# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:04:13 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 9-(3,5-dichloro-4-hydroxyphenyl)-1-{trans-4-[(dimethylamino)methyl]cyclohexyl}-3,4-dihydropyrimido[5,4-c]quinolin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C[C@H]1CC[C@@H](CC1)N2C(=O)NCc3cnc4ccc(cc4c23)c5cc(Cl)c(O)c(Cl)c5
#
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
 H91  H91  9-(3,5-dichloro-4-hydroxyphenyl)-1-{trans-4-[(dimethylamino)methyl]cyclohexyl}-3,4-dihydropyrimido[5,4-c]quinolin-2(1H)-one  ligand  62  34  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H91
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
 H91  N    N   NT    0  -0.405  -1.3292   5.4100  -0.6339
 H91  C    C   CH3   0  -0.518  -2.5167   5.8935  -1.3040
 H91  O    O   O     0  -0.492   3.3714   1.5117   2.6929
 H91  C1   C   CH3   0  -0.527  -0.8636   6.3736   0.3402
 H91  C10  C   C     0  -0.326   5.4081   0.0879   0.1709
 H91  C11  C   CR66  0  -0.083   4.4091  -0.8595  -0.4058
 H91  C12  C   CR16  0  -0.124   4.7500  -1.8595  -1.3301
 H91  C13  C   CR66  0   0.169   2.6175  -2.6353  -1.4313
 H91  C14  C   CR16  0  -0.278   1.6989  -3.5832  -1.9395
 H91  C15  C   CR16  0  -0.308   0.4137  -3.6352  -1.4830
 H91  C16  C   CR6   0   0.104  -0.0270  -2.7545  -0.4666
 H91  C17  C   CR16  0  -0.378   0.8495  -1.8159   0.0221
 H91  C18  C   CR66  0   0.070   2.1643  -1.6953  -0.4704
 H91  C19  C   CR66  0   0.424   3.1012  -0.7237  -0.0102
 H91  C2   C   CH2   0  -0.236  -1.5698   4.1041  -0.0494
 H91  C20  C   CR6   0   0.055  -1.3947  -2.8448   0.0754
 H91  C21  C   CR16  0  -0.265  -2.0283  -4.0751   0.2397
 H91  C22  C   CR6   0  -0.133  -3.3021  -4.1423   0.7708
 H91  C23  C   CR6   0   0.476  -3.9995  -2.9991   1.1637
 H91  C24  C   CR6   0  -0.160  -3.3516  -1.7763   0.9872
 H91  C25  C   CR16  0  -0.269  -2.0819  -1.6941   0.4502
 H91  C3   C   CH1   0  -0.271  -0.3274   3.4200   0.5109
 H91  C4   C   CH2   0  -0.436  -0.6953   2.0366   1.0468
 H91  C5   C   CH2   0  -0.456   0.5224   1.3120   1.6130
 H91  C6   C   CH1   0  -0.105   1.5743   1.1691   0.5171
 H91  C7   C   CH2   0  -0.432   1.9955   2.5453  -0.0016
 H91  C8   C   CH2   0  -0.417   0.7810   3.3032  -0.5322
 H91  C9   C   CR6   0   0.664   3.6889   0.8150   1.7443
 H91  N1   N   NR6   0  -0.620   2.7411   0.3211   0.8475
 H91  N2   N   NR16  0  -0.648   4.9636   0.4306   1.5054
 H91  N3   N   N     0  -0.436   3.8976  -2.6931  -1.8625
 H91  O1   O   OH1   0  -0.586  -5.2223  -3.1363   1.6723
 H91  CL   CL  CL    0  -0.089  -4.0680  -5.6743   0.9788
 H91  CL1  CL  CL    0  -0.095  -4.1832  -0.3283   1.4441
 H91  H2   H   HCH3  0   0.187  -3.3783   6.0166  -0.6278
 H91  H3   H   HCH3  0   0.230  -2.3191   6.8617  -1.7663
 H91  H4   H   HCH3  0   0.231  -2.8137   5.2018  -2.0941
 H91  H5   H   HCH3  0   0.190  -1.5626   6.5089   1.1816
 H91  H6   H   HCH3  0   0.235   0.1009   6.0779   0.7539
 H91  H7   H   HCH3  0   0.233  -0.7263   7.3444  -0.1377
 H91  H8   H   H     0   0.279   6.3894  -0.3797   0.2394
 H91  H9   H   H     0   0.260   5.5155   0.9773  -0.4620
 H91  H10  H   HCR6  0   0.267   5.7840  -1.9390  -1.6536
 H91  H11  H   HCR6  0   0.266   2.0452  -4.2737  -2.6975
 H91  H12  H   HCR6  0   0.264  -0.2719  -4.3606  -1.9024
 H91  H13  H   HCR6  0   0.273   0.5427  -1.2011   0.8547
 H91  H14  H   HCH2  0   0.192  -2.3347   4.1601   0.7479
 H91  H15  H   HCH2  0   0.219  -1.9874   3.4612  -0.8324
 H91  H16  H   HCR6  0   0.285  -1.5232  -4.9945  -0.0251
 H91  H17  H   HCR6  0   0.286  -1.6406  -0.7184   0.2977
 H91  H18  H   HCH1  0   0.225   0.0550   3.9997   1.3609
 H91  H19  H   HCH2  0   0.238  -1.4671   2.1211   1.8162
 H91  H20  H   HCH2  0   0.212  -1.1320   1.4460   0.2314
 H91  H21  H   HCH2  0   0.246   0.9247   1.8784   2.4528
 H91  H22  H   HCH2  0   0.243   0.2309   0.3377   2.0129
 H91  H23  H   HCH1  0   0.259   1.0951   0.6698  -0.3288
 H91  H24  H   HCH2  0   0.231   2.4688   3.1246   0.7949
 H91  H25  H   HCH2  0   0.238   2.7347   2.4254  -0.7982
 H91  H26  H   HCH2  0   0.211   0.3867   2.7814  -1.4128
 H91  H27  H   HCH2  0   0.240   1.0876   4.2933  -0.8734
 H91  H28  H   HNR6  0   0.407   5.6504   0.7998   2.1449
 H91  H29  H   HOH1  0   0.480  -5.6084  -2.2783   1.8942

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
 H91  C1   N    single    1.447  0.020  1.447
 H91  N    C    single    1.447  0.020  1.447
 H91  N    C2   single    1.451  0.020  1.451
 H91  O1   C23  single    1.331  0.020  1.331
 H91  C2   C3   single    1.525  0.020  1.525
 H91  CL1  C24  single    1.731  0.020  1.731
 H91  C23  C24  aromatic  1.395  0.020  1.395
 H91  C23  C22  aromatic  1.396  0.020  1.396
 H91  CL   C22  single    1.725  0.020  1.725
 H91  C24  C25  aromatic  1.381  0.020  1.381
 H91  C3   C4   single    1.529  0.020  1.529
 H91  C3   C8   single    1.526  0.020  1.526
 H91  C22  C21  aromatic  1.382  0.020  1.382
 H91  C4   C5   single    1.526  0.020  1.526
 H91  C8   C7   single    1.527  0.020  1.527
 H91  C25  C20  aromatic  1.392  0.020  1.392
 H91  C21  C20  aromatic  1.394  0.020  1.394
 H91  C20  C16  single    1.474  0.020  1.474
 H91  C5   C6   single    1.526  0.020  1.526
 H91  C7   C6   single    1.530  0.020  1.530
 H91  C6   N1   single    1.480  0.020  1.480
 H91  C16  C17  aromatic  1.374  0.020  1.374
 H91  C16  C15  aromatic  1.415  0.020  1.415
 H91  C17  C18  aromatic  1.409  0.020  1.409
 H91  C15  C14  aromatic  1.365  0.020  1.365
 H91  N1   C19  single    1.399  0.020  1.399
 H91  N1   C9   single    1.395  0.020  1.395
 H91  C18  C19  aromatic  1.426  0.020  1.426
 H91  C18  C13  aromatic  1.419  0.020  1.419
 H91  O    C9   double    1.219  0.020  1.219
 H91  C19  C11  aromatic  1.373  0.020  1.373
 H91  C14  C13  aromatic  1.414  0.020  1.414
 H91  C9   N2   single    1.353  0.020  1.353
 H91  C13  N3   aromatic  1.352  0.020  1.352
 H91  C11  C10  single    1.493  0.020  1.493
 H91  C11  C12  aromatic  1.404  0.020  1.404
 H91  N2   C10  single    1.448  0.020  1.448
 H91  N3   C12  aromatic  1.306  0.020  1.306
 H91  C    H2   single    0.970  0.020  1.090
 H91  C    H3   single    0.970  0.020  1.090
 H91  C    H4   single    0.970  0.020  1.090
 H91  C1   H5   single    0.970  0.020  1.090
 H91  C1   H6   single    0.970  0.020  1.090
 H91  C1   H7   single    0.970  0.020  1.090
 H91  C10  H8   single    0.970  0.020  1.090
 H91  C10  H9   single    0.970  0.020  1.090
 H91  C12  H10  single    0.930  0.020  1.080
 H91  C14  H11  single    0.930  0.020  1.080
 H91  C15  H12  single    0.930  0.020  1.080
 H91  C17  H13  single    0.930  0.020  1.080
 H91  C2   H14  single    0.970  0.020  1.090
 H91  C2   H15  single    0.970  0.020  1.090
 H91  C21  H16  single    0.930  0.020  1.080
 H91  C25  H17  single    0.930  0.020  1.080
 H91  C3   H18  single    0.970  0.020  1.090
 H91  C4   H19  single    0.970  0.020  1.090
 H91  C4   H20  single    0.970  0.020  1.090
 H91  C5   H21  single    0.970  0.020  1.090
 H91  C5   H22  single    0.970  0.020  1.090
 H91  C6   H23  single    0.970  0.020  1.090
 H91  C7   H24  single    0.970  0.020  1.090
 H91  C7   H25  single    0.970  0.020  1.090
 H91  C8   H26  single    0.970  0.020  1.090
 H91  C8   H27  single    0.970  0.020  1.090
 H91  N2   H28  single    0.890  0.020  1.040
 H91  O1   H29  single    0.850  0.020  0.980

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
 H91  C2   N    C1   112.43  3.000
 H91  C2   N    C    110.56  3.000
 H91  C1   N    C    110.69  3.000
 H91  H4   C    H3   107.76  3.000
 H91  H4   C    H2   107.59  3.000
 H91  H3   C    H2   107.60  3.000
 H91  H4   C    N    110.30  3.000
 H91  H3   C    N    110.13  3.000
 H91  H2   C    N    113.26  3.000
 H91  H7   C1   H6   107.23  3.000
 H91  H7   C1   H5   107.76  3.000
 H91  H6   C1   H5   107.74  3.000
 H91  H7   C1   N    109.77  3.000
 H91  H6   C1   N    111.07  3.000
 H91  H5   C1   N    113.05  3.000
 H91  H9   C10  H8   107.23  3.000
 H91  H9   C10  N2   111.71  3.000
 H91  H8   C10  N2   108.68  3.000
 H91  H9   C10  C11  110.94  3.000
 H91  H8   C10  C11  110.78  3.000
 H91  N2   C10  C11  107.51  3.000
 H91  C19  C11  C12  119.43  3.000
 H91  C12  C11  C10  122.96  3.000
 H91  C19  C11  C10  117.61  3.000
 H91  H10  C12  N3   116.95  3.000
 H91  H10  C12  C11  118.64  3.000
 H91  N3   C12  C11  124.39  3.000
 H91  N3   C13  C18  123.15  3.000
 H91  N3   C13  C14  118.14  3.000
 H91  C18  C13  C14  118.68  3.000
 H91  H11  C14  C15  120.74  3.000
 H91  H11  C14  C13  118.13  3.000
 H91  C15  C14  C13  121.13  3.000
 H91  H12  C15  C16  119.87  3.000
 H91  H12  C15  C14  119.49  3.000
 H91  C16  C15  C14  120.64  3.000
 H91  C20  C16  C17  120.20  3.000
 H91  C17  C16  C15  118.81  3.000
 H91  C20  C16  C15  120.99  3.000
 H91  H13  C17  C18  119.08  3.000
 H91  H13  C17  C16  118.82  3.000
 H91  C18  C17  C16  121.96  3.000
 H91  C19  C18  C17  123.95  3.000
 H91  C19  C18  C13  117.40  3.000
 H91  C17  C18  C13  118.56  3.000
 H91  N1   C19  C18  122.52  3.000
 H91  C18  C19  C11  117.74  3.000
 H91  N1   C19  C11  119.71  3.000
 H91  H15  C2   H14  106.34  3.000
 H91  H15  C2   C3   108.05  3.000
 H91  H14  C2   C3   108.74  3.000
 H91  H15  C2   N    107.66  3.000
 H91  H14  C2   N    111.06  3.000
 H91  C3   C2   N    114.62  3.000
 H91  C25  C20  C21  118.27  3.000
 H91  C21  C20  C16  121.29  3.000
 H91  C25  C20  C16  120.43  3.000
 H91  H16  C21  C22  118.89  3.000
 H91  H16  C21  C20  120.60  3.000
 H91  C22  C21  C20  120.49  3.000
 H91  CL   C22  C23  118.14  3.000
 H91  CL   C22  C21  119.92  3.000
 H91  C23  C22  C21  121.94  3.000
 H91  O1   C23  C24  124.42  3.000
 H91  C24  C23  C22  116.76  3.000
 H91  O1   C23  C22  118.82  3.000
 H91  CL1  C24  C25  119.63  3.000
 H91  C25  C24  C23  121.90  3.000
 H91  CL1  C24  C23  118.46  3.000
 H91  H17  C25  C24  118.92  3.000
 H91  H17  C25  C20  120.42  3.000
 H91  C24  C25  C20  120.63  3.000
 H91  H18  C3   C8   108.46  3.000
 H91  H18  C3   C4   106.87  3.000
 H91  C8   C3   C4   110.19  3.000
 H91  H18  C3   C2   109.36  3.000
 H91  C8   C3   C2   112.02  3.000
 H91  C4   C3   C2   109.79  3.000
 H91  H20  C4   H19  106.48  3.000
 H91  H20  C4   C5   109.73  3.000
 H91  H19  C4   C5   109.82  3.000
 H91  H20  C4   C3   108.80  3.000
 H91  H19  C4   C3   110.29  3.000
 H91  C5   C4   C3   111.58  3.000
 H91  H22  C5   H21  106.25  3.000
 H91  H22  C5   C6   111.30  3.000
 H91  H21  C5   C6   110.34  3.000
 H91  H22  C5   C4   110.26  3.000
 H91  H21  C5   C4   109.49  3.000
 H91  C6   C5   C4   109.16  3.000
 H91  H23  C6   N1   104.88  3.000
 H91  H23  C6   C7   105.62  3.000
 H91  N1   C6   C7   111.97  3.000
 H91  H23  C6   C5   107.24  3.000
 H91  N1   C6   C5   115.91  3.000
 H91  C7   C6   C5   110.43  3.000
 H91  H25  C7   H24  107.24  3.000
 H91  H25  C7   C8   109.82  3.000
 H91  H24  C7   C8   109.56  3.000
 H91  H25  C7   C6   109.54  3.000
 H91  H24  C7   C6   110.43  3.000
 H91  C8   C7   C6   110.21  3.000
 H91  H27  C8   H26  106.36  3.000
 H91  H27  C8   C7   109.61  3.000
 H91  H26  C8   C7   109.19  3.000
 H91  H27  C8   C3   110.39  3.000
 H91  H26  C8   C3   108.90  3.000
 H91  C7   C8   C3   112.22  3.000
 H91  N2   C9   N1   115.22  3.000
 H91  N2   C9   O    123.04  3.000
 H91  N1   C9   O    121.71  3.000
 H91  C9   N1   C6   118.44  3.000
 H91  C9   N1   C19  118.92  3.000
 H91  C6   N1   C19  119.61  3.000
 H91  H28  N2   C9   115.20  3.000
 H91  H28  N2   C10  117.52  3.000
 H91  C9   N2   C10  121.29  3.000
 H91  C13  N3   C12  117.44  3.000
 H91  H29  O1   C23  111.29  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
 H91  CONST_01  C17  C18  C19  C11  180.00   0.0  0
 H91  CONST_02  C13  C18  C19  C11    0.00   0.0  0
 H91  CONST_03  C13  N3   C12  C11    0.00   0.0  0
 H91  CONST_04  C18  C19  C11  C12    0.00   0.0  0
 H91  CONST_05  C18  C13  N3   C12    0.00   0.0  0
 H91  CONST_06  C14  C13  N3   C12  180.00   0.0  0
 H91  CONST_07  C16  C17  C18  C13    0.00   0.0  0
 H91  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 H91  CONST_09  C20  C16  C15  C14  180.00   0.0  0
 H91  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 H91  CONST_11  C17  C18  C13  C14    0.00   0.0  0
 H91  CONST_12  C19  C18  C13  C14  180.00   0.0  0
 H91  CONST_15  C18  C17  C16  C15    0.00   0.0  0
 H91  CONST_16  C18  C13  C14  C15    0.00   0.0  0
 H91  CONST_17  N3   C13  C14  C15  180.00   0.0  0
 H91  CONST_18  C24  C25  C20  C16  180.00   0.0  0
 H91  CONST_19  C22  C21  C20  C16  180.00   0.0  0
 H91  CONST_20  C19  C18  C17  C16  180.00   0.0  0
 H91  CONST_23  N3   C13  C18  C17  180.00   0.0  0
 H91  CONST_24  C20  C16  C17  C18  180.00   0.0  0
 H91  CONST_25  N3   C13  C18  C19    0.00   0.0  0
 H91  CONST_26  N3   C12  C11  C19    0.00   0.0  0
 H91  CONST_27  C23  C24  C25  C20    0.00   0.0  0
 H91  CONST_28  C23  C22  C21  C20    0.00   0.0  0
 H91  CONST_29  C24  C23  C22  C21    0.00   0.0  0
 H91  CONST_30  C24  C25  C20  C21    0.00   0.0  0
 H91  CONST_31  C25  C24  C23  C22    0.00   0.0  0
 H91  CONST_32  C25  C20  C21  C22    0.00   0.0  0
 H91  CONST_34  N2   C9   N1   C19    0.00   0.0  0
 H91  CONST_36  CL1  C24  C25  C20  180.00   0.0  0
 H91  CONST_37  CL   C22  C21  C20  180.00   0.0  0
 H91  CONST_38  O1   C23  C22  C21  180.00   0.0  0
 H91  CONST_39  CL1  C24  C23  C22  180.00   0.0  0
 H91  CONST_40  CL   C22  C23  C24  180.00   0.0  0
 H91  CONST_41  O1   C23  C24  C25  180.00   0.0  0
 H91  CONST_45  H10  C12  C11  C10    0.00   0.0  0
 H91  CONST_46  H13  C17  C18  C13  180.00   0.0  0
 H91  CONST_47  H12  C15  C14  C13  180.00   0.0  0
 H91  CONST_48  H17  C25  C20  C16    0.00   0.0  0
 H91  CONST_49  H16  C21  C20  C16    0.00   0.0  0
 H91  CONST_50  H11  C14  C15  C16  180.00   0.0  0
 H91  CONST_51  H28  N2   C9   N1   180.00   0.0  0
 H91  Var_01    C6   C5   C4   C3   -58.90  30.0  1
 H91  Var_02    C6   C7   C8   C3    55.40  30.0  1
 H91  Var_03    H8   C10  C11  C12  -30.46  30.0  1
 H91  Var_04    C3   C2   N    C    171.83  30.0  3
 H91  Var_05    H5   C1   N    C     66.27  30.0  3
 H91  Var_06    H2   C    N    C1   -64.10  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 H91  chir_01  C3  C2  C4  C8  negativ
 H91  chir_02  C6  N1  C5  C7  negativ

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
 H91  plan-1  C16  0.020
 H91  plan-1  C20  0.020
 H91  plan-1  C21  0.020
 H91  plan-1  C22  0.020
 H91  plan-1  C23  0.020
 H91  plan-1  C24  0.020
 H91  plan-1  C25  0.020
 H91  plan-1  O1   0.020
 H91  plan-1  CL   0.020
 H91  plan-1  CL1  0.020
 H91  plan-1  H16  0.020
 H91  plan-1  H17  0.020
 H91  plan-2  O    0.020
 H91  plan-2  C10  0.020
 H91  plan-2  C11  0.020
 H91  plan-2  C12  0.020
 H91  plan-2  C13  0.020
 H91  plan-2  C14  0.020
 H91  plan-2  C15  0.020
 H91  plan-2  C16  0.020
 H91  plan-2  C17  0.020
 H91  plan-2  C18  0.020
 H91  plan-2  C19  0.020
 H91  plan-2  C20  0.020
 H91  plan-2  C6   0.020
 H91  plan-2  C9   0.020
 H91  plan-2  N1   0.020
 H91  plan-2  N2   0.020
 H91  plan-2  N3   0.020
 H91  plan-2  H10  0.020
 H91  plan-2  H11  0.020
 H91  plan-2  H12  0.020
 H91  plan-2  H13  0.020
 H91  plan-2  H28  0.020

