# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:36:21 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: N-phenyl-N'-propan-2-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NC(=O)Nc1ccccc1
#
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
 XY4  XY4  N-phenyl-N'-propan-2-ylurea  ligand  27  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XY4
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
 XY4  N1   N  NH1   0  -0.687   2.9795  -0.4281  16.8257
 XY4  C4   C  C     0   0.730   2.0138  -1.2823  17.2314
 XY4  C5   C  CR6   0   0.367  -0.2535  -2.0416  16.5708
 XY4  C6   C  CR16  0  -0.340  -1.4392  -1.5033  16.0631
 XY4  C7   C  CR16  0  -0.245  -2.6320  -2.2015  16.1550
 XY4  C8   C  CR16  0  -0.274  -2.6726  -3.4464  16.7685
 XY4  C10  C  CR16  0  -0.303  -0.2924  -3.2998  17.1765
 XY4  C1   C  CH3   0  -0.656   4.0117   0.4400  18.9142
 XY4  C2   C  CH1   0  -0.075   4.2274  -0.1787  17.5370
 XY4  C3   C  CH3   0  -0.654   5.1362  -1.4028  17.5923
 XY4  C9   C  CR16  0  -0.248  -1.4969  -3.9824  17.2756
 XY4  N2   N  NH1   0  -0.782   0.9197  -1.3083  16.3896
 XY4  O1   O  O     0  -0.515   2.0914  -1.9707  18.2386
 XY4  H1   H  HNH1  0   0.395   2.8545   0.0748  15.9632
 XY4  H2   H  HCR6  0   0.262  -1.4248  -0.5270  15.5919
 XY4  H3   H  HCR6  0   0.254  -3.5351  -1.7630  15.7496
 XY4  H4   H  HCR6  0   0.250  -3.6037  -3.9920  16.8453
 XY4  H5   H  HCR6  0   0.263   0.6076  -3.7543  17.5592
 XY4  H6   H  HCH3  0   0.226   4.9706   0.7445  19.3354
 XY4  H7   H  HCH3  0   0.228   3.3799   1.3264  18.8497
 XY4  H8   H  HCH3  0   0.229   3.5506  -0.2621  19.6065
 XY4  H9   H  HCH1  0   0.243   4.7303   0.5700  16.9222
 XY4  H10  H  HCH3  0   0.226   6.1109  -1.1205  17.9920
 XY4  H11  H  HCH3  0   0.228   4.7258  -2.1828  18.2310
 XY4  H12  H  HCH3  0   0.228   5.2912  -1.8189  16.5965
 XY4  H13  H  HCR6  0   0.252  -1.5077  -4.9556  17.7501
 XY4  H14  H  HNH1  0   0.402   0.8548  -0.5778  15.6966

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
 XY4  N2   C5   single    1.395  0.020  1.395
 XY4  N2   C4   single    1.381  0.020  1.381
 XY4  C6   C5   aromatic  1.398  0.020  1.398
 XY4  C6   C7   aromatic  1.385  0.020  1.385
 XY4  C5   C10  aromatic  1.397  0.020  1.397
 XY4  C7   C8   aromatic  1.388  0.020  1.388
 XY4  N1   C4   single    1.352  0.020  1.352
 XY4  N1   C2   single    1.458  0.020  1.458
 XY4  C4   O1   double    1.222  0.020  1.222
 XY4  C10  C9   aromatic  1.388  0.020  1.388
 XY4  C8   C9   aromatic  1.388  0.020  1.388
 XY4  C3   C2   single    1.526  0.020  1.526
 XY4  C2   C1   single    1.525  0.020  1.525
 XY4  N1   H1   single    0.860  0.020  1.020
 XY4  C6   H2   single    0.930  0.020  1.080
 XY4  C7   H3   single    0.930  0.020  1.080
 XY4  C8   H4   single    0.930  0.020  1.080
 XY4  C10  H5   single    0.930  0.020  1.080
 XY4  C1   H6   single    0.970  0.020  1.090
 XY4  C1   H7   single    0.970  0.020  1.090
 XY4  C1   H8   single    0.970  0.020  1.090
 XY4  C2   H9   single    0.970  0.020  1.090
 XY4  C3   H10  single    0.970  0.020  1.090
 XY4  C3   H11  single    0.970  0.020  1.090
 XY4  C3   H12  single    0.970  0.020  1.090
 XY4  C9   H13  single    0.930  0.020  1.080
 XY4  N2   H14  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
 XY4  H1   N1   C2   116.04  3.000
 XY4  H1   N1   C4   118.98  3.000
 XY4  C2   N1   C4   124.98  3.000
 XY4  O1   C4   N2   122.82  3.000
 XY4  O1   C4   N1   123.91  3.000
 XY4  N2   C4   N1   113.27  3.000
 XY4  N2   C5   C10  123.58  3.000
 XY4  C10  C5   C6   118.74  3.000
 XY4  N2   C5   C6   117.63  3.000
 XY4  H2   C6   C7   119.62  3.000
 XY4  H2   C6   C5   119.57  3.000
 XY4  C7   C6   C5   120.82  3.000
 XY4  H3   C7   C8   120.28  3.000
 XY4  H3   C7   C6   119.29  3.000
 XY4  C8   C7   C6   120.43  3.000
 XY4  H4   C8   C9   120.55  3.000
 XY4  H4   C8   C7   120.57  3.000
 XY4  C9   C8   C7   118.88  3.000
 XY4  H5   C10  C9   119.44  3.000
 XY4  H5   C10  C5   120.68  3.000
 XY4  C9   C10  C5   119.87  3.000
 XY4  H8   C1   H7   108.45  3.000
 XY4  H8   C1   H6   107.87  3.000
 XY4  H7   C1   H6   107.78  3.000
 XY4  H8   C1   C2   111.87  3.000
 XY4  H7   C1   C2   111.00  3.000
 XY4  H6   C1   C2   109.74  3.000
 XY4  H9   C2   C3   107.23  3.000
 XY4  H9   C2   C1   107.19  3.000
 XY4  C3   C2   C1   112.15  3.000
 XY4  H9   C2   N1   103.70  3.000
 XY4  C1   C2   N1   112.89  3.000
 XY4  C3   C2   N1   112.98  3.000
 XY4  H12  C3   H11  108.42  3.000
 XY4  H12  C3   H10  107.85  3.000
 XY4  H11  C3   H10  107.90  3.000
 XY4  H12  C3   C2   110.96  3.000
 XY4  H11  C3   C2   111.82  3.000
 XY4  H10  C3   C2   109.76  3.000
 XY4  H13  C9   C10  118.82  3.000
 XY4  H13  C9   C8   119.92  3.000
 XY4  C10  C9   C8   121.26  3.000
 XY4  H14  N2   C5   114.55  3.000
 XY4  H14  N2   C4   117.14  3.000
 XY4  C5   N2   C4   126.65  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
 XY4  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 XY4  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 XY4  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 XY4  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 XY4  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 XY4  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 XY4  CONST_07  N2   C5   C6   C7   180.00   0.0  0
 XY4  CONST_08  N2   C5   C10  C9   180.00   0.0  0
 XY4  CONST_09  H3   C7   C6   C5   180.00   0.0  0
 XY4  CONST_10  H13  C9   C10  C5   180.00   0.0  0
 XY4  CONST_11  H5   C10  C5   C6   180.00   0.0  0
 XY4  CONST_12  H4   C8   C7   C6   180.00   0.0  0
 XY4  CONST_13  H2   C6   C7   C8   180.00   0.0  0
 XY4  CONST_17  O1   C4   N2   C5     0.00   0.0  0
 XY4  CONST_18  C5   N2   C4   N1   180.00   0.0  0
 XY4  CONST_19  O1   C4   N1   C2     0.00   0.0  0
 XY4  CONST_20  N2   C4   N1   C2   180.00   0.0  0
 XY4  CONST_21  H1   N1   C4   O1   180.00   0.0  0
 XY4  Var_01    C3   C2   N1   C4    65.23  30.0  3
 XY4  Var_02    H10  C3   C2   N1   171.13  30.0  3
 XY4  Var_03    H6   C1   C2   N1  -171.39  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
 XY4  plan-1  C5   0.020
 XY4  plan-1  C6   0.020
 XY4  plan-1  C7   0.020
 XY4  plan-1  C8   0.020
 XY4  plan-1  C10  0.020
 XY4  plan-1  C9   0.020
 XY4  plan-1  N2   0.020
 XY4  plan-1  H2   0.020
 XY4  plan-1  H3   0.020
 XY4  plan-1  H4   0.020
 XY4  plan-1  H5   0.020
 XY4  plan-1  H13  0.020
 XY4  plan-2  N1   0.020
 XY4  plan-2  C4   0.020
 XY4  plan-2  C5   0.020
 XY4  plan-2  C2   0.020
 XY4  plan-2  N2   0.020
 XY4  plan-2  O1   0.020
 XY4  plan-2  H1   0.020
 XY4  plan-2  H14  0.020

