# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:32:40 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 7,8-dimethyl-2-(pyrimidin-2-ylsulfanylmethyl)-3~{H}-quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2C(=O)NC(=Nc2c1C)CSc3ncccn3
#
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
 EBB  EBB  7,8-dimethyl-2-(pyrimidin-2-ylsulfanylmethyl)-3~{H}-quinazolin-4-one  ligand  35  21  .  2022-07-24  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_EBB
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
 EBB  C    C  CH3   0  -0.732   4.9948   2.7552  -0.0406
 EBB  C1   C  CR6   0   0.069   4.2507   1.4543  -0.0357
 EBB  C2   C  CR6   0  -0.007   2.8571   1.4408  -0.0143
 EBB  C3   C  CH3   0  -0.739   2.0901   2.7286   0.0121
 EBB  C4   C  CR66  0   0.253   2.1895   0.2009  -0.0153
 EBB  C5   C  CR66  0  -0.118   2.9246  -0.9965  -0.0335
 EBB  C6   C  CR16  0  -0.285   4.3174  -0.9646  -0.0525
 EBB  C7   C  CR16  0  -0.308   4.9653   0.2492  -0.0544
 EBB  C8   C  CR6   0   0.542   2.2192  -2.2722  -0.0326
 EBB  C9   C  CR6   0   0.517   0.2066  -0.9370  -0.0020
 EBB  C10  C  CH2   0  -0.656  -1.2873  -1.0023   0.0097
 EBB  C11  C  CR6   0   0.249  -3.6675   0.3510   0.0148
 EBB  C12  C  CR16  0  -0.019  -5.7198   1.2812   0.0168
 EBB  C13  C  CR16  0  -0.360  -6.3008   0.0215   0.0189
 EBB  C14  C  CR16  0  -0.004  -5.4295  -1.0517   0.0186
 EBB  O    O  O     0  -0.452   2.7442  -3.3709  -0.0456
 EBB  N    N  NR16  0  -0.702   0.8481  -2.1382  -0.0156
 EBB  S    S  S2    0   0.088  -1.9440   0.6828   0.0113
 EBB  N1   N  N     0  -0.477   0.8114   0.1897  -0.0000
 EBB  N3   N  N     0  -0.404  -4.1093  -0.8946   0.0166
 EBB  N2   N  N     0  -0.413  -4.4072   1.4547   0.0148
 EBB  H1   H  HCH3  0   0.250   4.7546   3.3583   0.8372
 EBB  H2   H  HCH3  0   0.255   6.0713   2.5946  -0.0495
 EBB  H3   H  HCH3  0   0.251   4.7408   3.3577  -0.9151
 EBB  H4   H  HCH3  0   0.244   2.3233   3.3458  -0.8579
 EBB  H5   H  HCH3  0   0.267   1.0178   2.5570   0.0228
 EBB  H6   H  HCH3  0   0.244   2.3448   3.3198   0.8942
 EBB  H7   H  HCR6  0   0.264   4.8815  -1.8874  -0.0665
 EBB  H8   H  HCR6  0   0.256   6.0476   0.2786  -0.0701
 EBB  H9   H  HCH2  0   0.319  -1.6452  -1.5458  -0.8668
 EBB  H10  H  HCH2  0   0.319  -1.6325  -1.5437   0.8926
 EBB  H11  H  HCR6  0   0.285  -6.3297   2.1773   0.0170
 EBB  H12  H  HCR6  0   0.287  -7.3720  -0.1121   0.0207
 EBB  H13  H  HCR6  0   0.285  -5.7955  -2.0718   0.0206
 EBB  H14  H  HNR6  0   0.431   0.3008  -2.9901  -0.0143

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
 EBB  O    C8   double    1.218  0.020  1.218
 EBB  C6   C7   aromatic  1.376  0.020  1.376
 EBB  C6   C5   aromatic  1.393  0.020  1.393
 EBB  C7   C1   aromatic  1.401  0.020  1.401
 EBB  C8   C5   single    1.458  0.020  1.458
 EBB  C8   N    single    1.378  0.020  1.378
 EBB  C5   C4   aromatic  1.405  0.020  1.405
 EBB  C1   C    single    1.499  0.020  1.499
 EBB  C1   C2   aromatic  1.394  0.020  1.394
 EBB  N    C9   single    1.362  0.020  1.362
 EBB  C4   C2   aromatic  1.408  0.020  1.408
 EBB  C4   N1   single    1.378  0.020  1.378
 EBB  C2   C3   single    1.499  0.020  1.499
 EBB  C9   N1   double    1.279  0.020  1.279
 EBB  C9   C10  single    1.495  0.020  1.495
 EBB  S    C10  single    1.808  0.020  1.808
 EBB  S    C11  single    1.755  0.020  1.755
 EBB  C11  N2   aromatic  1.329  0.020  1.329
 EBB  C11  N3   aromatic  1.322  0.020  1.322
 EBB  N2   C12  aromatic  1.324  0.020  1.324
 EBB  N3   C14  aromatic  1.329  0.020  1.329
 EBB  C12  C13  aromatic  1.387  0.020  1.387
 EBB  C14  C13  aromatic  1.382  0.020  1.382
 EBB  C    H1   single    0.970  0.020  1.090
 EBB  C    H2   single    0.970  0.020  1.090
 EBB  C    H3   single    0.970  0.020  1.090
 EBB  C3   H4   single    0.970  0.020  1.090
 EBB  C3   H5   single    0.970  0.020  1.090
 EBB  C3   H6   single    0.970  0.020  1.090
 EBB  C6   H7   single    0.930  0.020  1.080
 EBB  C7   H8   single    0.930  0.020  1.080
 EBB  C10  H9   single    0.970  0.020  1.090
 EBB  C10  H10  single    0.970  0.020  1.090
 EBB  C12  H11  single    0.930  0.020  1.080
 EBB  C13  H12  single    0.930  0.020  1.080
 EBB  C14  H13  single    0.930  0.020  1.080
 EBB  N    H14  single    0.860  0.020  1.020

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
 EBB  H3   C    H2   107.76  3.000
 EBB  H3   C    H1   106.74  3.000
 EBB  H2   C    H1   107.80  3.000
 EBB  H3   C    C1   111.47  3.000
 EBB  H2   C    C1   111.28  3.000
 EBB  H1   C    C1   111.57  3.000
 EBB  C7   C1   C2   120.12  3.000
 EBB  C2   C1   C    120.32  3.000
 EBB  C7   C1   C    119.56  3.000
 EBB  C4   C2   C3   120.92  3.000
 EBB  C3   C2   C1   120.24  3.000
 EBB  C4   C2   C1   118.84  3.000
 EBB  H6   C3   H5   107.93  3.000
 EBB  H6   C3   H4   106.72  3.000
 EBB  H5   C3   H4   107.94  3.000
 EBB  H6   C3   C2   111.10  3.000
 EBB  H5   C3   C2   111.70  3.000
 EBB  H4   C3   C2   111.24  3.000
 EBB  N1   C4   C5   121.08  3.000
 EBB  N1   C4   C2   118.76  3.000
 EBB  C5   C4   C2   120.15  3.000
 EBB  C8   C5   C6   120.25  3.000
 EBB  C8   C5   C4   119.51  3.000
 EBB  C6   C5   C4   120.24  3.000
 EBB  H7   C6   C7   120.47  3.000
 EBB  H7   C6   C5   120.13  3.000
 EBB  C7   C6   C5   119.40  3.000
 EBB  H8   C7   C6   119.65  3.000
 EBB  H8   C7   C1   119.12  3.000
 EBB  C6   C7   C1   121.24  3.000
 EBB  N    C8   O    121.12  3.000
 EBB  N    C8   C5   113.36  3.000
 EBB  O    C8   C5   125.51  3.000
 EBB  N1   C9   N    123.66  3.000
 EBB  N1   C9   C10  120.73  3.000
 EBB  N    C9   C10  115.61  3.000
 EBB  H10  C10  H9   107.38  3.000
 EBB  H10  C10  S    110.28  3.000
 EBB  H9   C10  S    110.22  3.000
 EBB  H10  C10  C9   110.11  3.000
 EBB  H9   C10  C9   110.06  3.000
 EBB  S    C10  C9   108.79  3.000
 EBB  N2   C11  N3   126.64  3.000
 EBB  N3   C11  S    120.43  3.000
 EBB  N2   C11  S    112.93  3.000
 EBB  H11  C12  N2   116.72  3.000
 EBB  H11  C12  C13  121.00  3.000
 EBB  N2   C12  C13  122.29  3.000
 EBB  H12  C13  C14  121.97  3.000
 EBB  H12  C13  C12  121.87  3.000
 EBB  C14  C13  C12  116.17  3.000
 EBB  H13  C14  N3   116.52  3.000
 EBB  H13  C14  C13  121.19  3.000
 EBB  N3   C14  C13  122.29  3.000
 EBB  H14  N    C9   119.17  3.000
 EBB  H14  N    C8   117.14  3.000
 EBB  C9   N    C8   123.69  3.000
 EBB  C11  S    C10  100.39  3.000
 EBB  C9   N1   C4   118.70  3.000
 EBB  C14  N3   C11  116.32  3.000
 EBB  C12  N2   C11  116.30  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
 EBB  CONST_01  C5   C6   C7   C1      0.00   0.0  0
 EBB  CONST_02  C5   C4   C2   C1      0.00   0.0  0
 EBB  CONST_03  C6   C7   C1   C2      0.00   0.0  0
 EBB  CONST_04  C6   C5   C4   C2      0.00   0.0  0
 EBB  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 EBB  CONST_06  C7   C1   C2   C4      0.00   0.0  0
 EBB  CONST_07  C13  C12  N2   C11     0.00   0.0  0
 EBB  CONST_08  C13  C14  N3   C11     0.00   0.0  0
 EBB  CONST_09  N3   C11  N2   C12     0.00   0.0  0
 EBB  CONST_10  N3   C14  C13  C12     0.00   0.0  0
 EBB  CONST_11  N2   C11  N3   C14     0.00   0.0  0
 EBB  CONST_12  N2   C12  C13  C14     0.00   0.0  0
 EBB  CONST_13  N    C9   N1   C4      0.00   0.0  0
 EBB  CONST_14  C9   N    C8   C5      0.00   0.0  0
 EBB  CONST_15  N1   C9   N    C8      0.00   0.0  0
 EBB  CONST_16  C6   C7   C1   C     180.00   0.0  0
 EBB  CONST_17  C4   C2   C1   C     180.00   0.0  0
 EBB  CONST_18  C7   C1   C2   C3    180.00   0.0  0
 EBB  CONST_19  C5   C4   C2   C3    180.00   0.0  0
 EBB  CONST_20  N1   C4   C2   C3      0.00   0.0  0
 EBB  CONST_21  S    C11  N2   C12   180.00   0.0  0
 EBB  CONST_22  S    C11  N3   C14   180.00   0.0  0
 EBB  CONST_23  C10  C9   N1   C4    180.00   0.0  0
 EBB  CONST_24  C10  C9   N    C8    180.00   0.0  0
 EBB  CONST_25  O    C8   N    C9    180.00   0.0  0
 EBB  CONST_26  H7   C6   C7   C1    180.00   0.0  0
 EBB  CONST_27  H8   C7   C1   C2    180.00   0.0  0
 EBB  CONST_28  H11  C12  N2   C11   180.00   0.0  0
 EBB  CONST_29  H13  C14  N3   C11   180.00   0.0  0
 EBB  CONST_30  H12  C13  C14  N3    180.00   0.0  0
 EBB  CONST_31  H14  N    C8   C5    180.00   0.0  0
 EBB  Var_01    N2   C11  S    C10  -179.92  30.0  2
 EBB  Var_02    S    C10  C9   N    -179.48  30.0  3
 EBB  Var_03    H4   C3   C2   C1     59.09  30.0  2
 EBB  Var_04    H1   C    C1   C2     59.07  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
 EBB  plan-1  C11  0.020
 EBB  plan-1  C12  0.020
 EBB  plan-1  C13  0.020
 EBB  plan-1  C14  0.020
 EBB  plan-1  S    0.020
 EBB  plan-1  N3   0.020
 EBB  plan-1  N2   0.020
 EBB  plan-1  H11  0.020
 EBB  plan-1  H12  0.020
 EBB  plan-1  H13  0.020
 EBB  plan-2  C    0.020
 EBB  plan-2  C1   0.020
 EBB  plan-2  C2   0.020
 EBB  plan-2  C3   0.020
 EBB  plan-2  C4   0.020
 EBB  plan-2  C5   0.020
 EBB  plan-2  C6   0.020
 EBB  plan-2  C7   0.020
 EBB  plan-2  C8   0.020
 EBB  plan-2  C9   0.020
 EBB  plan-2  C10  0.020
 EBB  plan-2  O    0.020
 EBB  plan-2  N    0.020
 EBB  plan-2  N1   0.020
 EBB  plan-2  H7   0.020
 EBB  plan-2  H8   0.020
 EBB  plan-2  H14  0.020

