# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 11:44:29 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(NC(=O)Nc2ccc(Cl)c(Cl)c2)cc1
#
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
 9EG  9EG  N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea  ligand  28  19  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9EG
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
 9EG  C12  C   CR16  0  -0.319  -2.8447  -1.2615  -0.3940
 9EG  C11  C   CR6   0   0.396  -1.8179  -0.3158  -0.3424
 9EG  CL2  CL  CL    0  -0.094  -5.3970  -2.0767  -0.4506
 9EG  CL1  CL  CL    0  -0.136   7.5381   0.1350   0.1966
 9EG  C8   C   C     0   0.756   0.6544  -0.1293  -0.1966
 9EG  N1   N   NH1   0  -0.799  -0.5211  -0.8148  -0.3697
 9EG  C4   C   CR6   0   0.388   3.0902  -0.6148  -0.1319
 9EG  C5   C   CR16  0  -0.355   4.0126  -1.6326  -0.3929
 9EG  C6   C   CR16  0  -0.200   5.3732  -1.4115  -0.2935
 9EG  C1   C   CR6   0  -0.060   5.8329  -0.1553   0.0695
 9EG  C2   C   CR16  0  -0.201   4.9369   0.8655   0.3325
 9EG  C3   C   CR16  0  -0.316   3.5704   0.6436   0.2359
 9EG  N7   N   NH1   0  -0.795   1.7433  -0.9547  -0.2474
 9EG  O9   O   O     0  -0.489   0.7175   1.0724  -0.0179
 9EG  C13  C   CR6   0   0.019  -4.1700  -0.8696  -0.3846
 9EG  C14  C   CR6   0  -0.028  -4.5059   0.4771  -0.3191
 9EG  C15  C   CR16  0  -0.204  -3.4886   1.4151  -0.2673
 9EG  C16  C   CR16  0  -0.315  -2.1565   1.0378  -0.2797
 9EG  CL3  CL  CL    0  -0.104  -6.1523   0.9846  -0.3044
 9EG  H1   H   HCR6  0   0.298  -2.6094  -2.3175  -0.4418
 9EG  H2   H   HNH1  0   0.421  -0.4610  -1.8152  -0.4831
 9EG  H3   H   HCR6  0   0.281   3.6630  -2.6160  -0.6832
 9EG  H4   H   HCR6  0   0.282   6.0645  -2.2166  -0.5019
 9EG  H5   H   HCR6  0   0.281   5.2921   1.8457   0.6205
 9EG  H6   H   HCR6  0   0.289   2.8991   1.4577   0.4516
 9EG  H7   H   HNH1  0   0.419   1.5777  -1.9326  -0.4324
 9EG  H8   H   HCR6  0   0.289  -3.7362   2.4669  -0.2184
 9EG  H9   H   HCR6  0   0.296  -1.4011   1.8032  -0.2435

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
 9EG  C6   C5   aromatic  1.382  0.020  1.382
 9EG  C6   C1   aromatic  1.386  0.020  1.386
 9EG  CL1  C1   single    1.734  0.020  1.734
 9EG  C5   C4   aromatic  1.398  0.020  1.398
 9EG  C1   C2   aromatic  1.384  0.020  1.384
 9EG  O9   C8   double    1.217  0.020  1.217
 9EG  C4   N7   single    1.394  0.020  1.394
 9EG  C4   C3   aromatic  1.396  0.020  1.396
 9EG  C15  C16  aromatic  1.385  0.020  1.385
 9EG  C15  C14  aromatic  1.385  0.020  1.385
 9EG  C8   N7   single    1.367  0.020  1.367
 9EG  C8   N1   single    1.372  0.020  1.372
 9EG  C16  C11  aromatic  1.397  0.020  1.397
 9EG  C2   C3   aromatic  1.388  0.020  1.388
 9EG  CL3  C14  single    1.723  0.020  1.723
 9EG  C14  C13  aromatic  1.390  0.020  1.390
 9EG  C11  N1   single    1.390  0.020  1.390
 9EG  C11  C12  aromatic  1.397  0.020  1.397
 9EG  C13  C12  aromatic  1.382  0.020  1.382
 9EG  C13  CL2  single    1.722  0.020  1.722
 9EG  C12  H1   single    0.930  0.020  1.080
 9EG  N1   H2   single    0.860  0.020  1.020
 9EG  C5   H3   single    0.930  0.020  1.080
 9EG  C6   H4   single    0.930  0.020  1.080
 9EG  C2   H5   single    0.930  0.020  1.080
 9EG  C3   H6   single    0.930  0.020  1.080
 9EG  N7   H7   single    0.860  0.020  1.020
 9EG  C15  H8   single    0.930  0.020  1.080
 9EG  C16  H9   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
 9EG  H1   C12  C13  119.02  3.000
 9EG  H1   C12  C11  120.14  3.000
 9EG  C13  C12  C11  120.84  3.000
 9EG  C16  C11  N1   125.11  3.000
 9EG  N1   C11  C12  116.24  3.000
 9EG  C16  C11  C12  118.66  3.000
 9EG  O9   C8   N7   124.08  3.000
 9EG  N7   C8   N1   112.09  3.000
 9EG  O9   C8   N1   123.83  3.000
 9EG  H2   N1   C8   117.31  3.000
 9EG  H2   N1   C11  114.45  3.000
 9EG  C8   N1   C11  128.15  3.000
 9EG  N7   C4   C3   125.02  3.000
 9EG  C3   C4   C5   118.58  3.000
 9EG  N7   C4   C5   116.39  3.000
 9EG  H3   C5   C6   118.83  3.000
 9EG  H3   C5   C4   119.86  3.000
 9EG  C6   C5   C4   121.31  3.000
 9EG  H4   C6   C1   120.88  3.000
 9EG  H4   C6   C5   119.76  3.000
 9EG  C1   C6   C5   119.36  3.000
 9EG  C2   C1   C6   120.25  3.000
 9EG  C2   C1   CL1  119.95  3.000
 9EG  C6   C1   CL1  119.80  3.000
 9EG  H5   C2   C3   119.13  3.000
 9EG  H5   C2   C1   120.44  3.000
 9EG  C3   C2   C1   120.43  3.000
 9EG  H6   C3   C2   118.62  3.000
 9EG  H6   C3   C4   121.31  3.000
 9EG  C2   C3   C4   120.07  3.000
 9EG  H7   N7   C4   114.22  3.000
 9EG  H7   N7   C8   117.46  3.000
 9EG  C4   N7   C8   128.26  3.000
 9EG  C14  C13  CL2  120.58  3.000
 9EG  CL2  C13  C12  118.96  3.000
 9EG  C14  C13  C12  120.46  3.000
 9EG  CL3  C14  C15  120.15  3.000
 9EG  CL3  C14  C13  121.12  3.000
 9EG  C15  C14  C13  118.73  3.000
 9EG  H8   C15  C16  119.05  3.000
 9EG  H8   C15  C14  119.49  3.000
 9EG  C16  C15  C14  121.46  3.000
 9EG  H9   C16  C15  118.77  3.000
 9EG  H9   C16  C11  121.38  3.000
 9EG  C15  C16  C11  119.85  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
 9EG  CONST_01  C15  C16  C11  C12    0.00  0.0  0
 9EG  CONST_02  C15  C14  C13  C12    0.00  0.0  0
 9EG  CONST_03  C14  C15  C16  C11    0.00  0.0  0
 9EG  CONST_04  C14  C13  C12  C11    0.00  0.0  0
 9EG  CONST_05  C1   C6   C5   C4     0.00  0.0  0
 9EG  CONST_06  C1   C2   C3   C4     0.00  0.0  0
 9EG  CONST_07  C2   C1   C6   C5     0.00  0.0  0
 9EG  CONST_08  C2   C3   C4   C5     0.00  0.0  0
 9EG  CONST_09  C3   C4   C5   C6     0.00  0.0  0
 9EG  CONST_10  C3   C2   C1   C6     0.00  0.0  0
 9EG  CONST_11  C16  C15  C14  C13    0.00  0.0  0
 9EG  CONST_12  C16  C11  C12  C13    0.00  0.0  0
 9EG  CONST_13  CL3  C14  C13  C12  180.00  0.0  0
 9EG  CONST_14  CL2  C13  C12  C11  180.00  0.0  0
 9EG  CONST_15  C15  C14  C13  CL2  180.00  0.0  0
 9EG  CONST_16  C5   C6   C1   CL1  180.00  0.0  0
 9EG  CONST_17  C3   C2   C1   CL1  180.00  0.0  0
 9EG  CONST_18  C15  C16  C11  N1   180.00  0.0  0
 9EG  CONST_19  C13  C12  C11  N1   180.00  0.0  0
 9EG  CONST_20  N7   C4   C5   C6   180.00  0.0  0
 9EG  CONST_21  N7   C4   C3   C2   180.00  0.0  0
 9EG  CONST_22  CL3  C14  C15  C16  180.00  0.0  0
 9EG  CONST_23  H9   C16  C11  C12  180.00  0.0  0
 9EG  CONST_24  H8   C15  C16  C11  180.00  0.0  0
 9EG  CONST_25  H4   C6   C5   C4   180.00  0.0  0
 9EG  CONST_26  H5   C2   C3   C4   180.00  0.0  0
 9EG  CONST_27  H6   C3   C4   C5   180.00  0.0  0
 9EG  CONST_28  H3   C5   C6   C1   180.00  0.0  0
 9EG  CONST_29  H1   C12  C13  C14  180.00  0.0  0
 9EG  CONST_30  C8   N1   C11  C12  180.00  0.0  0
 9EG  CONST_31  C5   C4   N7   C8   180.00  0.0  0
 9EG  CONST_32  C3   C4   N7   C8     0.00  0.0  0
 9EG  CONST_33  C16  C11  N1   C8     0.00  0.0  0
 9EG  CONST_34  H2   N1   C11  C12    0.00  0.0  0
 9EG  CONST_35  H7   N7   C4   C5     0.00  0.0  0
 9EG  CONST_36  O9   C8   N1   C11    0.00  0.0  0
 9EG  CONST_37  O9   C8   N7   C4     0.00  0.0  0
 9EG  CONST_38  N7   C8   N1   C11  180.00  0.0  0
 9EG  CONST_39  C4   N7   C8   N1   180.00  0.0  0

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
 9EG  plan-1  CL1  0.020
 9EG  plan-1  C4   0.020
 9EG  plan-1  C5   0.020
 9EG  plan-1  C6   0.020
 9EG  plan-1  C1   0.020
 9EG  plan-1  C2   0.020
 9EG  plan-1  C3   0.020
 9EG  plan-1  N7   0.020
 9EG  plan-1  H3   0.020
 9EG  plan-1  H4   0.020
 9EG  plan-1  H5   0.020
 9EG  plan-1  H6   0.020
 9EG  plan-2  C12  0.020
 9EG  plan-2  C11  0.020
 9EG  plan-2  CL2  0.020
 9EG  plan-2  N1   0.020
 9EG  plan-2  C13  0.020
 9EG  plan-2  C14  0.020
 9EG  plan-2  C15  0.020
 9EG  plan-2  C16  0.020
 9EG  plan-2  CL3  0.020
 9EG  plan-2  H1   0.020
 9EG  plan-2  H8   0.020
 9EG  plan-2  H9   0.020
 9EG  plan-3  C11  0.020
 9EG  plan-3  C8   0.020
 9EG  plan-3  N1   0.020
 9EG  plan-3  C4   0.020
 9EG  plan-3  N7   0.020
 9EG  plan-3  O9   0.020
 9EG  plan-3  H2   0.020
 9EG  plan-3  H7   0.020

