# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:46:49 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-(2,5-dimethylphenyl)-3-(2-oxidanyl-5-sulfamoyl-phenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C)c(NC(=O)Nc2cc(ccc2O)[S](N)(=O)=O)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
 D3B  D3B  1-(2,5-dimethylphenyl)-3-(2-oxidanyl-5-sulfamoyl-phenyl)urea  ligand  40  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D3B
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
 D3B  C3   C  CR16  0  -0.370   3.3089   2.5342   0.2921
 D3B  C4   C  CR16  0  -0.239   4.0211   1.3474   0.3207
 D3B  C5   C  CR6   0  -0.235   3.3527   0.1616   0.0691
 D3B  C6   C  CR16  0  -0.256   1.9923   0.1399  -0.2201
 D3B  C7   C  CR6   0   0.313  -3.4455   0.0734  -0.2003
 D3B  C8   C  CR16  0  -0.317  -3.4865  -1.3021  -0.4027
 D3B  N20  N  NH1   0  -0.784  -2.2925   0.8124  -0.5197
 D3B  C22  C  C     0   0.712  -1.0274   0.4797  -0.1271
 D3B  O23  O  O     0  -0.496  -0.7588  -0.5191   0.5150
 D3B  C1   C  CR6   0   0.301   1.2735   1.3233  -0.2345
 D3B  C2   C  CR6   0   0.319   1.9462   2.5326   0.0271
 D3B  C9   C  CR6   0   0.078  -4.6281  -2.0404  -0.1080
 D3B  C10  C  CR16  0  -0.298  -5.7412  -1.3645   0.3806
 D3B  C11  C  CR16  0  -0.296  -5.7073   0.0103   0.5628
 D3B  C12  C  CR6   0   0.046  -4.5666   0.7559   0.2880
 D3B  O1   O  OH1   0  -0.614   1.2086   3.6496  -0.0080
 D3B  S2   S  S     0   1.360   4.2348  -1.3636   0.0907
 D3B  O3   O  OS    0  -0.670   3.6902  -2.2684  -0.9127
 D3B  O4   O  OS    0  -0.655   5.6588  -1.0576   0.0351
 D3B  N5   N  NC2   0  -0.887   3.7695  -1.9865   1.5503
 D3B  C13  C  CH3   0  -0.744  -4.5368   2.2380   0.5209
 D3B  C14  C  CH3   0  -0.723  -4.6642  -3.5211  -0.3556
 D3B  H1   H  HCR6  0   0.289   3.8171   3.4700   0.4905
 D3B  H2   H  HCR6  0   0.286   5.0801   1.3641   0.5348
 D3B  H3   H  HCR6  0   0.291   1.4976  -0.7925  -0.4462
 D3B  H4   H  HCR6  0   0.252  -2.6204  -1.8067  -0.8103
 D3B  H5   H  HNH1  0   0.407  -2.4396   1.7214  -0.9312
 D3B  H6   H  HNH1  0   0.411  -0.4053   2.2423  -0.9694
 D3B  H7   H  HCR6  0   0.245  -6.6432  -1.9139   0.6225
 D3B  H8   H  HCR6  0   0.248  -6.5855   0.5165   0.9453
 D3B  H9   H  HOH1  0   0.488   1.7570   4.4306   0.1321
 D3B  H10  H  HNC2  0   0.417   3.9764  -2.9795   1.6108
 D3B  H11  H  HNC2  0   0.414   4.1897  -1.4961   2.3333
 D3B  H12  H  HCH3  0   0.245  -4.3974   2.8032  -0.4041
 D3B  H13  H  HCH3  0   0.256  -5.4716   2.5779   0.9634
 D3B  H14  H  HCH3  0   0.249  -3.7268   2.5229   1.1951
 D3B  H15  H  HCH3  0   0.247  -4.8606  -3.7370  -1.4078
 D3B  H16  H  HCH3  0   0.243  -3.7172  -3.9964  -0.1000
 D3B  H17  H  HCH3  0   0.243  -5.4504  -4.0020   0.2255
 D3B  N24  N  NH1   0  -0.776  -0.0857   1.3862  -0.5422

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
 D3B  C14  C9   single    1.502  0.020  1.502
 D3B  C9   C10  aromatic  1.391  0.020  1.391
 D3B  C9   C8   aromatic  1.391  0.020  1.391
 D3B  C10  C11  aromatic  1.387  0.020  1.387
 D3B  C8   C7   aromatic  1.391  0.020  1.391
 D3B  O23  C22  double    1.217  0.020  1.217
 D3B  C11  C12  aromatic  1.390  0.020  1.390
 D3B  C7   C12  aromatic  1.400  0.020  1.400
 D3B  C7   N20  single    1.406  0.020  1.406
 D3B  C22  N20  single    1.366  0.020  1.366
 D3B  C22  N24  single    1.371  0.020  1.371
 D3B  C12  C13  single    1.501  0.020  1.501
 D3B  N24  C1   single    1.395  0.020  1.395
 D3B  O1   C2   single    1.339  0.020  1.339
 D3B  C1   C2   aromatic  1.408  0.020  1.408
 D3B  C1   C6   aromatic  1.385  0.020  1.385
 D3B  C2   C3   aromatic  1.388  0.020  1.388
 D3B  C6   C5   aromatic  1.391  0.020  1.391
 D3B  C3   C4   aromatic  1.384  0.020  1.384
 D3B  C5   C4   aromatic  1.384  0.020  1.384
 D3B  C5   S2   single    1.762  0.020  1.762
 D3B  N5   S2   single    1.654  0.020  1.654
 D3B  S2   O4   double    1.458  0.020  1.458
 D3B  S2   O3   double    1.457  0.020  1.457
 D3B  C3   H1   single    0.930  0.020  1.080
 D3B  C4   H2   single    0.930  0.020  1.080
 D3B  C6   H3   single    0.930  0.020  1.080
 D3B  C8   H4   single    0.930  0.020  1.080
 D3B  N20  H5   single    0.860  0.020  1.020
 D3B  N24  H6   single    0.860  0.020  1.020
 D3B  C10  H7   single    0.930  0.020  1.080
 D3B  C11  H8   single    0.930  0.020  1.080
 D3B  O1   H9   single    0.850  0.020  0.980
 D3B  N5   H10  single    0.890  0.020  1.040
 D3B  N5   H11  single    0.890  0.020  1.040
 D3B  C13  H12  single    0.970  0.020  1.090
 D3B  C13  H13  single    0.970  0.020  1.090
 D3B  C13  H14  single    0.970  0.020  1.090
 D3B  C14  H15  single    0.970  0.020  1.090
 D3B  C14  H16  single    0.970  0.020  1.090
 D3B  C14  H17  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
 D3B  H1   C3   C2   119.77  3.000
 D3B  H1   C3   C4   119.70  3.000
 D3B  C2   C3   C4   120.53  3.000
 D3B  H2   C4   C5   121.50  3.000
 D3B  H2   C4   C3   119.67  3.000
 D3B  C5   C4   C3   118.83  3.000
 D3B  S2   C5   C6   118.60  3.000
 D3B  S2   C5   C4   119.83  3.000
 D3B  C6   C5   C4   121.56  3.000
 D3B  H3   C6   C1   119.87  3.000
 D3B  H3   C6   C5   120.35  3.000
 D3B  C1   C6   C5   119.77  3.000
 D3B  C12  C7   N20  118.65  3.000
 D3B  N20  C7   C8   120.72  3.000
 D3B  C12  C7   C8   120.60  3.000
 D3B  H4   C8   C9   119.29  3.000
 D3B  H4   C8   C7   119.50  3.000
 D3B  C9   C8   C7   121.21  3.000
 D3B  H5   N20  C22  118.16  3.000
 D3B  H5   N20  C7   116.53  3.000
 D3B  C22  N20  C7   124.48  3.000
 D3B  N24  C22  O23  123.40  3.000
 D3B  N24  C22  N20  112.83  3.000
 D3B  O23  C22  N20  123.77  3.000
 D3B  C2   C1   N24  117.89  3.000
 D3B  C2   C1   C6   118.94  3.000
 D3B  N24  C1   C6   123.13  3.000
 D3B  O1   C2   C1   116.63  3.000
 D3B  C1   C2   C3   120.36  3.000
 D3B  O1   C2   C3   123.01  3.000
 D3B  C14  C9   C10  121.19  3.000
 D3B  C10  C9   C8   118.25  3.000
 D3B  C14  C9   C8   120.54  3.000
 D3B  H7   C10  C11  119.57  3.000
 D3B  H7   C10  C9   119.89  3.000
 D3B  C11  C10  C9   120.54  3.000
 D3B  H8   C11  C12  118.96  3.000
 D3B  H8   C11  C10  119.32  3.000
 D3B  C12  C11  C10  121.71  3.000
 D3B  C13  C12  C11  121.02  3.000
 D3B  C13  C12  C7   121.30  3.000
 D3B  C11  C12  C7   117.67  3.000
 D3B  H9   O1   C2   111.01  3.000
 D3B  N5   S2   O4   112.80  3.000
 D3B  O4   S2   O3   117.99  3.000
 D3B  N5   S2   O3   105.59  3.000
 D3B  O3   S2   C5   110.00  3.000
 D3B  O4   S2   C5   107.88  3.000
 D3B  N5   S2   C5   101.30  3.000
 D3B  H11  N5   H10  110.00  3.000
 D3B  H11  N5   S2   112.48  3.000
 D3B  H10  N5   S2   111.31  3.000
 D3B  H14  C13  H13  107.73  3.000
 D3B  H14  C13  H12  107.04  3.000
 D3B  H13  C13  H12  106.98  3.000
 D3B  H14  C13  C12  111.62  3.000
 D3B  H13  C13  C12  110.76  3.000
 D3B  H12  C13  C12  112.46  3.000
 D3B  H17  C14  H16  108.03  3.000
 D3B  H17  C14  H15  107.27  3.000
 D3B  H16  C14  H15  107.21  3.000
 D3B  H17  C14  C9   111.39  3.000
 D3B  H16  C14  C9   111.74  3.000
 D3B  H15  C14  C9   110.99  3.000
 D3B  H6   N24  C1   116.12  3.000
 D3B  H6   N24  C22  118.14  3.000
 D3B  C1   N24  C22  124.92  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
 D3B  CONST_01  C6   C1   C2   C3     0.00   0.0  0
 D3B  CONST_02  C6   C5   C4   C3     0.00   0.0  0
 D3B  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 D3B  CONST_04  C1   C6   C5   C4     0.00   0.0  0
 D3B  CONST_05  C2   C1   C6   C5     0.00   0.0  0
 D3B  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 D3B  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 D3B  CONST_08  C10  C11  C12  C7     0.00   0.0  0
 D3B  CONST_09  C11  C10  C9   C8     0.00   0.0  0
 D3B  CONST_10  C11  C12  C7   C8     0.00   0.0  0
 D3B  CONST_11  C12  C11  C10  C9     0.00   0.0  0
 D3B  CONST_12  C12  C7   C8   C9     0.00   0.0  0
 D3B  CONST_13  N24  C1   C2   C3   180.00   0.0  0
 D3B  CONST_14  S2   C5   C4   C3   180.00   0.0  0
 D3B  CONST_15  O1   C2   C3   C4   180.00   0.0  0
 D3B  CONST_16  N24  C1   C6   C5   180.00   0.0  0
 D3B  CONST_17  O1   C2   C1   C6   180.00   0.0  0
 D3B  CONST_18  C14  C9   C8   C7   180.00   0.0  0
 D3B  CONST_19  C13  C12  C7   C8   180.00   0.0  0
 D3B  CONST_20  C9   C8   C7   N20  180.00   0.0  0
 D3B  CONST_21  C11  C12  C7   N20  180.00   0.0  0
 D3B  CONST_22  S2   C5   C6   C1   180.00   0.0  0
 D3B  CONST_23  C13  C12  C11  C10  180.00   0.0  0
 D3B  CONST_24  C14  C9   C10  C11  180.00   0.0  0
 D3B  CONST_25  H3   C6   C5   C4   180.00   0.0  0
 D3B  CONST_26  H1   C3   C4   C5   180.00   0.0  0
 D3B  CONST_27  H2   C4   C5   C6   180.00   0.0  0
 D3B  CONST_28  H8   C11  C12  C7   180.00   0.0  0
 D3B  CONST_29  H7   C10  C9   C8   180.00   0.0  0
 D3B  CONST_30  H4   C8   C9   C10  180.00   0.0  0
 D3B  CONST_37  O23  C22  N20  C7     0.00   0.0  0
 D3B  CONST_38  C1   N24  C22  O23    0.00   0.0  0
 D3B  CONST_39  N24  C22  N20  C7   180.00   0.0  0
 D3B  CONST_40  C1   N24  C22  N20  180.00   0.0  0
 D3B  Var_01    N5   S2   C5   C4   103.64  30.0  2
 D3B  Var_02    H12  C13  C12  C7    64.20  30.0  2
 D3B  Var_03    H15  C14  C9   C8   -80.44  30.0  2
 D3B  Var_04    H10  N5   S2   C5   163.80  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
 D3B  plan-1  C3   0.020
 D3B  plan-1  C4   0.020
 D3B  plan-1  C5   0.020
 D3B  plan-1  C6   0.020
 D3B  plan-1  C1   0.020
 D3B  plan-1  C2   0.020
 D3B  plan-1  O1   0.020
 D3B  plan-1  S2   0.020
 D3B  plan-1  H1   0.020
 D3B  plan-1  H2   0.020
 D3B  plan-1  H3   0.020
 D3B  plan-1  N24  0.020
 D3B  plan-2  C7   0.020
 D3B  plan-2  C8   0.020
 D3B  plan-2  N20  0.020
 D3B  plan-2  C9   0.020
 D3B  plan-2  C10  0.020
 D3B  plan-2  C11  0.020
 D3B  plan-2  C12  0.020
 D3B  plan-2  C13  0.020
 D3B  plan-2  C14  0.020
 D3B  plan-2  H4   0.020
 D3B  plan-2  H7   0.020
 D3B  plan-2  H8   0.020
 D3B  plan-3  C7   0.020
 D3B  plan-3  N20  0.020
 D3B  plan-3  C22  0.020
 D3B  plan-3  O23  0.020
 D3B  plan-3  C1   0.020
 D3B  plan-3  H5   0.020
 D3B  plan-3  H6   0.020
 D3B  plan-3  N24  0.020

