# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 03:55:36 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-(11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-3-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccccc1c2ccc3C(=O)Nc4ccccc4Nc3c2
#
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
 HK7  HK7  2-(11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-3-yl)benzamide  ligand  40  25  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HK7
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
 HK7  O2   O  O     0  -0.466  -3.2564   1.6909   1.5736
 HK7  C16  C  C     0   0.434  -3.9410   1.3130   0.6362
 HK7  N3   N  NH2   0  -0.789  -4.7817   2.1063  -0.0417
 HK7  C15  C  CR6   0  -0.083  -3.9218  -0.1179   0.1871
 HK7  C14  C  CR16  0  -0.256  -5.1216  -0.8201   0.1260
 HK7  C13  C  CR16  0  -0.252  -5.1343  -2.1779  -0.1594
 HK7  C12  C  CR16  0  -0.239  -3.9391  -2.8401  -0.3931
 HK7  C11  C  CR16  0  -0.293  -2.7415  -2.1416  -0.3483
 HK7  C10  C  CR6   0   0.086  -2.7126  -0.7791  -0.0586
 HK7  C8   C  CR6   0   0.080  -1.4161  -0.0685  -0.0818
 HK7  C7   C  CR16  0  -0.303  -1.2381   1.0728  -0.8659
 HK7  C6   C  CR16  0  -0.268  -0.0127   1.7032  -0.8913
 HK7  C5   C  CR6   0  -0.131   1.0807   1.2087  -0.1770
 HK7  C1   C  C     0   0.515   2.3019   2.0560  -0.1510
 HK7  O1   O  O     0  -0.462   2.2136   3.2656  -0.2959
 HK7  C9   C  CR16  0  -0.380  -0.3329  -0.5748   0.6203
 HK7  C4   C  CR6   0   0.337   0.9188   0.0394   0.5729
 HK7  N2   N  NH1   0  -0.746   1.9707  -0.5131   1.3066
 HK7  C3   C  CR6   0   0.254   3.1558  -0.8515   0.6341
 HK7  C17  C  CR16  0  -0.326   3.6212  -2.1629   0.6329
 HK7  C18  C  CR16  0  -0.261   4.8178  -2.4917   0.0156
 HK7  C19  C  CR16  0  -0.264   5.5489  -1.5094  -0.6377
 HK7  C20  C  CR16  0  -0.319   5.0802  -0.2054  -0.6587
 HK7  C2   C  CR6   0   0.337   3.8937   0.1351  -0.0164
 HK7  N1   N  NH1   0  -0.740   3.5178   1.4850   0.0380
 HK7  H16  H  HNH2  0   0.406  -4.8811   3.0770   0.2094
 HK7  H17  H  HNH2  0   0.414  -5.2690   1.7876  -0.8615
 HK7  H9   H  HCR6  0   0.270  -6.0548  -0.3107   0.3312
 HK7  H8   H  HCR6  0   0.265  -6.0733  -2.7138  -0.1951
 HK7  H7   H  HCR6  0   0.266  -3.9361  -3.8982  -0.6186
 HK7  H6   H  HCR6  0   0.263  -1.8138  -2.6567  -0.5640
 HK7  H4   H  HCR6  0   0.255  -2.0559   1.4680  -1.4546
 HK7  H3   H  HCR6  0   0.266   0.1056   2.6024  -1.4805
 HK7  H5   H  HCR6  0   0.267  -0.4545  -1.4647   1.2270
 HK7  H2   H  HNH1  0   0.395   1.6581  -1.2556   1.9158
 HK7  H12  H  HCR6  0   0.266   3.0430  -2.9278   1.1374
 HK7  H13  H  HCR6  0   0.261   5.1693  -3.5145   0.0378
 HK7  H14  H  HCR6  0   0.261   6.4800  -1.7534  -1.1308
 HK7  H15  H  HCR6  0   0.273   5.6475   0.5664  -1.1642
 HK7  H1   H  HNH1  0   0.407   4.2815   2.1465  -0.0053

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
 HK7  C19  C20  aromatic  1.386  0.020  1.386
 HK7  C19  C18  aromatic  1.388  0.020  1.388
 HK7  C20  C2   aromatic  1.392  0.020  1.392
 HK7  C18  C17  aromatic  1.386  0.020  1.386
 HK7  N1   C2   single    1.402  0.020  1.402
 HK7  N1   C1   single    1.357  0.020  1.357
 HK7  C2   C3   aromatic  1.393  0.020  1.393
 HK7  O1   C1   double    1.221  0.020  1.221
 HK7  C1   C5   single    1.487  0.020  1.487
 HK7  C6   C5   aromatic  1.397  0.020  1.397
 HK7  C6   C7   aromatic  1.378  0.020  1.378
 HK7  C17  C3   aromatic  1.392  0.020  1.392
 HK7  C3   N2   single    1.404  0.020  1.404
 HK7  C5   C4   aromatic  1.399  0.020  1.399
 HK7  C7   C8   aromatic  1.396  0.020  1.396
 HK7  C4   N2   single    1.396  0.020  1.396
 HK7  C4   C9   aromatic  1.395  0.020  1.395
 HK7  C8   C9   aromatic  1.387  0.020  1.387
 HK7  C8   C10  single    1.479  0.020  1.479
 HK7  C11  C10  aromatic  1.393  0.020  1.393
 HK7  C11  C12  aromatic  1.387  0.020  1.387
 HK7  C10  C15  aromatic  1.400  0.020  1.400
 HK7  C12  C13  aromatic  1.386  0.020  1.386
 HK7  C15  C16  single    1.500  0.020  1.500
 HK7  C15  C14  aromatic  1.391  0.020  1.391
 HK7  C13  C14  aromatic  1.387  0.020  1.387
 HK7  C16  N3   single    1.340  0.020  1.340
 HK7  C16  O2   double    1.221  0.020  1.221
 HK7  N3   H16  single    0.860  0.020  1.020
 HK7  N3   H17  single    0.860  0.020  1.020
 HK7  C14  H9   single    0.930  0.020  1.080
 HK7  C13  H8   single    0.930  0.020  1.080
 HK7  C12  H7   single    0.930  0.020  1.080
 HK7  C11  H6   single    0.930  0.020  1.080
 HK7  C7   H4   single    0.930  0.020  1.080
 HK7  C6   H3   single    0.930  0.020  1.080
 HK7  C9   H5   single    0.930  0.020  1.080
 HK7  N2   H2   single    0.890  0.020  1.040
 HK7  C17  H12  single    0.930  0.020  1.080
 HK7  C18  H13  single    0.930  0.020  1.080
 HK7  C19  H14  single    0.930  0.020  1.080
 HK7  C20  H15  single    0.930  0.020  1.080
 HK7  N1   H1   single    0.860  0.020  1.020

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
 HK7  C15  C16  N3   114.92  3.000
 HK7  N3   C16  O2   123.86  3.000
 HK7  C15  C16  O2   121.20  3.000
 HK7  H17  N3   H16  117.44  3.000
 HK7  H17  N3   C16  121.92  3.000
 HK7  H16  N3   C16  120.40  3.000
 HK7  C10  C15  C14  119.92  3.000
 HK7  C14  C15  C16  118.92  3.000
 HK7  C10  C15  C16  120.94  3.000
 HK7  H9   C14  C13  119.44  3.000
 HK7  H9   C14  C15  119.82  3.000
 HK7  C13  C14  C15  120.72  3.000
 HK7  H8   C13  C12  120.41  3.000
 HK7  H8   C13  C14  119.97  3.000
 HK7  C12  C13  C14  119.62  3.000
 HK7  H7   C12  C11  119.79  3.000
 HK7  H7   C12  C13  120.31  3.000
 HK7  C11  C12  C13  119.90  3.000
 HK7  H6   C11  C10  119.27  3.000
 HK7  H6   C11  C12  119.59  3.000
 HK7  C10  C11  C12  121.13  3.000
 HK7  C8   C10  C11  119.00  3.000
 HK7  C11  C10  C15  118.71  3.000
 HK7  C8   C10  C15  122.22  3.000
 HK7  C9   C8   C7   118.90  3.000
 HK7  C9   C8   C10  120.10  3.000
 HK7  C7   C8   C10  120.90  3.000
 HK7  H4   C7   C6   119.65  3.000
 HK7  H4   C7   C8   120.50  3.000
 HK7  C6   C7   C8   119.84  3.000
 HK7  H3   C6   C5   119.17  3.000
 HK7  H3   C6   C7   119.18  3.000
 HK7  C5   C6   C7   121.65  3.000
 HK7  C4   C5   C1   124.21  3.000
 HK7  C4   C5   C6   118.66  3.000
 HK7  C1   C5   C6   116.77  3.000
 HK7  N1   C1   O1   119.88  3.000
 HK7  O1   C1   C5   120.19  3.000
 HK7  N1   C1   C5   119.93  3.000
 HK7  H5   C9   C4   118.76  3.000
 HK7  H5   C9   C8   119.71  3.000
 HK7  C4   C9   C8   121.53  3.000
 HK7  N2   C4   C9   118.94  3.000
 HK7  C9   C4   C5   119.35  3.000
 HK7  N2   C4   C5   121.69  3.000
 HK7  H2   N2   C3   111.89  3.000
 HK7  H2   N2   C4   112.00  3.000
 HK7  C3   N2   C4   118.66  3.000
 HK7  C2   C3   C17  119.33  3.000
 HK7  C17  C3   N2   120.66  3.000
 HK7  C2   C3   N2   120.00  3.000
 HK7  H12  C17  C18  120.05  3.000
 HK7  H12  C17  C3   119.10  3.000
 HK7  C18  C17  C3   120.84  3.000
 HK7  H13  C18  C19  120.51  3.000
 HK7  H13  C18  C17  119.71  3.000
 HK7  C19  C18  C17  119.77  3.000
 HK7  H14  C19  C20  119.77  3.000
 HK7  H14  C19  C18  120.56  3.000
 HK7  C20  C19  C18  119.67  3.000
 HK7  H15  C20  C2   119.19  3.000
 HK7  H15  C20  C19  120.03  3.000
 HK7  C2   C20  C19  120.77  3.000
 HK7  N1   C2   C20  118.81  3.000
 HK7  N1   C2   C3   121.44  3.000
 HK7  C20  C2   C3   119.60  3.000
 HK7  H1   N1   C2   115.19  3.000
 HK7  H1   N1   C1   113.31  3.000
 HK7  C2   N1   C1   129.79  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
 HK7  CONST_03  C12  C11  C10  C15    0.00   0.0  0
 HK7  CONST_04  C12  C13  C14  C15    0.00   0.0  0
 HK7  CONST_05  C8   C10  C15  C14  180.00   0.0  0
 HK7  CONST_06  C11  C10  C15  C14    0.00   0.0  0
 HK7  CONST_07  C11  C12  C13  C14    0.00   0.0  0
 HK7  CONST_08  C10  C11  C12  C13    0.00   0.0  0
 HK7  CONST_09  C10  C15  C14  C13    0.00   0.0  0
 HK7  CONST_10  C8   C10  C11  C12  180.00   0.0  0
 HK7  CONST_13  C6   C7   C8   C10  180.00   0.0  0
 HK7  CONST_14  C4   C9   C8   C10  180.00   0.0  0
 HK7  CONST_15  C5   C6   C7   C8     0.00   0.0  0
 HK7  CONST_16  C4   C9   C8   C7     0.00   0.0  0
 HK7  CONST_17  C9   C8   C7   C6     0.00   0.0  0
 HK7  CONST_18  C19  C18  C17  C3     0.00   0.0  0
 HK7  CONST_19  C20  C19  C18  C17    0.00   0.0  0
 HK7  CONST_20  C2   C20  C19  C18    0.00   0.0  0
 HK7  CONST_21  C8   C10  C15  C16    0.00   0.0  0
 HK7  CONST_22  C11  C10  C15  C16  180.00   0.0  0
 HK7  CONST_23  C13  C14  C15  C16  180.00   0.0  0
 HK7  CONST_24  H6   C11  C10  C15  180.00   0.0  0
 HK7  CONST_25  H8   C13  C14  C15  180.00   0.0  0
 HK7  CONST_26  H7   C12  C13  C14  180.00   0.0  0
 HK7  CONST_27  H9   C14  C13  C12  180.00   0.0  0
 HK7  CONST_28  H4   C7   C8   C10    0.00   0.0  0
 HK7  CONST_29  H5   C9   C8   C10    0.00   0.0  0
 HK7  CONST_30  H3   C6   C7   C8   180.00   0.0  0
 HK7  CONST_31  H13  C18  C17  C3   180.00   0.0  0
 HK7  CONST_32  H14  C19  C18  C17  180.00   0.0  0
 HK7  CONST_33  H15  C20  C19  C18  180.00   0.0  0
 HK7  CONST_34  H12  C17  C18  C19  180.00   0.0  0
 HK7  CONST_35  H16  N3   C16  C15  180.00   0.0  0
 HK7  CONST_36  H17  N3   C16  C15    0.00   0.0  0
 HK7  Var_01    C10  C15  C16  O2   -50.17  30.0  2

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
 HK7  plan-1  C16  0.020
 HK7  plan-1  C15  0.020
 HK7  plan-1  C14  0.020
 HK7  plan-1  C13  0.020
 HK7  plan-1  C12  0.020
 HK7  plan-1  C11  0.020
 HK7  plan-1  C10  0.020
 HK7  plan-1  C8   0.020
 HK7  plan-1  H9   0.020
 HK7  plan-1  H8   0.020
 HK7  plan-1  H7   0.020
 HK7  plan-1  H6   0.020
 HK7  plan-2  C10  0.020
 HK7  plan-2  C8   0.020
 HK7  plan-2  C7   0.020
 HK7  plan-2  C6   0.020
 HK7  plan-2  C5   0.020
 HK7  plan-2  C1   0.020
 HK7  plan-2  C9   0.020
 HK7  plan-2  C4   0.020
 HK7  plan-2  N2   0.020
 HK7  plan-2  H4   0.020
 HK7  plan-2  H3   0.020
 HK7  plan-2  H5   0.020
 HK7  plan-3  N2   0.020
 HK7  plan-3  C3   0.020
 HK7  plan-3  C17  0.020
 HK7  plan-3  C18  0.020
 HK7  plan-3  C19  0.020
 HK7  plan-3  C20  0.020
 HK7  plan-3  C2   0.020
 HK7  plan-3  N1   0.020
 HK7  plan-3  H12  0.020
 HK7  plan-3  H13  0.020
 HK7  plan-3  H14  0.020
 HK7  plan-3  H15  0.020
 HK7  plan-4  O2   0.020
 HK7  plan-4  C16  0.020
 HK7  plan-4  N3   0.020
 HK7  plan-4  C15  0.020
 HK7  plan-4  H16  0.020
 HK7  plan-4  H17  0.020
 HK7  plan-5  C5   0.020
 HK7  plan-5  C1   0.020
 HK7  plan-5  O1   0.020
 HK7  plan-5  C2   0.020
 HK7  plan-5  N1   0.020
 HK7  plan-5  H1   0.020

