# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:37:57 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-({2-[(4-methyl-1,3-thiazol-2-yl)amino]pyridin-3-yl}oxy)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1csc(Nc2ncccc2Oc3ccccc3C#N)n1
#
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
 HKM  HKM  2-({2-[(4-methyl-1,3-thiazol-2-yl)amino]pyridin-3-yl}oxy)benzonitrile  ligand  34  22  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HKM
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
 HKM  C18  C  CR16  0  -0.235  -4.9209   0.9024  -1.5726
 HKM  C13  C  CR6   0   0.183  -0.8842  -1.0458  -0.5916
 HKM  C12  C  CR16  0  -0.206  -1.6064  -2.1883  -0.3453
 HKM  C17  C  CR16  0  -0.310  -3.6266   0.4981  -1.8712
 HKM  C16  C  CR6   0   0.355  -2.6840   0.4385  -0.8624
 HKM  C15  C  CSP   0   0.060  -2.0391   0.7725   1.4713
 HKM  C11  C  CR16  0  -0.352  -0.9582  -3.2834   0.2260
 HKM  C10  C  CR16  0  -0.051   0.3848  -3.1697   0.5131
 HKM  C8   C  CR6   0   0.522   0.4814  -1.0192  -0.2565
 HKM  N2   N  N     0  -0.454   3.1214   1.4276  -0.4676
 HKM  C6   C  CH3   0  -0.726   5.2826   2.6136  -0.3461
 HKM  C1   C  CR5   0   0.282   2.5428   0.2957  -0.2097
 HKM  C4   C  CR15  0  -0.569   4.8737   0.2237   0.4015
 HKM  C19  C  CR16  0  -0.247  -5.2792   1.2346  -0.2725
 HKM  C20  C  CR16  0  -0.250  -4.3352   1.1800   0.7380
 HKM  C21  C  CR6   0  -0.032  -3.0295   0.7862   0.4471
 HKM  C3   C  CR5   0   0.325   4.4484   1.3983  -0.1236
 HKM  S5   S  S2    0   0.205   3.5753  -0.9151   0.4808
 HKM  N7   N  NH1   0  -0.727   1.2168   0.1147  -0.4799
 HKM  N9   N  N     0  -0.470   1.0844  -2.0626   0.2733
 HKM  O14  O  O2    0  -0.514  -1.4037   0.0815  -1.1692
 HKM  N22  N  NS    0  -0.235  -1.2394   0.7757   2.3007
 HKM  H1   H  HCR6  0   0.284  -5.6564   0.9486  -2.3638
 HKM  H2   H  HCR6  0   0.299  -2.6600  -2.2426  -0.5905
 HKM  H3   H  HCR6  0   0.293  -3.3461   0.2324  -2.8816
 HKM  H4   H  HCR6  0   0.277  -1.4951  -4.1970   0.4360
 HKM  H5   H  HCR6  0   0.271   0.9303  -3.9943   0.9554
 HKM  H6   H  HCH3  0   0.246   4.8866   3.4665   0.2072
 HKM  H7   H  HCH3  0   0.244   6.3101   2.4503  -0.0269
 HKM  H8   H  HCH3  0   0.246   5.2949   2.8913  -1.4012
 HKM  H9   H  HCR5  0   0.290   5.8637  -0.0364   0.7415
 HKM  H10  H  HCR6  0   0.280  -6.2906   1.5407  -0.0455
 HKM  H11  H  HCR6  0   0.292  -4.5982   1.4469   1.7523
 HKM  H12  H  HNH1  0   0.423   0.7571   0.9189  -0.8811

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
 HKM  C6   C3   single    1.491  0.020  1.491
 HKM  C3   N2   aromatic  1.371  0.020  1.371
 HKM  C3   C4   aromatic  1.355  0.020  1.355
 HKM  N2   C1   aromatic  1.297  0.020  1.297
 HKM  C4   S5   aromatic  1.729  0.020  1.729
 HKM  N22  C15  triple    1.152  0.020  1.152
 HKM  C1   N7   single    1.365  0.020  1.365
 HKM  C1   S5   aromatic  1.735  0.020  1.735
 HKM  C15  C21  single    1.425  0.020  1.425
 HKM  N7   C8   single    1.370  0.020  1.370
 HKM  C21  C20  aromatic  1.394  0.020  1.394
 HKM  C21  C16  aromatic  1.398  0.020  1.398
 HKM  C20  C19  aromatic  1.384  0.020  1.384
 HKM  O14  C16  single    1.364  0.020  1.364
 HKM  O14  C13  single    1.369  0.020  1.369
 HKM  C16  C17  aromatic  1.382  0.020  1.382
 HKM  C19  C18  aromatic  1.389  0.020  1.389
 HKM  C17  C18  aromatic  1.388  0.020  1.388
 HKM  C8   C13  aromatic  1.406  0.020  1.406
 HKM  C8   N9   aromatic  1.316  0.020  1.316
 HKM  C13  C12  aromatic  1.374  0.020  1.374
 HKM  N9   C10  aromatic  1.331  0.020  1.331
 HKM  C12  C11  aromatic  1.395  0.020  1.395
 HKM  C10  C11  aromatic  1.378  0.020  1.378
 HKM  C18  H1   single    0.930  0.020  1.080
 HKM  C12  H2   single    0.930  0.020  1.080
 HKM  C17  H3   single    0.930  0.020  1.080
 HKM  C11  H4   single    0.930  0.020  1.080
 HKM  C10  H5   single    0.930  0.020  1.080
 HKM  C6   H6   single    0.970  0.020  1.090
 HKM  C6   H7   single    0.970  0.020  1.090
 HKM  C6   H8   single    0.970  0.020  1.090
 HKM  C4   H9   single    0.930  0.020  1.080
 HKM  C19  H10  single    0.930  0.020  1.080
 HKM  C20  H11  single    0.930  0.020  1.080
 HKM  N7   H12  single    0.860  0.020  1.020

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
 HKM  H1   C18  C19  119.96  3.000
 HKM  H1   C18  C17  119.28  3.000
 HKM  C19  C18  C17  120.76  3.000
 HKM  O14  C13  C8   116.97  3.000
 HKM  C8   C13  C12  118.91  3.000
 HKM  O14  C13  C12  124.12  3.000
 HKM  H2   C12  C11  120.36  3.000
 HKM  H2   C12  C13  120.83  3.000
 HKM  C11  C12  C13  118.82  3.000
 HKM  H3   C17  C16  119.62  3.000
 HKM  H3   C17  C18  120.94  3.000
 HKM  C16  C17  C18  119.43  3.000
 HKM  O14  C16  C21  120.51  3.000
 HKM  O14  C16  C17  119.17  3.000
 HKM  C21  C16  C17  120.29  3.000
 HKM  N22  C15  C21  180.00  3.000
 HKM  H4   C11  C10  120.91  3.000
 HKM  H4   C11  C12  120.83  3.000
 HKM  C10  C11  C12  118.26  3.000
 HKM  H5   C10  N9   116.23  3.000
 HKM  H5   C10  C11  120.87  3.000
 HKM  N9   C10  C11  122.90  3.000
 HKM  N9   C8   N7   118.41  3.000
 HKM  N9   C8   C13  121.72  3.000
 HKM  N7   C8   C13  119.87  3.000
 HKM  C3   N2   C1   111.29  3.000
 HKM  H8   C6   H7   108.13  3.000
 HKM  H8   C6   H6   107.19  3.000
 HKM  H7   C6   H6   108.13  3.000
 HKM  H8   C6   C3   110.99  3.000
 HKM  H7   C6   C3   111.24  3.000
 HKM  H6   C6   C3   111.00  3.000
 HKM  N7   C1   S5   124.36  3.000
 HKM  S5   C1   N2   115.01  3.000
 HKM  N7   C1   N2   120.63  3.000
 HKM  H9   C4   S5   121.07  3.000
 HKM  H9   C4   C3   128.26  3.000
 HKM  S5   C4   C3   110.67  3.000
 HKM  H10  C19  C20  119.74  3.000
 HKM  H10  C19  C18  120.38  3.000
 HKM  C20  C19  C18  119.88  3.000
 HKM  H11  C20  C21  119.55  3.000
 HKM  H11  C20  C19  120.62  3.000
 HKM  C21  C20  C19  119.83  3.000
 HKM  C20  C21  C15  120.23  3.000
 HKM  C20  C21  C16  119.80  3.000
 HKM  C15  C21  C16  119.94  3.000
 HKM  C4   C3   C6   126.07  3.000
 HKM  C4   C3   N2   114.80  3.000
 HKM  C6   C3   N2   119.13  3.000
 HKM  C4   S5   C1    88.22  3.000
 HKM  H12  N7   C1   114.54  3.000
 HKM  H12  N7   C8   118.67  3.000
 HKM  C1   N7   C8   126.79  3.000
 HKM  C8   N9   C10  119.40  3.000
 HKM  C16  O14  C13  118.48  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
 HKM  CONST_01  C21  C20  C19  C18     0.00   0.0  0
 HKM  CONST_02  C21  C16  C17  C18     0.00   0.0  0
 HKM  CONST_03  C10  N9   C8   C13     0.00   0.0  0
 HKM  CONST_04  C10  C11  C12  C13     0.00   0.0  0
 HKM  CONST_05  N9   C8   C13  C12     0.00   0.0  0
 HKM  CONST_06  N9   C10  C11  C12     0.00   0.0  0
 HKM  CONST_07  C20  C21  C16  C17     0.00   0.0  0
 HKM  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 HKM  CONST_09  C19  C20  C21  C16     0.00   0.0  0
 HKM  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 HKM  CONST_11  C8   C13  C12  C11     0.00   0.0  0
 HKM  CONST_12  C8   N9   C10  C11     0.00   0.0  0
 HKM  CONST_13  S5   C4   C3   N2      0.00   0.0  0
 HKM  CONST_14  C4   S5   C1   N2      0.00   0.0  0
 HKM  CONST_15  C4   C3   N2   C1      0.00   0.0  0
 HKM  CONST_16  C3   C4   S5   C1      0.00   0.0  0
 HKM  CONST_17  S5   C1   N2   C3      0.00   0.0  0
 HKM  CONST_18  O14  C16  C17  C18   180.00   0.0  0
 HKM  CONST_19  N7   C8   C13  C12   180.00   0.0  0
 HKM  CONST_20  C15  C21  C16  C17   180.00   0.0  0
 HKM  CONST_21  C19  C20  C21  C15   180.00   0.0  0
 HKM  CONST_22  O14  C13  C12  C11   180.00   0.0  0
 HKM  CONST_23  N7   C8   N9   C10   180.00   0.0  0
 HKM  CONST_24  C1   N2   C3   C6    180.00   0.0  0
 HKM  CONST_25  S5   C4   C3   C6    180.00   0.0  0
 HKM  CONST_26  N7   C1   S5   C4    180.00   0.0  0
 HKM  CONST_27  O14  C16  C21  C20   180.00   0.0  0
 HKM  CONST_28  N7   C1   N2   C3    180.00   0.0  0
 HKM  CONST_29  O14  C13  C8   N9    180.00   0.0  0
 HKM  CONST_30  H11  C20  C19  C18   180.00   0.0  0
 HKM  CONST_31  H4   C11  C12  C13   180.00   0.0  0
 HKM  CONST_32  H5   C10  C11  C12   180.00   0.0  0
 HKM  CONST_33  H10  C19  C18  C17   180.00   0.0  0
 HKM  CONST_34  H1   C18  C17  C16   180.00   0.0  0
 HKM  CONST_35  H2   C12  C11  C10   180.00   0.0  0
 HKM  CONST_36  H9   C4   C3   N2    180.00   0.0  0
 HKM  CONST_37  H3   C17  C18  C19   180.00   0.0  0
 HKM  Var_01    C21  C16  O14  C13    63.45  30.0  2
 HKM  Var_02    C1   N7   C8   C13   179.96  30.0  2
 HKM  Var_03    C8   C13  O14  C16  -144.35  30.0  2
 HKM  Var_04    N2   C1   N7   C8   -179.79  30.0  2
 HKM  Var_05    H6   C6   C3   N2     59.40  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
 HKM  plan-1  N2   0.020
 HKM  plan-1  C6   0.020
 HKM  plan-1  C1   0.020
 HKM  plan-1  C4   0.020
 HKM  plan-1  C3   0.020
 HKM  plan-1  S5   0.020
 HKM  plan-1  N7   0.020
 HKM  plan-1  H9   0.020
 HKM  plan-2  C13  0.020
 HKM  plan-2  C12  0.020
 HKM  plan-2  C11  0.020
 HKM  plan-2  C10  0.020
 HKM  plan-2  C8   0.020
 HKM  plan-2  N7   0.020
 HKM  plan-2  N9   0.020
 HKM  plan-2  O14  0.020
 HKM  plan-2  H2   0.020
 HKM  plan-2  H4   0.020
 HKM  plan-2  H5   0.020
 HKM  plan-3  C18  0.020
 HKM  plan-3  C17  0.020
 HKM  plan-3  C16  0.020
 HKM  plan-3  C15  0.020
 HKM  plan-3  C19  0.020
 HKM  plan-3  C20  0.020
 HKM  plan-3  C21  0.020
 HKM  plan-3  O14  0.020
 HKM  plan-3  N22  0.020
 HKM  plan-3  H1   0.020
 HKM  plan-3  H3   0.020
 HKM  plan-3  H10  0.020
 HKM  plan-3  H11  0.020

