# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 03:38:03 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: methyl [3-(1-methyl-1H-imidazol-5-yl)-11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-8-yl]acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Cc1ccc2Nc3cc(ccc3C(=O)Nc2c1)c4cncn4C
#
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
 6HK  6HK  'methyl [3-(1-methyl-1H-imidazol-5-yl)-11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-8-yl]acetate'  ligand  45  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6HK
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
 6HK  O2    O  O     0  -0.461   0.3196  -3.6598  -0.3613
 6HK  C13   C  C     0   0.517   0.0997  -2.4715  -0.1843
 6HK  N2    N  NH1   0  -0.745  -1.1632  -2.0510   0.0805
 6HK  C14   C  CR6   0   0.360  -1.6978  -0.7554   0.0582
 6HK  C6    C  CR6   0   0.242  -1.0472   0.3115   0.6709
 6HK  C5    C  CR16  0  -0.314  -1.6675   1.5564   0.6925
 6HK  C4    C  CR16  0  -0.305  -2.9259   1.7339   0.1424
 6HK  C15   C  CR16  0  -0.372  -2.9498  -0.5606  -0.5148
 6HK  C3    C  CR6   0   0.143  -3.5819   0.6738  -0.4720
 6HK  C2    C  CH2   0  -0.691  -4.9457   0.8474  -1.0679
 6HK  C1    C  C     0   0.605  -6.0488   0.6112  -0.0620
 6HK  O3    O  O2    0  -0.452  -7.2408   0.7478  -0.6253
 6HK  C20   C  CH3   0  -0.422  -8.3895   0.5480   0.1995
 6HK  O1    O  O     0  -0.442  -5.8831   0.3354   1.0979
 6HK  C12   C  CR6   0  -0.134   1.2135  -1.4890  -0.2476
 6HK  C7    C  CR6   0   0.350   1.2783  -0.3140   0.5113
 6HK  N1    N  NH1   0  -0.748   0.2014   0.1211   1.2826
 6HK  C11   C  CR16  0  -0.266   2.3290  -1.8575  -1.0012
 6HK  C10   C  CR16  0  -0.309   3.4856  -1.1072  -1.0072
 6HK  C9    C  CR6   0   0.083   3.5768   0.0352  -0.2052
 6HK  C8    C  CR16  0  -0.401   2.4653   0.4156   0.5396
 6HK  C16   C  CR5   0   0.275   4.7674   0.8759  -0.1641
 6HK  N4    N  NR5   0  -0.452   6.0675   0.4299  -0.1962
 6HK  C19   C  CH3   0  -0.542   6.5482  -0.9353  -0.2113
 6HK  C18   C  CR15  0   0.086   6.8566   1.5213  -0.1426
 6HK  N3    N  N     0  -0.440   6.1673   2.6336  -0.0872
 6HK  C17   C  CR15  0  -0.246   4.8659   2.2448  -0.0957
 6HK  H9    H  HNH1  0   0.407  -1.8454  -2.7971   0.0633
 6HK  H4    H  HCR6  0   0.267  -1.1596   2.3906   1.1614
 6HK  H3    H  HCR6  0   0.257  -3.3902   2.7116   0.1818
 6HK  H10   H  HCR6  0   0.270  -3.4433  -1.4004  -0.9913
 6HK  H1    H  HCH2  0   0.304  -5.0672   1.8541  -1.4775
 6HK  H2    H  HCH2  0   0.303  -5.0945   0.1621  -1.9065
 6HK  H203  H  HCH3  0   0.252  -9.2497   0.6695  -0.4520
 6HK  H202  H  HCH3  0   0.239  -8.4015  -0.4524   0.6310
 6HK  H201  H  HCH3  0   0.240  -8.4369   1.2850   1.0008
 6HK  H5    H  HNH1  0   0.397   0.4499   0.8943   1.8833
 6HK  H8    H  HCR6  0   0.267   2.2835  -2.7566  -1.6005
 6HK  H7    H  HCR6  0   0.258   4.3050  -1.4088  -1.6443
 6HK  H6    H  HCR6  0   0.265   2.5214   1.2964   1.1680
 6HK  H193  H  HCH3  0   0.263   6.5157  -1.3582  -1.2134
 6HK  H191  H  HCH3  0   0.276   7.5785  -0.9460   0.1338
 6HK  H192  H  HCH3  0   0.268   5.9536  -1.5533   0.4569
 6HK  H12   H  HCR5  0   0.282   7.9337   1.4423  -0.1372
 6HK  H11   H  HCR5  0   0.262   4.0536   2.9559  -0.0757

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
 6HK  C2   C1    single    1.511  0.020  1.511
 6HK  C2   C3    single    1.498  0.020  1.498
 6HK  O1   C1    double    1.204  0.020  1.204
 6HK  C1   O3    single    1.325  0.020  1.325
 6HK  C15  C3    aromatic  1.387  0.020  1.387
 6HK  C15  C14   aromatic  1.391  0.020  1.391
 6HK  C3   C4    aromatic  1.390  0.020  1.390
 6HK  O2   C13   double    1.221  0.020  1.221
 6HK  N2   C14   single    1.402  0.020  1.402
 6HK  N2   C13   single    1.357  0.020  1.357
 6HK  O3   C20   single    1.428  0.020  1.428
 6HK  C14  C6    aromatic  1.392  0.020  1.392
 6HK  C13  C12   single    1.487  0.020  1.487
 6HK  C4   C5    aromatic  1.385  0.020  1.385
 6HK  C11  C12   aromatic  1.396  0.020  1.396
 6HK  C11  C10   aromatic  1.379  0.020  1.379
 6HK  C12  C7    aromatic  1.400  0.020  1.400
 6HK  C6   C5    aromatic  1.391  0.020  1.391
 6HK  C6   N1    single    1.403  0.020  1.403
 6HK  C10  C9    aromatic  1.399  0.020  1.399
 6HK  C7   N1    single    1.394  0.020  1.394
 6HK  C7   C8    aromatic  1.394  0.020  1.394
 6HK  C9   C8    aromatic  1.391  0.020  1.391
 6HK  C9   C16   single    1.458  0.020  1.458
 6HK  C16  N4    aromatic  1.375  0.020  1.375
 6HK  C16  C17   aromatic  1.374  0.020  1.374
 6HK  C19  N4    single    1.447  0.020  1.447
 6HK  N4   C18   aromatic  1.348  0.020  1.348
 6HK  C17  N3    aromatic  1.358  0.020  1.358
 6HK  C18  N3    aromatic  1.310  0.020  1.310
 6HK  N2   H9    single    0.860  0.020  1.020
 6HK  C5   H4    single    0.930  0.020  1.080
 6HK  C4   H3    single    0.930  0.020  1.080
 6HK  C15  H10   single    0.930  0.020  1.080
 6HK  C2   H1    single    0.970  0.020  1.090
 6HK  C2   H2    single    0.970  0.020  1.090
 6HK  C20  H203  single    0.970  0.020  1.090
 6HK  C20  H202  single    0.970  0.020  1.090
 6HK  C20  H201  single    0.970  0.020  1.090
 6HK  N1   H5    single    0.890  0.020  1.040
 6HK  C11  H8    single    0.930  0.020  1.080
 6HK  C10  H7    single    0.930  0.020  1.080
 6HK  C8   H6    single    0.930  0.020  1.080
 6HK  C19  H193  single    0.970  0.020  1.090
 6HK  C19  H191  single    0.970  0.020  1.090
 6HK  C19  H192  single    0.970  0.020  1.090
 6HK  C18  H12   single    0.930  0.020  1.080
 6HK  C17  H11   single    0.930  0.020  1.080

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
 6HK  C12   C13  N2    120.05  3.000
 6HK  C12   C13  O2    120.13  3.000
 6HK  N2    C13  O2    119.82  3.000
 6HK  H9    N2   C14   115.12  3.000
 6HK  H9    N2   C13   113.32  3.000
 6HK  C14   N2   C13   129.66  3.000
 6HK  C15   C14  C6    119.66  3.000
 6HK  C6    C14  N2    121.55  3.000
 6HK  C15   C14  N2    118.65  3.000
 6HK  N1    C6   C5    120.76  3.000
 6HK  N1    C6   C14   120.25  3.000
 6HK  C5    C6   C14   118.98  3.000
 6HK  H4    C5   C4    119.95  3.000
 6HK  H4    C5   C6    119.13  3.000
 6HK  C4    C5   C6    120.91  3.000
 6HK  H3    C4   C3    120.15  3.000
 6HK  H3    C4   C5    119.39  3.000
 6HK  C3    C4   C5    120.45  3.000
 6HK  H10   C15  C3    119.68  3.000
 6HK  H10   C15  C14   118.84  3.000
 6HK  C3    C15  C14   121.47  3.000
 6HK  C2    C3   C15   120.36  3.000
 6HK  C15   C3   C4    118.50  3.000
 6HK  C2    C3   C4    121.13  3.000
 6HK  H2    C2   H1    105.94  3.000
 6HK  H2    C2   C1    108.25  3.000
 6HK  H1    C2   C1    108.18  3.000
 6HK  H2    C2   C3    110.87  3.000
 6HK  H1    C2   C3    110.90  3.000
 6HK  C1    C2   C3    112.43  3.000
 6HK  O1    C1   O3    123.85  3.000
 6HK  O3    C1   C2    110.94  3.000
 6HK  O1    C1   C2    125.21  3.000
 6HK  C20   O3   C1    117.61  3.000
 6HK  H201  C20  H202  109.22  3.000
 6HK  H201  C20  H203  109.33  3.000
 6HK  H202  C20  H203  109.36  3.000
 6HK  H201  C20  O3    111.41  3.000
 6HK  H202  C20  O3    111.47  3.000
 6HK  H203  C20  O3    105.96  3.000
 6HK  C11   C12  C7    118.51  3.000
 6HK  C7    C12  C13   124.48  3.000
 6HK  C11   C12  C13   116.57  3.000
 6HK  C8    C7   N1    118.90  3.000
 6HK  C8    C7   C12   119.32  3.000
 6HK  N1    C7   C12   121.74  3.000
 6HK  H5    N1   C7    112.20  3.000
 6HK  H5    N1   C6    111.98  3.000
 6HK  C7    N1   C6    119.24  3.000
 6HK  H8    C11  C10   119.03  3.000
 6HK  H8    C11  C12   119.02  3.000
 6HK  C10   C11  C12   121.95  3.000
 6HK  H7    C10  C9    121.09  3.000
 6HK  H7    C10  C11   119.13  3.000
 6HK  C9    C10  C11   119.78  3.000
 6HK  C16   C9   C8    118.67  3.000
 6HK  C16   C9   C10   122.70  3.000
 6HK  C8    C9   C10   118.57  3.000
 6HK  H6    C8   C9    119.43  3.000
 6HK  H6    C8   C7    118.79  3.000
 6HK  C9    C8   C7    121.78  3.000
 6HK  C17   C16  N4    104.86  3.000
 6HK  C17   C16  C9    129.37  3.000
 6HK  N4    C16  C9    125.76  3.000
 6HK  C18   N4   C19   124.73  3.000
 6HK  C18   N4   C16   106.86  3.000
 6HK  C19   N4   C16   128.33  3.000
 6HK  H192  C19  H191  108.53  3.000
 6HK  H192  C19  H193  109.19  3.000
 6HK  H191  C19  H193  108.48  3.000
 6HK  H192  C19  N4    110.37  3.000
 6HK  H191  C19  N4    108.71  3.000
 6HK  H193  C19  N4    111.48  3.000
 6HK  H12   C18  N3    125.93  3.000
 6HK  H12   C18  N4    121.66  3.000
 6HK  N3    C18  N4    112.41  3.000
 6HK  C17   N3   C18   105.13  3.000
 6HK  H11   C17  N3    122.16  3.000
 6HK  H11   C17  C16   127.09  3.000
 6HK  N3    C17  C16   110.74  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
 6HK  CONST_01  C4    C3   C15  C14     0.00   0.0  0
 6HK  CONST_02  C3    C4   C5   C6      0.00   0.0  0
 6HK  CONST_03  C15   C3   C4   C5      0.00   0.0  0
 6HK  CONST_04  C9    C10  C11  C12     0.00   0.0  0
 6HK  CONST_05  C10   C9   C8   C7      0.00   0.0  0
 6HK  CONST_06  C16   C9   C8   C7    180.00   0.0  0
 6HK  CONST_07  C8    C9   C10  C11     0.00   0.0  0
 6HK  CONST_08  C16   C9   C10  C11   180.00   0.0  0
 6HK  CONST_11  C18   N4   C16  C9    180.00   0.0  0
 6HK  CONST_12  N3    C17  C16  C9    180.00   0.0  0
 6HK  CONST_15  N3    C18  N4   C16     0.00   0.0  0
 6HK  CONST_16  C18   N3   C17  C16     0.00   0.0  0
 6HK  CONST_17  N3    C17  C16  N4      0.00   0.0  0
 6HK  CONST_18  C17   N3   C18  N4      0.00   0.0  0
 6HK  CONST_19  C17   C16  N4   C18     0.00   0.0  0
 6HK  CONST_20  C2    C3   C15  C14   180.00   0.0  0
 6HK  CONST_21  C2    C3   C4   C5    180.00   0.0  0
 6HK  CONST_22  C19   N4   C16  C9      0.00   0.0  0
 6HK  CONST_23  C17   C16  N4   C19   180.00   0.0  0
 6HK  CONST_24  N3    C18  N4   C19   180.00   0.0  0
 6HK  CONST_25  H3    C4   C5   C6    180.00   0.0  0
 6HK  CONST_26  H10   C15  C3   C4    180.00   0.0  0
 6HK  CONST_27  H4    C5   C4   C3    180.00   0.0  0
 6HK  CONST_28  H7    C10  C11  C12   180.00   0.0  0
 6HK  CONST_29  H6    C8   C9   C10   180.00   0.0  0
 6HK  CONST_30  H8    C11  C10  C9    180.00   0.0  0
 6HK  CONST_31  H11   C17  C16  C9      0.00   0.0  0
 6HK  CONST_32  H12   C18  N4   C16   180.00   0.0  0
 6HK  Var_01    C1    C2   C3   C4    -87.99  30.0  2
 6HK  Var_02    H193  C19  N4   C16    81.50  30.0  2
 6HK  Var_03    O1    C1   C2   C3      1.17  30.0  3
 6HK  Var_04    H203  C20  O3   C1   -178.05  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
 6HK  plan-1  C9   0.020
 6HK  plan-1  C16  0.020
 6HK  plan-1  N4   0.020
 6HK  plan-1  C19  0.020
 6HK  plan-1  C18  0.020
 6HK  plan-1  N3   0.020
 6HK  plan-1  C17  0.020
 6HK  plan-1  H12  0.020
 6HK  plan-1  H11  0.020
 6HK  plan-2  N2   0.020
 6HK  plan-2  C14  0.020
 6HK  plan-2  C6   0.020
 6HK  plan-2  C5   0.020
 6HK  plan-2  C4   0.020
 6HK  plan-2  C15  0.020
 6HK  plan-2  C3   0.020
 6HK  plan-2  C2   0.020
 6HK  plan-2  N1   0.020
 6HK  plan-2  H4   0.020
 6HK  plan-2  H3   0.020
 6HK  plan-2  H10  0.020
 6HK  plan-3  C13  0.020
 6HK  plan-3  C12  0.020
 6HK  plan-3  C7   0.020
 6HK  plan-3  N1   0.020
 6HK  plan-3  C11  0.020
 6HK  plan-3  C10  0.020
 6HK  plan-3  C9   0.020
 6HK  plan-3  C8   0.020
 6HK  plan-3  C16  0.020
 6HK  plan-3  H8   0.020
 6HK  plan-3  H7   0.020
 6HK  plan-3  H6   0.020
 6HK  plan-4  O2   0.020
 6HK  plan-4  C13  0.020
 6HK  plan-4  N2   0.020
 6HK  plan-4  C14  0.020
 6HK  plan-4  C12  0.020
 6HK  plan-4  H9   0.020
 6HK  plan-5  C2   0.020
 6HK  plan-5  C1   0.020
 6HK  plan-5  O3   0.020
 6HK  plan-5  O1   0.020

