# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:57:54 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 6-benzyl-3-[3-(benzyloxy)phenyl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC2=CC(=O)N(Cc3ccccc3)C=C2CN1c4cccc(OCc5ccccc5)c4
#
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
 8LP  8LP  6-benzyl-3-[3-(benzyloxy)phenyl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(1H,3H)-dione  ligand  56  33  .  2022-07-23  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_8LP
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
 8LP  N1   N  NH1   0  -0.768  -1.4933  -2.6776  -0.8346
 8LP  N3   N  NR6   0  -0.511  -3.7494   0.1437   1.1334
 8LP  C4   C  CR16  0  -0.241  -6.8289   2.5311  -0.9087
 8LP  C5   C  CR16  0  -0.242   7.3897   2.3371   2.2972
 8LP  C6   C  CR16  0  -0.242   8.2497   0.0931   2.2288
 8LP  C7   C  CR16  0  -0.246   2.9673  -0.3865  -3.5432
 8LP  C8   C  CR16  0  -0.289  -7.0438   1.2048   1.5182
 8LP  C10  C  CR16  0  -0.289   6.6777   2.0977   1.1305
 8LP  C13  C  CR16  0  -0.379   3.9859  -0.0601  -2.6544
 8LP  C15  C  CR6   0   0.146  -5.7849   1.5307   1.0261
 8LP  C17  C  CR6   0   0.334   1.4807  -0.8048  -1.7216
 8LP  C20  C  CR16  0   0.014  -2.6603   0.4956   0.4096
 8LP  C21  C  CR6   0  -0.142  -1.9141  -0.4045  -0.2702
 8LP  C22  C  CR6   0   0.541  -2.2875  -1.7682  -0.1800
 8LP  C24  C  C     0   0.668  -0.1977  -2.4323  -1.2454
 8LP  C26  C  CH2   0  -0.428  -4.5390   1.1792   1.7981
 8LP  C1   C  CR16  0  -0.265  -8.0836   2.2043  -0.4087
 8LP  C2   C  CR16  0  -0.261   8.1769   1.3336   2.8484
 8LP  C3   C  CR16  0  -0.245  -8.1885   1.5447   0.8081
 8LP  C9   C  CR16  0  -0.300  -5.6881   2.1988  -0.1924
 8LP  C11  C  CR16  0  -0.294   7.5349  -0.1430   1.0620
 8LP  C12  C  CR16  0  -0.291   1.7124  -0.7567  -3.0925
 8LP  C14  C  CR16  0  -0.375   2.4794  -0.4840  -0.8218
 8LP  C16  C  CR6   0   0.099   6.7460   0.8571   0.5025
 8LP  C18  C  CR6   0   0.395   3.7424  -0.1072  -1.2842
 8LP  C19  C  CR16  0  -0.563  -3.3874  -2.1395   0.5402
 8LP  C23  C  CR6   0   0.576  -4.1897  -1.1779   1.2297
 8LP  C25  C  CH2   0  -0.305  -0.7760  -0.0359  -1.1643
 8LP  C27  C  CH2   0  -0.271   5.9518   0.5964  -0.7410
 8LP  N2   N  NT    0  -0.602   0.1883  -1.1291  -1.2224
 8LP  O1   O  O     0  -0.515  -5.1918  -1.4420   1.8893
 8LP  O2   O  O     0  -0.492   0.5349  -3.3466  -1.5748
 8LP  O3   O  O2    0  -0.469   4.6500   0.1908  -0.3354
 8LP  H1   H  HNH1  0   0.418  -1.7431  -3.6545  -0.7799
 8LP  H2   H  HCR6  0   0.257  -6.7386   3.0522  -1.8531
 8LP  H4   H  HCR6  0   0.259   8.8654  -0.6896   2.6521
 8LP  H5   H  HCR6  0   0.266   3.1662  -0.3458  -4.6059
 8LP  H6   H  HCR6  0   0.251  -7.1299   0.6812   2.4617
 8LP  H7   H  HCR6  0   0.255   6.0697   2.8843   0.6994
 8LP  H8   H  HCR6  0   0.286   4.9504   0.2276  -3.0489
 8LP  H9   H  HCR6  0   0.309  -2.4204   1.5500   0.3952
 8LP  H10  H  HCH2  0   0.288  -4.7904   0.8403   2.8012
 8LP  H11  H  HCH2  0   0.286  -3.8983   2.0547   1.9022
 8LP  H12  H  HCR6  0   0.257  -8.9751   2.4643  -0.9647
 8LP  H13  H  HCR6  0   0.259   8.7347   1.5196   3.7570
 8LP  H14  H  HCR6  0   0.256  -9.1628   1.2904   1.2048
 8LP  H15  H  HCR6  0   0.251  -4.7154   2.4693  -0.5878
 8LP  H16  H  HCR6  0   0.255   7.5951  -1.1119   0.5807
 8LP  H17  H  HCR6  0   0.261   0.9232  -1.0028  -3.7910
 8LP  H18  H  HCR6  0   0.268   2.2837  -0.5232   0.2428
 8LP  H19  H  HCR6  0   0.278  -3.6770  -3.1788   0.6229
 8LP  H20  H  HCH2  0   0.268  -1.1363   0.1983  -2.1730
 8LP  H21  H  HCH2  0   0.280  -0.2656   0.8513  -0.7909
 8LP  H22  H  HCH2  0   0.243   5.8932   1.5031  -1.3525
 8LP  H23  H  HCH2  0   0.244   6.4251  -0.1851  -1.3445
 8LP  H3   H  HCR6  0   0.258   7.3350   3.3074   2.7734

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
 8LP  O1   C23  double    1.228  0.020  1.228
 8LP  C19  C23  single    1.430  0.020  1.430
 8LP  C19  C22  double    1.366  0.020  1.366
 8LP  C23  N3   single    1.396  0.020  1.396
 8LP  N1   C22  single    1.373  0.020  1.373
 8LP  N1   C24  single    1.381  0.020  1.381
 8LP  O2   C24  double    1.217  0.020  1.217
 8LP  C1   C3   aromatic  1.388  0.020  1.388
 8LP  C1   C4   aromatic  1.390  0.020  1.390
 8LP  C3   C8   aromatic  1.389  0.020  1.389
 8LP  C22  C21  single    1.417  0.020  1.417
 8LP  C4   C9   aromatic  1.387  0.020  1.387
 8LP  C24  N2   single    1.359  0.020  1.359
 8LP  C8   C15  aromatic  1.390  0.020  1.390
 8LP  C9   C15  aromatic  1.393  0.020  1.393
 8LP  C15  C26  single    1.507  0.020  1.507
 8LP  N3   C26  single    1.462  0.020  1.462
 8LP  N3   C20  single    1.354  0.020  1.354
 8LP  C21  C20  double    1.352  0.020  1.352
 8LP  C21  C25  single    1.494  0.020  1.494
 8LP  N2   C25  single    1.459  0.020  1.459
 8LP  N2   C17  single    1.423  0.020  1.423
 8LP  C17  C12  aromatic  1.391  0.020  1.391
 8LP  C17  C14  aromatic  1.382  0.020  1.382
 8LP  C12  C7   aromatic  1.384  0.020  1.384
 8LP  C14  C18  aromatic  1.397  0.020  1.397
 8LP  C7   C13  aromatic  1.391  0.020  1.391
 8LP  C18  C13  aromatic  1.392  0.020  1.392
 8LP  C18  O3   single    1.346  0.020  1.346
 8LP  C27  C16  single    1.498  0.020  1.498
 8LP  C27  O3   single    1.423  0.020  1.423
 8LP  C11  C16  aromatic  1.391  0.020  1.391
 8LP  C11  C6   aromatic  1.389  0.020  1.389
 8LP  C16  C10  aromatic  1.392  0.020  1.392
 8LP  C6   C2   aromatic  1.389  0.020  1.389
 8LP  C10  C5   aromatic  1.388  0.020  1.388
 8LP  C2   C5   aromatic  1.389  0.020  1.389
 8LP  N1   H1   single    0.860  0.020  1.020
 8LP  C4   H2   single    0.930  0.020  1.080
 8LP  C5   H3   single    0.930  0.020  1.080
 8LP  C6   H4   single    0.930  0.020  1.080
 8LP  C7   H5   single    0.930  0.020  1.080
 8LP  C8   H6   single    0.930  0.020  1.080
 8LP  C10  H7   single    0.930  0.020  1.080
 8LP  C13  H8   single    0.930  0.020  1.080
 8LP  C20  H9   single    0.930  0.020  1.080
 8LP  C26  H10  single    0.970  0.020  1.090
 8LP  C26  H11  single    0.970  0.020  1.090
 8LP  C1   H12  single    0.930  0.020  1.080
 8LP  C2   H13  single    0.930  0.020  1.080
 8LP  C3   H14  single    0.930  0.020  1.080
 8LP  C9   H15  single    0.930  0.020  1.080
 8LP  C11  H16  single    0.930  0.020  1.080
 8LP  C12  H17  single    0.930  0.020  1.080
 8LP  C14  H18  single    0.930  0.020  1.080
 8LP  C19  H19  single    0.930  0.020  1.080
 8LP  C25  H20  single    0.970  0.020  1.090
 8LP  C25  H21  single    0.970  0.020  1.090
 8LP  C27  H22  single    0.970  0.020  1.090
 8LP  C27  H23  single    0.970  0.020  1.090

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
 8LP  H1   N1   C24  114.83  3.000
 8LP  H1   N1   C22  118.15  3.000
 8LP  C24  N1   C22  124.52  3.000
 8LP  C23  N3   C26  117.95  3.000
 8LP  C26  N3   C20  119.56  3.000
 8LP  C23  N3   C20  122.44  3.000
 8LP  H2   C4   C9   119.81  3.000
 8LP  H2   C4   C1   120.16  3.000
 8LP  C9   C4   C1   120.02  3.000
 8LP  H3   C5   C2   120.11  3.000
 8LP  H3   C5   C10  119.91  3.000
 8LP  C2   C5   C10  119.98  3.000
 8LP  H4   C6   C11  119.91  3.000
 8LP  H4   C6   C2   120.10  3.000
 8LP  C11  C6   C2   119.99  3.000
 8LP  H5   C7   C12  119.78  3.000
 8LP  H5   C7   C13  118.96  3.000
 8LP  C12  C7   C13  121.26  3.000
 8LP  H6   C8   C3   119.89  3.000
 8LP  H6   C8   C15  119.59  3.000
 8LP  C3   C8   C15  120.52  3.000
 8LP  H7   C10  C16  119.67  3.000
 8LP  H7   C10  C5   119.81  3.000
 8LP  C16  C10  C5   120.52  3.000
 8LP  H8   C13  C18  121.61  3.000
 8LP  H8   C13  C7   118.86  3.000
 8LP  C18  C13  C7   119.52  3.000
 8LP  C9   C15  C26  120.16  3.000
 8LP  C26  C15  C8   120.83  3.000
 8LP  C9   C15  C8   119.01  3.000
 8LP  N2   C17  C14  118.74  3.000
 8LP  C14  C17  C12  120.88  3.000
 8LP  N2   C17  C12  120.32  3.000
 8LP  H9   C20  C21  121.32  3.000
 8LP  H9   C20  N3   116.03  3.000
 8LP  C21  C20  N3   122.64  3.000
 8LP  C25  C21  C22  118.45  3.000
 8LP  C25  C21  C20  123.86  3.000
 8LP  C22  C21  C20  117.59  3.000
 8LP  C19  C22  C21  120.49  3.000
 8LP  C21  C22  N1   117.04  3.000
 8LP  C19  C22  N1   122.47  3.000
 8LP  O2   C24  N2   123.63  3.000
 8LP  N2   C24  N1   115.57  3.000
 8LP  O2   C24  N1   120.78  3.000
 8LP  H11  C26  H10  107.33  3.000
 8LP  H11  C26  C15  110.34  3.000
 8LP  H10  C26  C15  110.72  3.000
 8LP  H11  C26  N3   107.15  3.000
 8LP  H10  C26  N3   108.86  3.000
 8LP  C15  C26  N3   112.25  3.000
 8LP  H12  C1   C3   120.15  3.000
 8LP  H12  C1   C4   120.15  3.000
 8LP  C3   C1   C4   119.70  3.000
 8LP  H13  C2   C6   120.07  3.000
 8LP  H13  C2   C5   120.07  3.000
 8LP  C6   C2   C5   119.86  3.000
 8LP  H14  C3   C1   120.07  3.000
 8LP  H14  C3   C8   119.80  3.000
 8LP  C1   C3   C8   120.13  3.000
 8LP  H15  C9   C15  120.07  3.000
 8LP  H15  C9   C4   119.31  3.000
 8LP  C15  C9   C4   120.62  3.000
 8LP  H16  C11  C16  119.72  3.000
 8LP  H16  C11  C6   119.78  3.000
 8LP  C16  C11  C6   120.50  3.000
 8LP  H17  C12  C17  120.44  3.000
 8LP  H17  C12  C7   120.79  3.000
 8LP  C17  C12  C7   118.77  3.000
 8LP  H18  C14  C18  119.90  3.000
 8LP  H18  C14  C17  120.06  3.000
 8LP  C18  C14  C17  120.03  3.000
 8LP  C27  C16  C11  120.61  3.000
 8LP  C11  C16  C10  119.14  3.000
 8LP  C27  C16  C10  120.23  3.000
 8LP  O3   C18  C14  115.84  3.000
 8LP  O3   C18  C13  124.61  3.000
 8LP  C14  C18  C13  119.54  3.000
 8LP  H19  C19  C23  117.32  3.000
 8LP  H19  C19  C22  121.12  3.000
 8LP  C23  C19  C22  121.55  3.000
 8LP  O1   C23  C19  124.91  3.000
 8LP  C19  C23  N3   115.24  3.000
 8LP  O1   C23  N3   119.85  3.000
 8LP  H21  C25  H20  107.17  3.000
 8LP  H21  C25  N2   108.31  3.000
 8LP  H20  C25  N2   109.92  3.000
 8LP  H21  C25  C21  110.66  3.000
 8LP  H20  C25  C21  110.68  3.000
 8LP  N2   C25  C21  110.04  3.000
 8LP  H23  C27  H22  107.83  3.000
 8LP  H23  C27  O3   110.44  3.000
 8LP  H22  C27  O3   110.26  3.000
 8LP  H23  C27  C16  110.64  3.000
 8LP  H22  C27  C16  110.35  3.000
 8LP  O3   C27  C16  107.34  3.000
 8LP  C25  N2   C24  122.10  3.000
 8LP  C25  N2   C17  116.33  3.000
 8LP  C24  N2   C17  118.06  3.000
 8LP  C27  O3   C18  118.62  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
 8LP  CONST_01  C8   C3   C1   C4     0.00   0.0  0
 8LP  CONST_02  C8   C15  C9   C4     0.00   0.0  0
 8LP  CONST_03  C11  C16  C10  C5     0.00   0.0  0
 8LP  CONST_04  C11  C6   C2   C5     0.00   0.0  0
 8LP  CONST_05  C10  C16  C11  C6     0.00   0.0  0
 8LP  CONST_06  C10  C5   C2   C6     0.00   0.0  0
 8LP  CONST_07  C14  C17  C12  C7     0.00   0.0  0
 8LP  CONST_08  C14  C18  C13  C7     0.00   0.0  0
 8LP  CONST_09  C17  C12  C7   C13    0.00   0.0  0
 8LP  CONST_10  C17  C14  C18  C13    0.00   0.0  0
 8LP  CONST_11  C1   C3   C8   C15    0.00   0.0  0
 8LP  CONST_12  C1   C4   C9   C15    0.00   0.0  0
 8LP  CONST_13  C16  C11  C6   C2     0.00   0.0  0
 8LP  CONST_14  C16  C10  C5   C2     0.00   0.0  0
 8LP  CONST_15  C9   C4   C1   C3     0.00   0.0  0
 8LP  CONST_16  C9   C15  C8   C3     0.00   0.0  0
 8LP  CONST_17  C18  C14  C17  C12    0.00   0.0  0
 8LP  CONST_18  C18  C13  C7   C12    0.00   0.0  0
 8LP  CONST_19  N2   C17  C12  C7   180.00   0.0  0
 8LP  CONST_20  N2   C17  C14  C18  180.00   0.0  0
 8LP  CONST_22  C17  N2   C24  N1   180.00   0.0  0
 8LP  CONST_23  C19  C23  N3   C20    0.00   0.0  0
 8LP  CONST_24  N2   C24  N1   C22    0.00   0.0  0
 8LP  CONST_25  C26  C15  C9   C4   180.00   0.0  0
 8LP  CONST_26  C27  C16  C10  C5   180.00   0.0  0
 8LP  CONST_27  C27  C16  C11  C6   180.00   0.0  0
 8LP  CONST_28  O3   C18  C13  C7   180.00   0.0  0
 8LP  CONST_29  O3   C18  C14  C17  180.00   0.0  0
 8LP  CONST_30  C3   C8   C15  C26  180.00   0.0  0
 8LP  CONST_31  O2   C24  N2   C17    0.00   0.0  0
 8LP  CONST_32  O1   C23  N3   C20  180.00   0.0  0
 8LP  CONST_33  O2   C24  N1   C22  180.00   0.0  0
 8LP  CONST_34  C19  C23  N3   C26  180.00   0.0  0
 8LP  CONST_36  H14  C3   C1   C4   180.00   0.0  0
 8LP  CONST_37  H4   C6   C2   C5   180.00   0.0  0
 8LP  CONST_38  H3   C5   C2   C6   180.00   0.0  0
 8LP  CONST_39  H12  C1   C3   C8   180.00   0.0  0
 8LP  CONST_40  H15  C9   C15  C8   180.00   0.0  0
 8LP  CONST_41  H16  C11  C16  C10  180.00   0.0  0
 8LP  CONST_42  H13  C2   C5   C10  180.00   0.0  0
 8LP  CONST_43  H17  C12  C7   C13  180.00   0.0  0
 8LP  CONST_44  H18  C14  C18  C13  180.00   0.0  0
 8LP  CONST_45  H2   C4   C9   C15  180.00   0.0  0
 8LP  CONST_46  H5   C7   C12  C17  180.00   0.0  0
 8LP  CONST_47  H6   C8   C3   C1   180.00   0.0  0
 8LP  CONST_48  H7   C10  C5   C2   180.00   0.0  0
 8LP  CONST_49  H8   C13  C7   C12  180.00   0.0  0
 8LP  CONST_50  H1   N1   C24  N2   180.00   0.0  0
 8LP  CONST_51  O1   C23  N3   C26    0.00   0.0  0
 8LP  Var_01    C12  C17  N2   C24   76.82  30.0  2
 8LP  Var_02    C8   C15  C26  N3   111.39  30.0  2
 8LP  Var_03    C23  N3   C26  C15  -77.13  30.0  2
 8LP  Var_04    H20  C25  N2   C17   74.58  30.0  1
 8LP  Var_05    O3   C27  C16  C10  -85.17  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
 8LP  plan-1  C7   0.020
 8LP  plan-1  C13  0.020
 8LP  plan-1  C17  0.020
 8LP  plan-1  C12  0.020
 8LP  plan-1  C14  0.020
 8LP  plan-1  C18  0.020
 8LP  plan-1  N2   0.020
 8LP  plan-1  O3   0.020
 8LP  plan-1  H5   0.020
 8LP  plan-1  H8   0.020
 8LP  plan-1  H17  0.020
 8LP  plan-1  H18  0.020
 8LP  plan-2  C4   0.020
 8LP  plan-2  C8   0.020
 8LP  plan-2  C15  0.020
 8LP  plan-2  C26  0.020
 8LP  plan-2  C1   0.020
 8LP  plan-2  C3   0.020
 8LP  plan-2  C9   0.020
 8LP  plan-2  H2   0.020
 8LP  plan-2  H6   0.020
 8LP  plan-2  H12  0.020
 8LP  plan-2  H14  0.020
 8LP  plan-2  H15  0.020
 8LP  plan-3  C5   0.020
 8LP  plan-3  C6   0.020
 8LP  plan-3  C10  0.020
 8LP  plan-3  C2   0.020
 8LP  plan-3  C11  0.020
 8LP  plan-3  C16  0.020
 8LP  plan-3  C27  0.020
 8LP  plan-3  H4   0.020
 8LP  plan-3  H7   0.020
 8LP  plan-3  H13  0.020
 8LP  plan-3  H16  0.020
 8LP  plan-3  H3   0.020
 8LP  plan-4  N1   0.020
 8LP  plan-4  N3   0.020
 8LP  plan-4  C17  0.020
 8LP  plan-4  C20  0.020
 8LP  plan-4  C21  0.020
 8LP  plan-4  C22  0.020
 8LP  plan-4  C24  0.020
 8LP  plan-4  C26  0.020
 8LP  plan-4  C19  0.020
 8LP  plan-4  C23  0.020
 8LP  plan-4  C25  0.020
 8LP  plan-4  N2   0.020
 8LP  plan-4  O1   0.020
 8LP  plan-4  O2   0.020
 8LP  plan-4  H1   0.020
 8LP  plan-4  H9   0.020
 8LP  plan-4  H19  0.020

