# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:07:08 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 7-benzyl-4-[(2-methylphenyl)methyl]-6,7,8,9-tetrahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1CN2C(=O)C3=C(CCN(Cc4ccccc4)C3)n5ccnc25
#
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
 ONC  ONC  7-benzyl-4-[(2-methylphenyl)methyl]-6,7,8,9-tetrahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(4H)-one  ligand  53  29  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ONC
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
 ONC  C01  C  CH3   0  -0.747  -4.7515  -2.4555  -1.8903
 ONC  C02  C  CR6   0   0.080  -4.6245  -1.9372  -0.4872
 ONC  C03  C  CR16  0  -0.299  -5.5253  -2.3408   0.4932
 ONC  C04  C  CR16  0  -0.255  -5.4343  -1.8708   1.7966
 ONC  C05  C  CR16  0  -0.261  -4.4276  -0.9805   2.1325
 ONC  C06  C  CR16  0  -0.289  -3.5196  -0.5699   1.1646
 ONC  C07  C  CR6   0   0.072  -3.6053  -1.0389  -0.1401
 ONC  C08  C  CH2   0  -0.363  -2.6392  -0.6059  -1.2155
 ONC  C10  C  CR6   0   0.589  -0.4242  -0.3208  -0.2125
 ONC  C12  C  CR6   0  -0.251   0.6070   0.6049   0.2344
 ONC  C13  C  CR6   0   0.453   0.4276   1.9381   0.1783
 ONC  C14  C  CH2   0  -0.533   1.4377   2.9127   0.6711
 ONC  C15  C  CH2   0  -0.292   2.4990   2.2056   1.4989
 ONC  C17  C  CH2   0  -0.285   1.8749   0.0169   0.7742
 ONC  C19  C  CR6   0   0.083   4.7532  -0.6185   0.5206
 ONC  C20  C  CR16  0  -0.280   4.9160  -0.4018  -0.8469
 ONC  C21  C  CR16  0  -0.242   5.4970  -1.3704  -1.6516
 ONC  C22  C  CR16  0  -0.270   5.9263  -2.5727  -1.0997
 ONC  C23  C  CR16  0  -0.241   5.7680  -2.7969   0.2601
 ONC  C24  C  CR16  0  -0.314   5.1810  -1.8251   1.0628
 ONC  C26  C  CR56  0   0.750  -1.7348   1.6027  -0.8058
 ONC  C28  C  CR15  0  -0.189  -2.4251   3.5806  -1.1024
 ONC  C29  C  CR15  0  -0.111  -1.1937   3.7178  -0.5488
 ONC  N09  N  NR6   0  -0.611  -1.5677   0.2485  -0.7415
 ONC  N16  N  NT    0  -0.423   2.9346   1.0012   0.8226
 ONC  N25  N  N     0  -0.594  -0.7448   2.4219  -0.3548
 ONC  N27  N  N     0  -0.483  -2.7624   2.2577  -1.2589
 ONC  H1   H  HCH3  0   0.245  -3.8495  -2.9796  -2.2141
 ONC  H2   H  HCH3  0   0.257  -5.5840  -3.1520  -1.9772
 ONC  H3   H  HCH3  0   0.249  -4.9209  -1.6485  -2.6070
 ONC  H4   H  HCR6  0   0.248  -6.3145  -3.0355   0.2300
 ONC  H5   H  HCR6  0   0.253  -6.1473  -2.1994   2.5417
 ONC  H6   H  HCR6  0   0.254  -4.3438  -0.6030   3.1433
 ONC  H7   H  HCR6  0   0.235  -2.7392   0.1256   1.4468
 ONC  H8   H  HCH2  0   0.280  -2.1878  -1.4776  -1.6890
 ONC  H9   H  HCH2  0   0.289  -3.1709  -0.0664  -2.0005
 ONC  H10  H  HCH2  0   0.285   1.8906   3.4233  -0.1839
 ONC  H11  H  HCH2  0   0.276   0.9529   3.6810   1.2780
 ONC  H12  H  HCH2  0   0.256   3.3511   2.8743   1.6249
 ONC  H13  H  HCH2  0   0.215   2.1033   1.9966   2.5059
 ONC  H14  H  HCH2  0   0.223   1.6756  -0.4214   1.7686
 ONC  H15  H  HCH2  0   0.262   2.1846  -0.8122   0.1344
 ONC  H16  H  HCH2  0   0.218   3.9883   0.0504   2.4072
 ONC  H17  H  HCH2  0   0.257   4.8663   1.2694   1.4952
 ONC  H18  H  HCR6  0   0.249   4.5739   0.5295  -1.2814
 ONC  H19  H  HCR6  0   0.253   5.6163  -1.1884  -2.7121
 ONC  H20  H  HCR6  0   0.254   6.3782  -3.3300  -1.7275
 ONC  H21  H  HCR6  0   0.254   6.0963  -3.7308   0.6980
 ONC  H22  H  HCR6  0   0.248   5.0518  -2.0107   2.1229
 ONC  H23  H  HCR5  0   0.263  -3.0981   4.3687  -1.4008
 ONC  H24  H  HCR5  0   0.300  -0.6089   4.5816  -0.2869
 ONC  O11  O  O     0  -0.486  -0.3108  -1.5342  -0.1355
 ONC  C18  C  CH2   0  -0.332   4.1475   0.4511   1.3924

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
 ONC  C03  C04  aromatic  1.389  0.020  1.389
 ONC  C03  C02  aromatic  1.391  0.020  1.391
 ONC  C04  C05  aromatic  1.385  0.020  1.385
 ONC  C01  C02  single    1.501  0.020  1.501
 ONC  C02  C07  aromatic  1.402  0.020  1.402
 ONC  C05  C06  aromatic  1.389  0.020  1.389
 ONC  C07  C06  aromatic  1.389  0.020  1.389
 ONC  C07  C08  single    1.509  0.020  1.509
 ONC  C08  N09  single    1.450  0.020  1.450
 ONC  O11  C10  double    1.221  0.020  1.221
 ONC  N09  C10  single    1.383  0.020  1.383
 ONC  N09  C26  single    1.366  0.020  1.366
 ONC  C10  C12  single    1.456  0.020  1.456
 ONC  C22  C21  aromatic  1.391  0.020  1.391
 ONC  C22  C23  aromatic  1.387  0.020  1.387
 ONC  C21  C20  aromatic  1.387  0.020  1.387
 ONC  C23  C24  aromatic  1.390  0.020  1.390
 ONC  C20  C19  aromatic  1.394  0.020  1.394
 ONC  C26  N27  aromatic  1.300  0.020  1.300
 ONC  C26  N25  aromatic  1.362  0.020  1.362
 ONC  C12  C17  single    1.498  0.020  1.498
 ONC  C12  C13  double    1.346  0.020  1.346
 ONC  N27  C28  aromatic  1.374  0.020  1.374
 ONC  C17  N16  single    1.447  0.020  1.447
 ONC  C24  C19  aromatic  1.390  0.020  1.390
 ONC  C19  C18  single    1.507  0.020  1.507
 ONC  N25  C13  single    1.376  0.020  1.376
 ONC  N25  C29  aromatic  1.385  0.020  1.385
 ONC  C13  C14  single    1.488  0.020  1.488
 ONC  N16  C18  single    1.449  0.020  1.449
 ONC  N16  C15  single    1.448  0.020  1.448
 ONC  C28  C29  aromatic  1.357  0.020  1.357
 ONC  C14  C15  single    1.520  0.020  1.520
 ONC  C01  H1   single    0.970  0.020  1.090
 ONC  C01  H2   single    0.970  0.020  1.090
 ONC  C01  H3   single    0.970  0.020  1.090
 ONC  C03  H4   single    0.930  0.020  1.080
 ONC  C04  H5   single    0.930  0.020  1.080
 ONC  C05  H6   single    0.930  0.020  1.080
 ONC  C06  H7   single    0.930  0.020  1.080
 ONC  C08  H8   single    0.970  0.020  1.090
 ONC  C08  H9   single    0.970  0.020  1.090
 ONC  C14  H10  single    0.970  0.020  1.090
 ONC  C14  H11  single    0.970  0.020  1.090
 ONC  C15  H12  single    0.970  0.020  1.090
 ONC  C15  H13  single    0.970  0.020  1.090
 ONC  C17  H14  single    0.970  0.020  1.090
 ONC  C17  H15  single    0.970  0.020  1.090
 ONC  C18  H16  single    0.970  0.020  1.090
 ONC  C18  H17  single    0.970  0.020  1.090
 ONC  C20  H18  single    0.930  0.020  1.080
 ONC  C21  H19  single    0.930  0.020  1.080
 ONC  C22  H20  single    0.930  0.020  1.080
 ONC  C23  H21  single    0.930  0.020  1.080
 ONC  C24  H22  single    0.930  0.020  1.080
 ONC  C28  H23  single    0.930  0.020  1.080
 ONC  C29  H24  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
 ONC  H3   C01  H2   107.55  3.000
 ONC  H3   C01  H1   106.73  3.000
 ONC  H2   C01  H1   107.51  3.000
 ONC  H3   C01  C02  111.79  3.000
 ONC  H2   C01  C02  111.11  3.000
 ONC  H1   C01  C02  111.89  3.000
 ONC  C07  C02  C03  118.82  3.000
 ONC  C07  C02  C01  120.94  3.000
 ONC  C03  C02  C01  120.25  3.000
 ONC  H4   C03  C04  119.51  3.000
 ONC  H4   C03  C02  119.10  3.000
 ONC  C04  C03  C02  121.39  3.000
 ONC  H5   C04  C05  120.46  3.000
 ONC  H5   C04  C03  120.02  3.000
 ONC  C05  C04  C03  119.52  3.000
 ONC  H6   C05  C06  119.80  3.000
 ONC  H6   C05  C04  120.46  3.000
 ONC  C06  C05  C04  119.74  3.000
 ONC  H7   C06  C07  120.41  3.000
 ONC  H7   C06  C05  118.64  3.000
 ONC  C07  C06  C05  120.95  3.000
 ONC  C08  C07  C06  122.20  3.000
 ONC  C08  C07  C02  118.21  3.000
 ONC  C06  C07  C02  119.58  3.000
 ONC  H9   C08  H8   106.54  3.000
 ONC  H9   C08  N09  107.70  3.000
 ONC  H8   C08  N09  107.89  3.000
 ONC  H9   C08  C07  110.04  3.000
 ONC  H8   C08  C07  110.20  3.000
 ONC  N09  C08  C07  114.15  3.000
 ONC  O11  C10  N09  120.67  3.000
 ONC  N09  C10  C12  116.20  3.000
 ONC  O11  C10  C12  123.14  3.000
 ONC  C17  C12  C13  121.09  3.000
 ONC  C13  C12  C10  121.49  3.000
 ONC  C17  C12  C10  117.42  3.000
 ONC  N25  C13  C14  118.47  3.000
 ONC  C14  C13  C12  122.99  3.000
 ONC  N25  C13  C12  118.55  3.000
 ONC  H11  C14  H10  106.84  3.000
 ONC  H11  C14  C15  109.53  3.000
 ONC  H10  C14  C15  110.71  3.000
 ONC  H11  C14  C13  110.09  3.000
 ONC  H10  C14  C13  109.14  3.000
 ONC  C15  C14  C13  110.47  3.000
 ONC  H13  C15  H12  106.94  3.000
 ONC  H13  C15  N16  112.15  3.000
 ONC  H12  C15  N16  109.20  3.000
 ONC  H13  C15  C14  109.58  3.000
 ONC  H12  C15  C14  108.85  3.000
 ONC  N16  C15  C14  110.03  3.000
 ONC  H15  C17  H14  106.10  3.000
 ONC  H15  C17  N16  109.16  3.000
 ONC  H14  C17  N16  111.82  3.000
 ONC  H15  C17  C12  109.08  3.000
 ONC  H14  C17  C12  109.11  3.000
 ONC  N16  C17  C12  111.40  3.000
 ONC  C24  C19  C20  118.79  3.000
 ONC  C24  C19  C18  120.93  3.000
 ONC  C20  C19  C18  120.27  3.000
 ONC  H18  C20  C21  120.01  3.000
 ONC  H18  C20  C19  119.36  3.000
 ONC  C21  C20  C19  120.63  3.000
 ONC  H19  C21  C22  120.00  3.000
 ONC  H19  C21  C20  119.81  3.000
 ONC  C22  C21  C20  120.19  3.000
 ONC  H20  C22  C23  120.20  3.000
 ONC  H20  C22  C21  120.24  3.000
 ONC  C23  C22  C21  119.57  3.000
 ONC  H21  C23  C24  119.84  3.000
 ONC  H21  C23  C22  120.09  3.000
 ONC  C24  C23  C22  120.07  3.000
 ONC  H22  C24  C23  119.68  3.000
 ONC  H22  C24  C19  119.56  3.000
 ONC  C23  C24  C19  120.75  3.000
 ONC  N27  C26  N25  112.76  3.000
 ONC  N25  C26  N09  119.46  3.000
 ONC  N27  C26  N09  127.78  3.000
 ONC  H23  C28  N27  121.26  3.000
 ONC  H23  C28  C29  127.24  3.000
 ONC  N27  C28  C29  111.50  3.000
 ONC  H24  C29  N25  122.75  3.000
 ONC  H24  C29  C28  132.38  3.000
 ONC  N25  C29  C28  104.87  3.000
 ONC  C26  N09  C10  121.83  3.000
 ONC  C26  N09  C08  118.58  3.000
 ONC  C10  N09  C08  119.58  3.000
 ONC  C18  N16  C17  111.59  3.000
 ONC  C18  N16  C15  112.58  3.000
 ONC  C17  N16  C15  111.16  3.000
 ONC  C29  N25  C26  106.31  3.000
 ONC  C29  N25  C13  131.26  3.000
 ONC  C26  N25  C13  122.43  3.000
 ONC  C28  N27  C26  104.56  3.000
 ONC  H17  C18  H16  106.27  3.000
 ONC  H17  C18  N16  107.64  3.000
 ONC  H16  C18  N16  112.28  3.000
 ONC  H17  C18  C19  108.73  3.000
 ONC  H16  C18  C19  109.43  3.000
 ONC  N16  C18  C19  112.24  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
 ONC  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 ONC  CONST_02  C05  C06  C07  C02     0.00   0.0  0
 ONC  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 ONC  CONST_04  C06  C07  C02  C03     0.00   0.0  0
 ONC  CONST_05  C07  C02  C03  C04     0.00   0.0  0
 ONC  CONST_06  C07  C06  C05  C04     0.00   0.0  0
 ONC  CONST_07  C22  C21  C20  C19     0.00   0.0  0
 ONC  CONST_08  C22  C23  C24  C19     0.00   0.0  0
 ONC  CONST_09  C23  C22  C21  C20     0.00   0.0  0
 ONC  CONST_10  C23  C24  C19  C20     0.00   0.0  0
 ONC  CONST_11  C24  C23  C22  C21     0.00   0.0  0
 ONC  CONST_12  C24  C19  C20  C21     0.00   0.0  0
 ONC  CONST_13  C29  C28  N27  C26     0.00   0.0  0
 ONC  CONST_14  C28  C29  N25  C26     0.00   0.0  0
 ONC  CONST_15  N25  C26  N27  C28     0.00   0.0  0
 ONC  CONST_16  N27  C26  N25  C29     0.00   0.0  0
 ONC  CONST_17  N27  C28  C29  N25     0.00   0.0  0
 ONC  CONST_18  C26  N09  C10  C12     0.00   0.0  0
 ONC  CONST_19  C04  C03  C02  C01   180.00   0.0  0
 ONC  CONST_20  C06  C07  C02  C01   180.00   0.0  0
 ONC  CONST_21  C08  C07  C02  C03   180.00   0.0  0
 ONC  CONST_22  C08  C07  C06  C05   180.00   0.0  0
 ONC  CONST_23  C21  C20  C19  C18   180.00   0.0  0
 ONC  CONST_24  C23  C24  C19  C18   180.00   0.0  0
 ONC  CONST_25  C12  C10  N09  C08   180.00   0.0  0
 ONC  CONST_26  O11  C10  N09  C26   180.00   0.0  0
 ONC  CONST_27  H5   C04  C03  C02   180.00   0.0  0
 ONC  CONST_28  H7   C06  C07  C02   180.00   0.0  0
 ONC  CONST_29  H6   C05  C04  C03   180.00   0.0  0
 ONC  CONST_30  H4   C03  C04  C05   180.00   0.0  0
 ONC  CONST_31  H24  C29  N25  C13     0.00   0.0  0
 ONC  CONST_32  H19  C21  C20  C19   180.00   0.0  0
 ONC  CONST_33  H21  C23  C24  C19   180.00   0.0  0
 ONC  CONST_34  H20  C22  C21  C20   180.00   0.0  0
 ONC  CONST_35  H22  C24  C19  C20   180.00   0.0  0
 ONC  CONST_36  H18  C20  C21  C22   180.00   0.0  0
 ONC  CONST_37  H23  C28  N27  C26   180.00   0.0  0
 ONC  CONST_38  O11  C10  N09  C08     0.00   0.0  0
 ONC  Var_01    N16  C17  C12  C10   163.71  30.0  1
 ONC  Var_02    C15  N16  C17  C12    51.18  30.0  1
 ONC  Var_03    C15  C14  C13  C12   -12.71  30.0  1
 ONC  Var_04    N16  C15  C14  C13    45.68  30.0  1
 ONC  Var_05    C17  N16  C15  C14   -67.41  30.0  1
 ONC  Var_06    N09  C08  C07  C02  -175.92  30.0  2
 ONC  Var_07    C10  N09  C08  C07    85.43  30.0  3
 ONC  Var_08    C19  C18  N16  C15  -167.98  30.0  3
 ONC  Var_09    N16  C18  C19  C20    47.71  30.0  2
 ONC  Var_10    H1   C01  C02  C03  -121.31  30.0  2

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
 ONC  plan-1  C01  0.020
 ONC  plan-1  C02  0.020
 ONC  plan-1  C03  0.020
 ONC  plan-1  C04  0.020
 ONC  plan-1  C05  0.020
 ONC  plan-1  C06  0.020
 ONC  plan-1  C07  0.020
 ONC  plan-1  C08  0.020
 ONC  plan-1  H4   0.020
 ONC  plan-1  H5   0.020
 ONC  plan-1  H6   0.020
 ONC  plan-1  H7   0.020
 ONC  plan-2  C19  0.020
 ONC  plan-2  C20  0.020
 ONC  plan-2  C21  0.020
 ONC  plan-2  C22  0.020
 ONC  plan-2  C23  0.020
 ONC  plan-2  C24  0.020
 ONC  plan-2  H18  0.020
 ONC  plan-2  H19  0.020
 ONC  plan-2  H20  0.020
 ONC  plan-2  H21  0.020
 ONC  plan-2  H22  0.020
 ONC  plan-2  C18  0.020
 ONC  plan-3  C08  0.020
 ONC  plan-3  C10  0.020
 ONC  plan-3  C12  0.020
 ONC  plan-3  C13  0.020
 ONC  plan-3  C14  0.020
 ONC  plan-3  C17  0.020
 ONC  plan-3  C26  0.020
 ONC  plan-3  C28  0.020
 ONC  plan-3  C29  0.020
 ONC  plan-3  N09  0.020
 ONC  plan-3  N25  0.020
 ONC  plan-3  N27  0.020
 ONC  plan-3  H23  0.020
 ONC  plan-3  H24  0.020
 ONC  plan-3  O11  0.020

