# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 16:24:06 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 3-{[4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-yl]amino}phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(c(C)n1)c2ccnc(Nc3cccc(O)c3)n2
#
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
 CK5  CK5  3-{[4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-yl]amino}phenol  ligand  35  21  .  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_CK5
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
 CK5  O7B   O  OH1   0  -0.637  -1.6317  -0.1624  -6.0466
 CK5  C3B   C  CR6   0   0.400  -0.5025  -0.0610  -5.3165
 CK5  C2B   C  CR16  0  -0.476  -0.5392  -0.0681  -3.9238
 CK5  C1B   C  CR6   0   0.382   0.6489   0.0335  -3.1993
 CK5  C6B   C  CR16  0  -0.385   1.8641   0.1427  -3.8866
 CK5  C5B   C  CR16  0  -0.233   1.8756   0.1489  -5.2695
 CK5  C4B   C  CR16  0  -0.369   0.7027   0.0482  -6.0027
 CK5  N7    N  NH1   0  -0.774   0.7266   0.0328  -1.8124
 CK5  C2    C  CR6   0   0.605  -0.2294  -0.0368  -0.8448
 CK5  N1    N  N     0  -0.472  -1.5127  -0.1269  -1.1746
 CK5  C6    C  CR16  0   0.008  -2.3669  -0.1924  -0.1600
 CK5  N3    N  N     0  -0.496   0.2581   0.0008   0.3971
 CK5  C4    C  CR6   0   0.305  -0.6021  -0.0705   1.4022
 CK5  C5    C  CR16  0  -0.402  -1.9783  -0.1729   1.1613
 CK5  C5A   C  CR5   0  -0.341  -0.0572  -0.0369   2.7508
 CK5  C1A   C  CR5   0   0.350   1.2443  -0.1646   3.1741
 CK5  C6A   C  CH3   0  -0.726   2.4551  -0.3829   2.3301
 CK5  S4A   S  S2    0   0.229  -1.0839   0.1864   4.1249
 CK5  C3A   C  CR5   0   0.076   0.2886   0.0960   5.1567
 CK5  N2A   N  N     0  -0.392   1.4073  -0.0868   4.5275
 CK5  C7A   C  CH3   0  -0.724   0.1570   0.2107   6.6332
 CK5  H7B   H  HOH1  0   0.473  -2.3999  -0.2316  -5.4689
 CK5  H2B   H  HCR6  0   0.298  -1.4827  -0.1546  -3.4049
 CK5  H6B   H  HCR6  0   0.263   2.7922   0.2248  -3.3340
 CK5  H5B   H  HCR6  0   0.258   2.8210   0.2358  -5.7894
 CK5  H4B   H  HCR6  0   0.258   0.7189   0.0530  -7.0847
 CK5  HN7   H  HNH1  0   0.409   1.6603   0.1002  -1.4355
 CK5  H6    H  HCR6  0   0.277  -3.4166  -0.2680  -0.4198
 CK5  H5    H  HCR6  0   0.274  -2.7114  -0.2438   1.9514
 CK5  H6A1  H  HCH3  0   0.254   2.7398   0.5292   1.8046
 CK5  H6A2  H  HCH3  0   0.247   3.2880  -0.6856   2.9617
 CK5  H6A3  H  HCH3  0   0.252   2.2883  -1.1425   1.5699
 CK5  H7A1  H  HCH3  0   0.268   1.1454   0.2452   7.0855
 CK5  H7A2  H  HCH3  0   0.268  -0.3886   1.1110   6.9149
 CK5  H7A3  H  HCH3  0   0.271  -0.3826  -0.6430   7.0449

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
 CK5  O7B  C3B   single    1.348  0.020  1.348
 CK5  O7B  H7B   single    0.850  0.020  0.980
 CK5  C3B  C2B   aromatic  1.393  0.020  1.393
 CK5  C3B  C4B   aromatic  1.391  0.020  1.391
 CK5  C2B  C1B   aromatic  1.395  0.020  1.395
 CK5  C2B  H2B   single    0.930  0.020  1.080
 CK5  C1B  C6B   aromatic  1.400  0.020  1.400
 CK5  C1B  N7    single    1.389  0.020  1.389
 CK5  C6B  C5B   aromatic  1.383  0.020  1.383
 CK5  C6B  H6B   single    0.930  0.020  1.080
 CK5  C5B  C4B   aromatic  1.387  0.020  1.387
 CK5  C5B  H5B   single    0.930  0.020  1.080
 CK5  C4B  H4B   single    0.930  0.020  1.080
 CK5  N7   C2    single    1.362  0.020  1.362
 CK5  N7   HN7   single    0.860  0.020  1.020
 CK5  C2   N1    aromatic  1.328  0.020  1.328
 CK5  C2   N3    aromatic  1.335  0.020  1.335
 CK5  N1   C6    aromatic  1.328  0.020  1.328
 CK5  C6   C5    aromatic  1.377  0.020  1.377
 CK5  C6   H6    single    0.930  0.020  1.080
 CK5  N3   C4    aromatic  1.325  0.020  1.325
 CK5  C4   C5    aromatic  1.401  0.020  1.401
 CK5  C4   C5A   single    1.455  0.020  1.455
 CK5  C5   H5    single    0.930  0.020  1.080
 CK5  C5A  C1A   aromatic  1.375  0.020  1.375
 CK5  C5A  S4A   aromatic  1.730  0.020  1.730
 CK5  C1A  C6A   single    1.492  0.020  1.492
 CK5  C1A  N2A   aromatic  1.365  0.020  1.365
 CK5  C6A  H6A1  single    0.970  0.020  1.090
 CK5  C6A  H6A2  single    0.970  0.020  1.090
 CK5  C6A  H6A3  single    0.970  0.020  1.090
 CK5  S4A  C3A   aromatic  1.719  0.020  1.719
 CK5  C3A  N2A   aromatic  1.297  0.020  1.297
 CK5  C3A  C7A   single    1.487  0.020  1.487
 CK5  C7A  H7A1  single    0.970  0.020  1.090
 CK5  C7A  H7A2  single    0.970  0.020  1.090
 CK5  C7A  H7A3  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
 CK5  H7B   O7B  C3B   110.39  3.000
 CK5  C4B   C3B  C2B   121.08  3.000
 CK5  C4B   C3B  O7B   117.66  3.000
 CK5  C2B   C3B  O7B   121.26  3.000
 CK5  H2B   C2B  C1B   120.01  3.000
 CK5  H2B   C2B  C3B   120.24  3.000
 CK5  C1B   C2B  C3B   119.75  3.000
 CK5  N7    C1B  C6B   116.20  3.000
 CK5  N7    C1B  C2B   124.47  3.000
 CK5  C6B   C1B  C2B   119.33  3.000
 CK5  H6B   C6B  C5B   120.18  3.000
 CK5  H6B   C6B  C1B   119.94  3.000
 CK5  C5B   C6B  C1B   119.88  3.000
 CK5  H5B   C5B  C4B   119.38  3.000
 CK5  H5B   C5B  C6B   119.19  3.000
 CK5  C4B   C5B  C6B   121.42  3.000
 CK5  H4B   C4B  C5B   121.04  3.000
 CK5  H4B   C4B  C3B   120.43  3.000
 CK5  C5B   C4B  C3B   118.53  3.000
 CK5  HN7   N7   C2    112.80  3.000
 CK5  HN7   N7   C1B   115.13  3.000
 CK5  C2    N7   C1B   132.07  3.000
 CK5  N3    C2   N1    125.87  3.000
 CK5  N3    C2   N7    113.78  3.000
 CK5  N1    C2   N7    120.35  3.000
 CK5  C6    N1   C2    115.79  3.000
 CK5  H6    C6   C5    120.28  3.000
 CK5  H6    C6   N1    116.30  3.000
 CK5  C5    C6   N1    123.42  3.000
 CK5  C4    N3   C2    117.86  3.000
 CK5  C5A   C4   C5    121.94  3.000
 CK5  C5A   C4   N3    117.31  3.000
 CK5  C5    C4   N3    120.75  3.000
 CK5  H5    C5   C4    123.08  3.000
 CK5  H5    C5   C6    120.61  3.000
 CK5  C4    C5   C6    116.31  3.000
 CK5  S4A   C5A  C1A   109.23  3.000
 CK5  S4A   C5A  C4    121.13  3.000
 CK5  C1A   C5A  C4    129.64  3.000
 CK5  N2A   C1A  C6A   118.18  3.000
 CK5  N2A   C1A  C5A   114.39  3.000
 CK5  C6A   C1A  C5A   127.43  3.000
 CK5  H6A3  C6A  H6A2  109.20  3.000
 CK5  H6A3  C6A  H6A1  106.70  3.000
 CK5  H6A2  C6A  H6A1  108.21  3.000
 CK5  H6A3  C6A  C1A   111.91  3.000
 CK5  H6A2  C6A  C1A   109.48  3.000
 CK5  H6A1  C6A  C1A   111.23  3.000
 CK5  C3A   S4A  C5A    89.78  3.000
 CK5  C7A   C3A  N2A   124.69  3.000
 CK5  C7A   C3A  S4A   121.42  3.000
 CK5  N2A   C3A  S4A   113.89  3.000
 CK5  C3A   N2A  C1A   112.71  3.000
 CK5  H7A3  C7A  H7A2  107.54  3.000
 CK5  H7A3  C7A  H7A1  108.52  3.000
 CK5  H7A2  C7A  H7A1  108.75  3.000
 CK5  H7A3  C7A  C3A   110.99  3.000
 CK5  H7A2  C7A  C3A   111.39  3.000
 CK5  H7A1  C7A  C3A   109.58  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
 CK5  CONST_01  C6B   C1B  C2B  C3B     0.00   0.0  0
 CK5  CONST_02  C6B   C5B  C4B  C3B     0.00   0.0  0
 CK5  CONST_03  C5B   C4B  C3B  C2B     0.00   0.0  0
 CK5  CONST_04  C5B   C6B  C1B  C2B     0.00   0.0  0
 CK5  CONST_05  C4B   C3B  C2B  C1B     0.00   0.0  0
 CK5  CONST_06  C4B   C5B  C6B  C1B     0.00   0.0  0
 CK5  CONST_07  C5    C6   N1   C2      0.00   0.0  0
 CK5  CONST_08  C5    C4   N3   C2      0.00   0.0  0
 CK5  CONST_09  C5A   C4   N3   C2    180.00   0.0  0
 CK5  CONST_10  C4    N3   C2   N1      0.00   0.0  0
 CK5  CONST_11  C4    C5   C6   N1      0.00   0.0  0
 CK5  CONST_12  N3    C2   N1   C6      0.00   0.0  0
 CK5  CONST_13  N3    C4   C5   C6      0.00   0.0  0
 CK5  CONST_14  C5A   C4   C5   C6    180.00   0.0  0
 CK5  CONST_15  C1A   C5A  C4   N3      0.00   0.0  0
 CK5  CONST_16  S4A   C5A  C4   N3    180.00   0.0  0
 CK5  CONST_17  N2A   C1A  C5A  C4    180.00   0.0  0
 CK5  CONST_18  C3A   S4A  C5A  C4    180.00   0.0  0
 CK5  CONST_19  C1A   C5A  C4   C5    180.00   0.0  0
 CK5  CONST_20  S4A   C5A  C4   C5      0.00   0.0  0
 CK5  CONST_21  C3A   N2A  C1A  C5A     0.00   0.0  0
 CK5  CONST_22  N2A   C3A  S4A  C5A     0.00   0.0  0
 CK5  CONST_23  C3A   S4A  C5A  C1A     0.00   0.0  0
 CK5  CONST_24  S4A   C3A  N2A  C1A     0.00   0.0  0
 CK5  CONST_25  N2A   C1A  C5A  S4A     0.00   0.0  0
 CK5  CONST_26  C1B   C2B  C3B  O7B   180.00   0.0  0
 CK5  CONST_27  C5B   C4B  C3B  O7B   180.00   0.0  0
 CK5  CONST_28  N7    C1B  C2B  C3B   180.00   0.0  0
 CK5  CONST_29  N7    C1B  C6B  C5B   180.00   0.0  0
 CK5  CONST_30  C6    N1   C2   N7    180.00   0.0  0
 CK5  CONST_31  C4    N3   C2   N7    180.00   0.0  0
 CK5  CONST_32  C6A   C1A  C5A  C4      0.00   0.0  0
 CK5  CONST_33  C7A   C3A  S4A  C5A   180.00   0.0  0
 CK5  CONST_34  C7A   C3A  N2A  C1A   180.00   0.0  0
 CK5  CONST_35  S4A   C5A  C1A  C6A   180.00   0.0  0
 CK5  CONST_36  C3A   N2A  C1A  C6A   180.00   0.0  0
 CK5  CONST_37  H5B   C5B  C4B  C3B   180.00   0.0  0
 CK5  CONST_38  H4B   C4B  C3B  C2B   180.00   0.0  0
 CK5  CONST_39  H6B   C6B  C1B  C2B   180.00   0.0  0
 CK5  CONST_40  H2B   C2B  C1B  C6B   180.00   0.0  0
 CK5  CONST_41  H6    C6   N1   C2    180.00   0.0  0
 CK5  CONST_42  H5    C5   C6   N1    180.00   0.0  0
 CK5  Var_01    C2    N7   C1B  C2B    -1.16  30.0  2
 CK5  Var_02    N1    C2   N7   C1B     0.19  30.0  2
 CK5  Var_03    H6A1  C6A  C1A  C5A    74.40  30.0  2
 CK5  Var_04    H7A1  C7A  C3A  S4A  -173.38  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
 CK5  plan-1  C4   0.020
 CK5  plan-1  C5A  0.020
 CK5  plan-1  C1A  0.020
 CK5  plan-1  C6A  0.020
 CK5  plan-1  S4A  0.020
 CK5  plan-1  C3A  0.020
 CK5  plan-1  N2A  0.020
 CK5  plan-1  C7A  0.020
 CK5  plan-2  O7B  0.020
 CK5  plan-2  C3B  0.020
 CK5  plan-2  C2B  0.020
 CK5  plan-2  C1B  0.020
 CK5  plan-2  C6B  0.020
 CK5  plan-2  C5B  0.020
 CK5  plan-2  C4B  0.020
 CK5  plan-2  N7   0.020
 CK5  plan-2  H2B  0.020
 CK5  plan-2  H6B  0.020
 CK5  plan-2  H5B  0.020
 CK5  plan-2  H4B  0.020
 CK5  plan-3  N7   0.020
 CK5  plan-3  C2   0.020
 CK5  plan-3  N1   0.020
 CK5  plan-3  C6   0.020
 CK5  plan-3  N3   0.020
 CK5  plan-3  C4   0.020
 CK5  plan-3  C5   0.020
 CK5  plan-3  C5A  0.020
 CK5  plan-3  H6   0.020
 CK5  plan-3  H5   0.020

