# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 01:36:20 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-methoxy-4-(11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-3-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1C(O)=O)c2ccc3C(=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
 HK9  HK9  '2-methoxy-4-(11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-3-yl)benzoic acid'  ligand  42  27  .  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_HK9
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
 HK9  O4   O  O      0  -0.462  -3.8736  -2.8944   1.2335
 HK9  C14  C  C      0   0.516  -3.6868  -1.7676   0.8003
 HK9  N2   N  NH1    0  -0.741  -4.7481  -0.9682   0.5236
 HK9  C13  C  C      0   0.335  -4.8063   0.2262  -0.2087
 HK9  C18  C  C1     0  -0.321  -5.8579   0.4157  -1.1000
 HK9  C19  C  C1     0  -0.263  -6.0227   1.6250  -1.7567
 HK9  C20  C  C1     0  -0.261  -5.1178   2.6541  -1.5385
 HK9  C21  C  C1     0  -0.327  -4.0523   2.4610  -0.6731
 HK9  C12  C  C      0   0.257  -3.8938   1.2566   0.0061
 HK9  N1   N  NH1    0  -0.748  -2.8468   1.0892   0.9251
 HK9  C15  C  CR6    0  -0.142  -2.3040  -1.2680   0.5853
 HK9  C11  C  CR6    0   0.351  -1.9161   0.0701   0.7227
 HK9  C10  C  CR16   0  -0.397  -0.5613   0.3966   0.6873
 HK9  C16  C  CR16   0  -0.264  -1.3122  -2.2298   0.3834
 HK9  C17  C  CR16   0  -0.326   0.0241  -1.8954   0.3221
 HK9  C9   C  CR6    0   0.107   0.4221  -0.5668   0.4969
 HK9  C4   C  CR6    0   0.110   1.8462  -0.1803   0.4668
 HK9  C3   C  CR16   0  -0.469   2.7416  -0.8583  -0.3624
 HK9  C5   C  CR16   0  -0.334   2.3224   0.8561   1.2626
 HK9  C6   C  CR16   0  -0.263   3.6648   1.1994   1.2139
 HK9  C7   C  CR6    0  -0.165   4.5648   0.5668   0.3661
 HK9  C8   C  C      0   0.378   6.0034   1.0692   0.3191
 HK9  O3   O  OC    -1  -0.600   6.4930   1.4092   1.4131
 HK9  O2   O  O      0  -0.591   6.5437   1.1353  -0.7983
 HK9  C2   C  CR6    0   0.389   4.0842  -0.4927  -0.4224
 HK9  O1   O  O2     0  -0.457   4.9770  -1.1394  -1.1943
 HK9  C1   C  CH3    0  -0.440   4.5473  -2.2502  -1.9516
 HK9  H9   H  HNH1   0   0.406  -5.6389  -1.4240   0.6700
 HK9  H12  H  H      0   0.273  -6.5640  -0.3894  -1.2638
 HK9  H13  H  H      0   0.260  -6.8545   1.7581  -2.4350
 HK9  H14  H  H      0   0.261  -5.2319   3.6031  -2.0454
 HK9  H15  H  H      0   0.266  -3.3373   3.2576  -0.5039
 HK9  H8   H  HNH1   0   0.396  -2.4049   1.9674   1.1565
 HK9  H7   H  HCR6   0   0.265  -0.2787   1.4382   0.7855
 HK9  H10  H  HCR6   0   0.265  -1.5989  -3.2685   0.2895
 HK9  H11  H  HCR6   0   0.254   0.7600  -2.6756   0.1813
 HK9  H4   H  HCR6   0   0.275   2.3678  -1.6640  -0.9798
 HK9  H5   H  HCR6   0   0.247   1.6597   1.3761   1.9423
 HK9  H6   H  HCR6   0   0.249   4.0280   1.9951   1.8515
 HK9  H3   H  HCH3   0   0.224   4.1517  -3.0513  -1.3207
 HK9  H2   H  HCH3   0   0.226   3.7882  -1.9790  -2.6908
 HK9  H1   H  HCH3   0   0.259   5.4242  -2.6221  -2.4764

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
 HK9  C18  C19  aromatic  1.386  0.020  1.386
 HK9  C18  C13  aromatic  1.392  0.020  1.392
 HK9  C19  C20  aromatic  1.388  0.020  1.388
 HK9  N2   C13  single    1.402  0.020  1.402
 HK9  N2   C14  single    1.357  0.020  1.357
 HK9  O4   C14  double    1.221  0.020  1.221
 HK9  C13  C12  aromatic  1.393  0.020  1.393
 HK9  C20  C21  aromatic  1.386  0.020  1.386
 HK9  C14  C15  single    1.486  0.020  1.486
 HK9  C16  C15  aromatic  1.396  0.020  1.396
 HK9  C16  C17  aromatic  1.379  0.020  1.379
 HK9  C15  C11  aromatic  1.400  0.020  1.400
 HK9  C12  C21  aromatic  1.392  0.020  1.392
 HK9  C12  N1   single    1.403  0.020  1.403
 HK9  C17  C9   aromatic  1.398  0.020  1.398
 HK9  C11  N1   single    1.395  0.020  1.395
 HK9  C11  C10  aromatic  1.394  0.020  1.394
 HK9  C9   C10  aromatic  1.390  0.020  1.390
 HK9  C9   C4   single    1.476  0.020  1.476
 HK9  C4   C5   aromatic  1.391  0.020  1.391
 HK9  C4   C3   aromatic  1.396  0.020  1.396
 HK9  C5   C6   aromatic  1.387  0.020  1.387
 HK9  C3   C2   aromatic  1.393  0.020  1.393
 HK9  C1   O1   single    1.411  0.020  1.411
 HK9  C6   C7   aromatic  1.389  0.020  1.389
 HK9  C2   C7   aromatic  1.405  0.020  1.405
 HK9  C2   O1   single    1.346  0.020  1.346
 HK9  C7   C8   single    1.525  0.020  1.525
 HK9  O2   C8   deloc     1.243  0.020  1.243
 HK9  C8   O3   deloc     1.246  0.020  1.246
 HK9  N2   H9   single    0.860  0.020  1.020
 HK9  C18  H12  single    0.930  0.020  1.080
 HK9  C19  H13  single    0.930  0.020  1.080
 HK9  C20  H14  single    0.930  0.020  1.080
 HK9  C21  H15  single    0.930  0.020  1.080
 HK9  N1   H8   single    0.890  0.020  1.040
 HK9  C10  H7   single    0.930  0.020  1.080
 HK9  C16  H10  single    0.930  0.020  1.080
 HK9  C17  H11  single    0.930  0.020  1.080
 HK9  C3   H4   single    0.930  0.020  1.080
 HK9  C5   H5   single    0.930  0.020  1.080
 HK9  C6   H6   single    0.930  0.020  1.080
 HK9  C1   H3   single    0.970  0.020  1.090
 HK9  C1   H2   single    0.970  0.020  1.090
 HK9  C1   H1   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
 HK9  C15  C14  N2   120.01  3.000
 HK9  C15  C14  O4   120.25  3.000
 HK9  N2   C14  O4   119.74  3.000
 HK9  H9   N2   C13  115.03  3.000
 HK9  H9   N2   C14  113.19  3.000
 HK9  C13  N2   C14  129.84  3.000
 HK9  C12  C13  C18  119.55  3.000
 HK9  C12  C13  N2   121.49  3.000
 HK9  C18  C13  N2   118.80  3.000
 HK9  H12  C18  C19  119.96  3.000
 HK9  H12  C18  C13  119.23  3.000
 HK9  C19  C18  C13  120.81  3.000
 HK9  H13  C19  C20  120.59  3.000
 HK9  H13  C19  C18  119.74  3.000
 HK9  C20  C19  C18  119.68  3.000
 HK9  H14  C20  C21  119.73  3.000
 HK9  H14  C20  C19  120.53  3.000
 HK9  C21  C20  C19  119.74  3.000
 HK9  H15  C21  C12  119.00  3.000
 HK9  H15  C21  C20  120.14  3.000
 HK9  C12  C21  C20  120.85  3.000
 HK9  N1   C12  C21  120.52  3.000
 HK9  N1   C12  C13  120.10  3.000
 HK9  C21  C12  C13  119.35  3.000
 HK9  H8   N1   C11  112.12  3.000
 HK9  H8   N1   C12  111.89  3.000
 HK9  C11  N1   C12  119.34  3.000
 HK9  C16  C15  C11  118.41  3.000
 HK9  C11  C15  C14  124.41  3.000
 HK9  C16  C15  C14  116.76  3.000
 HK9  C10  C11  C15  119.39  3.000
 HK9  C10  C11  N1   118.75  3.000
 HK9  C15  C11  N1   121.85  3.000
 HK9  H7   C10  C9   119.62  3.000
 HK9  H7   C10  C11  118.44  3.000
 HK9  C9   C10  C11  121.92  3.000
 HK9  H10  C16  C17  119.07  3.000
 HK9  H10  C16  C15  119.06  3.000
 HK9  C17  C16  C15  121.86  3.000
 HK9  H11  C17  C9   120.54  3.000
 HK9  H11  C17  C16  119.35  3.000
 HK9  C9   C17  C16  120.05  3.000
 HK9  C4   C9   C17  121.40  3.000
 HK9  C4   C9   C10  120.27  3.000
 HK9  C17  C9   C10  118.33  3.000
 HK9  C5   C4   C3   118.83  3.000
 HK9  C3   C4   C9   120.25  3.000
 HK9  C5   C4   C9   120.92  3.000
 HK9  H4   C3   C2   120.27  3.000
 HK9  H4   C3   C4   118.62  3.000
 HK9  C2   C3   C4   121.09  3.000
 HK9  H5   C5   C6   119.73  3.000
 HK9  H5   C5   C4   120.51  3.000
 HK9  C6   C5   C4   119.73  3.000
 HK9  H6   C6   C7   118.49  3.000
 HK9  H6   C6   C5   119.09  3.000
 HK9  C7   C6   C5   122.42  3.000
 HK9  C2   C7   C8   123.63  3.000
 HK9  C8   C7   C6   118.70  3.000
 HK9  C2   C7   C6   117.66  3.000
 HK9  O2   C8   O3   127.16  3.000
 HK9  O3   C8   C7   115.70  3.000
 HK9  O2   C8   C7   117.10  3.000
 HK9  O1   C2   C7   117.21  3.000
 HK9  O1   C2   C3   122.55  3.000
 HK9  C7   C2   C3   120.22  3.000
 HK9  C1   O1   C2   118.95  3.000
 HK9  H1   C1   H2   108.56  3.000
 HK9  H1   C1   H3   108.63  3.000
 HK9  H2   C1   H3   108.69  3.000
 HK9  H1   C1   O1   106.42  3.000
 HK9  H2   C1   O1   112.26  3.000
 HK9  H3   C1   O1   112.15  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
 HK9  CONST_01  C20  C19  C18  C13     0.00   0.0  0
 HK9  CONST_02  C21  C20  C19  C18     0.00   0.0  0
 HK9  CONST_03  C12  C21  C20  C19     0.00   0.0  0
 HK9  CONST_04  C9   C17  C16  C15     0.00   0.0  0
 HK9  CONST_05  C17  C9   C10  C11     0.00   0.0  0
 HK9  CONST_06  C4   C9   C10  C11   180.00   0.0  0
 HK9  CONST_07  C16  C17  C9   C10     0.00   0.0  0
 HK9  CONST_10  C4   C9   C17  C16   180.00   0.0  0
 HK9  CONST_13  C6   C5   C4   C9    180.00   0.0  0
 HK9  CONST_14  C2   C3   C4   C9    180.00   0.0  0
 HK9  CONST_15  C7   C6   C5   C4      0.00   0.0  0
 HK9  CONST_16  C7   C2   C3   C4      0.00   0.0  0
 HK9  CONST_17  C6   C5   C4   C3      0.00   0.0  0
 HK9  CONST_18  C6   C7   C2   C3      0.00   0.0  0
 HK9  CONST_19  C2   C3   C4   C5      0.00   0.0  0
 HK9  CONST_20  C2   C7   C6   C5      0.00   0.0  0
 HK9  CONST_21  O1   C2   C3   C4    180.00   0.0  0
 HK9  CONST_22  C8   C7   C2   C3    180.00   0.0  0
 HK9  CONST_23  C8   C7   C6   C5    180.00   0.0  0
 HK9  CONST_24  O1   C2   C7   C6    180.00   0.0  0
 HK9  CONST_25  H13  C19  C18  C13   180.00   0.0  0
 HK9  CONST_26  H14  C20  C19  C18   180.00   0.0  0
 HK9  CONST_27  H15  C21  C20  C19   180.00   0.0  0
 HK9  CONST_28  H12  C18  C19  C20   180.00   0.0  0
 HK9  CONST_29  H11  C17  C16  C15   180.00   0.0  0
 HK9  CONST_30  H7   C10  C9   C17   180.00   0.0  0
 HK9  CONST_31  H10  C16  C17  C9    180.00   0.0  0
 HK9  CONST_32  H5   C5   C4   C9      0.00   0.0  0
 HK9  CONST_33  H4   C3   C4   C9      0.00   0.0  0
 HK9  CONST_34  H6   C6   C5   C4    180.00   0.0  0
 HK9  Var_01    O2   C8   C7   C6   -138.80  30.0  2
 HK9  Var_02    H3   C1   O1   C2    -60.32  30.0  3

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
 HK9  plan-1  C9   0.020
 HK9  plan-1  C4   0.020
 HK9  plan-1  C3   0.020
 HK9  plan-1  C5   0.020
 HK9  plan-1  C6   0.020
 HK9  plan-1  C7   0.020
 HK9  plan-1  C8   0.020
 HK9  plan-1  C2   0.020
 HK9  plan-1  O1   0.020
 HK9  plan-1  H4   0.020
 HK9  plan-1  H5   0.020
 HK9  plan-1  H6   0.020
 HK9  plan-2  N2   0.020
 HK9  plan-2  C13  0.020
 HK9  plan-2  C18  0.020
 HK9  plan-2  C19  0.020
 HK9  plan-2  C20  0.020
 HK9  plan-2  C21  0.020
 HK9  plan-2  C12  0.020
 HK9  plan-2  N1   0.020
 HK9  plan-2  H12  0.020
 HK9  plan-2  H13  0.020
 HK9  plan-2  H14  0.020
 HK9  plan-2  H15  0.020
 HK9  plan-3  C14  0.020
 HK9  plan-3  N1   0.020
 HK9  plan-3  C15  0.020
 HK9  plan-3  C11  0.020
 HK9  plan-3  C10  0.020
 HK9  plan-3  C16  0.020
 HK9  plan-3  C17  0.020
 HK9  plan-3  C9   0.020
 HK9  plan-3  C4   0.020
 HK9  plan-3  H7   0.020
 HK9  plan-3  H10  0.020
 HK9  plan-3  H11  0.020
 HK9  plan-4  O4   0.020
 HK9  plan-4  C14  0.020
 HK9  plan-4  N2   0.020
 HK9  plan-4  C13  0.020
 HK9  plan-4  C15  0.020
 HK9  plan-4  H9   0.020
 HK9  plan-5  C7   0.020
 HK9  plan-5  C8   0.020
 HK9  plan-5  O3   0.020
 HK9  plan-5  O2   0.020

