# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:43:04 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: N-(2-aminoethyl)-N'-phenylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNC(=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
 WUY  WUY  N-(2-aminoethyl)-N'-phenylurea  ligand  26  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 GRAND
;

data_comp_WUY
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
 WUY  C10  C  CR16  0  -0.277  17.6675  -81.0054  29.5830
 WUY  N01  N  NH2   0  -0.801  17.5901  -85.3484  21.1485
 WUY  C02  C  CH2   0  -0.284  17.3811  -85.2405  22.5835
 WUY  C03  C  CH2   0  -0.291  16.2015  -84.3174  22.8658
 WUY  N04  N  NH1   0  -0.677  15.9303  -84.1566  24.2745
 WUY  C05  C  C     0   0.727  16.5667  -83.2325  25.0320
 WUY  N06  N  NH1   0  -0.784  16.2643  -83.3160  26.3717
 WUY  C07  C  CR6   0   0.369  16.7657  -82.5155  27.3982
 WUY  C08  C  CR16  0  -0.308  17.1881  -81.1959  27.2186
 WUY  C09  C  CR16  0  -0.249  17.6383  -80.4608  28.3069
 WUY  C11  C  CR16  0  -0.246  17.2345  -82.3124  29.7634
 WUY  C12  C  CR16  0  -0.345  16.7938  -83.0614  28.6847
 WUY  O13  O  O     0  -0.522  17.3210  -82.3908  24.5657
 WUY  H1   H  HCR6  0   0.252  18.0158  -80.4203  30.4238
 WUY  H2   H  HNH2  0   0.351  18.4288  -85.8850  20.9706
 WUY  H3   H  HNH2  0   0.341  16.8350  -85.8827  20.7361
 WUY  H5   H  HCH2  0   0.195  17.2058  -86.2034  23.0838
 WUY  H6   H  HCH2  0   0.222  18.2792  -84.8124  23.0339
 WUY  H7   H  HCH2  0   0.240  16.3840  -83.3411  22.4179
 WUY  H8   H  HCH2  0   0.243  15.2986  -84.7172  22.3999
 WUY  H9   H  HNH1  0   0.397  15.3763  -84.8686  24.7211
 WUY  H10  H  HNH1  0   0.405  15.7636  -84.1361  26.6788
 WUY  H11  H  HCR6  0   0.268  17.1618  -80.7357  26.2442
 WUY  H12  H  HCR6  0   0.255  17.9616  -79.4401  28.1465
 WUY  H13  H  HCR6  0   0.256  17.2425  -82.7585  30.7496
 WUY  H14  H  HCR6  0   0.264  16.4679  -84.0834  28.8401

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
 WUY  N01  C02  single    1.454  0.020  1.454
 WUY  C02  C03  single    1.524  0.020  1.524
 WUY  C03  N04  single    1.444  0.020  1.444
 WUY  N04  C05  single    1.354  0.020  1.354
 WUY  O13  C05  double    1.223  0.020  1.223
 WUY  C05  N06  single    1.376  0.020  1.376
 WUY  N06  C07  single    1.395  0.020  1.395
 WUY  C08  C07  aromatic  1.397  0.020  1.397
 WUY  C08  C09  aromatic  1.388  0.020  1.388
 WUY  C07  C12  aromatic  1.398  0.020  1.398
 WUY  C09  C10  aromatic  1.388  0.020  1.388
 WUY  C12  C11  aromatic  1.385  0.020  1.385
 WUY  C10  C11  aromatic  1.389  0.020  1.389
 WUY  C10  H1   single    0.930  0.020  1.080
 WUY  N01  H2   single    0.890  0.020  1.040
 WUY  N01  H3   single    0.890  0.020  1.040
 WUY  C02  H5   single    0.970  0.020  1.090
 WUY  C02  H6   single    0.970  0.020  1.090
 WUY  C03  H7   single    0.970  0.020  1.090
 WUY  C03  H8   single    0.970  0.020  1.090
 WUY  N04  H9   single    0.860  0.020  1.020
 WUY  N06  H10  single    0.860  0.020  1.020
 WUY  C08  H11  single    0.930  0.020  1.080
 WUY  C09  H12  single    0.930  0.020  1.080
 WUY  C11  H13  single    0.930  0.020  1.080
 WUY  C12  H14  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
 WUY  H1   C10  C11  120.56  3.000
 WUY  H1   C10  C09  120.60  3.000
 WUY  C11  C10  C09  118.84  3.000
 WUY  H3   N01  H2   105.47  3.000
 WUY  H3   N01  C02  109.50  3.000
 WUY  H2   N01  C02  109.40  3.000
 WUY  H6   C02  H5   106.67  3.000
 WUY  H6   C02  C03  108.82  3.000
 WUY  H5   C02  C03  108.83  3.000
 WUY  H6   C02  N01  108.54  3.000
 WUY  H5   C02  N01  114.02  3.000
 WUY  C03  C02  N01  109.81  3.000
 WUY  H8   C03  H7   106.93  3.000
 WUY  H8   C03  N04  107.57  3.000
 WUY  H7   C03  N04  109.43  3.000
 WUY  H8   C03  C02  109.83  3.000
 WUY  H7   C03  C02  109.69  3.000
 WUY  N04  C03  C02  113.18  3.000
 WUY  H9   N04  C05  119.55  3.000
 WUY  H9   N04  C03  117.23  3.000
 WUY  C05  N04  C03  122.26  3.000
 WUY  O13  C05  N06  123.28  3.000
 WUY  N06  C05  N04  113.58  3.000
 WUY  O13  C05  N04  123.13  3.000
 WUY  H10  N06  C07  114.90  3.000
 WUY  H10  N06  C05  117.05  3.000
 WUY  C07  N06  C05  127.06  3.000
 WUY  C12  C07  C08  118.76  3.000
 WUY  C12  C07  N06  117.41  3.000
 WUY  C08  C07  N06  123.79  3.000
 WUY  H11  C08  C09  119.37  3.000
 WUY  H11  C08  C07  120.80  3.000
 WUY  C09  C08  C07  119.83  3.000
 WUY  H12  C09  C08  118.68  3.000
 WUY  H12  C09  C10  120.00  3.000
 WUY  C08  C09  C10  121.32  3.000
 WUY  H13  C11  C12  119.27  3.000
 WUY  H13  C11  C10  120.27  3.000
 WUY  C12  C11  C10  120.46  3.000
 WUY  H14  C12  C11  119.59  3.000
 WUY  H14  C12  C07  119.61  3.000
 WUY  C11  C12  C07  120.79  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
 WUY  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 WUY  CONST_02  C07  C12  C11  C10     0.00   0.0  0
 WUY  CONST_03  C11  C12  C07  C08     0.00   0.0  0
 WUY  CONST_04  C11  C10  C09  C08     0.00   0.0  0
 WUY  CONST_05  C12  C07  C08  C09     0.00   0.0  0
 WUY  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 WUY  CONST_07  C09  C08  C07  N06   180.00   0.0  0
 WUY  CONST_08  C11  C12  C07  N06   180.00   0.0  0
 WUY  CONST_09  H11  C08  C09  C10   180.00   0.0  0
 WUY  CONST_10  H14  C12  C11  C10   180.00   0.0  0
 WUY  CONST_11  H12  C09  C08  C07   180.00   0.0  0
 WUY  CONST_12  H13  C11  C12  C07   180.00   0.0  0
 WUY  CONST_13  H1   C10  C09  C08   180.00   0.0  0
 WUY  CONST_17  O13  C05  N06  C07     0.00   0.0  0
 WUY  CONST_18  C07  N06  C05  N04   180.00   0.0  0
 WUY  CONST_19  O13  C05  N04  C03     0.00   0.0  0
 WUY  CONST_20  N06  C05  N04  C03   180.00   0.0  0
 WUY  CONST_21  H9   N04  C05  O13   180.00   0.0  0
 WUY  Var_01    N04  C03  C02  N01  -179.91  30.0  3
 WUY  Var_02    C05  N04  C03  C02    85.80  30.0  3
 WUY  Var_03    H2   N01  C02  C03   174.31  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
 WUY  plan-1  C10  0.020
 WUY  plan-1  N06  0.020
 WUY  plan-1  C07  0.020
 WUY  plan-1  C08  0.020
 WUY  plan-1  C09  0.020
 WUY  plan-1  C11  0.020
 WUY  plan-1  C12  0.020
 WUY  plan-1  H1   0.020
 WUY  plan-1  H11  0.020
 WUY  plan-1  H12  0.020
 WUY  plan-1  H13  0.020
 WUY  plan-1  H14  0.020
 WUY  plan-2  C03  0.020
 WUY  plan-2  N04  0.020
 WUY  plan-2  C05  0.020
 WUY  plan-2  N06  0.020
 WUY  plan-2  C07  0.020
 WUY  plan-2  O13  0.020
 WUY  plan-2  H9   0.020
 WUY  plan-2  H10  0.020

