# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 11:41:49 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (7S)-2-amino-4-methyl-7-phenyl-7,8-dihydroquinazolin-5(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)nc2C[C@@H](CC(=O)c12)c3ccccc3
#
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
 3JC  3JC  (7S)-2-amino-4-methyl-7-phenyl-7,8-dihydroquinazolin-5(6H)-one  ligand  34  19  .  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_3JC
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
 3JC  C1   C  CR6   0   0.312   3.0520  -0.7768   0.0015
 3JC  C2   C  CR6   0  -0.179   1.6465  -0.6421   0.1099
 3JC  C3   C  CR6   0   0.307   1.1564   0.6757   0.1121
 3JC  C11  C  CR16  0  -0.238  -4.5740   0.5738   1.1993
 3JC  C12  C  CR16  0  -0.272  -5.3898   0.5633   0.0744
 3JC  C13  C  CR16  0  -0.237  -4.8314   0.3179  -1.1718
 3JC  C14  C  CR16  0  -0.334  -3.4667   0.0842  -1.2896
 3JC  C15  C  CH3   0  -0.724   3.7639  -2.0910  -0.0389
 3JC  N1   N  N     0  -0.474   3.8340   0.2818  -0.0718
 3JC  N2   N  N     0  -0.486   1.9453   1.7291   0.0330
 3JC  C4   C  CR6   0   0.558   3.2589   1.4932  -0.0456
 3JC  C5   C  C     0   0.347   0.7263  -1.7785   0.2217
 3JC  C6   C  CH2   0  -0.541  -0.7440  -1.4659   0.3840
 3JC  C7   C  CH1   0  -0.391  -1.1623  -0.1762  -0.3158
 3JC  C8   C  CR6   0   0.204  -2.6392   0.0911  -0.1704
 3JC  C9   C  CH2   0  -0.500  -0.3090   0.9658   0.2211
 3JC  C10  C  CR16  0  -0.320  -3.2120   0.3391   1.0767
 3JC  H1   H  HCR6  0   0.255  -4.9994   0.7655   2.1760
 3JC  H2   H  HCR6  0   0.255  -6.4527   0.7433   0.1705
 3JC  H3   H  HCR6  0   0.255  -5.4576   0.3082  -2.0546
 3JC  H4   H  HCR6  0   0.250  -3.0400  -0.1085  -2.2672
 3JC  H5   H  HCH3  0   0.256   3.4375  -2.6923  -0.8863
 3JC  H6   H  HCH3  0   0.245   4.8333  -1.9133  -0.1231
 3JC  H7   H  HCH3  0   0.257   3.5714  -2.6804   0.8563
 3JC  H8   H  HNH2  0   0.407   5.0651   2.4243  -0.1656
 3JC  H9   H  HNH2  0   0.407   3.6976   3.4820  -0.0911
 3JC  H10  H  HCH2  0   0.275  -1.3201  -2.3197   0.0239
 3JC  H11  H  HCH2  0   0.271  -0.9398  -1.3807   1.4600
 3JC  H12  H  HCH1  0   0.269  -0.9489  -0.2863  -1.3842
 3JC  H13  H  HCH2  0   0.271  -0.5366   1.1374   1.2796
 3JC  H14  H  HCH2  0   0.275  -0.5239   1.9009  -0.2975
 3JC  H15  H  HCR6  0   0.249  -2.5949   0.3507   1.9680
 3JC  O1   O  O     0  -0.416   1.0991  -2.9384   0.2155
 3JC  N3   N  NH2   0  -0.810   4.0696   2.5487  -0.1123

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
 3JC  O1   C5   double    1.218  0.020  1.218
 3JC  C15  C1   single    1.495  0.020  1.495
 3JC  C5   C6   single    1.512  0.020  1.512
 3JC  C5   C2   single    1.467  0.020  1.467
 3JC  C1   C2   aromatic  1.416  0.020  1.416
 3JC  C1   N1   aromatic  1.318  0.020  1.318
 3JC  C6   C7   single    1.526  0.020  1.526
 3JC  C2   C3   aromatic  1.406  0.020  1.406
 3JC  N1   C4   aromatic  1.341  0.020  1.341
 3JC  C7   C8   single    1.508  0.020  1.508
 3JC  C7   C9   single    1.523  0.020  1.523
 3JC  C3   C9   single    1.498  0.020  1.498
 3JC  C3   N2   aromatic  1.318  0.020  1.318
 3JC  C4   N2   aromatic  1.337  0.020  1.337
 3JC  C4   N3   single    1.333  0.020  1.333
 3JC  C8   C14  aromatic  1.392  0.020  1.392
 3JC  C8   C10  aromatic  1.395  0.020  1.395
 3JC  C14  C13  aromatic  1.390  0.020  1.390
 3JC  C10  C11  aromatic  1.387  0.020  1.387
 3JC  C13  C12  aromatic  1.387  0.020  1.387
 3JC  C11  C12  aromatic  1.390  0.020  1.390
 3JC  C11  H1   single    0.930  0.020  1.080
 3JC  C12  H2   single    0.930  0.020  1.080
 3JC  C13  H3   single    0.930  0.020  1.080
 3JC  C14  H4   single    0.930  0.020  1.080
 3JC  C15  H5   single    0.970  0.020  1.090
 3JC  C15  H6   single    0.970  0.020  1.090
 3JC  C15  H7   single    0.970  0.020  1.090
 3JC  N3   H8   single    0.860  0.020  1.020
 3JC  N3   H9   single    0.860  0.020  1.020
 3JC  C6   H10  single    0.970  0.020  1.090
 3JC  C6   H11  single    0.970  0.020  1.090
 3JC  C7   H12  single    0.970  0.020  1.090
 3JC  C9   H13  single    0.970  0.020  1.090
 3JC  C9   H14  single    0.970  0.020  1.090
 3JC  C10  H15  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
 3JC  N1   C1   C15  114.96  3.000
 3JC  N1   C1   C2   121.11  3.000
 3JC  C15  C1   C2   123.93  3.000
 3JC  C5   C2   C3   120.49  3.000
 3JC  C3   C2   C1   115.80  3.000
 3JC  C5   C2   C1   123.71  3.000
 3JC  C9   C3   N2   115.79  3.000
 3JC  N2   C3   C2   122.70  3.000
 3JC  C9   C3   C2   121.51  3.000
 3JC  H1   C11  C10  119.70  3.000
 3JC  H1   C11  C12  120.07  3.000
 3JC  C10  C11  C12  120.23  3.000
 3JC  H2   C12  C13  120.29  3.000
 3JC  H2   C12  C11  120.23  3.000
 3JC  C13  C12  C11  119.48  3.000
 3JC  H3   C13  C14  119.83  3.000
 3JC  H3   C13  C12  120.09  3.000
 3JC  C14  C13  C12  120.08  3.000
 3JC  H4   C14  C8   119.48  3.000
 3JC  H4   C14  C13  119.54  3.000
 3JC  C8   C14  C13  120.98  3.000
 3JC  H7   C15  H6   109.02  3.000
 3JC  H7   C15  H5   106.72  3.000
 3JC  H6   C15  H5   108.94  3.000
 3JC  H7   C15  C1   111.68  3.000
 3JC  H6   C15  C1   109.07  3.000
 3JC  H5   C15  C1   111.32  3.000
 3JC  C4   N1   C1   118.03  3.000
 3JC  C4   N2   C3   116.77  3.000
 3JC  N3   C4   N2   117.45  3.000
 3JC  N3   C4   N1   116.98  3.000
 3JC  N2   C4   N1   125.57  3.000
 3JC  C6   C5   O1   119.66  3.000
 3JC  C6   C5   C2   117.27  3.000
 3JC  O1   C5   C2   123.05  3.000
 3JC  H11  C6   H10  106.87  3.000
 3JC  H11  C6   C7   109.59  3.000
 3JC  H10  C6   C7   111.43  3.000
 3JC  H11  C6   C5   107.15  3.000
 3JC  H10  C6   C5   108.44  3.000
 3JC  C7   C6   C5   113.09  3.000
 3JC  H12  C7   C9   108.06  3.000
 3JC  H12  C7   C8   107.62  3.000
 3JC  C9   C7   C8   112.45  3.000
 3JC  H12  C7   C6   108.00  3.000
 3JC  C9   C7   C6   108.57  3.000
 3JC  C8   C7   C6   111.97  3.000
 3JC  C10  C8   C7   121.33  3.000
 3JC  C10  C8   C14  118.41  3.000
 3JC  C7   C8   C14  120.26  3.000
 3JC  H14  C9   H13  106.50  3.000
 3JC  H14  C9   C7   111.39  3.000
 3JC  H13  C9   C7   109.96  3.000
 3JC  H14  C9   C3   108.92  3.000
 3JC  H13  C9   C3   107.68  3.000
 3JC  C7   C9   C3   112.16  3.000
 3JC  H15  C10  C8   120.22  3.000
 3JC  H15  C10  C11  118.96  3.000
 3JC  C8   C10  C11  120.82  3.000
 3JC  H9   N3   H8   118.88  3.000
 3JC  H9   N3   C4   120.62  3.000
 3JC  H8   N3   C4   120.49  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
 3JC  CONST_01  N2   C3   C2   C1     0.00   0.0  0
 3JC  CONST_02  N2   C4   N1   C1     0.00   0.0  0
 3JC  CONST_03  C4   N1   C1   C2     0.00   0.0  0
 3JC  CONST_04  C4   N2   C3   C2     0.00   0.0  0
 3JC  CONST_05  N1   C1   C2   C3     0.00   0.0  0
 3JC  CONST_06  N1   C4   N2   C3     0.00   0.0  0
 3JC  CONST_07  C14  C8   C10  C11    0.00   0.0  0
 3JC  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 3JC  CONST_09  C8   C14  C13  C12    0.00   0.0  0
 3JC  CONST_10  C8   C10  C11  C12    0.00   0.0  0
 3JC  CONST_11  C10  C8   C14  C13    0.00   0.0  0
 3JC  CONST_12  C10  C11  C12  C13    0.00   0.0  0
 3JC  CONST_13  C7   C8   C10  C11  180.00   0.0  0
 3JC  CONST_14  C7   C8   C14  C13  180.00   0.0  0
 3JC  CONST_15  N3   C4   N1   C1   180.00   0.0  0
 3JC  CONST_16  C15  C1   C2   C3   180.00   0.0  0
 3JC  CONST_17  N3   C4   N2   C3   180.00   0.0  0
 3JC  CONST_18  C5   C2   C1   C15    0.00   0.0  0
 3JC  CONST_19  C4   N1   C1   C15  180.00   0.0  0
 3JC  CONST_20  H3   C13  C12  C11  180.00   0.0  0
 3JC  CONST_21  H4   C14  C13  C12  180.00   0.0  0
 3JC  CONST_22  H15  C10  C11  C12  180.00   0.0  0
 3JC  CONST_23  H1   C11  C12  C13  180.00   0.0  0
 3JC  CONST_24  H2   C12  C13  C14  180.00   0.0  0
 3JC  CONST_25  H8   N3   C4   N1     0.00   0.0  0
 3JC  CONST_26  H9   N3   C4   N1   180.00   0.0  0
 3JC  Var_01    C6   C5   C2   C1   177.68  30.0  1
 3JC  Var_02    C7   C6   C5   C2    31.44  30.0  1
 3JC  Var_03    C7   C9   C3   C2   -26.74  30.0  1
 3JC  Var_04    H5   C15  C1   C2    59.84  30.0  2

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
 3JC  chir_01  C7  C6  C8  C9  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
 3JC  plan-1  C11  0.020
 3JC  plan-1  C12  0.020
 3JC  plan-1  C13  0.020
 3JC  plan-1  C14  0.020
 3JC  plan-1  C7   0.020
 3JC  plan-1  C8   0.020
 3JC  plan-1  C10  0.020
 3JC  plan-1  H1   0.020
 3JC  plan-1  H2   0.020
 3JC  plan-1  H3   0.020
 3JC  plan-1  H4   0.020
 3JC  plan-1  H15  0.020
 3JC  plan-2  C4   0.020
 3JC  plan-2  H8   0.020
 3JC  plan-2  H9   0.020
 3JC  plan-2  N3   0.020
 3JC  plan-3  C1   0.020
 3JC  plan-3  C2   0.020
 3JC  plan-3  C3   0.020
 3JC  plan-3  C15  0.020
 3JC  plan-3  N1   0.020
 3JC  plan-3  N2   0.020
 3JC  plan-3  C4   0.020
 3JC  plan-3  C5   0.020
 3JC  plan-3  C9   0.020
 3JC  plan-3  N3   0.020
 3JC  plan-4  C2   0.020
 3JC  plan-4  C5   0.020
 3JC  plan-4  C6   0.020
 3JC  plan-4  O1   0.020

