# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 03:23:25 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 2-{3,5-dimethyl-4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}-5,7-dimethoxyquinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)c2C(=O)NC(=Nc2c1)c3cc(C)c(OCCN4CCCC4)c(C)c3
#
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
 5GD  5GD  2-{3,5-dimethyl-4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}-5,7-dimethoxyquinazolin-4(3H)-one  ligand  60  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5GD
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
 5GD  C3   C  CR66  0   0.306  -3.5856  -0.5449  -0.1563
 5GD  C5   C  CR6   0   0.544  -3.2762   1.8199   0.4604
 5GD  C2   C  CR16  0  -0.475  -4.3877  -1.6470  -0.4331
 5GD  C1   C  CR6   0   0.451  -5.7673  -1.5202  -0.3979
 5GD  C8   C  CR16  0  -0.374   0.8724   1.1411  -0.2268
 5GD  C12  C  CH2   0  -0.185   4.7737  -0.3791   1.1747
 5GD  C9   C  CR6   0   0.040   2.2499   0.9590  -0.2520
 5GD  C11  C  CR6   0   0.299   2.7508  -0.3243  -0.0274
 5GD  C10  C  CH3   0  -0.725   3.1680   2.1118  -0.5313
 5GD  C13  C  CH2   0  -0.299   6.1908  -0.8951   1.0603
 5GD  C14  C  CH2   0  -0.277   6.8803   0.0998  -1.0802
 5GD  C20  C  CR16  0  -0.351   0.5358  -1.1961   0.2095
 5GD  C21  C  CR6   0   0.436  -5.5704   0.8148   0.1840
 5GD  C17  C  CH2   0  -0.273   8.4879  -0.4339   0.4918
 5GD  C18  C  CR6   0   0.040   1.9047  -1.4150   0.1988
 5GD  O1   O  O     0  -0.451  -3.5850   2.9565   0.7712
 5GD  C4   C  CR66  0  -0.255  -4.1603   0.7083   0.1588
 5GD  O3   O  O2    0  -0.445  -6.0875   2.0069   0.4801
 5GD  C23  C  CR16  0  -0.568  -6.3627  -0.2909  -0.0920
 5GD  O    O  O2    0  -0.466  -6.4705  -2.6245  -0.6698
 5GD  C    C  CH3   0  -0.444  -7.8862  -2.5775  -0.6411
 5GD  N    N  NR16  0  -0.728  -1.9332   1.4849   0.3832
 5GD  C6   C  CR6   0   0.487  -1.4544   0.2565   0.0534
 5GD  N1   N  N     0  -0.487  -2.2273  -0.7377  -0.2106
 5GD  C7   C  CR6   0   0.041   0.0073   0.0777   0.0142
 5GD  N2   N  NT    0  -0.429   7.1008  -0.0250   0.3546
 5GD  C16  C  CH2   0  -0.460   9.2165   0.4755  -0.4861
 5GD  C15  C  CH2   0  -0.475   8.2044   0.6525  -1.6332
 5GD  H1   H  HCR6  0   0.265  -3.9250  -2.5948  -0.6742
 5GD  H2   H  HCR6  0   0.255   0.4900   2.1346  -0.4314
 5GD  H3   H  HCH2  0   0.232   4.2549  -0.9481   1.9533
 5GD  H4   H  HCH2  0   0.228   4.7772   0.6731   1.4790
 5GD  H5   H  HCH3  0   0.250   3.7005   2.4287   0.3671
 5GD  H6   H  HCH3  0   0.254   3.9192   1.8628  -1.2808
 5GD  H7   H  HCH3  0   0.252   2.6063   2.9715  -0.8934
 5GD  H8   H  HCH2  0   0.242   6.5607  -1.0036   2.0835
 5GD  H9   H  HCH2  0   0.198   6.1642  -1.9126   0.6312
 5GD  H11  H  HCH2  0   0.236   6.0370   0.7563  -1.2939
 5GD  H15  H  HCR6  0   0.256  -0.1355  -2.0276   0.3809
 5GD  H16  H  HCH2  0   0.232   8.8264  -0.3220   1.5246
 5GD  H17  H  HCH2  0   0.189   8.6349  -1.4913   0.2107
 5GD  H21  H  HCR6  0   0.310  -7.4380  -0.2009  -0.0714
 5GD  H22  H  HCH3  0   0.235  -8.2652  -2.3084   0.3474
 5GD  H23  H  HCH3  0   0.235  -8.2863  -1.8798  -1.3802
 5GD  H24  H  HCH3  0   0.267  -8.2285  -3.5793  -0.8858
 5GD  H25  H  HNR6  0   0.426  -1.2864   2.2188   0.6402
 5GD  H27  H  HCH2  0   0.231   9.4367   1.4345  -0.0149
 5GD  H28  H  HCH2  0   0.233  10.1629   0.0488  -0.8169
 5GD  H29  H  HCH2  0   0.233   8.5069   0.1035  -2.5248
 5GD  H30  H  HCH2  0   0.236   8.1137   1.6996  -1.9221
 5GD  O2   O  O2    0  -0.486   4.0927  -0.5396  -0.0707
 5GD  C19  C  CH3   0  -0.715   2.4677  -2.7911   0.4008
 5GD  C22  C  CH3   0  -0.447  -7.4950   2.1607   0.5289
 5GD  H10  H  HCH2  0   0.190   6.6525  -0.8762  -1.5378
 5GD  H12  H  HCH3  0   0.250   3.0673  -3.1063  -0.4539
 5GD  H13  H  HCH3  0   0.247   3.1109  -2.8471   1.2807
 5GD  H14  H  HCH3  0   0.249   1.6679  -3.5174   0.5335
 5GD  H18  H  HCH3  0   0.235  -7.9606   1.9498  -0.4363
 5GD  H19  H  HCH3  0   0.236  -7.9465   1.5216   1.2911
 5GD  H20  H  HCH3  0   0.268  -7.6767   3.2001   0.7880

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
 5GD  C22  O3   single    1.417  0.020  1.417
 5GD  O3   C21  single    1.333  0.020  1.333
 5GD  O1   C5   double    1.218  0.020  1.218
 5GD  C21  C23  aromatic  1.388  0.020  1.388
 5GD  C21  C4   aromatic  1.414  0.020  1.414
 5GD  C5   C4   single    1.452  0.020  1.452
 5GD  C5   N    single    1.386  0.020  1.386
 5GD  C23  C1   aromatic  1.400  0.020  1.400
 5GD  C4   C3   aromatic  1.414  0.020  1.414
 5GD  N    C6   single    1.359  0.020  1.359
 5GD  C1   O    single    1.337  0.020  1.337
 5GD  C1   C2   aromatic  1.386  0.020  1.386
 5GD  C3   C2   aromatic  1.391  0.020  1.391
 5GD  C3   N1   single    1.373  0.020  1.373
 5GD  C6   N1   double    1.287  0.020  1.287
 5GD  C6   C7   single    1.473  0.020  1.473
 5GD  O    C    single    1.417  0.020  1.417
 5GD  C20  C7   aromatic  1.393  0.020  1.393
 5GD  C20  C18  aromatic  1.386  0.020  1.386
 5GD  C19  C18  single    1.500  0.020  1.500
 5GD  C7   C8   aromatic  1.392  0.020  1.392
 5GD  C18  C11  aromatic  1.399  0.020  1.399
 5GD  C8   C9   aromatic  1.390  0.020  1.390
 5GD  C11  C9   aromatic  1.396  0.020  1.396
 5GD  C11  O2   single    1.360  0.020  1.360
 5GD  C9   C10  single    1.500  0.020  1.500
 5GD  O2   C12  single    1.428  0.020  1.428
 5GD  C17  C16  single    1.521  0.020  1.521
 5GD  C17  N2   single    1.453  0.020  1.453
 5GD  C12  C13  single    1.513  0.020  1.513
 5GD  C16  C15  single    1.540  0.020  1.540
 5GD  N2   C13  single    1.443  0.020  1.443
 5GD  N2   C14  single    1.457  0.020  1.457
 5GD  C15  C14  single    1.538  0.020  1.538
 5GD  C2   H1   single    0.930  0.020  1.080
 5GD  C8   H2   single    0.930  0.020  1.080
 5GD  C12  H3   single    0.970  0.020  1.090
 5GD  C12  H4   single    0.970  0.020  1.090
 5GD  C10  H5   single    0.970  0.020  1.090
 5GD  C10  H6   single    0.970  0.020  1.090
 5GD  C10  H7   single    0.970  0.020  1.090
 5GD  C13  H8   single    0.970  0.020  1.090
 5GD  C13  H9   single    0.970  0.020  1.090
 5GD  C14  H10  single    0.970  0.020  1.090
 5GD  C14  H11  single    0.970  0.020  1.090
 5GD  C19  H12  single    0.970  0.020  1.090
 5GD  C19  H13  single    0.970  0.020  1.090
 5GD  C19  H14  single    0.970  0.020  1.090
 5GD  C20  H15  single    0.930  0.020  1.080
 5GD  C17  H16  single    0.970  0.020  1.090
 5GD  C17  H17  single    0.970  0.020  1.090
 5GD  C22  H18  single    0.970  0.020  1.090
 5GD  C22  H19  single    0.970  0.020  1.090
 5GD  C22  H20  single    0.970  0.020  1.090
 5GD  C23  H21  single    0.930  0.020  1.080
 5GD  C    H22  single    0.970  0.020  1.090
 5GD  C    H23  single    0.970  0.020  1.090
 5GD  C    H24  single    0.970  0.020  1.090
 5GD  N    H25  single    0.860  0.020  1.020
 5GD  C16  H27  single    0.970  0.020  1.090
 5GD  C16  H28  single    0.970  0.020  1.090
 5GD  C15  H29  single    0.970  0.020  1.090
 5GD  C15  H30  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
 5GD  N1   C3   C4   122.36  3.000
 5GD  N1   C3   C2   116.83  3.000
 5GD  C4   C3   C2   120.81  3.000
 5GD  N    C5   C4   113.16  3.000
 5GD  N    C5   O1   119.03  3.000
 5GD  C4   C5   O1   127.81  3.000
 5GD  H1   C2   C1   120.77  3.000
 5GD  H1   C2   C3   119.46  3.000
 5GD  C1   C2   C3   119.77  3.000
 5GD  O    C1   C23  123.10  3.000
 5GD  O    C1   C2   116.28  3.000
 5GD  C23  C1   C2   120.62  3.000
 5GD  H2   C8   C7   120.90  3.000
 5GD  H2   C8   C9   117.80  3.000
 5GD  C7   C8   C9   121.27  3.000
 5GD  H4   C12  H3   107.65  3.000
 5GD  H4   C12  O2   110.59  3.000
 5GD  H3   C12  O2   109.62  3.000
 5GD  H4   C12  C13  110.22  3.000
 5GD  H3   C12  C13  108.68  3.000
 5GD  O2   C12  C13  110.02  3.000
 5GD  C10  C9   C11  121.13  3.000
 5GD  C10  C9   C8   120.62  3.000
 5GD  C11  C9   C8   118.25  3.000
 5GD  O2   C11  C18  118.60  3.000
 5GD  O2   C11  C9   119.64  3.000
 5GD  C18  C11  C9   121.72  3.000
 5GD  H7   C10  H6   107.89  3.000
 5GD  H7   C10  H5   107.23  3.000
 5GD  H6   C10  H5   107.22  3.000
 5GD  H7   C10  C9   110.67  3.000
 5GD  H6   C10  C9   111.98  3.000
 5GD  H5   C10  C9   111.62  3.000
 5GD  H9   C13  H8   106.27  3.000
 5GD  H9   C13  N2   112.37  3.000
 5GD  H8   C13  N2   107.71  3.000
 5GD  H9   C13  C12  108.73  3.000
 5GD  H8   C13  C12  106.26  3.000
 5GD  N2   C13  C12  114.96  3.000
 5GD  H11  C14  H10  106.99  3.000
 5GD  H11  C14  C15  112.29  3.000
 5GD  H10  C14  C15  110.31  3.000
 5GD  H11  C14  N2   111.21  3.000
 5GD  H10  C14  N2   111.37  3.000
 5GD  C15  C14  N2   104.75  3.000
 5GD  H15  C20  C7   119.30  3.000
 5GD  H15  C20  C18  119.49  3.000
 5GD  C7   C20  C18  121.20  3.000
 5GD  C23  C21  O3   122.36  3.000
 5GD  C23  C21  C4   120.38  3.000
 5GD  O3   C21  C4   117.27  3.000
 5GD  H17  C17  H16  107.31  3.000
 5GD  H17  C17  C16  110.19  3.000
 5GD  H16  C17  C16  113.45  3.000
 5GD  H17  C17  N2   111.89  3.000
 5GD  H16  C17  N2   110.87  3.000
 5GD  C16  C17  N2   103.20  3.000
 5GD  C20  C18  C19  120.95  3.000
 5GD  C19  C18  C11  120.65  3.000
 5GD  C20  C18  C11  118.39  3.000
 5GD  C21  C4   C5   123.08  3.000
 5GD  C5   C4   C3   118.51  3.000
 5GD  C21  C4   C3   118.41  3.000
 5GD  C22  O3   C21  119.36  3.000
 5GD  H21  C23  C21  119.90  3.000
 5GD  H21  C23  C1   120.08  3.000
 5GD  C21  C23  C1   120.02  3.000
 5GD  C    O    C1   119.60  3.000
 5GD  H24  C    H23  108.73  3.000
 5GD  H24  C    H22  108.76  3.000
 5GD  H23  C    H22  109.14  3.000
 5GD  H24  C    O    106.24  3.000
 5GD  H23  C    O    111.94  3.000
 5GD  H22  C    O    111.91  3.000
 5GD  H25  N    C6   119.49  3.000
 5GD  H25  N    C5   115.47  3.000
 5GD  C6   N    C5   124.98  3.000
 5GD  C7   C6   N1   119.79  3.000
 5GD  C7   C6   N    117.76  3.000
 5GD  N1   C6   N    122.45  3.000
 5GD  C6   N1   C3   118.53  3.000
 5GD  C6   C7   C20  118.93  3.000
 5GD  C20  C7   C8   119.15  3.000
 5GD  C6   C7   C8   121.91  3.000
 5GD  C17  N2   C14  105.17  3.000
 5GD  C14  N2   C13  115.95  3.000
 5GD  C17  N2   C13  112.72  3.000
 5GD  H28  C16  H27  107.46  3.000
 5GD  H28  C16  C15  112.93  3.000
 5GD  H27  C16  C15  110.70  3.000
 5GD  H28  C16  C17  112.15  3.000
 5GD  H27  C16  C17  110.15  3.000
 5GD  C15  C16  C17  103.46  3.000
 5GD  H30  C15  H29  106.87  3.000
 5GD  H30  C15  C16  111.25  3.000
 5GD  H29  C15  C16  111.66  3.000
 5GD  H30  C15  C14  111.65  3.000
 5GD  H29  C15  C14  110.62  3.000
 5GD  C16  C15  C14  104.88  3.000
 5GD  C11  O2   C12  115.14  3.000
 5GD  H14  C19  H13  107.48  3.000
 5GD  H14  C19  H12  107.86  3.000
 5GD  H13  C19  H12  107.04  3.000
 5GD  H14  C19  C18  110.65  3.000
 5GD  H13  C19  C18  112.13  3.000
 5GD  H12  C19  C18  111.47  3.000
 5GD  H20  C22  H19  108.92  3.000
 5GD  H20  C22  H18  108.91  3.000
 5GD  H19  C22  H18  109.12  3.000
 5GD  H20  C22  O3   106.15  3.000
 5GD  H19  C22  O3   111.79  3.000
 5GD  H18  C22  O3   111.84  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
 5GD  CONST_01  C23  C21  C4   C3     0.00   0.0  0
 5GD  CONST_02  C23  C1   C2   C3     0.00   0.0  0
 5GD  CONST_03  C21  C23  C1   C2     0.00   0.0  0
 5GD  CONST_04  C21  C4   C3   C2     0.00   0.0  0
 5GD  CONST_05  C4   C21  C23  C1     0.00   0.0  0
 5GD  CONST_06  C4   C3   C2   C1     0.00   0.0  0
 5GD  CONST_07  C18  C20  C7   C8     0.00   0.0  0
 5GD  CONST_08  C18  C11  C9   C8     0.00   0.0  0
 5GD  CONST_09  C20  C7   C8   C9     0.00   0.0  0
 5GD  CONST_10  C20  C18  C11  C9     0.00   0.0  0
 5GD  CONST_11  C7   C20  C18  C11    0.00   0.0  0
 5GD  CONST_12  C7   C8   C9   C11    0.00   0.0  0
 5GD  CONST_13  C6   C7   C8   C9   180.00   0.0  0
 5GD  CONST_14  C6   C7   C20  C18  180.00   0.0  0
 5GD  CONST_15  N    C6   N1   C3     0.00   0.0  0
 5GD  CONST_16  C7   C6   N1   C3   180.00   0.0  0
 5GD  CONST_17  N1   C6   N    C5     0.00   0.0  0
 5GD  CONST_18  C7   C6   N    C5   180.00   0.0  0
 5GD  CONST_19  C6   N    C5   C4     0.00   0.0  0
 5GD  CONST_20  O3   C21  C4   C3   180.00   0.0  0
 5GD  CONST_21  O    C1   C2   C3   180.00   0.0  0
 5GD  CONST_22  O3   C21  C4   C5     0.00   0.0  0
 5GD  CONST_23  O3   C21  C23  C1   180.00   0.0  0
 5GD  CONST_24  O2   C11  C9   C8   180.00   0.0  0
 5GD  CONST_25  C19  C18  C11  C9   180.00   0.0  0
 5GD  CONST_26  C7   C8   C9   C10  180.00   0.0  0
 5GD  CONST_27  C18  C11  C9   C10  180.00   0.0  0
 5GD  CONST_28  C7   C20  C18  C19  180.00   0.0  0
 5GD  CONST_29  O2   C11  C18  C20  180.00   0.0  0
 5GD  CONST_30  O    C1   C23  C21  180.00   0.0  0
 5GD  CONST_31  C6   N    C5   O1   180.00   0.0  0
 5GD  CONST_32  H21  C23  C1   C2   180.00   0.0  0
 5GD  CONST_33  H15  C20  C7   C8   180.00   0.0  0
 5GD  CONST_34  H2   C8   C9   C11  180.00   0.0  0
 5GD  CONST_35  H1   C2   C3   C4   180.00   0.0  0
 5GD  CONST_36  H25  N    C5   C4   180.00   0.0  0
 5GD  Var_01    N    C6   C7   C8   -25.89  30.0  2
 5GD  Var_02    C16  C17  N2   C14   44.39  30.0  1
 5GD  Var_03    C17  C16  C15  C14   12.34  30.0  1
 5GD  Var_04    C15  C14  N2   C17  -36.15  30.0  1
 5GD  Var_05    C15  C16  C17  N2   -34.17  30.0  1
 5GD  Var_06    C16  C15  C14  N2    13.65  30.0  1
 5GD  Var_07    C18  C11  O2   C12  -92.28  30.0  2
 5GD  Var_08    C17  N2   C13  C12  168.90  30.0  2
 5GD  Var_09    C23  C21  O3   C22    0.54  30.0  2
 5GD  Var_10    H5   C10  C9   C8   107.68  30.0  2
 5GD  Var_11    H12  C19  C18  C11  -58.32  30.0  2
 5GD  Var_12    C13  C12  O2   C11  169.25  30.0  3
 5GD  Var_13    N2   C13  C12  O2    76.25  30.0  3
 5GD  Var_14    H22  C    O    C1   -61.15  30.0  3
 5GD  Var_15    H18  C22  O3   C21  -61.50  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
 5GD  plan-1  C8   0.020
 5GD  plan-1  C9   0.020
 5GD  plan-1  C11  0.020
 5GD  plan-1  C10  0.020
 5GD  plan-1  C20  0.020
 5GD  plan-1  C18  0.020
 5GD  plan-1  C6   0.020
 5GD  plan-1  C7   0.020
 5GD  plan-1  H2   0.020
 5GD  plan-1  H15  0.020
 5GD  plan-1  O2   0.020
 5GD  plan-1  C19  0.020
 5GD  plan-2  C3   0.020
 5GD  plan-2  C5   0.020
 5GD  plan-2  C2   0.020
 5GD  plan-2  C1   0.020
 5GD  plan-2  C21  0.020
 5GD  plan-2  O1   0.020
 5GD  plan-2  C4   0.020
 5GD  plan-2  O3   0.020
 5GD  plan-2  C23  0.020
 5GD  plan-2  O    0.020
 5GD  plan-2  N    0.020
 5GD  plan-2  C6   0.020
 5GD  plan-2  N1   0.020
 5GD  plan-2  C7   0.020
 5GD  plan-2  H1   0.020
 5GD  plan-2  H21  0.020
 5GD  plan-2  H25  0.020

