# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 02:07:53 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: methyl [11-oxo-3-(pyridin-4-ylamino)-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(Nc4ccncc4)ccc3C(=O)Nc2c1
#
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
 7HK  7HK  'methyl [11-oxo-3-(pyridin-4-ylamino)-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-8-yl]acetate'  ligand  46  28  .  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_7HK
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
 7HK  O2    O  O     0  -0.465  -0.0323  -3.5098  -0.2320
 7HK  C18   C  C     0   0.513  -0.2861  -2.3288  -0.0441
 7HK  N4    N  NH1   0  -0.747  -1.5719  -1.9496   0.1845
 7HK  C19   C  CR6   0   0.358  -2.1479  -0.6740   0.1252
 7HK  C6    C  CR6   0   0.241  -1.5555   0.4218   0.7467
 7HK  C5    C  CR16  0  -0.314  -2.2139   1.6466   0.7259
 7HK  C4    C  CR16  0  -0.307  -3.4547   1.7775   0.1243
 7HK  C20   C  CR16  0  -0.372  -3.3822  -0.5256  -0.4983
 7HK  C3    C  CR6   0   0.143  -4.0529   0.6891  -0.4993
 7HK  C2    C  CH2   0  -0.691  -5.3950   0.8131  -1.1542
 7HK  C1    C  C     0   0.605  -6.5321   0.5253  -0.2013
 7HK  O3    O  O2    0  -0.452  -7.7030   0.6494  -0.8098
 7HK  C21   C  CH3   0  -0.422  -8.8792   0.4038  -0.0378
 7HK  O1    O  O     0  -0.442  -6.4073   0.2219   0.9569
 7HK  C17   C  CR6   0  -0.146   0.7968  -1.3185  -0.0525
 7HK  C7    C  CR6   0   0.350   0.7955  -0.1338   0.6978
 7HK  N1    N  NH1   0  -0.750  -0.3274   0.2806   1.4106
 7HK  C16   C  CR16  0  -0.272   1.9637  -1.6543  -0.7430
 7HK  C15   C  CR16  0  -0.335   3.1011  -0.8790  -0.7023
 7HK  C9    C  CR6   0   0.400   3.1165   0.2684   0.0995
 7HK  C8    C  CR16  0  -0.443   1.9554   0.6292   0.7795
 7HK  N2    N  NH1   0  -0.798   4.2072   1.1117   0.1929
 7HK  C10   C  CR6   0   0.456   5.5376   0.8364  -0.0052
 7HK  C14   C  CR16  0  -0.419   6.4224   1.9022  -0.2093
 7HK  C13   C  CR16  0  -0.064   7.7663   1.6393  -0.3823
 7HK  N3    N  N     0  -0.427   8.2980   0.4193  -0.3715
 7HK  C12   C  CR16  0  -0.070   7.4560  -0.5863  -0.1612
 7HK  C11   C  CR16  0  -0.397   6.0928  -0.4464   0.0312
 7HK  H14   H  HNH1  0   0.405  -2.2277  -2.7173   0.1333
 7HK  H4    H  HCR6  0   0.267  -1.7502   2.5030   1.2006
 7HK  H3    H  HCR6  0   0.257  -3.9494   2.7409   0.1299
 7HK  H15   H  HCR6  0   0.269  -3.8308  -1.3871  -0.9805
 7HK  H1    H  HCH2  0   0.304  -5.5378   1.8164  -1.5650
 7HK  H2    H  HCH2  0   0.303  -5.4789   0.1278  -2.0022
 7HK  H212  H  HCH3  0   0.239  -8.8913  -0.6113   0.3579
 7HK  H211  H  HCH3  0   0.240  -8.9696   1.1114   0.7859
 7HK  H213  H  HCH3  0   0.252  -9.7155   0.5353  -0.7180
 7HK  H5    H  HNH1  0   0.397  -0.1308   1.0686   2.0111
 7HK  H13   H  HCR6  0   0.267   1.9731  -2.5548  -1.3420
 7HK  H12   H  HCR6  0   0.283   3.9544  -1.1589  -1.3023
 7HK  H6    H  HCR6  0   0.276   1.9549   1.5284   1.3858
 7HK  H7    H  HNH1  0   0.412   3.9975   2.0642   0.4486
 7HK  H11   H  HCR6  0   0.278   6.0624   2.9232  -0.2375
 7HK  H10   H  HCR6  0   0.264   8.4499   2.4648  -0.5467
 7HK  H9    H  HCR6  0   0.263   7.8876  -1.5812  -0.1330
 7HK  H8    H  HCR6  0   0.289   5.4980  -1.3258   0.2295

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
 7HK  C21  O3    single    1.428  0.020  1.428
 7HK  O1   C1    double    1.204  0.020  1.204
 7HK  O3   C1    single    1.325  0.020  1.325
 7HK  C1   C2    single    1.511  0.020  1.511
 7HK  C2   C3    single    1.499  0.020  1.499
 7HK  C3   C20   aromatic  1.388  0.020  1.388
 7HK  C3   C4    aromatic  1.390  0.020  1.390
 7HK  C20  C19   aromatic  1.391  0.020  1.391
 7HK  C4   C5    aromatic  1.385  0.020  1.385
 7HK  O2   C18   double    1.223  0.020  1.223
 7HK  N4   C19   single    1.401  0.020  1.401
 7HK  N4   C18   single    1.360  0.020  1.360
 7HK  C19  C6    aromatic  1.392  0.020  1.392
 7HK  C18  C17   single    1.481  0.020  1.481
 7HK  C16  C17   aromatic  1.397  0.020  1.397
 7HK  C16  C15   aromatic  1.377  0.020  1.377
 7HK  C5   C6    aromatic  1.391  0.020  1.391
 7HK  C17  C7    aromatic  1.402  0.020  1.402
 7HK  C6   N1    single    1.403  0.020  1.403
 7HK  C15  C9    aromatic  1.400  0.020  1.400
 7HK  C7   N1    single    1.393  0.020  1.393
 7HK  C7   C8    aromatic  1.391  0.020  1.391
 7HK  C9   C8    aromatic  1.393  0.020  1.393
 7HK  C9   N2    single    1.382  0.020  1.382
 7HK  N2   C10   single    1.373  0.020  1.373
 7HK  C11  C10   aromatic  1.398  0.020  1.398
 7HK  C11  C12   aromatic  1.384  0.020  1.384
 7HK  C10  C14   aromatic  1.400  0.020  1.400
 7HK  C12  N3    aromatic  1.328  0.020  1.328
 7HK  C14  C13   aromatic  1.380  0.020  1.380
 7HK  N3   C13   aromatic  1.331  0.020  1.331
 7HK  N4   H14   single    0.860  0.020  1.020
 7HK  C5   H4    single    0.930  0.020  1.080
 7HK  C4   H3    single    0.930  0.020  1.080
 7HK  C20  H15   single    0.930  0.020  1.080
 7HK  C2   H1    single    0.970  0.020  1.090
 7HK  C2   H2    single    0.970  0.020  1.090
 7HK  C21  H212  single    0.970  0.020  1.090
 7HK  C21  H211  single    0.970  0.020  1.090
 7HK  C21  H213  single    0.970  0.020  1.090
 7HK  N1   H5    single    0.890  0.020  1.040
 7HK  C16  H13   single    0.930  0.020  1.080
 7HK  C15  H12   single    0.930  0.020  1.080
 7HK  C8   H6    single    0.930  0.020  1.080
 7HK  N2   H7    single    0.860  0.020  1.020
 7HK  C14  H11   single    0.930  0.020  1.080
 7HK  C13  H10   single    0.930  0.020  1.080
 7HK  C12  H9    single    0.930  0.020  1.080
 7HK  C11  H8    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
 7HK  C17   C18  N4    120.14  3.000
 7HK  C17   C18  O2    120.42  3.000
 7HK  N4    C18  O2    119.44  3.000
 7HK  H14   N4   C19   115.00  3.000
 7HK  H14   N4   C18   113.14  3.000
 7HK  C19   N4   C18   129.46  3.000
 7HK  C20   C19  C6    119.60  3.000
 7HK  C6    C19  N4    121.52  3.000
 7HK  C20   C19  N4    118.75  3.000
 7HK  N1    C6   C5    120.67  3.000
 7HK  N1    C6   C19   120.30  3.000
 7HK  C5    C6   C19   119.02  3.000
 7HK  H4    C5   C4    119.93  3.000
 7HK  H4    C5   C6    119.14  3.000
 7HK  C4    C5   C6    120.92  3.000
 7HK  H3    C4   C3    120.16  3.000
 7HK  H3    C4   C5    119.41  3.000
 7HK  C3    C4   C5    120.43  3.000
 7HK  H15   C20  C3    119.68  3.000
 7HK  H15   C20  C19   118.80  3.000
 7HK  C3    C20  C19   121.51  3.000
 7HK  C2    C3   C20   120.38  3.000
 7HK  C20   C3   C4    118.50  3.000
 7HK  C2    C3   C4    121.12  3.000
 7HK  H2    C2   H1    105.88  3.000
 7HK  H2    C2   C1    108.17  3.000
 7HK  H1    C2   C1    108.26  3.000
 7HK  H2    C2   C3    110.83  3.000
 7HK  H1    C2   C3    110.92  3.000
 7HK  C1    C2   C3    112.49  3.000
 7HK  O1    C1   O3    123.84  3.000
 7HK  O3    C1   C2    110.94  3.000
 7HK  O1    C1   C2    125.22  3.000
 7HK  C21   O3   C1    117.60  3.000
 7HK  H213  C21  H211  109.33  3.000
 7HK  H213  C21  H212  109.37  3.000
 7HK  H211  C21  H212  109.24  3.000
 7HK  H213  C21  O3    105.95  3.000
 7HK  H211  C21  O3    111.42  3.000
 7HK  H212  C21  O3    111.45  3.000
 7HK  C16   C17  C7    117.93  3.000
 7HK  C7    C17  C18   124.93  3.000
 7HK  C16   C17  C18   116.72  3.000
 7HK  C8    C7   N1    118.61  3.000
 7HK  C8    C7   C17   119.62  3.000
 7HK  N1    C7   C17   121.73  3.000
 7HK  H5    N1   C7    112.30  3.000
 7HK  H5    N1   C6    111.91  3.000
 7HK  C7    N1   C6    119.56  3.000
 7HK  H13   C16  C15   118.55  3.000
 7HK  H13   C16  C17   118.77  3.000
 7HK  C15   C16  C17   122.68  3.000
 7HK  H12   C15  C9    121.46  3.000
 7HK  H12   C15  C16   119.36  3.000
 7HK  C9    C15  C16   119.18  3.000
 7HK  N2    C9   C8    117.83  3.000
 7HK  N2    C9   C15   123.20  3.000
 7HK  C8    C9   C15   118.86  3.000
 7HK  H6    C8   C9    119.21  3.000
 7HK  H6    C8   C7    119.17  3.000
 7HK  C9    C8   C7    121.62  3.000
 7HK  H7    N2   C10   115.31  3.000
 7HK  H7    N2   C9    115.44  3.000
 7HK  C10   N2   C9    129.25  3.000
 7HK  C11   C10  C14   116.82  3.000
 7HK  C14   C10  N2    118.74  3.000
 7HK  C11   C10  N2    124.39  3.000
 7HK  H11   C14  C13   120.00  3.000
 7HK  H11   C14  C10   120.75  3.000
 7HK  C13   C14  C10   119.25  3.000
 7HK  H10   C13  N3    116.56  3.000
 7HK  H10   C13  C14   119.20  3.000
 7HK  N3    C13  C14   124.24  3.000
 7HK  C12   N3   C13   116.23  3.000
 7HK  H9    C12  C11   118.75  3.000
 7HK  H9    C12  N3    116.50  3.000
 7HK  C11   C12  N3    124.74  3.000
 7HK  H8    C11  C12   119.06  3.000
 7HK  H8    C11  C10   122.22  3.000
 7HK  C12   C11  C10   118.71  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
 7HK  CONST_01  C4    C3   C20  C19    0.00   0.0  0
 7HK  CONST_02  C3    C4   C5   C6     0.00   0.0  0
 7HK  CONST_03  C20   C3   C4   C5     0.00   0.0  0
 7HK  CONST_04  C9    C15  C16  C17    0.00   0.0  0
 7HK  CONST_05  C15   C9   C8   C7     0.00   0.0  0
 7HK  CONST_06  C8    C9   C15  C16    0.00   0.0  0
 7HK  CONST_07  N3    C12  C11  C10    0.00   0.0  0
 7HK  CONST_08  N3    C13  C14  C10    0.00   0.0  0
 7HK  CONST_09  C12   C11  C10  C14    0.00   0.0  0
 7HK  CONST_10  C12   N3   C13  C14    0.00   0.0  0
 7HK  CONST_11  C11   C10  C14  C13    0.00   0.0  0
 7HK  CONST_12  C11   C12  N3   C13    0.00   0.0  0
 7HK  CONST_13  C2    C3   C20  C19  180.00   0.0  0
 7HK  CONST_14  C2    C3   C4   C5   180.00   0.0  0
 7HK  CONST_15  N2    C9   C8   C7   180.00   0.0  0
 7HK  CONST_16  N2    C9   C15  C16  180.00   0.0  0
 7HK  CONST_17  C12   C11  C10  N2   180.00   0.0  0
 7HK  CONST_18  C13   C14  C10  N2   180.00   0.0  0
 7HK  CONST_19  H3    C4   C5   C6   180.00   0.0  0
 7HK  CONST_20  H15   C20  C3   C4   180.00   0.0  0
 7HK  CONST_21  H4    C5   C4   C3   180.00   0.0  0
 7HK  CONST_22  H12   C15  C16  C17  180.00   0.0  0
 7HK  CONST_23  H6    C8   C9   C15  180.00   0.0  0
 7HK  CONST_24  H13   C16  C15  C9   180.00   0.0  0
 7HK  CONST_25  H9    C12  C11  C10  180.00   0.0  0
 7HK  CONST_26  H10   C13  C14  C10  180.00   0.0  0
 7HK  CONST_27  H8    C11  C10  C14  180.00   0.0  0
 7HK  CONST_28  H11   C14  C13  N3   180.00   0.0  0
 7HK  Var_01    C10   N2   C9   C15  -25.91  30.0  2
 7HK  Var_02    C11   C10  N2   C9   -19.54  30.0  2
 7HK  Var_03    C1    C2   C3   C4   -89.45  30.0  2
 7HK  Var_04    O1    C1   C2   C3    -0.33  30.0  1
 7HK  Var_05    H212  C21  O3   C1   -59.91  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
 7HK  plan-1  N2   0.020
 7HK  plan-1  C10  0.020
 7HK  plan-1  C14  0.020
 7HK  plan-1  C13  0.020
 7HK  plan-1  N3   0.020
 7HK  plan-1  C12  0.020
 7HK  plan-1  C11  0.020
 7HK  plan-1  H11  0.020
 7HK  plan-1  H10  0.020
 7HK  plan-1  H9   0.020
 7HK  plan-1  H8   0.020
 7HK  plan-2  N4   0.020
 7HK  plan-2  C19  0.020
 7HK  plan-2  C6   0.020
 7HK  plan-2  C5   0.020
 7HK  plan-2  C4   0.020
 7HK  plan-2  C20  0.020
 7HK  plan-2  C3   0.020
 7HK  plan-2  C2   0.020
 7HK  plan-2  N1   0.020
 7HK  plan-2  H4   0.020
 7HK  plan-2  H3   0.020
 7HK  plan-2  H15  0.020
 7HK  plan-3  C18  0.020
 7HK  plan-3  C17  0.020
 7HK  plan-3  C7   0.020
 7HK  plan-3  N1   0.020
 7HK  plan-3  C16  0.020
 7HK  plan-3  C15  0.020
 7HK  plan-3  C9   0.020
 7HK  plan-3  C8   0.020
 7HK  plan-3  N2   0.020
 7HK  plan-3  H13  0.020
 7HK  plan-3  H12  0.020
 7HK  plan-3  H6   0.020
 7HK  plan-4  O2   0.020
 7HK  plan-4  C18  0.020
 7HK  plan-4  N4   0.020
 7HK  plan-4  C19  0.020
 7HK  plan-4  C17  0.020
 7HK  plan-4  H14  0.020
 7HK  plan-5  C2   0.020
 7HK  plan-5  C1   0.020
 7HK  plan-5  O3   0.020
 7HK  plan-5  O1   0.020

