# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:37:05 2021
#   Inital geometry file: a 63 line input string
#   Ligand name: 5-fluoranyl-1-[(2~{R})-oxolan-2-yl]pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC1=CN([C@H]2CCCO2)C(=O)NC1=O
#
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
 S7W  S7W  5-fluoranyl-1-[(2~{R})-oxolan-2-yl]pyrimidine-2,4-dione  ligand  23  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S7W
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
 S7W  C01   C  CH2   0  -0.494  15.4219  -20.0369   0.2036
 S7W  C02   C  CH2   0  -0.514  16.2605  -19.9090   1.4674
 S7W  C03   C  CR15  0   0.197  17.6755  -19.8252   0.8991
 S7W  C05   C  CH2   0  -0.176  16.1919  -19.1463  -0.7583
 S7W  C07   C  CR16  0  -0.069  18.3276  -17.6328   1.7398
 S7W  C08   C  CR6   0   0.283  19.1190  -16.7963   2.4151
 S7W  C09   C  CR6   0   0.472  20.2886  -17.2698   3.1212
 S7W  C12   C  CR6   0   0.742  19.6603  -19.5353   2.3224
 S7W  F14   F  F     0  -0.293  18.8733  -15.4853   2.4640
 S7W  N06   N  NR6   0  -0.554  18.5745  -18.9788   1.6868
 S7W  N11   N  NR16  0  -0.739  20.4482  -18.6348   3.0016
 S7W  O04   O  O     0  -0.494  17.5661  -19.2922  -0.3943
 S7W  O10   O  O     0  -0.445  21.0575  -16.5774   3.7535
 S7W  O13   O  O     0  -0.475  19.9190  -20.7200   2.3042
 S7W  H012  H  HCH2  0   0.262  14.3917  -19.7116   0.3397
 S7W  H011  H  HCH2  0   0.250  15.4077  -21.0689  -0.1512
 S7W  H022  H  HCH2  0   0.261  15.9989  -18.9981   2.0116
 S7W  H021  H  HCH2  0   0.274  16.1574  -20.7456   2.1563
 S7W  H031  H  HCR5  0   0.275  18.1434  -20.8085   0.8595
 S7W  H052  H  HCH2  0   0.219  15.8862  -18.0987  -0.6592
 S7W  H051  H  HCH2  0   0.244  16.0771  -19.4345  -1.8035
 S7W  H071  H  HCR6  0   0.337  17.4598  -17.2685   1.2077
 S7W  H111  H  HNR6  0   0.435  21.2511  -19.0364   3.4714

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
 S7W  C05  O04   single  1.429  0.020  1.429
 S7W  C05  C01   single  1.520  0.020  1.520
 S7W  O04  C03   single  1.403  0.020  1.403
 S7W  C01  C02   single  1.522  0.020  1.522
 S7W  C03  C02   single  1.527  0.020  1.527
 S7W  C03  N06   single  1.465  0.020  1.465
 S7W  C07  N06   single  1.369  0.020  1.369
 S7W  C07  C08   double  1.335  0.020  1.335
 S7W  N06  C12   single  1.376  0.020  1.376
 S7W  F14  C08   single  1.335  0.020  1.335
 S7W  C08  C09   single  1.446  0.020  1.446
 S7W  C12  O13   double  1.213  0.020  1.213
 S7W  C12  N11   single  1.376  0.020  1.376
 S7W  C09  N11   single  1.380  0.020  1.380
 S7W  C09  O10   double  1.213  0.020  1.213
 S7W  C01  H012  single  0.970  0.020  1.090
 S7W  C01  H011  single  0.970  0.020  1.090
 S7W  C02  H022  single  0.970  0.020  1.090
 S7W  C02  H021  single  0.970  0.020  1.090
 S7W  C03  H031  single  0.970  0.020  1.090
 S7W  C05  H052  single  0.970  0.020  1.090
 S7W  C05  H051  single  0.970  0.020  1.090
 S7W  C07  H071  single  0.930  0.020  1.080
 S7W  N11  H111  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
 S7W  H011  C01  H012  108.10  3.000
 S7W  H011  C01  C05   110.79  3.000
 S7W  H012  C01  C05   112.54  3.000
 S7W  H011  C01  C02   110.89  3.000
 S7W  H012  C01  C02   113.10  3.000
 S7W  C05   C01  C02   101.37  3.000
 S7W  H021  C02  H022  107.62  3.000
 S7W  H021  C02  C03   111.43  3.000
 S7W  H022  C02  C03   111.19  3.000
 S7W  H021  C02  C01   114.12  3.000
 S7W  H022  C02  C01   110.58  3.000
 S7W  C03   C02  C01   101.89  3.000
 S7W  H031  C03  O04   110.05  3.000
 S7W  H031  C03  N06   106.11  3.000
 S7W  O04   C03  N06   108.91  3.000
 S7W  H031  C03  C02   111.21  3.000
 S7W  N06   C03  C02   113.59  3.000
 S7W  O04   C03  C02   106.96  3.000
 S7W  H051  C05  H052  108.07  3.000
 S7W  H051  C05  O04   108.57  3.000
 S7W  H052  C05  O04   110.05  3.000
 S7W  H051  C05  C01   113.47  3.000
 S7W  H052  C05  C01   111.19  3.000
 S7W  O04   C05  C01   105.43  3.000
 S7W  H071  C07  N06   117.18  3.000
 S7W  H071  C07  C08   120.91  3.000
 S7W  N06   C07  C08   121.91  3.000
 S7W  F14   C08  C09   116.91  3.000
 S7W  C09   C08  C07   121.43  3.000
 S7W  F14   C08  C07   121.66  3.000
 S7W  O10   C09  N11   122.47  3.000
 S7W  O10   C09  C08   125.49  3.000
 S7W  N11   C09  C08   112.04  3.000
 S7W  O13   C12  N11   121.64  3.000
 S7W  N11   C12  N06   114.54  3.000
 S7W  O13   C12  N06   123.82  3.000
 S7W  C12   N06  C07   121.47  3.000
 S7W  C12   N06  C03   119.94  3.000
 S7W  C07   N06  C03   118.57  3.000
 S7W  H111  N11  C12   115.05  3.000
 S7W  H111  N11  C09   116.33  3.000
 S7W  C12   N11  C09   128.62  3.000
 S7W  C05   O04  C03   110.39  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
 S7W  CONST_01  N11   C12  N06  C03  180.00   0.0  0
 S7W  CONST_02  N11   C12  N06  C07    0.00   0.0  0
 S7W  CONST_03  C12   N11  C09  C08    0.00   0.0  0
 S7W  CONST_04  N06   C12  N11  C09    0.00   0.0  0
 S7W  CONST_05  O13   C12  N06  C03    0.00   0.0  0
 S7W  CONST_06  O13   C12  N06  C07  180.00   0.0  0
 S7W  CONST_07  O13   C12  N11  C09  180.00   0.0  0
 S7W  CONST_08  O10   C09  N11  C12  180.00   0.0  0
 S7W  CONST_09  H111  N11  C09  C08  180.00   0.0  0
 S7W  Var_01    O04   C05  C01  C02   33.82  30.0  1
 S7W  Var_02    C05   C01  C02  C03  -35.86  30.0  1

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
 S7W  chir_01  C03  O04  C02  N06  positiv

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
 S7W  plan-1  C03   0.020
 S7W  plan-1  C07   0.020
 S7W  plan-1  C08   0.020
 S7W  plan-1  C09   0.020
 S7W  plan-1  C12   0.020
 S7W  plan-1  F14   0.020
 S7W  plan-1  N06   0.020
 S7W  plan-1  N11   0.020
 S7W  plan-1  O10   0.020
 S7W  plan-1  O13   0.020
 S7W  plan-1  H071  0.020
 S7W  plan-1  H111  0.020

