# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:12:22 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: N-(5-methylthiophen-2-yl)-N'-pyridin-3-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(NC(=O)Nc2cccnc2)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
 UH4  UH4  N-(5-methylthiophen-2-yl)-N'-pyridin-3-ylurea  ligand  27  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UH4
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
 UH4  N1   N  NH1   0  -0.799   7.1927  -0.1202  20.8801
 UH4  C4   C  CR5   0   0.106  10.3643  -0.1786  22.5796
 UH4  C5   C  C     0   0.759   8.4755   0.2778  21.1230
 UH4  C6   C  CR6   0   0.301   6.3105   0.3566  19.9156
 UH4  C7   C  CR16  0  -0.252   5.0339  -0.2070  19.8854
 UH4  C8   C  CR16  0  -0.308   4.1199   0.2267  18.9463
 UH4  C10  C  CR16  0  -0.120   6.5970   1.3509  18.9742
 UH4  O    O  O     0  -0.494   9.0646   1.1442  20.4985
 UH4  N    N  NH1   0  -0.752   9.0658  -0.3927  22.1531
 UH4  C3   C  CR15  0  -0.294  10.9781  -0.8444  23.5981
 UH4  C2   C  CR15  0  -0.206  12.3173  -0.4068  23.8002
 UH4  S    S  S2    0   0.212  11.4186   0.9913  21.8596
 UH4  C1   C  CR5   0  -0.182  12.7056   0.5752  22.9461
 UH4  C    C  CH3   0  -0.714  14.0205   1.2733  22.8590
 UH4  N2   N  N     0  -0.391   5.7103   1.7612  18.0756
 UH4  C9   C  CR16  0  -0.090   4.5021   1.2187  18.0551
 UH4  H1   H  HNH1  0   0.420   6.8197  -0.8569  21.4597
 UH4  H2   H  HCR6  0   0.287   4.7629  -0.9793  20.5962
 UH4  H3   H  HCR6  0   0.275   3.1262  -0.1975  18.9070
 UH4  H4   H  HCR6  0   0.282   7.5651   1.8269  18.9443
 UH4  H5   H  HNH1  0   0.425   8.5488  -1.0941  22.6634
 UH4  H6   H  HCR5  0   0.267  10.4944  -1.6171  24.1798
 UH4  H7   H  HCR5  0   0.257  12.9668  -0.8192  24.5606
 UH4  H8   H  HCH3  0   0.248  14.4777   1.1644  21.8743
 UH4  H9   H  HCH3  0   0.248  13.9309   2.3424  23.0588
 UH4  H10  H  HCH3  0   0.253  14.7088   0.8552  23.5924
 UH4  H11  H  HCR6  0   0.262   3.8117   1.5845  17.3039

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
 UH4  N2   C9   aromatic  1.325  0.020  1.325
 UH4  N2   C10  aromatic  1.327  0.020  1.327
 UH4  C9   C8   aromatic  1.387  0.020  1.387
 UH4  C10  C6   aromatic  1.399  0.020  1.399
 UH4  C8   C7   aromatic  1.380  0.020  1.380
 UH4  C6   C7   aromatic  1.396  0.020  1.396
 UH4  C6   N1   single    1.391  0.020  1.391
 UH4  O    C5   double    1.220  0.020  1.220
 UH4  N1   C5   single    1.365  0.020  1.365
 UH4  C5   N    single    1.364  0.020  1.364
 UH4  N    C4   single    1.383  0.020  1.383
 UH4  S    C4   aromatic  1.732  0.020  1.732
 UH4  S    C1   aromatic  1.735  0.020  1.735
 UH4  C4   C3   aromatic  1.363  0.020  1.363
 UH4  C1   C    single    1.491  0.020  1.491
 UH4  C1   C2   aromatic  1.358  0.020  1.358
 UH4  C3   C2   aromatic  1.423  0.020  1.423
 UH4  N1   H1   single    0.860  0.020  1.020
 UH4  C7   H2   single    0.930  0.020  1.080
 UH4  C8   H3   single    0.930  0.020  1.080
 UH4  C10  H4   single    0.930  0.020  1.080
 UH4  N    H5   single    0.860  0.020  1.020
 UH4  C3   H6   single    0.930  0.020  1.080
 UH4  C2   H7   single    0.930  0.020  1.080
 UH4  C    H8   single    0.970  0.020  1.090
 UH4  C    H9   single    0.970  0.020  1.090
 UH4  C    H10  single    0.970  0.020  1.090
 UH4  C9   H11  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
 UH4  H1   N1   C6   114.46  3.000
 UH4  H1   N1   C5   117.27  3.000
 UH4  C6   N1   C5   128.27  3.000
 UH4  S    C4   C3   111.50  3.000
 UH4  C3   C4   N    125.28  3.000
 UH4  S    C4   N    123.22  3.000
 UH4  N    C5   O    121.81  3.000
 UH4  N    C5   N1   113.45  3.000
 UH4  O    C5   N1   124.74  3.000
 UH4  C10  C6   C7   117.37  3.000
 UH4  C7   C6   N1   117.16  3.000
 UH4  C10  C6   N1   125.47  3.000
 UH4  H2   C7   C8   120.29  3.000
 UH4  H2   C7   C6   120.14  3.000
 UH4  C8   C7   C6   119.57  3.000
 UH4  H3   C8   C9   120.69  3.000
 UH4  H3   C8   C7   120.67  3.000
 UH4  C9   C8   C7   118.64  3.000
 UH4  H4   C10  N2   116.36  3.000
 UH4  H4   C10  C6   121.06  3.000
 UH4  N2   C10  C6   122.58  3.000
 UH4  H5   N    C5   120.11  3.000
 UH4  H5   N    C4   115.62  3.000
 UH4  C5   N    C4   124.27  3.000
 UH4  H6   C3   C2   124.35  3.000
 UH4  H6   C3   C4   123.34  3.000
 UH4  C2   C3   C4   112.31  3.000
 UH4  H7   C2   C1   123.10  3.000
 UH4  H7   C2   C3   123.20  3.000
 UH4  C1   C2   C3   113.70  3.000
 UH4  C1   S    C4    91.68  3.000
 UH4  C    C1   S    120.35  3.000
 UH4  C    C1   C2   128.85  3.000
 UH4  S    C1   C2   110.80  3.000
 UH4  H10  C    H9   107.74  3.000
 UH4  H10  C    H8   107.73  3.000
 UH4  H9   C    H8   107.30  3.000
 UH4  H10  C    C1   109.76  3.000
 UH4  H9   C    C1   112.06  3.000
 UH4  H8   C    C1   112.06  3.000
 UH4  C9   N2   C10  119.55  3.000
 UH4  H11  C9   N2   116.97  3.000
 UH4  H11  C9   C8   120.73  3.000
 UH4  N2   C9   C8   122.29  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
 UH4  CONST_01  C2   C1   S    C4     0.00   0.0  0
 UH4  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 UH4  CONST_03  C9   N2   C10  C6     0.00   0.0  0
 UH4  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 UH4  CONST_05  N2   C9   C8   C7     0.00   0.0  0
 UH4  CONST_06  N2   C10  C6   C7     0.00   0.0  0
 UH4  CONST_07  C10  N2   C9   C8     0.00   0.0  0
 UH4  CONST_08  C10  C6   C7   C8     0.00   0.0  0
 UH4  CONST_09  C1   S    C4   C3     0.00   0.0  0
 UH4  CONST_10  S    C1   C2   C3     0.00   0.0  0
 UH4  CONST_11  S    C4   C3   C2     0.00   0.0  0
 UH4  CONST_12  N2   C10  C6   N1   180.00   0.0  0
 UH4  CONST_13  C8   C7   C6   N1   180.00   0.0  0
 UH4  CONST_14  C    C1   S    C4   180.00   0.0  0
 UH4  CONST_15  C1   S    C4   N    180.00   0.0  0
 UH4  CONST_16  C2   C3   C4   N    180.00   0.0  0
 UH4  CONST_17  C    C1   C2   C3   180.00   0.0  0
 UH4  CONST_18  H7   C2   C3   C4   180.00   0.0  0
 UH4  CONST_19  H3   C8   C7   C6   180.00   0.0  0
 UH4  CONST_20  H11  C9   C8   C7   180.00   0.0  0
 UH4  CONST_21  H4   C10  C6   C7   180.00   0.0  0
 UH4  CONST_22  H2   C7   C6   C10  180.00   0.0  0
 UH4  CONST_23  H6   C3   C4   S    180.00   0.0  0
 UH4  CONST_24  C10  C6   N1   C5     0.00   0.0  0
 UH4  CONST_25  C7   C6   N1   C5   180.00   0.0  0
 UH4  CONST_26  S    C4   N    C5     0.00   0.0  0
 UH4  CONST_27  C3   C4   N    C5   180.00   0.0  0
 UH4  CONST_28  H1   N1   C6   C7     0.00   0.0  0
 UH4  CONST_29  H5   N    C4   C3     0.00   0.0  0
 UH4  CONST_30  O    C5   N    C4     0.00   0.0  0
 UH4  CONST_31  O    C5   N1   C6     0.00   0.0  0
 UH4  CONST_32  C4   N    C5   N1   180.00   0.0  0
 UH4  CONST_33  N    C5   N1   C6   180.00   0.0  0
 UH4  Var_01    H8   C    C1   C2   121.73  30.0  2

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
 UH4  plan-1  C4   0.020
 UH4  plan-1  N    0.020
 UH4  plan-1  C3   0.020
 UH4  plan-1  C2   0.020
 UH4  plan-1  S    0.020
 UH4  plan-1  C1   0.020
 UH4  plan-1  C    0.020
 UH4  plan-1  H6   0.020
 UH4  plan-1  H7   0.020
 UH4  plan-2  N1   0.020
 UH4  plan-2  C6   0.020
 UH4  plan-2  C7   0.020
 UH4  plan-2  C8   0.020
 UH4  plan-2  C10  0.020
 UH4  plan-2  N2   0.020
 UH4  plan-2  C9   0.020
 UH4  plan-2  H2   0.020
 UH4  plan-2  H3   0.020
 UH4  plan-2  H4   0.020
 UH4  plan-2  H11  0.020
 UH4  plan-3  N1   0.020
 UH4  plan-3  C4   0.020
 UH4  plan-3  C5   0.020
 UH4  plan-3  C6   0.020
 UH4  plan-3  O    0.020
 UH4  plan-3  N    0.020
 UH4  plan-3  H1   0.020
 UH4  plan-3  H5   0.020

