# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:52:33 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 2-[3-(3-methoxy-4-nitrophenyl)-11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-8-yl]-N,N-dimethylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1[N+]([O-])=O)c2ccc3C(=O)Nc4cc(CC(=O)N(C)C)ccc4Nc3c2
#
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
 5HK  5HK  2-[3-(3-methoxy-4-nitrophenyl)-11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-8-yl]-N,N-dimethylacetamide  ligand  55  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5HK
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
 5HK  O5    O  O      0  -0.493   6.9212   0.7818   0.8623
 5HK  C17   C  C      0   0.566   7.0255   0.9447  -0.3451
 5HK  N3    N  NT     0  -0.449   8.2086   1.1828  -0.9502
 5HK  C19   C  CH3    0  -0.523   9.4064   1.3734  -0.1585
 5HK  C18   C  CH3    0  -0.525   8.3332   1.5158  -2.3549
 5HK  C16   C  CH2    0  -0.716   5.8035   0.8733  -1.2530
 5HK  C15   C  CR6    0   0.178   4.5392   0.6510  -0.4808
 5HK  C14   C  CR16   0  -0.379   4.1030  -0.6337  -0.1903
 5HK  C20   C  CR16   0  -0.316   3.7742   1.7240  -0.0390
 5HK  C21   C  CR16   0  -0.312   2.5975   1.5107   0.6600
 5HK  C22   C  CR6    0   0.238   2.1740   0.2222   0.9659
 5HK  C13   C  CR6    0   0.361   2.9386  -0.8585   0.5357
 5HK  N2    N  NH1    0  -0.743   2.6112  -2.1745   0.8931
 5HK  C12   C  C      0   0.517   1.4139  -2.8092   0.8579
 5HK  O4    O  O      0  -0.460   1.3612  -4.0221   0.9893
 5HK  N4    N  NH1    0  -0.747   1.0065   0.0058   1.7163
 5HK  C23   C  CR6    0   0.348  -0.0334  -0.7267   1.1463
 5HK  C11   C  CR6    0  -0.134   0.1639  -2.0251   0.6631
 5HK  C10   C  CR16   0  -0.267  -0.9163  -2.6996   0.0937
 5HK  C9    C  CR16   0  -0.314  -2.1645  -2.1202  -0.0005
 5HK  C24   C  CR16   0  -0.383  -1.3058  -0.1595   1.0805
 5HK  C8    C  CR6    0   0.100  -2.3760  -0.8405   0.5162
 5HK  C4    C  CR6    0   0.128  -3.7069  -0.2068   0.4477
 5HK  C5    C  CR16   0  -0.466  -4.5072  -0.4026  -0.6733
 5HK  C6    C  CR6    0   0.446  -5.7658   0.1859  -0.7849
 5HK  O3    O  O2     0  -0.444  -6.5718   0.0048  -1.8255
 5HK  C7    C  CH3    0  -0.447  -6.1797  -0.8901  -2.8557
 5HK  C3    C  CR16   0  -0.332  -4.1737   0.5846   1.4971
 5HK  C2    C  CR16   0  -0.254  -5.4228   1.1631   1.4156
 5HK  C1    C  CR6    0   0.146  -6.2072   0.9836   0.2854
 5HK  N1    N  N      1   0.337  -7.4926   1.6465   0.2501
 5HK  O1    O  O      0  -0.387  -8.0746   1.7930   1.3024
 5HK  O2    O  O     -1  -0.374  -7.9118   2.0394  -0.8119
 5HK  H191  H  HCH3   0   0.256   9.2776   0.9583   0.8355
 5HK  H193  H  HCH3   0   0.242  10.2453   0.8708  -0.6396
 5HK  H192  H  HCH3   0   0.237   9.6551   2.4335  -0.0635
 5HK  H182  H  HCH3   0   0.242   8.2078   2.5866  -2.5348
 5HK  H181  H  HCH3   0   0.254   9.3258   1.2294  -2.6982
 5HK  H183  H  HCH3   0   0.261   7.6149   0.9766  -2.9661
 5HK  H9    H  HCH2   0   0.294   5.7285   1.7976  -1.8323
 5HK  H8    H  HCH2   0   0.297   5.9465   0.0743  -1.9860
 5HK  H7    H  HCR6   0   0.266   4.6826  -1.4874  -0.5240
 5HK  H10   H  HCR6   0   0.254   4.0884   2.7378  -0.2538
 5HK  H11   H  HCR6   0   0.265   2.0019   2.3549   0.9866
 5HK  H6    H  HNH1   0   0.407   3.3969  -2.8044   0.9850
 5HK  H12   H  HNH1   0   0.396   0.6800   0.8514   2.1624
 5HK  H5    H  HCR6   0   0.270  -0.7738  -3.7079  -0.2699
 5HK  H4    H  HCR6   0   0.262  -2.9799  -2.6813  -0.4369
 5HK  H13   H  HCR6   0   0.272  -1.4428   0.8502   1.4494
 5HK  H3    H  HCR6   0   0.300  -4.1267  -1.0048  -1.4865
 5HK  H71   H  HCH3   0   0.242  -5.2839  -0.5420  -3.3734
 5HK  H72   H  HCH3   0   0.240  -6.0067  -1.8973  -2.4710
 5HK  H73   H  HCH3   0   0.272  -7.0063  -0.9161  -3.5595
 5HK  H2    H  HCR6   0   0.273  -3.5761   0.7322   2.3860
 5HK  H1    H  HCR6   0   0.298  -5.7853   1.7709   2.2326

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
 5HK  C17  C16   single    1.524  0.020  1.524
 5HK  C17  O5    double    1.223  0.020  1.223
 5HK  N3   C17   single    1.350  0.020  1.350
 5HK  C19  N3    single    1.448  0.020  1.448
 5HK  C19  H191  single    0.970  0.020  1.090
 5HK  C19  H193  single    0.970  0.020  1.090
 5HK  C19  H192  single    0.970  0.020  1.090
 5HK  C18  N3    single    1.449  0.020  1.449
 5HK  C18  H182  single    0.970  0.020  1.090
 5HK  C18  H181  single    0.970  0.020  1.090
 5HK  C18  H183  single    0.970  0.020  1.090
 5HK  C16  C15   single    1.498  0.020  1.498
 5HK  C16  H9    single    0.970  0.020  1.090
 5HK  C16  H8    single    0.970  0.020  1.090
 5HK  C15  C20   aromatic  1.390  0.020  1.390
 5HK  C14  C15   aromatic  1.388  0.020  1.388
 5HK  C14  C13   aromatic  1.390  0.020  1.390
 5HK  C14  H7    single    0.930  0.020  1.080
 5HK  C20  C21   aromatic  1.385  0.020  1.385
 5HK  C20  H10   single    0.930  0.020  1.080
 5HK  C21  H11   single    0.930  0.020  1.080
 5HK  C22  C21   aromatic  1.390  0.020  1.390
 5HK  C22  N4    single    1.405  0.020  1.405
 5HK  C13  C22   aromatic  1.392  0.020  1.392
 5HK  N2   C13   single    1.402  0.020  1.402
 5HK  N2   C12   single    1.356  0.020  1.356
 5HK  N2   H6    single    0.860  0.020  1.020
 5HK  C12  C11   single    1.488  0.020  1.488
 5HK  O4   C12   double    1.221  0.020  1.221
 5HK  N4   H12   single    0.890  0.020  1.040
 5HK  C23  N4    single    1.394  0.020  1.394
 5HK  C23  C24   aromatic  1.395  0.020  1.395
 5HK  C11  C23   aromatic  1.399  0.020  1.399
 5HK  C10  C11   aromatic  1.395  0.020  1.395
 5HK  C10  C9    aromatic  1.379  0.020  1.379
 5HK  C10  H5    single    0.930  0.020  1.080
 5HK  C9   C8    aromatic  1.396  0.020  1.396
 5HK  C9   H4    single    0.930  0.020  1.080
 5HK  C24  H13   single    0.930  0.020  1.080
 5HK  C8   C24   aromatic  1.388  0.020  1.388
 5HK  C8   C4    single    1.476  0.020  1.476
 5HK  C4   C5    aromatic  1.391  0.020  1.391
 5HK  C4   C3    aromatic  1.395  0.020  1.395
 5HK  C5   C6    aromatic  1.394  0.020  1.394
 5HK  C5   H3    single    0.930  0.020  1.080
 5HK  C6   O3    single    1.329  0.020  1.329
 5HK  C6   C1    aromatic  1.406  0.020  1.406
 5HK  C7   O3    single    1.420  0.020  1.420
 5HK  C7   H71   single    0.970  0.020  1.090
 5HK  C7   H72   single    0.970  0.020  1.090
 5HK  C7   H73   single    0.970  0.020  1.090
 5HK  C3   C2    aromatic  1.379  0.020  1.379
 5HK  C3   H2    single    0.930  0.020  1.080
 5HK  C2   C1    aromatic  1.387  0.020  1.387
 5HK  C2   H1    single    0.930  0.020  1.080
 5HK  C1   N1    single    1.447  0.020  1.447
 5HK  N1   O1    double    1.211  0.020  1.211
 5HK  O2   N1    single    1.207  0.020  1.207

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
 5HK  C16   C17  N3    116.36  3.000
 5HK  N3    C17  O5    122.74  3.000
 5HK  C16   C17  O5    120.90  3.000
 5HK  C18   N3   C19   115.37  3.000
 5HK  C18   N3   C17   123.40  3.000
 5HK  C19   N3   C17   120.19  3.000
 5HK  H192  C19  H193  108.10  3.000
 5HK  H192  C19  H191  108.57  3.000
 5HK  H193  C19  H191  108.62  3.000
 5HK  H192  C19  N3    111.30  3.000
 5HK  H193  C19  N3    109.55  3.000
 5HK  H191  C19  N3    110.63  3.000
 5HK  H183  C18  H181  107.15  3.000
 5HK  H183  C18  H182  108.53  3.000
 5HK  H181  C18  H182  108.09  3.000
 5HK  H183  C18  N3    111.99  3.000
 5HK  H181  C18  N3    108.88  3.000
 5HK  H182  C18  N3    112.01  3.000
 5HK  H8    C16  H9    105.75  3.000
 5HK  H8    C16  C15   110.33  3.000
 5HK  H9    C16  C15   109.91  3.000
 5HK  H8    C16  C17   109.18  3.000
 5HK  H9    C16  C17   109.33  3.000
 5HK  C15   C16  C17   112.13  3.000
 5HK  C20   C15  C14   118.38  3.000
 5HK  C14   C15  C16   120.71  3.000
 5HK  C20   C15  C16   120.92  3.000
 5HK  H7    C14  C13   118.75  3.000
 5HK  H7    C14  C15   119.76  3.000
 5HK  C13   C14  C15   121.48  3.000
 5HK  H10   C20  C21   119.38  3.000
 5HK  H10   C20  C15   120.00  3.000
 5HK  C21   C20  C15   120.60  3.000
 5HK  H11   C21  C22   119.23  3.000
 5HK  C22   C21  C20   120.83  3.000
 5HK  H11   C21  C20   119.94  3.000
 5HK  N4    C22  C13   120.14  3.000
 5HK  C13   C22  C21   118.96  3.000
 5HK  N4    C22  C21   120.90  3.000
 5HK  N2    C13  C22   121.44  3.000
 5HK  N2    C13  C14   118.70  3.000
 5HK  C22   C13  C14   119.73  3.000
 5HK  H6    N2   C12   113.39  3.000
 5HK  H6    N2   C13   115.23  3.000
 5HK  C12   N2   C13   129.71  3.000
 5HK  C11   C12  O4    120.07  3.000
 5HK  O4    C12  N2    120.03  3.000
 5HK  C11   C12  N2    119.90  3.000
 5HK  H12   N4   C23   112.29  3.000
 5HK  C23   N4   C22   118.86  3.000
 5HK  H12   N4   C22   112.06  3.000
 5HK  C24   C23  C11   119.32  3.000
 5HK  C11   C23  N4    121.57  3.000
 5HK  C24   C23  N4    119.09  3.000
 5HK  C10   C11  C23   118.71  3.000
 5HK  C10   C11  C12   116.68  3.000
 5HK  C23   C11  C12   124.20  3.000
 5HK  H5    C10  C9    119.21  3.000
 5HK  H5    C10  C11   119.08  3.000
 5HK  C9    C10  C11   121.70  3.000
 5HK  H4    C9   C8    120.69  3.000
 5HK  H4    C9   C10   119.46  3.000
 5HK  C8    C9   C10   119.79  3.000
 5HK  H13   C24  C8    119.86  3.000
 5HK  C8    C24  C23   121.53  3.000
 5HK  H13   C24  C23   118.57  3.000
 5HK  C4    C8   C24   120.23  3.000
 5HK  C4    C8   C9    120.87  3.000
 5HK  C24   C8   C9    118.90  3.000
 5HK  C3    C4   C5    119.57  3.000
 5HK  C3    C4   C8    120.71  3.000
 5HK  C5    C4   C8    119.72  3.000
 5HK  H3    C5   C6    119.52  3.000
 5HK  H3    C5   C4    118.82  3.000
 5HK  C6    C5   C4    121.63  3.000
 5HK  C1    C6   O3    118.89  3.000
 5HK  C1    C6   C5    117.52  3.000
 5HK  O3    C6   C5    123.57  3.000
 5HK  C7    O3   C6    119.12  3.000
 5HK  H73   C7   H72   109.08  3.000
 5HK  H73   C7   H71   108.96  3.000
 5HK  H72   C7   H71   109.34  3.000
 5HK  H73   C7   O3    105.97  3.000
 5HK  H72   C7   O3    111.68  3.000
 5HK  H71   C7   O3    111.70  3.000
 5HK  H2    C3   C2    119.47  3.000
 5HK  H2    C3   C4    120.73  3.000
 5HK  C2    C3   C4    119.79  3.000
 5HK  H1    C2   C1    119.92  3.000
 5HK  H1    C2   C3    119.68  3.000
 5HK  C1    C2   C3    120.39  3.000
 5HK  N1    C1   C2    117.58  3.000
 5HK  N1    C1   C6    121.35  3.000
 5HK  C2    C1   C6    121.07  3.000
 5HK  O2    N1   O1    123.91  3.000
 5HK  O2    N1   C1    118.62  3.000
 5HK  O1    N1   C1    117.45  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
 5HK  CONST_01  C22   C21  C20  C15     0.00   0.0  0
 5HK  CONST_02  C22   C13  C14  C15     0.00   0.0  0
 5HK  CONST_03  C21   C20  C15  C14     0.00   0.0  0
 5HK  CONST_04  C21   C22  C13  C14     0.00   0.0  0
 5HK  CONST_05  C13   C14  C15  C20     0.00   0.0  0
 5HK  CONST_06  C13   C22  C21  C20     0.00   0.0  0
 5HK  CONST_07  C9    C8   C24  C23     0.00   0.0  0
 5HK  CONST_08  C4    C8   C24  C23   180.00   0.0  0
 5HK  CONST_09  C9    C10  C11  C23     0.00   0.0  0
 5HK  CONST_10  C8    C24  C23  C11     0.00   0.0  0
 5HK  CONST_11  C8    C9   C10  C11     0.00   0.0  0
 5HK  CONST_12  C24   C23  C11  C10     0.00   0.0  0
 5HK  CONST_13  C24   C8   C9   C10     0.00   0.0  0
 5HK  CONST_14  C4    C8   C9   C10   180.00   0.0  0
 5HK  CONST_19  C6    C5   C4   C8    180.00   0.0  0
 5HK  CONST_20  C2    C3   C4   C8    180.00   0.0  0
 5HK  CONST_21  C1    C6   C5   C4      0.00   0.0  0
 5HK  CONST_22  C1    C2   C3   C4      0.00   0.0  0
 5HK  CONST_23  C2    C3   C4   C5      0.00   0.0  0
 5HK  CONST_24  C2    C1   C6   C5      0.00   0.0  0
 5HK  CONST_25  C3    C4   C5   C6      0.00   0.0  0
 5HK  CONST_26  C3    C2   C1   C6      0.00   0.0  0
 5HK  CONST_27  C11   C12  N2   C13     0.00   0.0  0
 5HK  CONST_28  C21   C20  C15  C16   180.00   0.0  0
 5HK  CONST_29  C13   C14  C15  C16   180.00   0.0  0
 5HK  CONST_30  O3    C6   C5   C4    180.00   0.0  0
 5HK  CONST_31  N1    C1   C6   C5    180.00   0.0  0
 5HK  CONST_32  C2    C1   C6   O3    180.00   0.0  0
 5HK  CONST_33  N1    C1   C2   C3    180.00   0.0  0
 5HK  CONST_34  O4    C12  N2   C13   180.00   0.0  0
 5HK  CONST_35  H11   C21  C20  C15   180.00   0.0  0
 5HK  CONST_36  H10   C20  C15  C14   180.00   0.0  0
 5HK  CONST_37  H7    C14  C15  C20   180.00   0.0  0
 5HK  CONST_38  H5    C10  C11  C12     0.00   0.0  0
 5HK  CONST_39  H13   C24  C23  N4      0.00   0.0  0
 5HK  CONST_40  H4    C9   C10  C11   180.00   0.0  0
 5HK  CONST_41  H3    C5   C4   C8      0.00   0.0  0
 5HK  CONST_42  H2    C3   C4   C8      0.00   0.0  0
 5HK  CONST_43  H1    C2   C3   C4    180.00   0.0  0
 5HK  CONST_44  H6    N2   C12  C11   180.00   0.0  0
 5HK  CONST_49  C19   N3   C17  O5      0.00   0.0  0
 5HK  CONST_50  C18   N3   C17  O5    180.00   0.0  0
 5HK  CONST_51  C16   C17  N3   C19   180.00   0.0  0
 5HK  CONST_52  C16   C17  N3   C18     0.00   0.0  0
 5HK  Var_01    C12   N2   C13  C14  -137.18  30.0  1
 5HK  Var_02    C23   N4   C22  C21   120.06  30.0  1
 5HK  Var_03    C24   C23  N4   C22  -124.71  30.0  1
 5HK  Var_04    C23   C11  C12  N2    -33.34  30.0  1
 5HK  Var_05    C20   C15  C16  C17    91.61  30.0  2
 5HK  Var_06    C1    C6   O3   C7   -174.66  30.0  2
 5HK  Var_07    C15   C16  C17  O5      2.45  30.0  3
 5HK  Var_08    H71   C7   O3   C6    -64.47  30.0  3
 5HK  Var_09    H191  C19  N3   C17    20.15  30.0  3
 5HK  Var_10    H182  C18  N3   C17    85.53  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
 5HK  plan-1  C8   0.020
 5HK  plan-1  C4   0.020
 5HK  plan-1  C5   0.020
 5HK  plan-1  C6   0.020
 5HK  plan-1  O3   0.020
 5HK  plan-1  C3   0.020
 5HK  plan-1  C2   0.020
 5HK  plan-1  C1   0.020
 5HK  plan-1  N1   0.020
 5HK  plan-1  H3   0.020
 5HK  plan-1  H2   0.020
 5HK  plan-1  H1   0.020
 5HK  plan-2  C16  0.020
 5HK  plan-2  C15  0.020
 5HK  plan-2  C14  0.020
 5HK  plan-2  C20  0.020
 5HK  plan-2  C21  0.020
 5HK  plan-2  C22  0.020
 5HK  plan-2  C13  0.020
 5HK  plan-2  N2   0.020
 5HK  plan-2  N4   0.020
 5HK  plan-2  H7   0.020
 5HK  plan-2  H10  0.020
 5HK  plan-2  H11  0.020
 5HK  plan-3  C12  0.020
 5HK  plan-3  N4   0.020
 5HK  plan-3  C23  0.020
 5HK  plan-3  C11  0.020
 5HK  plan-3  C10  0.020
 5HK  plan-3  C9   0.020
 5HK  plan-3  C24  0.020
 5HK  plan-3  C8   0.020
 5HK  plan-3  C4   0.020
 5HK  plan-3  H5   0.020
 5HK  plan-3  H4   0.020
 5HK  plan-3  H13  0.020
 5HK  plan-4  O5   0.020
 5HK  plan-4  C17  0.020
 5HK  plan-4  N3   0.020
 5HK  plan-4  C19  0.020
 5HK  plan-4  C18  0.020
 5HK  plan-4  C16  0.020
 5HK  plan-5  C13  0.020
 5HK  plan-5  N2   0.020
 5HK  plan-5  C12  0.020
 5HK  plan-5  O4   0.020
 5HK  plan-5  C11  0.020
 5HK  plan-5  H6   0.020
 5HK  plan-6  C1   0.020
 5HK  plan-6  N1   0.020
 5HK  plan-6  O1   0.020
 5HK  plan-6  O2   0.020

