
 69E  plan-2  N22  0.020
 69E  plan-2  N23  0.020
 69E  plan-2  C24  0.020
 69E  plan-2  C25  0.020
 69E  plan-2  H12  0.020
 69E  plan-2  H13  0.020
 69E  plan-2  H14  0.020
 69E  plan-3  C11  0.020
 69E  plan-3  C8   0.020
 69E  plan-3  C9   0.020
 69E  plan-3  C10  0.020
 69E  plan-3  C12  0.020
 69E  plan-3  C13  0.020
 69E  plan-3  N7   0.020
 69E  plan-3  N14  0.020
 69E  plan-3  C15  0.020
 69E  plan-3  H3   0.020
 69E  plan-3  H4   0.020
 69E  plan-3  H5   0.020
 69E  plan-4  C4   0.020
 69E  plan-4  C5   0.020
 69E  plan-4  C8   0.020
 69E  plan-4  O6   0.020
 69E  plan-4  N7   0.020
 69E  plan-4  H10  0.020

