# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 17:40:49 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-methyl-1-(oxan-4-yl)-8-pyridin-3-yl-imidazo[4,5-c]quinolin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C2CCOCC2)c3c1cnc4ccc(cc34)c5cccnc5
#
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
 DD8  DD8  3-methyl-1-(oxan-4-yl)-8-pyridin-3-yl-imidazo[4,5-c]quinolin-2-one  ligand  47  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DD8
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
 DD8  C1   C  CH3   0  -0.540   4.9682   1.6678  -0.1299
 DD8  C3   C  CR5   0   0.693   3.3583  -0.2307  -0.1538
 DD8  O4   O  O     0  -0.497   4.1605  -1.1408  -0.2499
 DD8  C7   C  CH2   0  -0.456   1.4783  -2.4156  -1.3589
 DD8  C8   C  CH2   0  -0.186   0.7438  -3.7448  -1.2465
 DD8  C10  C  CH2   0  -0.187   0.9728  -3.8295   1.0767
 DD8  C11  C  CH2   0  -0.451   1.7245  -2.5058   1.1409
 DD8  C12  C  CR56  0   0.375   1.4177   0.9168   0.0148
 DD8  C13  C  CR56  0   0.226   2.4732   1.8142   0.0090
 DD8  C14  C  CR16  0  -0.129   2.2700   3.1891   0.1141
 DD8  C16  C  CR66  0   0.146   0.0062   2.8517   0.2057
 DD8  C19  C  CR6   0   0.113  -2.3384   1.2889   0.1566
 DD8  C20  C  CR16  0  -0.389  -1.1065   0.6880   0.0618
 DD8  C21  C  CR66  0   0.125   0.0975   1.4287   0.0971
 DD8  C22  C  CR6   0  -0.009  -3.5700   0.4827   0.1172
 DD8  C24  C  CR16  0  -0.314  -5.8393   0.1179  -0.5637
 DD8  N26  N  N     0  -0.396  -4.7201  -1.5309   0.7475
 DD8  C27  C  CR16  0  -0.102  -3.6461  -0.7559   0.7564
 DD8  N2   N  NR5   0  -0.585   3.6407   1.1051  -0.1021
 DD8  N5   N  NR5   0  -0.622   1.9751  -0.3425  -0.0752
 DD8  C6   C  CH1   0  -0.115   1.3146  -1.6456  -0.0523
 DD8  O9   O  O2    0  -0.479   1.1888  -4.5016  -0.1435
 DD8  N15  N  N     0  -0.441   1.0663   3.6898   0.2167
 DD8  C17  C  CR16  0  -0.274  -1.2740   3.4451   0.3021
 DD8  C18  C  CR16  0  -0.316  -2.4122   2.6958   0.2833
 DD8  C23  C  CR16  0  -0.193  -4.7114   0.9202  -0.5516
 DD8  C25  C  CR16  0  -0.069  -5.7946  -1.1013   0.0958
 DD8  H1   H  HCH3  0   0.261   5.2097   2.1394   0.8220
 DD8  H2   H  HCH3  0   0.272   5.6840   0.8732  -0.3168
 DD8  H3   H  HCH3  0   0.261   5.0530   2.4058  -0.9261
 DD8  H4   H  HCH2  0   0.250   2.5333  -2.5934  -1.5695
 DD8  H5   H  HCH2  0   0.251   1.0610  -1.8440  -2.1910
 DD8  H6   H  HCH2  0   0.200  -0.3397  -3.5642  -1.1729
 DD8  H7   H  HCH2  0   0.246   0.9120  -4.3468  -2.1402
 DD8  H8   H  HCH2  0   0.246   1.3098  -4.4924   1.8744
 DD8  H9   H  HCH2  0   0.198  -0.1033  -3.6548   1.2299
 DD8  H10  H  HCH2  0   0.252   1.4765  -1.9982   2.0755
 DD8  H11  H  HCH2  0   0.252   2.7978  -2.6936   1.1351
 DD8  H12  H  HCR6  0   0.284   3.1075   3.8782   0.1182
 DD8  H13  H  HCR6  0   0.250  -1.0813  -0.3794  -0.0815
 DD8  H14  H  HCR6  0   0.276  -6.7367   0.4263  -1.0819
 DD8  H15  H  HCR6  0   0.258  -2.7961  -1.1244   1.3228
 DD8  H16  H  HCH1  0   0.245   0.2546  -1.4434   0.0688
 DD8  H17  H  HCR6  0   0.266  -1.3236   4.5221   0.3952
 DD8  H18  H  HCR6  0   0.263  -3.3757   3.1797   0.3789
 DD8  H19  H  HCR6  0   0.273  -4.7139   1.8694  -1.0733
 DD8  H20  H  HCR6  0   0.269  -6.6600  -1.7539   0.1016

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
 DD8  C17  C18  aromatic  1.363  0.020  1.363
 DD8  C17  C16  aromatic  1.414  0.020  1.414
 DD8  N15  C16  aromatic  1.351  0.020  1.351
 DD8  N15  C14  aromatic  1.308  0.020  1.308
 DD8  C18  C19  aromatic  1.414  0.020  1.414
 DD8  C16  C21  aromatic  1.430  0.020  1.430
 DD8  C14  C13  aromatic  1.394  0.020  1.394
 DD8  C27  N26  aromatic  1.325  0.020  1.325
 DD8  C27  C22  aromatic  1.396  0.020  1.396
 DD8  C19  C20  aromatic  1.374  0.020  1.374
 DD8  C19  C22  single    1.473  0.020  1.473
 DD8  N26  C25  aromatic  1.328  0.020  1.328
 DD8  C21  C20  aromatic  1.414  0.020  1.414
 DD8  C21  C12  aromatic  1.418  0.020  1.418
 DD8  C13  C12  aromatic  1.385  0.020  1.385
 DD8  C13  N2   single    1.371  0.020  1.371
 DD8  C1   N2   single    1.442  0.020  1.442
 DD8  C22  C23  aromatic  1.393  0.020  1.393
 DD8  C12  N5   single    1.380  0.020  1.380
 DD8  N2   C3   single    1.366  0.020  1.366
 DD8  C11  C10  single    1.524  0.020  1.524
 DD8  C11  C6   single    1.527  0.020  1.527
 DD8  N5   C3   single    1.390  0.020  1.390
 DD8  N5   C6   single    1.461  0.020  1.461
 DD8  C3   O4   double    1.217  0.020  1.217
 DD8  C25  C24  aromatic  1.387  0.020  1.387
 DD8  C10  O9   single    1.410  0.020  1.410
 DD8  C6   C7   single    1.525  0.020  1.525
 DD8  C23  C24  aromatic  1.384  0.020  1.384
 DD8  O9   C8   single    1.410  0.020  1.410
 DD8  C7   C8   single    1.523  0.020  1.523
 DD8  C1   H1   single    0.970  0.020  1.090
 DD8  C1   H2   single    0.970  0.020  1.090
 DD8  C1   H3   single    0.970  0.020  1.090
 DD8  C7   H4   single    0.970  0.020  1.090
 DD8  C7   H5   single    0.970  0.020  1.090
 DD8  C8   H6   single    0.970  0.020  1.090
 DD8  C8   H7   single    0.970  0.020  1.090
 DD8  C10  H8   single    0.970  0.020  1.090
 DD8  C10  H9   single    0.970  0.020  1.090
 DD8  C11  H10  single    0.970  0.020  1.090
 DD8  C11  H11  single    0.970  0.020  1.090
 DD8  C14  H12  single    0.930  0.020  1.080
 DD8  C20  H13  single    0.930  0.020  1.080
 DD8  C24  H14  single    0.930  0.020  1.080
 DD8  C27  H15  single    0.930  0.020  1.080
 DD8  C6   H16  single    0.970  0.020  1.090
 DD8  C17  H17  single    0.930  0.020  1.080
 DD8  C18  H18  single    0.930  0.020  1.080
 DD8  C23  H19  single    0.930  0.020  1.080
 DD8  C25  H20  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
 DD8  H3   C1   H2   108.59  3.000
 DD8  H3   C1   H1   109.16  3.000
 DD8  H2   C1   H1   108.73  3.000
 DD8  H3   C1   N2   110.50  3.000
 DD8  H2   C1   N2   108.95  3.000
 DD8  H1   C1   N2   110.87  3.000
 DD8  N5   C3   N2   106.39  3.000
 DD8  N5   C3   O4   126.89  3.000
 DD8  N2   C3   O4   126.72  3.000
 DD8  H5   C7   H4   107.93  3.000
 DD8  H5   C7   C6   110.33  3.000
 DD8  H4   C7   C6   110.59  3.000
 DD8  H5   C7   C8   109.19  3.000
 DD8  H4   C7   C8   109.79  3.000
 DD8  C6   C7   C8   109.00  3.000
 DD8  H7   C8   H6   107.28  3.000
 DD8  H7   C8   O9   107.23  3.000
 DD8  H6   C8   O9   110.27  3.000
 DD8  H7   C8   C7   110.30  3.000
 DD8  H6   C8   C7   109.66  3.000
 DD8  O9   C8   C7   111.97  3.000
 DD8  H9   C10  H8   107.26  3.000
 DD8  H9   C10  O9   110.23  3.000
 DD8  H8   C10  O9   107.22  3.000
 DD8  H9   C10  C11  109.79  3.000
 DD8  H8   C10  C11  110.17  3.000
 DD8  O9   C10  C11  112.03  3.000
 DD8  H11  C11  H10  107.96  3.000
 DD8  H11  C11  C6   110.94  3.000
 DD8  H10  C11  C6   110.24  3.000
 DD8  H11  C11  C10  109.64  3.000
 DD8  H10  C11  C10  109.13  3.000
 DD8  C6   C11  C10  108.91  3.000
 DD8  N5   C12  C21  135.16  3.000
 DD8  N5   C12  C13  106.45  3.000
 DD8  C21  C12  C13  118.40  3.000
 DD8  N2   C13  C14  129.84  3.000
 DD8  N2   C13  C12  108.31  3.000
 DD8  C14  C13  C12  121.84  3.000
 DD8  H12  C14  N15  117.85  3.000
 DD8  H12  C14  C13  120.96  3.000
 DD8  N15  C14  C13  121.19  3.000
 DD8  C17  C16  N15  116.70  3.000
 DD8  N15  C16  C21  124.59  3.000
 DD8  C17  C16  C21  118.72  3.000
 DD8  C18  C19  C22  120.22  3.000
 DD8  C22  C19  C20  120.57  3.000
 DD8  C18  C19  C20  119.21  3.000
 DD8  H13  C20  C21  120.15  3.000
 DD8  H13  C20  C19  117.62  3.000
 DD8  C21  C20  C19  122.18  3.000
 DD8  C20  C21  C16  117.95  3.000
 DD8  C20  C21  C12  127.02  3.000
 DD8  C16  C21  C12  115.02  3.000
 DD8  C23  C22  C27  116.98  3.000
 DD8  C23  C22  C19  121.74  3.000
 DD8  C27  C22  C19  121.28  3.000
 DD8  H14  C24  C25  120.36  3.000
 DD8  H14  C24  C23  121.01  3.000
 DD8  C25  C24  C23  118.62  3.000
 DD8  C25  N26  C27  118.04  3.000
 DD8  H15  C27  N26  116.08  3.000
 DD8  H15  C27  C22  119.82  3.000
 DD8  N26  C27  C22  124.08  3.000
 DD8  C13  N2   C3   109.44  3.000
 DD8  C3   N2   C1   124.82  3.000
 DD8  C13  N2   C1   125.72  3.000
 DD8  C6   N5   C12  129.07  3.000
 DD8  C6   N5   C3   121.50  3.000
 DD8  C12  N5   C3   109.40  3.000
 DD8  H16  C6   N5   106.08  3.000
 DD8  H16  C6   C11  106.25  3.000
 DD8  N5   C6   C11  113.16  3.000
 DD8  H16  C6   C7   107.11  3.000
 DD8  N5   C6   C7   112.84  3.000
 DD8  C11  C6   C7   110.86  3.000
 DD8  C10  O9   C8   111.90  3.000
 DD8  C16  N15  C14  118.94  3.000
 DD8  H17  C17  C18  120.67  3.000
 DD8  H17  C17  C16  117.71  3.000
 DD8  C18  C17  C16  121.62  3.000
 DD8  H18  C18  C17  119.76  3.000
 DD8  H18  C18  C19  119.93  3.000
 DD8  C17  C18  C19  120.30  3.000
 DD8  H19  C23  C24  120.12  3.000
 DD8  H19  C23  C22  120.54  3.000
 DD8  C24  C23  C22  119.32  3.000
 DD8  H20  C25  N26  116.65  3.000
 DD8  H20  C25  C24  120.40  3.000
 DD8  N26  C25  C24  122.95  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
 DD8  CONST_01  C17  C16  C21  C12   180.00   0.0  0
 DD8  CONST_02  N15  C16  C21  C12     0.00   0.0  0
 DD8  CONST_03  C19  C20  C21  C12   180.00   0.0  0
 DD8  CONST_04  N15  C14  C13  C12     0.00   0.0  0
 DD8  CONST_05  C16  N15  C14  C13     0.00   0.0  0
 DD8  CONST_06  C16  C21  C12  C13     0.00   0.0  0
 DD8  CONST_07  C20  C21  C12  C13   180.00   0.0  0
 DD8  CONST_08  C17  C16  N15  C14   180.00   0.0  0
 DD8  CONST_09  C21  C16  N15  C14     0.00   0.0  0
 DD8  CONST_10  C21  C12  C13  C14     0.00   0.0  0
 DD8  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 DD8  CONST_12  C19  C20  C21  C16     0.00   0.0  0
 DD8  CONST_13  N26  C27  C22  C19   180.00   0.0  0
 DD8  CONST_14  C24  C23  C22  C19   180.00   0.0  0
 DD8  CONST_15  C17  C18  C19  C20     0.00   0.0  0
 DD8  CONST_18  C17  C16  C21  C20     0.00   0.0  0
 DD8  CONST_19  N15  C16  C21  C20   180.00   0.0  0
 DD8  CONST_20  C18  C17  C16  C21     0.00   0.0  0
 DD8  CONST_21  C18  C19  C20  C21     0.00   0.0  0
 DD8  CONST_22  C22  C19  C20  C21   180.00   0.0  0
 DD8  CONST_23  C25  N26  C27  C22     0.00   0.0  0
 DD8  CONST_24  C17  C18  C19  C22   180.00   0.0  0
 DD8  CONST_25  C25  C24  C23  C22     0.00   0.0  0
 DD8  CONST_26  C27  N26  C25  C24     0.00   0.0  0
 DD8  CONST_27  C27  C22  C23  C24     0.00   0.0  0
 DD8  CONST_28  C23  C22  C27  N26     0.00   0.0  0
 DD8  CONST_29  C23  C24  C25  N26     0.00   0.0  0
 DD8  CONST_31  C18  C17  C16  N15   180.00   0.0  0
 DD8  CONST_33  C12  C13  N2   C3      0.00   0.0  0
 DD8  CONST_34  C13  C12  N5   C3      0.00   0.0  0
 DD8  CONST_35  N2   C3   N5   C12     0.00   0.0  0
 DD8  CONST_36  C6   N5   C12  C13   180.00   0.0  0
 DD8  CONST_37  N5   C3   N2   C13     0.00   0.0  0
 DD8  CONST_38  N5   C12  C13  N2      0.00   0.0  0
 DD8  CONST_39  C6   N5   C3   N2    180.00   0.0  0
 DD8  CONST_40  C12  C13  N2   C1    180.00   0.0  0
 DD8  CONST_41  N5   C3   N2   C1    180.00   0.0  0
 DD8  CONST_42  C13  N2   C3   O4    180.00   0.0  0
 DD8  CONST_43  C12  N5   C3   O4    180.00   0.0  0
 DD8  CONST_44  C6   N5   C3   O4      0.00   0.0  0
 DD8  CONST_45  H13  C20  C21  C12     0.00   0.0  0
 DD8  CONST_46  H12  C14  C13  C12   180.00   0.0  0
 DD8  CONST_47  H18  C18  C17  C16   180.00   0.0  0
 DD8  CONST_48  H17  C17  C18  C19   180.00   0.0  0
 DD8  CONST_49  H15  C27  C22  C19     0.00   0.0  0
 DD8  CONST_50  H19  C23  C22  C19     0.00   0.0  0
 DD8  CONST_51  H14  C24  C23  C22   180.00   0.0  0
 DD8  CONST_52  H20  C25  N26  C27   180.00   0.0  0
 DD8  CONST_53  O4   C3   N2   C1      0.00   0.0  0
 DD8  Var_01    C11  C10  O9   C8    -60.95  30.0  1
 DD8  Var_02    O9   C10  C11  C6     56.17  30.0  1
 DD8  Var_03    O9   C8   C7   C6    -56.25  30.0  1
 DD8  Var_04    H6   C8   O9   C10   -61.45  30.0  1
 DD8  Var_05    H1   C1   N2   C3   -112.92  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
 DD8  chir_01  C6  C11  N5  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
 DD8  plan-1  C19  0.020
 DD8  plan-1  C22  0.020
 DD8  plan-1  C24  0.020
 DD8  plan-1  N26  0.020
 DD8  plan-1  C27  0.020
 DD8  plan-1  C23  0.020
 DD8  plan-1  C25  0.020
 DD8  plan-1  H14  0.020
 DD8  plan-1  H15  0.020
 DD8  plan-1  H19  0.020
 DD8  plan-1  H20  0.020
 DD8  plan-2  C1   0.020
 DD8  plan-2  C3   0.020
 DD8  plan-2  O4   0.020
 DD8  plan-2  C12  0.020
 DD8  plan-2  C13  0.020
 DD8  plan-2  C14  0.020
 DD8  plan-2  C16  0.020
 DD8  plan-2  C19  0.020
 DD8  plan-2  C20  0.020
 DD8  plan-2  C21  0.020
 DD8  plan-2  C22  0.020
 DD8  plan-2  N2   0.020
 DD8  plan-2  N5   0.020
 DD8  plan-2  C6   0.020
 DD8  plan-2  N15  0.020
 DD8  plan-2  C17  0.020
 DD8  plan-2  C18  0.020
 DD8  plan-2  H12  0.020
 DD8  plan-2  H13  0.020
 DD8  plan-2  H17  0.020
 DD8  plan-2  H18  0.020

