# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 18:34:37 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-[(4-methylphenyl)methyl]-3-(2-oxidanyl-5-sulfamoyl-phenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CNC(=O)Nc2cc(ccc2O)[S](N)(=O)=O)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
 CJK  CJK  1-[(4-methylphenyl)methyl]-3-(2-oxidanyl-5-sulfamoyl-phenyl)urea  ligand  40  23  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CJK
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
 CJK  C1   C  CH3   0  -0.722   6.4484   2.0815   1.4546
 CJK  C3   C  CR16  0  -0.284   4.3636   1.5257   0.1532
 CJK  C5   C  CR6   0   0.109   4.0561  -0.6099  -0.9336
 CJK  C6   C  CR16  0  -0.292   5.2946  -1.0040  -0.4433
 CJK  C7   C  CR16  0  -0.287   6.0607  -0.1439   0.3346
 CJK  C8   C  CH2   0  -0.389   3.2141  -1.5487  -1.7609
 CJK  C10  C  C     0   0.726   0.8199  -1.5036  -1.1996
 CJK  N12  N  NH1   0  -0.790  -0.1430  -2.0685  -0.3842
 CJK  C13  C  CR6   0   0.199  -1.4202  -1.4717  -0.3020
 CJK  C14  C  CR16  0  -0.223  -1.6955  -0.4432   0.5771
 CJK  C15  C  CR6   0  -0.245  -2.9746   0.0958   0.6270
 CJK  C16  C  CR16  0  -0.223  -3.9805  -0.3830  -0.2029
 CJK  C17  C  CR16  0  -0.344  -3.7090  -1.4097  -1.0868
 CJK  C18  C  CR6   0   0.354  -2.4320  -1.9641  -1.1400
 CJK  O21  O  OS    0  -0.654  -4.7538   1.5307   1.8853
 CJK  C2   C  CR6   0   0.085   5.6104   1.1353   0.6443
 CJK  C4   C  CR16  0  -0.281   3.5990   0.6697  -0.6227
 CJK  N9   N  NH1   0  -0.657   2.0509  -2.0359  -1.0528
 CJK  O11  O  O     0  -0.518   0.5372  -0.6265  -2.0015
 CJK  O19  O  OH1   0  -0.600  -2.1980  -2.9649  -1.9871
 CJK  S20  S  S     0   1.360  -3.3072   1.4003   1.7621
 CJK  O22  O  OS    0  -0.669  -2.5299   1.2038   2.9781
 CJK  N23  N  NC2   0  -0.887  -2.6110   2.6869   0.9901
 CJK  H1   H  HCH3  0   0.248   7.0510   2.7208   0.8061
 CJK  H2   H  HCH3  0   0.243   5.8304   2.7366   2.0681
 CJK  H3   H  HCH3  0   0.243   7.1342   1.5496   2.1135
 CJK  H4   H  HCR6  0   0.245   3.9869   2.5166   0.3804
 CJK  H5   H  HCR6  0   0.249   5.6704  -1.9961  -0.6669
 CJK  H6   H  HCR6  0   0.246   7.0223  -0.4772   0.7069
 CJK  H7   H  HCH2  0   0.266   2.8756  -1.0543  -2.6705
 CJK  H8   H  HCH2  0   0.266   3.8101  -2.4081  -2.0713
 CJK  H9   H  HNH1  0   0.410   0.1526  -2.6267   0.4040
 CJK  H10  H  HCR6  0   0.290  -0.9059  -0.0737   1.2189
 CJK  H11  H  HCR6  0   0.286  -4.9777   0.0329  -0.1640
 CJK  H12  H  HCR6  0   0.283  -4.4875  -1.7920  -1.7335
 CJK  H13  H  HCR6  0   0.248   2.6362   1.0006  -0.9939
 CJK  H14  H  HNH1  0   0.399   2.2082  -2.7217  -0.3317
 CJK  H15  H  HOH1  0   0.479  -1.2927  -3.2850  -1.8566
 CJK  H16  H  HNC2  0   0.414  -3.1341   2.9738   0.1688
 CJK  H17  H  HNC2  0   0.418  -2.4937   3.4763   1.6192

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
 CJK  C1   C2   single    1.501  0.020  1.501
 CJK  C2   C7   aromatic  1.391  0.020  1.391
 CJK  C2   C3   aromatic  1.396  0.020  1.396
 CJK  C7   C6   aromatic  1.390  0.020  1.390
 CJK  C3   C4   aromatic  1.385  0.020  1.385
 CJK  C6   C5   aromatic  1.389  0.020  1.389
 CJK  C4   C5   aromatic  1.394  0.020  1.394
 CJK  C5   C8   single    1.508  0.020  1.508
 CJK  O19  C18  single    1.332  0.020  1.332
 CJK  O11  C10  double    1.222  0.020  1.222
 CJK  C10  N12  single    1.382  0.020  1.382
 CJK  C10  N9   single    1.349  0.020  1.349
 CJK  C8   N9   single    1.446  0.020  1.446
 CJK  C18  C17  aromatic  1.393  0.020  1.393
 CJK  C18  C13  aromatic  1.403  0.020  1.403
 CJK  N12  C13  single    1.412  0.020  1.412
 CJK  C17  C16  aromatic  1.382  0.020  1.382
 CJK  C13  C14  aromatic  1.381  0.020  1.381
 CJK  C16  C15  aromatic  1.389  0.020  1.389
 CJK  C14  C15  aromatic  1.389  0.020  1.389
 CJK  C15  S20  single    1.761  0.020  1.761
 CJK  N23  S20  single    1.654  0.020  1.654
 CJK  S20  O21  double    1.458  0.020  1.458
 CJK  S20  O22  double    1.457  0.020  1.457
 CJK  C1   H1   single    0.970  0.020  1.090
 CJK  C1   H2   single    0.970  0.020  1.090
 CJK  C1   H3   single    0.970  0.020  1.090
 CJK  C3   H4   single    0.930  0.020  1.080
 CJK  C6   H5   single    0.930  0.020  1.080
 CJK  C7   H6   single    0.930  0.020  1.080
 CJK  C8   H7   single    0.970  0.020  1.090
 CJK  C8   H8   single    0.970  0.020  1.090
 CJK  N12  H9   single    0.890  0.020  1.040
 CJK  C14  H10  single    0.930  0.020  1.080
 CJK  C16  H11  single    0.930  0.020  1.080
 CJK  C17  H12  single    0.930  0.020  1.080
 CJK  C4   H13  single    0.930  0.020  1.080
 CJK  N9   H14  single    0.860  0.020  1.020
 CJK  O19  H15  single    0.850  0.020  0.980
 CJK  N23  H16  single    0.890  0.020  1.040
 CJK  N23  H17  single    0.890  0.020  1.040

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
 CJK  H3   C1   H2   108.05  3.000
 CJK  H3   C1   H1   107.31  3.000
 CJK  H2   C1   H1   107.18  3.000
 CJK  H3   C1   C2   111.71  3.000
 CJK  H2   C1   C2   111.48  3.000
 CJK  H1   C1   C2   110.88  3.000
 CJK  H4   C3   C4   119.36  3.000
 CJK  H4   C3   C2   119.49  3.000
 CJK  C4   C3   C2   121.15  3.000
 CJK  C4   C5   C8   120.71  3.000
 CJK  C8   C5   C6   120.98  3.000
 CJK  C4   C5   C6   118.30  3.000
 CJK  H5   C6   C7   119.38  3.000
 CJK  H5   C6   C5   119.73  3.000
 CJK  C7   C6   C5   120.90  3.000
 CJK  H6   C7   C2   119.58  3.000
 CJK  H6   C7   C6   119.41  3.000
 CJK  C2   C7   C6   121.01  3.000
 CJK  H8   C8   H7   106.84  3.000
 CJK  H8   C8   N9   108.26  3.000
 CJK  H7   C8   N9   108.17  3.000
 CJK  H8   C8   C5   109.96  3.000
 CJK  H7   C8   C5   110.43  3.000
 CJK  N9   C8   C5   112.96  3.000
 CJK  O11  C10  N9   124.46  3.000
 CJK  N9   C10  N12  114.21  3.000
 CJK  O11  C10  N12  121.29  3.000
 CJK  H9   N12  C13  116.93  3.000
 CJK  H9   N12  C10  118.83  3.000
 CJK  C13  N12  C10  119.44  3.000
 CJK  C18  C13  C14  119.86  3.000
 CJK  C14  C13  N12  122.15  3.000
 CJK  C18  C13  N12  117.98  3.000
 CJK  H10  C14  C15  121.19  3.000
 CJK  H10  C14  C13  119.10  3.000
 CJK  C15  C14  C13  119.71  3.000
 CJK  S20  C15  C16  120.24  3.000
 CJK  S20  C15  C14  118.99  3.000
 CJK  C16  C15  C14  120.77  3.000
 CJK  H11  C16  C17  119.35  3.000
 CJK  H11  C16  C15  120.91  3.000
 CJK  C17  C16  C15  119.74  3.000
 CJK  H12  C17  C18  119.75  3.000
 CJK  H12  C17  C16  120.24  3.000
 CJK  C18  C17  C16  120.02  3.000
 CJK  O19  C18  C17  118.97  3.000
 CJK  C17  C18  C13  119.91  3.000
 CJK  O19  C18  C13  121.12  3.000
 CJK  C7   C2   C3   117.91  3.000
 CJK  C3   C2   C1   120.81  3.000
 CJK  C7   C2   C1   121.27  3.000
 CJK  H13  C4   C5   119.68  3.000
 CJK  H13  C4   C3   119.58  3.000
 CJK  C5   C4   C3   120.74  3.000
 CJK  H14  N9   C10  119.26  3.000
 CJK  H14  N9   C8   117.01  3.000
 CJK  C10  N9   C8   123.21  3.000
 CJK  H15  O19  C18  109.07  3.000
 CJK  N23  S20  O22  105.66  3.000
 CJK  O22  S20  O21  118.11  3.000
 CJK  N23  S20  O21  112.80  3.000
 CJK  O22  S20  C15  109.72  3.000
 CJK  O21  S20  C15  107.95  3.000
 CJK  N23  S20  C15  101.30  3.000
 CJK  H17  N23  H16  109.92  3.000
 CJK  H17  N23  S20  111.34  3.000
 CJK  H16  N23  S20  112.37  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
 CJK  CONST_01  C6   C7   C2   C3     0.00   0.0  0
 CJK  CONST_02  C6   C5   C4   C3     0.00   0.0  0
 CJK  CONST_03  C2   C7   C6   C5     0.00   0.0  0
 CJK  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 CJK  CONST_05  C4   C3   C2   C7     0.00   0.0  0
 CJK  CONST_06  C4   C5   C6   C7     0.00   0.0  0
 CJK  CONST_07  C16  C17  C18  C13    0.00   0.0  0
 CJK  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 CJK  CONST_09  C17  C18  C13  C14    0.00   0.0  0
 CJK  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 CJK  CONST_11  C18  C17  C16  C15    0.00   0.0  0
 CJK  CONST_12  C18  C13  C14  C15    0.00   0.0  0
 CJK  CONST_13  C6   C7   C2   C1   180.00   0.0  0
 CJK  CONST_14  C4   C3   C2   C1   180.00   0.0  0
 CJK  CONST_15  C8   C5   C4   C3   180.00   0.0  0
 CJK  CONST_16  C8   C5   C6   C7   180.00   0.0  0
 CJK  CONST_17  C17  C18  C13  N12  180.00   0.0  0
 CJK  CONST_18  C15  C14  C13  N12  180.00   0.0  0
 CJK  CONST_19  S20  C15  C14  C13  180.00   0.0  0
 CJK  CONST_20  O19  C18  C13  C14  180.00   0.0  0
 CJK  CONST_21  O19  C18  C17  C16  180.00   0.0  0
 CJK  CONST_22  S20  C15  C16  C17  180.00   0.0  0
 CJK  CONST_23  H6   C7   C2   C3   180.00   0.0  0
 CJK  CONST_24  H4   C3   C4   C5   180.00   0.0  0
 CJK  CONST_25  H13  C4   C5   C6   180.00   0.0  0
 CJK  CONST_26  H12  C17  C18  C13  180.00   0.0  0
 CJK  CONST_27  H11  C16  C15  C14  180.00   0.0  0
 CJK  CONST_28  H10  C14  C15  C16  180.00   0.0  0
 CJK  CONST_29  H5   C6   C7   C2   180.00   0.0  0
 CJK  CONST_33  O11  C10  N12  C13    0.00   0.0  0
 CJK  CONST_34  N9   C10  N12  C13  180.00   0.0  0
 CJK  CONST_35  O11  C10  N9   C8     0.00   0.0  0
 CJK  CONST_36  N12  C10  N9   C8   180.00   0.0  0
 CJK  CONST_37  H14  N9   C10  O11  180.00   0.0  0
 CJK  Var_01    N9   C8   C5   C6   108.30  30.0  2
 CJK  Var_02    N23  S20  C15  C14   76.69  30.0  2
 CJK  Var_03    H1   C1   C2   C3   -85.54  30.0  2
 CJK  Var_04    C10  N9   C8   C5    98.20  30.0  3
 CJK  Var_05    H16  N23  S20  C15   71.39  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
 CJK  plan-1  N12  0.020
 CJK  plan-1  C13  0.020
 CJK  plan-1  C14  0.020
 CJK  plan-1  C15  0.020
 CJK  plan-1  C16  0.020
 CJK  plan-1  C17  0.020
 CJK  plan-1  C18  0.020
 CJK  plan-1  O19  0.020
 CJK  plan-1  S20  0.020
 CJK  plan-1  H10  0.020
 CJK  plan-1  H11  0.020
 CJK  plan-1  H12  0.020
 CJK  plan-2  C1   0.020
 CJK  plan-2  C3   0.020
 CJK  plan-2  C5   0.020
 CJK  plan-2  C6   0.020
 CJK  plan-2  C7   0.020
 CJK  plan-2  C8   0.020
 CJK  plan-2  C2   0.020
 CJK  plan-2  C4   0.020
 CJK  plan-2  H4   0.020
 CJK  plan-2  H5   0.020
 CJK  plan-2  H6   0.020
 CJK  plan-2  H13  0.020
 CJK  plan-3  C8   0.020
 CJK  plan-3  C10  0.020
 CJK  plan-3  N12  0.020
 CJK  plan-3  C13  0.020
 CJK  plan-3  N9   0.020
 CJK  plan-3  O11  0.020
 CJK  plan-3  H9   0.020
 CJK  plan-3  H14  0.020

