# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:19:10 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: [3-(4-chloro-3-nitrobenzyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN1C=CC(=O)N(Cc2ccc(Cl)c(c2)[N+]([O-])=O)C1=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
 48I  48I  '[3-(4-chloro-3-nitrobenzyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl]acetic acid'  ligand  33  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_48I
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
 48I  CL   CL  CL     0  -0.101   5.2772   0.3317  -0.4484
 48I  C10  C   CR6    0  -0.051   3.6484   0.5370   0.0602
 48I  C8   C   CR6    0   0.340   2.7457  -0.5185   0.1589
 48I  N16  N   N      1   0.308   3.1008  -1.8705  -0.2418
 48I  O18  O   O      0  -0.127   2.6854  -2.7766   0.4404
 48I  O17  O   O     -1  -0.500   3.7532  -2.0093  -1.2458
 48I  C7   C   CR16   0  -0.318   1.4641  -0.3194   0.6463
 48I  C19  C   CR16   0  -0.228   3.2353   1.7997   0.4537
 48I  C15  C   CR16   0  -0.265   1.9430   2.0045   0.9079
 48I  C1   C   CR6    0   0.032   1.0422   0.9510   1.0108
 48I  C3   C   CH2    0  -0.377  -0.3590   1.1710   1.5177
 48I  N5   N   NR6    0  -0.467  -1.3486   1.1243   0.4458
 48I  C20  C   CR6    0   0.783  -2.0283  -0.0579   0.2541
 48I  O4   O   O      0  -0.486  -1.8325  -1.0546   0.9186
 48I  N2   N   NR6    0  -0.472  -2.9499  -0.0610  -0.7700
 48I  C13  C   CH2    0  -0.451  -3.7108  -1.2717  -0.9604
 48I  C11  C   C      0   0.577  -4.7448  -1.4405   0.1328
 48I  O14  O   OH1    0  -0.613  -5.3016  -2.6375   0.0680
 48I  O9   O   O      0  -0.384  -5.0466  -0.5813   0.9147
 48I  C22  C   CR16   0   0.028  -3.1974   1.0493  -1.5187
 48I  C23  C   CR16   0  -0.481  -2.5279   2.1961  -1.3416
 48I  C6   C   CR6    0   0.596  -1.5186   2.2846  -0.3179
 48I  O21  O   O      0  -0.661  -0.8363   3.2664  -0.0990
 48I  H1   H   HCR6   0   0.310   0.7884  -1.1606   0.7255
 48I  H2   H   HCR6   0   0.300   3.9287   2.6271   0.4023
 48I  H3   H   HCR6   0   0.295   1.6398   3.0027   1.1921
 48I  H4   H   HCH2   0   0.317  -0.6160   0.4138   2.2532
 48I  H5   H   HCH2   0   0.309  -0.4339   2.1365   2.0120
 48I  H6   H   HCH2   0   0.328  -4.2236  -1.2141  -1.9220
 48I  H7   H   HCH2   0   0.343  -3.0547  -2.1403  -1.0069
 48I  H8   H   HOH1   0   0.493  -5.9922  -2.7258   0.7413
 48I  H9   H   HCR6   0   0.327  -3.9610   0.9443  -2.2759
 48I  H10  H   HCR6   0   0.296  -2.7300   3.0584  -1.9575

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
 48I  C23  C22  double    1.340  0.020  1.340
 48I  C23  C6   single    1.440  0.020  1.440
 48I  O21  C6   double    1.215  0.020  1.215
 48I  C22  N2   single    1.362  0.020  1.362
 48I  C6   N5   single    1.399  0.020  1.399
 48I  N2   C13  single    1.443  0.020  1.443
 48I  N2   C20  single    1.378  0.020  1.378
 48I  N5   C20  single    1.377  0.020  1.377
 48I  N5   C3   single    1.460  0.020  1.460
 48I  C13  C11  single    1.514  0.020  1.514
 48I  C20  O4   double    1.214  0.020  1.214
 48I  C3   C1   single    1.506  0.020  1.506
 48I  C15  C1   aromatic  1.390  0.020  1.390
 48I  C15  C19  aromatic  1.385  0.020  1.385
 48I  C11  O9   double    1.200  0.020  1.200
 48I  C11  O14  single    1.322  0.020  1.322
 48I  C1   C7   aromatic  1.387  0.020  1.387
 48I  C19  C10  aromatic  1.386  0.020  1.386
 48I  C7   C8   aromatic  1.386  0.020  1.386
 48I  C10  C8   aromatic  1.392  0.020  1.392
 48I  C10  CL   single    1.719  0.020  1.719
 48I  C8   N16  single    1.454  0.020  1.454
 48I  N16  O18  double    1.208  0.020  1.208
 48I  N16  O17  single    1.205  0.020  1.205
 48I  C7   H1   single    0.930  0.020  1.080
 48I  C19  H2   single    0.930  0.020  1.080
 48I  C15  H3   single    0.930  0.020  1.080
 48I  C3   H4   single    0.970  0.020  1.090
 48I  C3   H5   single    0.970  0.020  1.090
 48I  C13  H6   single    0.970  0.020  1.090
 48I  C13  H7   single    0.970  0.020  1.090
 48I  O14  H8   single    0.850  0.020  0.980
 48I  C22  H9   single    0.930  0.020  1.080
 48I  C23  H10  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
 48I  C19  C10  C8   118.51  3.000
 48I  C8   C10  CL   123.02  3.000
 48I  C19  C10  CL   118.39  3.000
 48I  C7   C8   N16  117.15  3.000
 48I  N16  C8   C10  121.80  3.000
 48I  C7   C8   C10  121.04  3.000
 48I  O17  N16  O18  124.77  3.000
 48I  O17  N16  C8   117.95  3.000
 48I  O18  N16  C8   117.25  3.000
 48I  H1   C7   C1   120.19  3.000
 48I  H1   C7   C8   119.45  3.000
 48I  C1   C7   C8   120.35  3.000
 48I  H2   C19  C15  120.07  3.000
 48I  H2   C19  C10  119.53  3.000
 48I  C15  C19  C10  120.40  3.000
 48I  H3   C15  C1   119.90  3.000
 48I  H3   C15  C19  118.97  3.000
 48I  C1   C15  C19  121.12  3.000
 48I  C3   C1   C15  121.14  3.000
 48I  C15  C1   C7   118.52  3.000
 48I  C3   C1   C7   120.33  3.000
 48I  H5   C3   H4   107.15  3.000
 48I  H5   C3   N5   108.40  3.000
 48I  H4   C3   N5   108.33  3.000
 48I  H5   C3   C1   110.29  3.000
 48I  H4   C3   C1   110.25  3.000
 48I  N5   C3   C1   112.27  3.000
 48I  C6   N5   C20  125.16  3.000
 48I  C20  N5   C3   117.67  3.000
 48I  C6   N5   C3   117.16  3.000
 48I  N2   C20  O4   120.87  3.000
 48I  O4   C20  N5   123.30  3.000
 48I  N2   C20  N5   115.82  3.000
 48I  C22  N2   C13  121.05  3.000
 48I  C13  N2   C20  116.93  3.000
 48I  C22  N2   C20  121.90  3.000
 48I  H7   C13  H6   106.71  3.000
 48I  H7   C13  C11  110.68  3.000
 48I  H6   C13  C11  108.73  3.000
 48I  H7   C13  N2   110.92  3.000
 48I  H6   C13  N2   108.66  3.000
 48I  C11  C13  N2   111.01  3.000
 48I  O9   C11  O14  125.05  3.000
 48I  O14  C11  C13  110.69  3.000
 48I  O9   C11  C13  124.21  3.000
 48I  H8   O14  C11  110.42  3.000
 48I  H9   C22  C23  121.94  3.000
 48I  H9   C22  N2   115.75  3.000
 48I  C23  C22  N2   122.30  3.000
 48I  H10  C23  C6   119.20  3.000
 48I  H10  C23  C22  121.01  3.000
 48I  C6   C23  C22  119.79  3.000
 48I  O21  C6   C23  124.82  3.000
 48I  O21  C6   N5   120.22  3.000
 48I  C23  C6   N5   114.96  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
 48I  CONST_01  C1   C15  C19  C10    0.00   0.0  0
 48I  CONST_02  C1   C7   C8   C10    0.00   0.0  0
 48I  CONST_03  C15  C1   C7   C8     0.00   0.0  0
 48I  CONST_04  C15  C19  C10  C8     0.00   0.0  0
 48I  CONST_05  C19  C15  C1   C7     0.00   0.0  0
 48I  CONST_06  C19  C10  C8   C7     0.00   0.0  0
 48I  CONST_07  C22  N2   C20  N5     0.00   0.0  0
 48I  CONST_08  C6   N5   C20  N2     0.00   0.0  0
 48I  CONST_09  C15  C19  C10  CL   180.00   0.0  0
 48I  CONST_10  C7   C8   C10  CL   180.00   0.0  0
 48I  CONST_11  C3   C1   C7   C8   180.00   0.0  0
 48I  CONST_12  C1   C7   C8   N16  180.00   0.0  0
 48I  CONST_13  C19  C10  C8   N16  180.00   0.0  0
 48I  CONST_14  C3   C1   C15  C19  180.00   0.0  0
 48I  CONST_15  N2   C20  N5   C3   180.00   0.0  0
 48I  CONST_16  C13  N2   C20  N5   180.00   0.0  0
 48I  CONST_17  C22  N2   C20  O4   180.00   0.0  0
 48I  CONST_18  C6   N5   C20  O4   180.00   0.0  0
 48I  CONST_19  H3   C15  C19  C10  180.00   0.0  0
 48I  CONST_20  H1   C7   C8   C10  180.00   0.0  0
 48I  CONST_21  H2   C19  C10  C8   180.00   0.0  0
 48I  CONST_26  O4   C20  N5   C3     0.00   0.0  0
 48I  CONST_27  C13  N2   C20  O4     0.00   0.0  0
 48I  CONST_28  H8   O14  C11  C13  180.00   0.0  0
 48I  Var_01    N5   C3   C1   C7   -74.95  30.0  3
 48I  Var_02    C6   N5   C3   C1   -81.44  30.0  2
 48I  Var_03    C11  C13  N2   C20   73.10  30.0  3
 48I  Var_04    O9   C11  C13  N2    11.83  30.0  3

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
 48I  plan-1  CL   0.020
 48I  plan-1  C10  0.020
 48I  plan-1  C8   0.020
 48I  plan-1  N16  0.020
 48I  plan-1  C7   0.020
 48I  plan-1  C19  0.020
 48I  plan-1  C15  0.020
 48I  plan-1  C1   0.020
 48I  plan-1  C3   0.020
 48I  plan-1  H1   0.020
 48I  plan-1  H2   0.020
 48I  plan-1  H3   0.020
 48I  plan-2  C3   0.020
 48I  plan-2  N5   0.020
 48I  plan-2  C20  0.020
 48I  plan-2  O4   0.020
 48I  plan-2  N2   0.020
 48I  plan-2  C13  0.020
 48I  plan-2  C22  0.020
 48I  plan-2  C23  0.020
 48I  plan-2  C6   0.020
 48I  plan-2  O21  0.020
 48I  plan-2  H9   0.020
 48I  plan-2  H10  0.020
 48I  plan-3  C8   0.020
 48I  plan-3  N16  0.020
 48I  plan-3  O18  0.020
 48I  plan-3  O17  0.020
 48I  plan-4  C13  0.020
 48I  plan-4  C11  0.020
 48I  plan-4  O14  0.020
 48I  plan-4  O9   0.020
 48I  plan-4  H8   0.020

