# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:11:06 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-(3,4-dichlorophenyl)-1,1-dimethylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)Nc1ccc(Cl)c(Cl)c1
#
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
 W9M  W9M  3-(3,4-dichlorophenyl)-1,1-dimethylurea  ligand  24  14  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W9M
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
 W9M  C1    C   CR6   0   0.018  -1.8175   0.6405   0.2375
 W9M  C2    C   CR6   0  -0.028  -2.2350  -0.6326  -0.1265
 W9M  C3    C   CR16  0  -0.314  -0.4701   0.9556   0.2622
 W9M  CL4   CL  CL    0  -0.098  -2.9655   1.8472   0.6791
 W9M  C5    C   CR16  0  -0.212  -1.2814  -1.5753  -0.4795
 W9M  CL6   CL  CL    0  -0.106  -3.9075  -1.0480  -0.1529
 W9M  C7    C   CR6   0   0.399   0.4900   0.0082  -0.0919
 W9M  C8    C   CR16  0  -0.299   0.0669  -1.2678  -0.4719
 W9M  N9    N   NH1   0  -0.797   1.8202   0.4125  -0.1010
 W9M  C10   C   C     0   0.721   2.9063  -0.3996   0.1664
 W9M  N11   N   NT    0  -0.480   4.1084   0.2072   0.0335
 W9M  O12   O   O     0  -0.524   2.7737  -1.5705   0.4954
 W9M  C13   C   CH3   0  -0.522   5.3140  -0.4858   0.4362
 W9M  C14   C   CH3   0  -0.564   4.2737   1.5405  -0.5096
 W9M  H3    H   HCR6  0   0.296  -0.1650   1.9487   0.5668
 W9M  H5    H   HCR6  0   0.289  -1.5980  -2.5648  -0.7799
 W9M  H8    H   HCR6  0   0.282   0.7746  -2.0230  -0.7741
 W9M  H9    H   HNH1  0   0.425   1.9576   1.4106  -0.0736
 W9M  H131  H   HCH3  0   0.238   5.8890  -0.8189  -0.4309
 W9M  H132  H   HCH3  0   0.244   5.9423   0.1815   1.0263
 W9M  H133  H   HCH3  0   0.257   5.0734  -1.3522   1.0432
 W9M  H141  H   HCH3  0   0.255   3.6334   1.7067  -1.3753
 W9M  H142  H   HCH3  0   0.249   4.0808   2.3220   0.2308
 W9M  H143  H   HCH3  0   0.272   5.3007   1.6550  -0.8480

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
 W9M  C1   C2    aromatic  1.388  0.020  1.388
 W9M  C1   C3    aromatic  1.384  0.020  1.384
 W9M  C1   CL4   single    1.723  0.020  1.723
 W9M  C2   C5    aromatic  1.387  0.020  1.387
 W9M  C2   CL6   single    1.723  0.020  1.723
 W9M  C3   C7    aromatic  1.395  0.020  1.395
 W9M  C5   C8    aromatic  1.383  0.020  1.383
 W9M  C7   C8    aromatic  1.397  0.020  1.397
 W9M  C7   N9    single    1.390  0.020  1.390
 W9M  N9   C10   single    1.382  0.020  1.382
 W9M  C10  N11   single    1.353  0.020  1.353
 W9M  C10  O12   double    1.224  0.020  1.224
 W9M  N11  C13   single    1.448  0.020  1.448
 W9M  N11  C14   single    1.449  0.020  1.449
 W9M  C3   H3    single    0.930  0.020  1.080
 W9M  C5   H5    single    0.930  0.020  1.080
 W9M  C8   H8    single    0.930  0.020  1.080
 W9M  N9   H9    single    0.860  0.020  1.020
 W9M  C13  H131  single    0.970  0.020  1.090
 W9M  C13  H132  single    0.970  0.020  1.090
 W9M  C13  H133  single    0.970  0.020  1.090
 W9M  C14  H141  single    0.970  0.020  1.090
 W9M  C14  H142  single    0.970  0.020  1.090
 W9M  C14  H143  single    0.970  0.020  1.090

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
 W9M  CL4   C1   C3    118.98  3.000
 W9M  CL4   C1   C2    120.60  3.000
 W9M  C3    C1   C2    120.42  3.000
 W9M  CL6   C2   C5    119.97  3.000
 W9M  CL6   C2   C1    121.12  3.000
 W9M  C5    C2   C1    118.90  3.000
 W9M  H3    C3   C7    120.04  3.000
 W9M  H3    C3   C1    119.22  3.000
 W9M  C7    C3   C1    120.73  3.000
 W9M  H5    C5   C8    119.37  3.000
 W9M  H5    C5   C2    119.43  3.000
 W9M  C8    C5   C2    121.19  3.000
 W9M  N9    C7   C8    123.61  3.000
 W9M  N9    C7   C3    117.57  3.000
 W9M  C8    C7   C3    118.76  3.000
 W9M  H8    C8   C7    121.15  3.000
 W9M  H8    C8   C5    118.86  3.000
 W9M  C7    C8   C5    119.99  3.000
 W9M  H9    N9   C10   118.00  3.000
 W9M  H9    N9   C7    114.72  3.000
 W9M  C10   N9   C7    125.43  3.000
 W9M  O12   C10  N11   123.50  3.000
 W9M  O12   C10  N9    121.94  3.000
 W9M  N11   C10  N9    114.56  3.000
 W9M  C14   N11  C13   116.72  3.000
 W9M  C14   N11  C10   123.42  3.000
 W9M  C13   N11  C10   119.86  3.000
 W9M  H133  C13  H132  108.29  3.000
 W9M  H133  C13  H131  108.50  3.000
 W9M  H132  C13  H131  108.24  3.000
 W9M  H133  C13  N11   110.69  3.000
 W9M  H132  C13  N11   109.72  3.000
 W9M  H131  C13  N11   111.31  3.000
 W9M  H143  C14  H142  107.58  3.000
 W9M  H143  C14  H141  106.96  3.000
 W9M  H142  C14  H141  108.99  3.000
 W9M  H143  C14  N11   108.74  3.000
 W9M  H142  C14  N11   112.56  3.000
 W9M  H141  C14  N11   111.79  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
 W9M  CONST_01  C8    C5   C2   C1     0.00   0.0  0
 W9M  CONST_02  C8    C7   C3   C1     0.00   0.0  0
 W9M  CONST_03  C7    C3   C1   C2     0.00   0.0  0
 W9M  CONST_04  C7    C8   C5   C2     0.00   0.0  0
 W9M  CONST_05  C5    C2   C1   C3     0.00   0.0  0
 W9M  CONST_06  C5    C8   C7   C3     0.00   0.0  0
 W9M  CONST_07  N9    C7   C3   C1   180.00   0.0  0
 W9M  CONST_08  CL6   C2   C1   C3   180.00   0.0  0
 W9M  CONST_09  C5    C2   C1   CL4  180.00   0.0  0
 W9M  CONST_10  C7    C3   C1   CL4  180.00   0.0  0
 W9M  CONST_11  N9    C7   C8   C5   180.00   0.0  0
 W9M  CONST_12  C8    C5   C2   CL6  180.00   0.0  0
 W9M  CONST_13  H5    C5   C2   C1   180.00   0.0  0
 W9M  CONST_14  H3    C3   C1   C2   180.00   0.0  0
 W9M  CONST_15  H8    C8   C5   C2   180.00   0.0  0
 W9M  CONST_18  H9    N9   C7   C3     0.00   0.0  0
 W9M  CONST_19  O12   C10  N9   C7     0.00   0.0  0
 W9M  CONST_20  N11   C10  N9   C7   180.00   0.0  0
 W9M  CONST_21  C13   N11  C10  O12    0.00   0.0  0
 W9M  CONST_22  C14   N11  C10  O12  180.00   0.0  0
 W9M  CONST_23  C13   N11  C10  N9   180.00   0.0  0
 W9M  CONST_24  C14   N11  C10  N9     0.00   0.0  0
 W9M  Var_01    H131  C13  N11  C10  106.38  30.0  3
 W9M  Var_02    H141  C14  N11  C10  -41.55  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
 W9M  plan-1  C1   0.020
 W9M  plan-1  C2   0.020
 W9M  plan-1  C3   0.020
 W9M  plan-1  CL4  0.020
 W9M  plan-1  C5   0.020
 W9M  plan-1  CL6  0.020
 W9M  plan-1  C7   0.020
 W9M  plan-1  C8   0.020
 W9M  plan-1  N9   0.020
 W9M  plan-1  H3   0.020
 W9M  plan-1  H5   0.020
 W9M  plan-1  H8   0.020
 W9M  plan-2  C7   0.020
 W9M  plan-2  N9   0.020
 W9M  plan-2  C10  0.020
 W9M  plan-2  N11  0.020
 W9M  plan-2  O12  0.020
 W9M  plan-2  C13  0.020
 W9M  plan-2  C14  0.020
 W9M  plan-2  H9   0.020

