# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 08:25:26 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-(3-nitrophenyl)dihydropyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccc(c1)N2CCC(=O)NC2=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
 1SF  1SF  1-(3-nitrophenyl)dihydropyrimidine-2,4(1H,3H)-dione  ligand  26  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1SF
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
 1SF  C1   C  CR16   0  -0.254   1.8449   2.2555   0.5732
 1SF  C2   C  CR16   0  -0.250   0.5175   1.8712   0.4831
 1SF  C3   C  CR6    0   0.368   0.1892   0.5398   0.2365
 1SF  C4   C  CR16   0  -0.328   1.1968  -0.4026   0.0956
 1SF  C5   C  CR6    0   0.271   2.5173   0.0056   0.2119
 1SF  C6   C  CR16   0  -0.274   2.8647   1.3260   0.4425
 1SF  N7   N  N      1   0.329   3.5700  -0.9925   0.0760
 1SF  O8   O  O     -1  -0.375   3.2447  -2.1384  -0.1263
 1SF  O9   O  O      0  -0.374   4.7158  -0.6236   0.1730
 1SF  N10  N  NT     0  -0.597  -1.1589   0.1328   0.1679
 1SF  C11  C  CH2    0  -0.327  -1.5644  -1.1132   0.8103
 1SF  C12  C  CH2    0  -0.592  -2.9954  -0.9976   1.2898
 1SF  C13  C  C      0   0.544  -3.9010  -0.5516   0.1817
 1SF  O14  O  O      0  -0.432  -5.0780  -0.8201   0.1016
 1SF  N15  N  NH1    0  -0.715  -3.2863   0.2399  -0.7575
 1SF  C16  C  C      0   0.710  -1.9848   0.7219  -0.7416
 1SF  O17  O  O      0  -0.472  -1.6459   1.6008  -1.5064
 1SF  H1   H  HCR6   0   0.284   2.0894   3.2906   0.7655
 1SF  H2   H  HCR6   0   0.288  -0.2617   2.6070   0.6234
 1SF  H3   H  HCR6   0   0.311   0.9558  -1.4364  -0.1069
 1SF  H4   H  HCR6   0   0.302   3.8963   1.6326   0.5306
 1SF  H5   H  HCH2   0   0.271  -1.4595  -1.9556   0.1206
 1SF  H6   H  HCH2   0   0.291  -0.9074  -1.2921   1.6581
 1SF  H7   H  HCH2   0   0.298  -3.3453  -1.9522   1.6797
 1SF  H8   H  HCH2   0   0.301  -3.0662  -0.2640   2.0988
 1SF  H9   H  HNH1   0   0.422  -3.8746   0.6354  -1.4804

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
 1SF  O8   N7   single    1.208  0.020  1.208
 1SF  O9   N7   double    1.208  0.020  1.208
 1SF  N7   C5   single    1.457  0.020  1.457
 1SF  C5   C4   aromatic  1.387  0.020  1.387
 1SF  C5   C6   aromatic  1.385  0.020  1.385
 1SF  O17  C16  double    1.213  0.020  1.213
 1SF  C4   C3   aromatic  1.387  0.020  1.387
 1SF  C6   C1   aromatic  1.386  0.020  1.386
 1SF  C16  N15  single    1.388  0.020  1.388
 1SF  C16  N10  single    1.362  0.020  1.362
 1SF  C3   N10  single    1.410  0.020  1.410
 1SF  C3   C2   aromatic  1.393  0.020  1.393
 1SF  N15  C13  single    1.373  0.020  1.373
 1SF  N10  C11  single    1.459  0.020  1.459
 1SF  C1   C2   aromatic  1.385  0.020  1.385
 1SF  C11  C12  single    1.514  0.020  1.514
 1SF  C13  O14  double    1.210  0.020  1.210
 1SF  C13  C12  single    1.499  0.020  1.499
 1SF  C1   H1   single    0.930  0.020  1.080
 1SF  C2   H2   single    0.930  0.020  1.080
 1SF  C4   H3   single    0.930  0.020  1.080
 1SF  C6   H4   single    0.930  0.020  1.080
 1SF  C11  H5   single    0.970  0.020  1.090
 1SF  C11  H6   single    0.970  0.020  1.090
 1SF  C12  H7   single    0.970  0.020  1.090
 1SF  C12  H8   single    0.970  0.020  1.090
 1SF  N15  H9   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
 1SF  H1   C1   C6   119.51  3.000
 1SF  H1   C1   C2   119.61  3.000
 1SF  C6   C1   C2   120.87  3.000
 1SF  H2   C2   C3   120.24  3.000
 1SF  H2   C2   C1   119.59  3.000
 1SF  C3   C2   C1   120.17  3.000
 1SF  N10  C3   C4   119.58  3.000
 1SF  N10  C3   C2   120.65  3.000
 1SF  C4   C3   C2   119.74  3.000
 1SF  H3   C4   C5   120.63  3.000
 1SF  H3   C4   C3   120.48  3.000
 1SF  C5   C4   C3   118.90  3.000
 1SF  N7   C5   C6   119.18  3.000
 1SF  C6   C5   C4   122.23  3.000
 1SF  N7   C5   C4   118.59  3.000
 1SF  H4   C6   C5   121.61  3.000
 1SF  H4   C6   C1   120.32  3.000
 1SF  C5   C6   C1   118.07  3.000
 1SF  O9   N7   O8   123.96  3.000
 1SF  O9   N7   C5   117.95  3.000
 1SF  O8   N7   C5   118.09  3.000
 1SF  C16  N10  C11  119.65  3.000
 1SF  C11  N10  C3   119.39  3.000
 1SF  C16  N10  C3   119.15  3.000
 1SF  H6   C11  H5   107.88  3.000
 1SF  H6   C11  C12  109.68  3.000
 1SF  H5   C11  C12  110.44  3.000
 1SF  H6   C11  N10  108.41  3.000
 1SF  H5   C11  N10  110.69  3.000
 1SF  C12  C11  N10  109.69  3.000
 1SF  H8   C12  H7   107.59  3.000
 1SF  H8   C12  C13  107.93  3.000
 1SF  H7   C12  C13  109.35  3.000
 1SF  H8   C12  C11  110.28  3.000
 1SF  H7   C12  C11  110.51  3.000
 1SF  C13  C12  C11  111.08  3.000
 1SF  N15  C13  O14  121.20  3.000
 1SF  O14  C13  C12  124.79  3.000
 1SF  N15  C13  C12  113.99  3.000
 1SF  H9   N15  C16  114.67  3.000
 1SF  H9   N15  C13  116.96  3.000
 1SF  C16  N15  C13  127.73  3.000
 1SF  O17  C16  N15  120.41  3.000
 1SF  N15  C16  N10  115.21  3.000
 1SF  O17  C16  N10  124.38  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
 1SF  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 1SF  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 1SF  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 1SF  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 1SF  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 1SF  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 1SF  CONST_07  N10  C3   C2   C1   180.00   0.0  0
 1SF  CONST_08  N10  C3   C4   C5   180.00   0.0  0
 1SF  CONST_09  N15  C16  N10  C3   180.00   0.0  0
 1SF  CONST_10  C13  N15  C16  N10    0.00   0.0  0
 1SF  CONST_11  N15  C16  N10  C11    0.00   0.0  0
 1SF  CONST_12  C16  N15  C13  C12    0.00   0.0  0
 1SF  CONST_13  N7   C5   C6   C1   180.00   0.0  0
 1SF  CONST_14  N7   C5   C4   C3   180.00   0.0  0
 1SF  CONST_15  O17  C16  N10  C3     0.00   0.0  0
 1SF  CONST_16  O17  C16  N10  C11  180.00   0.0  0
 1SF  CONST_17  O17  C16  N15  C13  180.00   0.0  0
 1SF  CONST_18  C16  N15  C13  O14  180.00   0.0  0
 1SF  CONST_19  H3   C4   C3   C2   180.00   0.0  0
 1SF  CONST_20  H4   C6   C1   C2   180.00   0.0  0
 1SF  CONST_21  H1   C1   C2   C3   180.00   0.0  0
 1SF  CONST_22  H2   C2   C3   C4   180.00   0.0  0
 1SF  CONST_23  H9   N15  C16  N10  180.00   0.0  0
 1SF  CONST_24  O8   N7   C5   C4     0.00   0.0  0
 1SF  CONST_25  O9   N7   C5   C4   180.00   0.0  0
 1SF  CONST_26  O8   N7   C5   C6   180.00   0.0  0
 1SF  CONST_27  O9   N7   C5   C6     0.00   0.0  0
 1SF  Var_01    C16  N10  C3   C2    57.78  30.0  2
 1SF  Var_02    H5   C11  N10  C3   -89.15  30.0  1
 1SF  Var_03    H7   C12  C11  N10  174.23  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
 1SF  plan-1  C1   0.020
 1SF  plan-1  C2   0.020
 1SF  plan-1  C3   0.020
 1SF  plan-1  C4   0.020
 1SF  plan-1  C5   0.020
 1SF  plan-1  C6   0.020
 1SF  plan-1  N7   0.020
 1SF  plan-1  N10  0.020
 1SF  plan-1  H1   0.020
 1SF  plan-1  H2   0.020
 1SF  plan-1  H3   0.020
 1SF  plan-1  H4   0.020
 1SF  plan-2  C5   0.020
 1SF  plan-2  N7   0.020
 1SF  plan-2  O8   0.020
 1SF  plan-2  O9   0.020
 1SF  plan-3  C3   0.020
 1SF  plan-3  N10  0.020
 1SF  plan-3  C11  0.020
 1SF  plan-3  C12  0.020
 1SF  plan-3  C13  0.020
 1SF  plan-3  O14  0.020
 1SF  plan-3  N15  0.020
 1SF  plan-3  C16  0.020
 1SF  plan-3  O17  0.020
 1SF  plan-3  H9   0.020

