# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:49:39 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: [(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]acetonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=NC(=C1)c2ccccc2)SCC#N
#
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
 H0X  H0X  '[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]acetonitrile'  ligand  26  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H0X
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
 H0X  C01   C  CH2   0  -0.636  -2.5247  -1.4772  -0.0796
 H0X  C02   C  CSP   0   0.141  -3.7883  -2.1730  -0.2294
 H0X  N03   N  NS    0  -0.235  -4.7885  -2.7263  -0.3488
 H0X  S04   S  S2    0   0.131  -2.8755   0.3065  -0.0406
 H0X  C05   C  CR6   0   0.374  -1.2278   0.9030   0.0151
 H0X  N06   N  NR16  0  -0.692  -1.1057   2.2438   0.0610
 H0X  C07   C  CR6   0   0.566   0.1330   2.8816   0.1275
 H0X  C08   C  CR16  0  -0.503   1.2376   1.9652   0.1280
 H0X  C09   C  CR6   0   0.316   1.0262   0.6209   0.0542
 H0X  C10   C  CR6   0   0.060   2.1252  -0.3638   0.0316
 H0X  C11   C  CR16  0  -0.279   1.8633  -1.7055   0.3143
 H0X  C12   C  CR16  0  -0.238   2.8874  -2.6403   0.3095
 H0X  C13   C  CR16  0  -0.255   4.1865  -2.2527   0.0115
 H0X  C14   C  CR16  0  -0.237   4.4555  -0.9217  -0.2829
 H0X  C15   C  CR16  0  -0.317   3.4345   0.0145  -0.2734
 H0X  N16   N  N     0  -0.471  -0.2322   0.0900   0.0084
 H0X  O17   O  O     0  -0.472   0.1949   4.0977   0.1797
 H0X  H01   H  HCH2  0   0.358  -2.0426  -1.7905   0.8455
 H0X  H01A  H  HCH2  0   0.359  -1.8724  -1.7153  -0.9192
 H0X  HN06  H  HNR6  0   0.436  -1.9267   2.8384   0.0587
 H0X  H08   H  HCR6  0   0.281   2.2290   2.3870   0.1999
 H0X  H11   H  HCR6  0   0.264   0.8546  -2.0164   0.5470
 H0X  H12   H  HCR6  0   0.262   2.6674  -3.6750   0.5372
 H0X  H13   H  HCR6  0   0.264   4.9846  -2.9831   0.0044
 H0X  H14   H  HCR6  0   0.264   5.4627  -0.6116  -0.5273
 H0X  H15   H  HCR6  0   0.259   3.6673   1.0411  -0.5238

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
 H0X  C01  C02   single    1.450  0.020  1.450
 H0X  C01  S04   single    1.818  0.020  1.818
 H0X  C02  N03   triple    1.149  0.020  1.149
 H0X  S04  C05   single    1.753  0.020  1.753
 H0X  C05  N06   single    1.347  0.020  1.347
 H0X  C05  N16   double    1.285  0.020  1.285
 H0X  N06  C07   single    1.395  0.020  1.395
 H0X  C07  C08   single    1.435  0.020  1.435
 H0X  C07  O17   double    1.219  0.020  1.219
 H0X  C08  C09   double    1.363  0.020  1.363
 H0X  C09  C10   single    1.476  0.020  1.476
 H0X  C09  N16   single    1.367  0.020  1.367
 H0X  C10  C11   aromatic  1.396  0.020  1.396
 H0X  C10  C15   aromatic  1.397  0.020  1.397
 H0X  C11  C12   aromatic  1.387  0.020  1.387
 H0X  C12  C13   aromatic  1.388  0.020  1.388
 H0X  C13  C14   aromatic  1.389  0.020  1.389
 H0X  C14  C15   aromatic  1.385  0.020  1.385
 H0X  C01  H01   single    0.970  0.020  1.090
 H0X  C01  H01A  single    0.970  0.020  1.090
 H0X  N06  HN06  single    0.860  0.020  1.020
 H0X  C08  H08   single    0.930  0.020  1.080
 H0X  C11  H11   single    0.930  0.020  1.080
 H0X  C12  H12   single    0.930  0.020  1.080
 H0X  C13  H13   single    0.930  0.020  1.080
 H0X  C14  H14   single    0.930  0.020  1.080
 H0X  C15  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
 H0X  H01A  C01  H01  109.07  3.000
 H0X  H01A  C01  S04  110.27  3.000
 H0X  H01   C01  S04  110.44  3.000
 H0X  H01A  C01  C02  109.71  3.000
 H0X  H01   C01  C02  109.59  3.000
 H0X  S04   C01  C02  107.75  3.000
 H0X  N03   C02  C01  180.00  3.000
 H0X  C05   S04  C01   98.81  3.000
 H0X  N16   C05  N06  124.02  3.000
 H0X  N16   C05  S04  120.83  3.000
 H0X  N06   C05  S04  115.14  3.000
 H0X  HN06  N06  C07  116.81  3.000
 H0X  HN06  N06  C05  120.69  3.000
 H0X  C07   N06  C05  122.50  3.000
 H0X  O17   C07  C08  126.72  3.000
 H0X  O17   C07  N06  120.23  3.000
 H0X  C08   C07  N06  113.05  3.000
 H0X  H08   C08  C09  122.10  3.000
 H0X  H08   C08  C07  117.21  3.000
 H0X  C09   C08  C07  120.69  3.000
 H0X  N16   C09  C10  115.21  3.000
 H0X  N16   C09  C08  121.87  3.000
 H0X  C10   C09  C08  122.92  3.000
 H0X  C15   C10  C11  118.71  3.000
 H0X  C15   C10  C09  121.39  3.000
 H0X  C11   C10  C09  119.90  3.000
 H0X  H11   C11  C12  119.74  3.000
 H0X  H11   C11  C10  119.68  3.000
 H0X  C12   C11  C10  120.58  3.000
 H0X  H12   C12  C13  120.16  3.000
 H0X  H12   C12  C11  119.59  3.000
 H0X  C13   C12  C11  120.24  3.000
 H0X  H13   C13  C14  120.17  3.000
 H0X  H13   C13  C12  120.22  3.000
 H0X  C14   C13  C12  119.62  3.000
 H0X  H14   C14  C15  119.60  3.000
 H0X  H14   C14  C13  120.18  3.000
 H0X  C15   C14  C13  120.22  3.000
 H0X  H15   C15  C14  118.76  3.000
 H0X  H15   C15  C10  120.61  3.000
 H0X  C14   C15  C10  120.63  3.000
 H0X  C09   N16  C05  117.86  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
 H0X  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 H0X  CONST_02  C13   C14  C15  C10     0.00   0.0  0
 H0X  CONST_03  C14   C15  C10  C11     0.00   0.0  0
 H0X  CONST_04  C14   C13  C12  C11     0.00   0.0  0
 H0X  CONST_05  C15   C10  C11  C12     0.00   0.0  0
 H0X  CONST_06  C15   C14  C13  C12     0.00   0.0  0
 H0X  CONST_07  C12   C11  C10  C09   180.00   0.0  0
 H0X  CONST_08  C14   C15  C10  C09   180.00   0.0  0
 H0X  CONST_09  C08   C07  N06  C05     0.00   0.0  0
 H0X  CONST_10  C09   N16  C05  N06     0.00   0.0  0
 H0X  CONST_11  N16   C05  N06  C07     0.00   0.0  0
 H0X  CONST_12  C07   N06  C05  S04   180.00   0.0  0
 H0X  CONST_13  C09   N16  C05  S04   180.00   0.0  0
 H0X  CONST_14  O17   C07  N06  C05   180.00   0.0  0
 H0X  CONST_15  H11   C11  C10  C09     0.00   0.0  0
 H0X  CONST_16  H15   C15  C10  C09     0.00   0.0  0
 H0X  CONST_17  H12   C12  C11  C10   180.00   0.0  0
 H0X  CONST_18  H14   C14  C15  C10   180.00   0.0  0
 H0X  CONST_19  H13   C13  C12  C11   180.00   0.0  0
 H0X  CONST_20  HN06  N06  C07  C08   180.00   0.0  0
 H0X  Var_01    C11   C10  C09  C08   162.84  30.0  2
 H0X  Var_02    N06   C05  S04  C01  -179.66  30.0  3
 H0X  Var_03    H01   C01  S04  C05    64.51  30.0  1
 H0X  Var_04    S04   C01  C02  N03   161.61  30.0  1

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
 H0X  plan-1  S04   0.020
 H0X  plan-1  C05   0.020
 H0X  plan-1  N06   0.020
 H0X  plan-1  C07   0.020
 H0X  plan-1  C08   0.020
 H0X  plan-1  C09   0.020
 H0X  plan-1  C10   0.020
 H0X  plan-1  N16   0.020
 H0X  plan-1  O17   0.020
 H0X  plan-1  HN06  0.020
 H0X  plan-1  H08   0.020
 H0X  plan-2  C09   0.020
 H0X  plan-2  C10   0.020
 H0X  plan-2  C11   0.020
 H0X  plan-2  C12   0.020
 H0X  plan-2  C13   0.020
 H0X  plan-2  C14   0.020
 H0X  plan-2  C15   0.020
 H0X  plan-2  H11   0.020
 H0X  plan-2  H12   0.020
 H0X  plan-2  H13   0.020
 H0X  plan-2  H14   0.020
 H0X  plan-2  H15   0.020

