# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 00:00:21 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 8-methyl-2-[(pyrimidin-2-ylsulfanyl)methyl]quinazolin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2C(=O)N=C(CSc3ncccn3)Nc12
#
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
 0RU  0RU  8-methyl-2-[(pyrimidin-2-ylsulfanyl)methyl]quinazolin-4(1H)-one  ligand  32  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0RU
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
 0RU  NAJ  N  N     0  -0.404  -3.6607  -1.1914  -0.0506
 0RU  CAE  C  CR16  0  -0.004  -4.8750  -1.7331  -0.0545
 0RU  CAC  C  CR16  0  -0.359  -6.0251  -0.9672  -0.0218
 0RU  CAF  C  CR16  0  -0.020  -5.8438   0.4077   0.0162
 0RU  NAK  N  N     0  -0.412  -4.6418   0.9627   0.0209
 0RU  CAQ  C  CR6   0   0.249  -3.6084   0.1284  -0.0131
 0RU  SAN  S  S2    0   0.090  -2.0602   0.9556  -0.0055
 0RU  CAI  C  CH2   0  -0.662  -0.9368  -0.4589  -0.0554
 0RU  CAP  C  CR6   0   0.517   0.4763   0.0346  -0.0316
 0RU  NAL  N  NR16  0  -0.722   1.4209  -0.9166  -0.0060
 0RU  CAT  C  CR66  0   0.391   2.7599  -0.5935   0.0118
 0RU  CAO  C  CR6   0   0.051   3.7396  -1.5992   0.0383
 0RU  CAA  C  CH3   0  -0.761   3.3562  -3.0481   0.0491
 0RU  CAG  C  CR16  0  -0.302   5.0596  -1.1902   0.0543
 0RU  CAD  C  CR16  0  -0.242   5.4171   0.1612   0.0455
 0RU  CAH  C  CR16  0  -0.306   4.4412   1.1313   0.0209
 0RU  CAS  C  CR66  0  -0.147   3.0938   0.7609   0.0036
 0RU  CAR  C  CR6   0   0.459   2.0192   1.7637  -0.0213
 0RU  OAB  O  O     0  -0.451   2.2480   2.9621  -0.0257
 0RU  NAM  N  N     0  -0.501   0.7198   1.3041  -0.0395
 0RU  H1   H  HCR6  0   0.286  -4.9226  -2.8152  -0.0847
 0RU  H2   H  HCR6  0   0.287  -7.0085  -1.4127  -0.0258
 0RU  H3   H  HCR6  0   0.286  -6.6911   1.0828   0.0440
 0RU  H4   H  HCH2  0   0.323  -1.1145  -1.1175   0.7965
 0RU  H5   H  HCH2  0   0.325  -1.1057  -1.0478  -0.9591
 0RU  H6   H  HNR6  0   0.446   1.1434  -1.8883  -0.0002
 0RU  H7   H  HCH3  0   0.259   2.7872  -3.3247  -0.8417
 0RU  H8   H  HCH3  0   0.271   4.2413  -3.6799   0.0783
 0RU  H9   H  HCH3  0   0.258   2.7461  -3.3005   0.9195
 0RU  H10  H  HCR6  0   0.266   5.8378  -1.9430   0.0743
 0RU  H11  H  HCR6  0   0.265   6.4627   0.4372   0.0588
 0RU  H12  H  HCR6  0   0.266   4.7037   2.1805   0.0146

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
 0RU  CAF  CAC  aromatic  1.387  0.020  1.387
 0RU  CAF  NAK  aromatic  1.324  0.020  1.324
 0RU  CAC  CAE  aromatic  1.382  0.020  1.382
 0RU  NAK  CAQ  aromatic  1.329  0.020  1.329
 0RU  CAE  NAJ  aromatic  1.330  0.020  1.330
 0RU  CAQ  NAJ  aromatic  1.321  0.020  1.321
 0RU  CAQ  SAN  single    1.755  0.020  1.755
 0RU  SAN  CAI  single    1.807  0.020  1.807
 0RU  CAI  CAP  single    1.497  0.020  1.497
 0RU  CAP  NAL  single    1.341  0.020  1.341
 0RU  CAP  NAM  double    1.293  0.020  1.293
 0RU  NAL  CAT  single    1.378  0.020  1.378
 0RU  NAM  CAR  single    1.378  0.020  1.378
 0RU  CAA  CAO  single    1.499  0.020  1.499
 0RU  CAT  CAO  aromatic  1.404  0.020  1.404
 0RU  CAT  CAS  aromatic  1.395  0.020  1.395
 0RU  CAR  CAS  single    1.470  0.020  1.470
 0RU  CAR  OAB  double    1.220  0.020  1.220
 0RU  CAO  CAG  aromatic  1.382  0.020  1.382
 0RU  CAS  CAH  aromatic  1.397  0.020  1.397
 0RU  CAG  CAD  aromatic  1.398  0.020  1.398
 0RU  CAH  CAD  aromatic  1.376  0.020  1.376
 0RU  CAE  H1   single    0.930  0.020  1.080
 0RU  CAC  H2   single    0.930  0.020  1.080
 0RU  CAF  H3   single    0.930  0.020  1.080
 0RU  CAI  H4   single    0.970  0.020  1.090
 0RU  CAI  H5   single    0.970  0.020  1.090
 0RU  NAL  H6   single    0.860  0.020  1.020
 0RU  CAA  H7   single    0.970  0.020  1.090
 0RU  CAA  H8   single    0.970  0.020  1.090
 0RU  CAA  H9   single    0.970  0.020  1.090
 0RU  CAG  H10  single    0.930  0.020  1.080
 0RU  CAD  H11  single    0.930  0.020  1.080
 0RU  CAH  H12  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
 0RU  CAQ  NAJ  CAE  116.30  3.000
 0RU  H1   CAE  CAC  121.16  3.000
 0RU  H1   CAE  NAJ  116.55  3.000
 0RU  CAC  CAE  NAJ  122.29  3.000
 0RU  H2   CAC  CAF  121.88  3.000
 0RU  H2   CAC  CAE  121.95  3.000
 0RU  CAF  CAC  CAE  116.17  3.000
 0RU  H3   CAF  NAK  116.66  3.000
 0RU  H3   CAF  CAC  121.05  3.000
 0RU  NAK  CAF  CAC  122.29  3.000
 0RU  CAQ  NAK  CAF  116.28  3.000
 0RU  SAN  CAQ  NAK  112.95  3.000
 0RU  SAN  CAQ  NAJ  120.38  3.000
 0RU  NAK  CAQ  NAJ  126.67  3.000
 0RU  CAI  SAN  CAQ  100.33  3.000
 0RU  H5   CAI  H4   107.18  3.000
 0RU  H5   CAI  CAP  109.70  3.000
 0RU  H4   CAI  CAP  109.89  3.000
 0RU  H5   CAI  SAN  110.42  3.000
 0RU  H4   CAI  SAN  110.46  3.000
 0RU  CAP  CAI  SAN  109.17  3.000
 0RU  NAM  CAP  NAL  124.35  3.000
 0RU  NAM  CAP  CAI  120.09  3.000
 0RU  NAL  CAP  CAI  115.56  3.000
 0RU  H6   NAL  CAT  119.50  3.000
 0RU  H6   NAL  CAP  119.26  3.000
 0RU  CAT  NAL  CAP  121.24  3.000
 0RU  CAS  CAT  CAO  121.90  3.000
 0RU  CAS  CAT  NAL  117.41  3.000
 0RU  CAO  CAT  NAL  120.69  3.000
 0RU  CAG  CAO  CAA  122.02  3.000
 0RU  CAG  CAO  CAT  117.05  3.000
 0RU  CAA  CAO  CAT  120.93  3.000
 0RU  H9   CAA  H8   107.39  3.000
 0RU  H9   CAA  H7   107.47  3.000
 0RU  H8   CAA  H7   107.37  3.000
 0RU  H9   CAA  CAO  111.83  3.000
 0RU  H8   CAA  CAO  110.70  3.000
 0RU  H7   CAA  CAO  111.85  3.000
 0RU  H10  CAG  CAD  119.24  3.000
 0RU  H10  CAG  CAO  118.75  3.000
 0RU  CAD  CAG  CAO  122.02  3.000
 0RU  H11  CAD  CAH  120.39  3.000
 0RU  H11  CAD  CAG  119.59  3.000
 0RU  CAH  CAD  CAG  120.02  3.000
 0RU  H12  CAH  CAS  119.41  3.000
 0RU  H12  CAH  CAD  120.78  3.000
 0RU  CAS  CAH  CAD  119.81  3.000
 0RU  CAR  CAS  CAH  121.62  3.000
 0RU  CAH  CAS  CAT  119.21  3.000
 0RU  CAR  CAS  CAT  119.17  3.000
 0RU  NAM  CAR  OAB  120.28  3.000
 0RU  OAB  CAR  CAS  122.21  3.000
 0RU  NAM  CAR  CAS  117.51  3.000
 0RU  CAR  NAM  CAP  120.32  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
 0RU  CONST_01  CAF  CAC  CAE  NAJ     0.00   0.0  0
 0RU  CONST_02  CAF  NAK  CAQ  NAJ     0.00   0.0  0
 0RU  CONST_03  NAK  CAF  CAC  CAE     0.00   0.0  0
 0RU  CONST_04  NAK  CAQ  NAJ  CAE     0.00   0.0  0
 0RU  CONST_05  CAQ  NAK  CAF  CAC     0.00   0.0  0
 0RU  CONST_06  CAQ  NAJ  CAE  CAC     0.00   0.0  0
 0RU  CONST_07  CAD  CAG  CAO  CAT     0.00   0.0  0
 0RU  CONST_08  CAD  CAH  CAS  CAT     0.00   0.0  0
 0RU  CONST_09  CAH  CAS  CAT  CAO     0.00   0.0  0
 0RU  CONST_10  CAH  CAD  CAG  CAO     0.00   0.0  0
 0RU  CONST_11  CAS  CAT  CAO  CAG     0.00   0.0  0
 0RU  CONST_12  CAS  CAH  CAD  CAG     0.00   0.0  0
 0RU  CONST_13  CAR  NAM  CAP  NAL     0.00   0.0  0
 0RU  CONST_14  NAM  CAP  NAL  CAT     0.00   0.0  0
 0RU  CONST_15  SAN  CAQ  NAJ  CAE   180.00   0.0  0
 0RU  CONST_16  SAN  CAQ  NAK  CAF   180.00   0.0  0
 0RU  CONST_17  CAA  CAO  CAT  NAL     0.00   0.0  0
 0RU  CONST_18  CAS  CAT  CAO  CAA   180.00   0.0  0
 0RU  CONST_19  CAD  CAG  CAO  CAA   180.00   0.0  0
 0RU  CONST_20  CAT  NAL  CAP  CAI   180.00   0.0  0
 0RU  CONST_21  CAR  NAM  CAP  CAI   180.00   0.0  0
 0RU  CONST_22  H2   CAC  CAE  NAJ   180.00   0.0  0
 0RU  CONST_23  H3   CAF  CAC  CAE   180.00   0.0  0
 0RU  CONST_24  H1   CAE  CAC  CAF   180.00   0.0  0
 0RU  CONST_25  H10  CAG  CAO  CAT   180.00   0.0  0
 0RU  CONST_26  H12  CAH  CAS  CAT   180.00   0.0  0
 0RU  CONST_27  H11  CAD  CAG  CAO   180.00   0.0  0
 0RU  CONST_28  H6   NAL  CAP  NAM   180.00   0.0  0
 0RU  Var_01    CAP  CAI  SAN  CAQ  -179.03  30.0  3
 0RU  Var_02    NAL  CAP  CAI  SAN   177.23  30.0  3
 0RU  Var_03    H7   CAA  CAO  CAT    60.77  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
 0RU  plan-1  NAJ  0.020
 0RU  plan-1  CAE  0.020
 0RU  plan-1  CAC  0.020
 0RU  plan-1  CAF  0.020
 0RU  plan-1  NAK  0.020
 0RU  plan-1  CAQ  0.020
 0RU  plan-1  SAN  0.020
 0RU  plan-1  H1   0.020
 0RU  plan-1  H2   0.020
 0RU  plan-1  H3   0.020
 0RU  plan-2  CAI  0.020
 0RU  plan-2  CAP  0.020
 0RU  plan-2  NAL  0.020
 0RU  plan-2  CAT  0.020
 0RU  plan-2  CAO  0.020
 0RU  plan-2  CAA  0.020
 0RU  plan-2  CAG  0.020
 0RU  plan-2  CAD  0.020
 0RU  plan-2  CAH  0.020
 0RU  plan-2  CAS  0.020
 0RU  plan-2  CAR  0.020
 0RU  plan-2  OAB  0.020
 0RU  plan-2  NAM  0.020
 0RU  plan-2  H6   0.020
 0RU  plan-2  H10  0.020
 0RU  plan-2  H11  0.020
 0RU  plan-2  H12  0.020

