# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:06:12 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-(5-amino-2-chloropyridin-4-yl)-N'-(4-bromo-3-{[3-(hydroxymethyl)phenyl]ethynyl}-1,2-thiazol-5-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cnc(Cl)cc1NC(=O)Nc2snc(C#Cc3cccc(CO)c3)c2Br
#
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
 J7J  J7J  N-(5-amino-2-chloropyridin-4-yl)-N'-(4-bromo-3-{[3-(hydroxymethyl)phenyl]ethynyl}-1,2-thiazol-5-yl)urea  ligand  41  28  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J7J
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
 J7J  C1   C   CR16  0  -0.327  -5.8867   0.4713  -0.2193
 J7J  C2   C   CR6   0   0.451  -5.2346  -0.7140   0.0908
 J7J  C3   C   CR16  0  -0.200  -7.3773  -1.7640   0.1907
 J7J  C12  C   CR5   0   0.145   1.5947   1.2801   0.2556
 J7J  C13  C   CR5   0  -0.295   0.7666   0.1243   0.1856
 J7J  C14  C   CR5   0   0.278  -0.5580   0.4683   0.2177
 J7J  C17  C   CSP   0  -0.013   3.0112   1.2269   0.2288
 J7J  C18  C   CSP   0   0.178   4.2145   1.1505   0.1968
 J7J  C19  C   CR6   0   0.073   5.6301   1.0341   0.1454
 J7J  C20  C   CR16  0  -0.400   6.2128  -0.2251  -0.0324
 J7J  C21  C   CR6   0   0.113   7.5900  -0.3683  -0.0991
 J7J  C22  C   CR16  0  -0.315   8.3912   0.7686   0.0025
 J7J  C23  C   CR16  0  -0.184   7.8201   2.0210   0.1767
 J7J  C24  C   CR16  0  -0.350   6.4438   2.1636   0.2506
 J7J  C26  C   CH2   0  -0.229   8.2026  -1.7329  -0.2505
 J7J  N4   N   N     0  -0.333  -8.0066  -0.6356  -0.1281
 J7J  C5   C   CR6   0   0.114  -7.2696   0.4279  -0.3065
 J7J  C6   C   CR6   0   0.253  -6.0040  -1.8715   0.3268
 J7J  CL7  CL  CL    0  -0.149  -8.1105   1.9012  -0.6897
 J7J  N8   N   NH1   0  -0.808  -3.8602  -0.8764   0.1449
 J7J  C9   C   C     0   0.802  -2.9153   0.0977   0.1976
 J7J  O10  O   O     0  -0.495  -3.1344   1.2919   0.2767
 J7J  N11  N   N     0  -0.449   0.9600   2.4218   0.3387
 J7J  S15  S   S2    0   0.302  -0.6738   2.1855   0.3350
 J7J  N16  N   NH1   0  -0.746  -1.6273  -0.3766   0.1644
 J7J  O27  O   OH1   0  -0.662   9.2449  -1.6721  -1.1942
 J7J  N28  N   NH2   0  -0.892  -5.3538  -3.0717   0.6177
 J7J  H1   H   HCR6  0   0.323  -5.3529   1.3869  -0.4114
 J7J  H2   H   HCR6  0   0.272  -8.0003  -2.6378   0.3493
 J7J  H3   H   HCR6  0   0.249   5.5734  -1.0949  -0.1230
 J7J  H4   H   HCR6  0   0.239   9.4683   0.6783  -0.0514
 J7J  H5   H   HCR6  0   0.280   8.4540   2.8940   0.2567
 J7J  H6   H   HCR6  0   0.231   5.9995   3.1403   0.3873
 J7J  H7   H   HCH2  0   0.222   8.5707  -2.0623   0.7297
 J7J  H8   H   HCH2  0   0.229   7.4228  -2.4463  -0.5451
 J7J  H9   H   HNH1  0   0.441  -3.5588  -1.8428   0.1109
 J7J  H10  H   HNH1  0   0.427  -1.4443  -1.3685   0.0886
 J7J  H11  H   HOH1  0   0.439   9.7236  -2.5054  -1.1643
 J7J  H12  H   HNH2  0   0.395  -5.9775  -3.8661   0.6044
 J7J  H13  H   HNH2  0   0.410  -4.8713  -3.0586   1.5081
 J7J  BR2  BR  BR    0  -0.017   1.4112  -1.6168   0.0655

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
 J7J  N28  C6   single    1.396  0.020  1.396
 J7J  BR2  C13  single    1.860  0.020  1.860
 J7J  C6   C3   aromatic  1.384  0.020  1.384
 J7J  C6   C2   aromatic  1.410  0.020  1.410
 J7J  C23  C24  aromatic  1.386  0.020  1.386
 J7J  C23  C22  aromatic  1.387  0.020  1.387
 J7J  C24  C19  aromatic  1.396  0.020  1.396
 J7J  C3   N4   aromatic  1.331  0.020  1.331
 J7J  N8   C2   single    1.385  0.020  1.385
 J7J  N8   C9   single    1.358  0.020  1.358
 J7J  N16  C9   single    1.373  0.020  1.373
 J7J  N16  C14  single    1.364  0.020  1.364
 J7J  C13  C14  aromatic  1.369  0.020  1.369
 J7J  C13  C12  aromatic  1.424  0.020  1.424
 J7J  C2   C1   aromatic  1.388  0.020  1.388
 J7J  C22  C21  aromatic  1.395  0.020  1.395
 J7J  C9   O10  double    1.217  0.020  1.217
 J7J  C14  S15  aromatic  1.725  0.020  1.725
 J7J  N4   C5   aromatic  1.306  0.020  1.306
 J7J  C19  C18  single    1.421  0.020  1.421
 J7J  C19  C20  aromatic  1.399  0.020  1.399
 J7J  C18  C17  triple    1.206  0.020  1.206
 J7J  C17  C12  single    1.418  0.020  1.418
 J7J  C12  N11  aromatic  1.309  0.020  1.309
 J7J  C1   C5   aromatic  1.386  0.020  1.386
 J7J  C5   CL7  single    1.739  0.020  1.739
 J7J  C21  C20  aromatic  1.386  0.020  1.386
 J7J  C21  C26  single    1.503  0.020  1.503
 J7J  S15  N11  aromatic  1.651  0.020  1.651
 J7J  C26  O27  single    1.407  0.020  1.407
 J7J  C1   H1   single    0.930  0.020  1.080
 J7J  C3   H2   single    0.930  0.020  1.080
 J7J  C20  H3   single    0.930  0.020  1.080
 J7J  C22  H4   single    0.930  0.020  1.080
 J7J  C23  H5   single    0.930  0.020  1.080
 J7J  C24  H6   single    0.930  0.020  1.080
 J7J  C26  H7   single    0.970  0.020  1.090
 J7J  C26  H8   single    0.970  0.020  1.090
 J7J  N8   H9   single    0.860  0.020  1.020
 J7J  N16  H10  single    0.860  0.020  1.020
 J7J  O27  H11  single    0.850  0.020  0.980
 J7J  N28  H12  single    0.890  0.020  1.040
 J7J  N28  H13  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
 J7J  H1   C1   C5   120.65  3.000
 J7J  H1   C1   C2   122.21  3.000
 J7J  C5   C1   C2   117.13  3.000
 J7J  N8   C2   C6   116.03  3.000
 J7J  N8   C2   C1   125.11  3.000
 J7J  C6   C2   C1   118.83  3.000
 J7J  H2   C3   C6   119.53  3.000
 J7J  H2   C3   N4   116.52  3.000
 J7J  C6   C3   N4   123.96  3.000
 J7J  N11  C12  C17  121.23  3.000
 J7J  N11  C12  C13  115.42  3.000
 J7J  C17  C12  C13  123.35  3.000
 J7J  BR2  C13  C14  124.89  3.000
 J7J  C14  C13  C12  110.96  3.000
 J7J  BR2  C13  C12  124.16  3.000
 J7J  N16  C14  S15  124.52  3.000
 J7J  S15  C14  C13  108.46  3.000
 J7J  N16  C14  C13  127.02  3.000
 J7J  C18  C17  C12  180.00  3.000
 J7J  C19  C18  C17  180.00  3.000
 J7J  C24  C19  C20  119.68  3.000
 J7J  C20  C19  C18  119.55  3.000
 J7J  C24  C19  C18  120.76  3.000
 J7J  H3   C20  C21  119.96  3.000
 J7J  H3   C20  C19  119.18  3.000
 J7J  C21  C20  C19  120.86  3.000
 J7J  C26  C21  C22  120.87  3.000
 J7J  C26  C21  C20  120.22  3.000
 J7J  C22  C21  C20  118.89  3.000
 J7J  H4   C22  C23  119.42  3.000
 J7J  H4   C22  C21  120.01  3.000
 J7J  C23  C22  C21  120.57  3.000
 J7J  H5   C23  C24  119.67  3.000
 J7J  H5   C23  C22  119.77  3.000
 J7J  C24  C23  C22  120.56  3.000
 J7J  H6   C24  C23  120.50  3.000
 J7J  H6   C24  C19  120.05  3.000
 J7J  C23  C24  C19  119.45  3.000
 J7J  H8   C26  H7   106.44  3.000
 J7J  H8   C26  O27  111.98  3.000
 J7J  H7   C26  O27  111.31  3.000
 J7J  H8   C26  C21  109.12  3.000
 J7J  H7   C26  C21  108.61  3.000
 J7J  O27  C26  C21  109.27  3.000
 J7J  C5   N4   C3   117.15  3.000
 J7J  CL7  C5   N4   116.55  3.000
 J7J  CL7  C5   C1   118.01  3.000
 J7J  N4   C5   C1   125.43  3.000
 J7J  N28  C6   C3   123.33  3.000
 J7J  C3   C6   C2   117.47  3.000
 J7J  N28  C6   C2   119.12  3.000
 J7J  H9   N8   C9   118.59  3.000
 J7J  H9   N8   C2   113.94  3.000
 J7J  C9   N8   C2   127.43  3.000
 J7J  N16  C9   O10  120.63  3.000
 J7J  O10  C9   N8   125.54  3.000
 J7J  N16  C9   N8   113.83  3.000
 J7J  S15  N11  C12  110.79  3.000
 J7J  N11  S15  C14   94.37  3.000
 J7J  H10  N16  C9   120.68  3.000
 J7J  H10  N16  C14  117.94  3.000
 J7J  C9   N16  C14  121.37  3.000
 J7J  H11  O27  C26  108.08  3.000
 J7J  H13  N28  H12  108.42  3.000
 J7J  H13  N28  C6   113.21  3.000
 J7J  H12  N28  C6   112.70  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
 J7J  CONST_01  C3   C6   C2   C1     0.00   0.0  0
 J7J  CONST_02  C3   N4   C5   C1     0.00   0.0  0
 J7J  CONST_03  N4   C3   C6   C2     0.00   0.0  0
 J7J  CONST_04  N4   C5   C1   C2     0.00   0.0  0
 J7J  CONST_05  S15  C14  C13  C12    0.00   0.0  0
 J7J  CONST_06  C14  S15  N11  C12    0.00   0.0  0
 J7J  CONST_07  N11  S15  C14  C13    0.00   0.0  0
 J7J  CONST_08  S15  N11  C12  C13    0.00   0.0  0
 J7J  CONST_09  N11  C12  C13  C14    0.00   0.0  0
 J7J  CONST_10  C22  C23  C24  C19    0.00   0.0  0
 J7J  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 J7J  CONST_12  C23  C24  C19  C20    0.00   0.0  0
 J7J  CONST_13  C23  C22  C21  C20    0.00   0.0  0
 J7J  CONST_14  C24  C23  C22  C21    0.00   0.0  0
 J7J  CONST_15  C24  C19  C20  C21    0.00   0.0  0
 J7J  CONST_16  C6   C3   N4   C5     0.00   0.0  0
 J7J  CONST_17  C6   C2   C1   C5     0.00   0.0  0
 J7J  CONST_18  N28  C6   C2   C1   180.00   0.0  0
 J7J  CONST_19  CL7  C5   C1   C2   180.00   0.0  0
 J7J  CONST_20  N8   C2   C6   C3   180.00   0.0  0
 J7J  CONST_21  CL7  C5   N4   C3   180.00   0.0  0
 J7J  CONST_22  N16  C14  C13  C12  180.00   0.0  0
 J7J  CONST_23  C17  C12  C13  C14  180.00   0.0  0
 J7J  CONST_24  S15  N11  C12  C17  180.00   0.0  0
 J7J  CONST_25  C23  C24  C19  C18  180.00   0.0  0
 J7J  CONST_26  C21  C20  C19  C18  180.00   0.0  0
 J7J  CONST_27  C26  C21  C20  C19  180.00   0.0  0
 J7J  CONST_28  C26  C21  C22  C23  180.00   0.0  0
 J7J  CONST_29  N28  C6   C3   N4   180.00   0.0  0
 J7J  CONST_30  N8   C2   C1   C5   180.00   0.0  0
 J7J  CONST_31  BR2  C13  C12  N11  180.00   0.0  0
 J7J  CONST_32  N16  C14  S15  N11  180.00   0.0  0
 J7J  CONST_33  BR2  C13  C14  S15  180.00   0.0  0
 J7J  CONST_34  H2   C3   C6   C2   180.00   0.0  0
 J7J  CONST_35  H5   C23  C24  C19  180.00   0.0  0
 J7J  CONST_36  H6   C24  C19  C20  180.00   0.0  0
 J7J  CONST_37  H4   C22  C21  C20  180.00   0.0  0
 J7J  CONST_38  H3   C20  C21  C22  180.00   0.0  0
 J7J  CONST_39  H1   C1   C5   N4   180.00   0.0  0
 J7J  CONST_41  C9   N16  C14  C13  180.00   0.0  0
 J7J  CONST_42  C9   N8   C2   C6   180.00   0.0  0
 J7J  CONST_43  S15  C14  N16  C9     0.00   0.0  0
 J7J  CONST_45  H12  N28  C6   C2   180.00   0.0  0
 J7J  CONST_47  H10  N16  C14  C13    0.00   0.0  0
 J7J  CONST_48  O10  C9   N8   C2     0.00   0.0  0
 J7J  CONST_49  O10  C9   N16  C14    0.00   0.0  0
 J7J  CONST_50  N16  C9   N8   C2   180.00   0.0  0
 J7J  CONST_51  N8   C9   N16  C14  180.00   0.0  0
 J7J  Var_01    O27  C26  C21  C20  137.09  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
 J7J  plan-1  C12  0.020
 J7J  plan-1  C13  0.020
 J7J  plan-1  C14  0.020
 J7J  plan-1  C17  0.020
 J7J  plan-1  C18  0.020
 J7J  plan-1  N11  0.020
 J7J  plan-1  S15  0.020
 J7J  plan-1  N16  0.020
 J7J  plan-1  BR2  0.020
 J7J  plan-2  C17  0.020
 J7J  plan-2  C18  0.020
 J7J  plan-2  C19  0.020
 J7J  plan-2  C20  0.020
 J7J  plan-2  C21  0.020
 J7J  plan-2  C22  0.020
 J7J  plan-2  C23  0.020
 J7J  plan-2  C24  0.020
 J7J  plan-2  C26  0.020
 J7J  plan-2  H3   0.020
 J7J  plan-2  H4   0.020
 J7J  plan-2  H5   0.020
 J7J  plan-2  H6   0.020
 J7J  plan-3  C1   0.020
 J7J  plan-3  C2   0.020
 J7J  plan-3  C3   0.020
 J7J  plan-3  N4   0.020
 J7J  plan-3  C5   0.020
 J7J  plan-3  C6   0.020
 J7J  plan-3  CL7  0.020
 J7J  plan-3  N8   0.020
 J7J  plan-3  N28  0.020
 J7J  plan-3  H1   0.020
 J7J  plan-3  H2   0.020
 J7J  plan-4  C2   0.020
 J7J  plan-4  C14  0.020
 J7J  plan-4  N8   0.020
 J7J  plan-4  C9   0.020
 J7J  plan-4  O10  0.020
 J7J  plan-4  N16  0.020
 J7J  plan-4  H9   0.020
 J7J  plan-4  H10  0.020
 J7J  plan-5  C6   0.020
 J7J  plan-5  N28  0.020
 J7J  plan-5  H12  0.020
 J7J  plan-5  H13  0.020

