# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 13:09:22 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: N-[4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-yl]-N'-hydroxyimidoformamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(c(C)n1)c2ccnc(N\C=N/O)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
 CK3  CK3  N-[4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-yl]-N'-hydroxyimidoformamide  ligand  28  17  .  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_CK3
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
 CK3  C7A   C  CH3   0  -0.725   5.4709  -0.5716   0.0396
 CK3  C3A   C  CR5   0   0.077   3.9845  -0.5537   0.0189
 CK3  S4A   S  S2    0   0.230   3.1057   0.9226   0.0454
 CK3  N2A   N  N     0  -0.391   3.2346  -1.6117  -0.0025
 CK3  C1A   C  CR5   0   0.351   1.9030  -1.3144   0.0022
 CK3  C6A   C  CH3   0  -0.726   0.9301  -2.4458  -0.0228
 CK3  C5A   C  CR5   0  -0.343   1.6222   0.0326   0.0274
 CK3  C4    C  CR6   0   0.313   0.3385   0.7137   0.0314
 CK3  N3    N  N     0  -0.490  -0.7533  -0.0439   0.0197
 CK3  C5    C  CR16  0  -0.390   0.2356   2.1090   0.0452
 CK3  C6    C  CR16  0  -0.005  -1.0403   2.6333   0.0452
 CK3  N1    N  N     0  -0.462  -2.1346   1.8834   0.0338
 CK3  C2    C  CR6   0   0.614  -1.9278   0.5727   0.0212
 CK3  N7    N  NH1   0  -0.700  -3.0191  -0.2550   0.0082
 CK3  C8    C  C1    0   0.121  -4.3181   0.1754   0.0053
 CK3  N9    N  N     0  -0.196  -5.3534  -0.5629  -0.0012
 CK3  O10   O  OH1   0  -0.583  -5.0337  -1.9045  -0.0041
 CK3  H7A1  H  HCH3  0   0.273   5.8496  -0.2854   1.0219
 CK3  H7A2  H  HCH3  0   0.269   5.8271  -1.5738  -0.1869
 CK3  H7A3  H  HCH3  0   0.268   5.8890   0.1225  -0.6884
 CK3  H6A1  H  HCH3  0   0.254   0.2803  -2.3978  -0.8951
 CK3  H6A2  H  HCH3  0   0.248   1.4736  -3.3882  -0.0427
 CK3  H6A3  H  HCH3  0   0.254   0.2804  -2.4350   0.8509
 CK3  H5    H  HCR6  0   0.276   1.0935   2.7655   0.0545
 CK3  H6    H  HCR6  0   0.281  -1.1899   3.7068   0.0550
 CK3  HN7   H  HNH1  0   0.416  -2.8267  -1.2457   0.0022
 CK3  H8    H  H     0   0.289  -4.4753   1.2440   0.0083
 CK3  H10   H  HOH1  0   0.477  -5.8869  -2.3489  -0.0073

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
 CK3  C7A  C3A   single    1.487  0.020  1.487
 CK3  C7A  H7A1  single    0.970  0.020  1.090
 CK3  C7A  H7A2  single    0.970  0.020  1.090
 CK3  C7A  H7A3  single    0.970  0.020  1.090
 CK3  C3A  S4A   aromatic  1.718  0.020  1.718
 CK3  C3A  N2A   aromatic  1.297  0.020  1.297
 CK3  S4A  C5A   aromatic  1.730  0.020  1.730
 CK3  N2A  C1A   aromatic  1.364  0.020  1.364
 CK3  C1A  C6A   single    1.492  0.020  1.492
 CK3  C1A  C5A   aromatic  1.376  0.020  1.376
 CK3  C6A  H6A1  single    0.970  0.020  1.090
 CK3  C6A  H6A2  single    0.970  0.020  1.090
 CK3  C6A  H6A3  single    0.970  0.020  1.090
 CK3  C5A  C4    single    1.453  0.020  1.453
 CK3  C4   N3    aromatic  1.329  0.020  1.329
 CK3  C4   C5    aromatic  1.399  0.020  1.399
 CK3  N3   C2    aromatic  1.326  0.020  1.326
 CK3  C5   C6    aromatic  1.379  0.020  1.379
 CK3  C5   H5    single    0.930  0.020  1.080
 CK3  C6   N1    aromatic  1.327  0.020  1.327
 CK3  C6   H6    single    0.930  0.020  1.080
 CK3  N1   C2    aromatic  1.327  0.020  1.327
 CK3  C2   N7    single    1.370  0.020  1.370
 CK3  N7   C8    single    1.368  0.020  1.368
 CK3  N7   HN7   single    0.860  0.020  1.020
 CK3  C8   N9    double    1.272  0.020  1.272
 CK3  C8   H8    single    0.930  0.020  1.080
 CK3  N9   O10   single    1.379  0.020  1.379
 CK3  O10  H10   single    0.850  0.020  0.980

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
 CK3  H7A3  C7A  H7A2  108.80  3.000
 CK3  H7A3  C7A  H7A1  107.54  3.000
 CK3  H7A2  C7A  H7A1  108.40  3.000
 CK3  H7A3  C7A  C3A   111.52  3.000
 CK3  H7A2  C7A  C3A   109.61  3.000
 CK3  H7A1  C7A  C3A   110.88  3.000
 CK3  N2A   C3A  S4A   113.92  3.000
 CK3  N2A   C3A  C7A   124.65  3.000
 CK3  S4A   C3A  C7A   121.43  3.000
 CK3  C5A   S4A  C3A    89.80  3.000
 CK3  C1A   N2A  C3A   112.74  3.000
 CK3  C5A   C1A  C6A   127.54  3.000
 CK3  C5A   C1A  N2A   114.36  3.000
 CK3  C6A   C1A  N2A   118.10  3.000
 CK3  H6A3  C6A  H6A2  108.74  3.000
 CK3  H6A3  C6A  H6A1  106.64  3.000
 CK3  H6A2  C6A  H6A1  108.77  3.000
 CK3  H6A3  C6A  C1A   111.59  3.000
 CK3  H6A2  C6A  C1A   109.34  3.000
 CK3  H6A1  C6A  C1A   111.66  3.000
 CK3  C4    C5A  C1A   129.72  3.000
 CK3  C4    C5A  S4A   121.09  3.000
 CK3  C1A   C5A  S4A   109.19  3.000
 CK3  C5    C4   N3    120.54  3.000
 CK3  C5    C4   C5A   122.17  3.000
 CK3  N3    C4   C5A   117.29  3.000
 CK3  C2    N3   C4    117.55  3.000
 CK3  H5    C5   C6    120.23  3.000
 CK3  H5    C5   C4    123.21  3.000
 CK3  C6    C5   C4    116.56  3.000
 CK3  H6    C6   N1    116.49  3.000
 CK3  H6    C6   C5    120.27  3.000
 CK3  N1    C6   C5    123.24  3.000
 CK3  C2    N1   C6    115.46  3.000
 CK3  N7    C2   N1    118.21  3.000
 CK3  N7    C2   N3    115.12  3.000
 CK3  N1    C2   N3    126.67  3.000
 CK3  HN7   N7   C8    119.32  3.000
 CK3  HN7   N7   C2    116.19  3.000
 CK3  C8    N7   C2    124.49  3.000
 CK3  H8    C8   N9    117.12  3.000
 CK3  H8    C8   N7    116.70  3.000
 CK3  N9    C8   N7    126.17  3.000
 CK3  O10   N9   C8    112.09  3.000
 CK3  H10   O10  N9    104.11  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
 CK3  CONST_01  C1A   C5A  S4A  C3A     0.00   0.0  0
 CK3  CONST_02  C4    C5A  S4A  C3A   180.00   0.0  0
 CK3  CONST_03  C5A   C1A  N2A  C3A     0.00   0.0  0
 CK3  CONST_04  C1A   N2A  C3A  S4A     0.00   0.0  0
 CK3  CONST_05  N2A   C1A  C5A  S4A     0.00   0.0  0
 CK3  CONST_06  N3    C4   C5A  S4A   180.00   0.0  0
 CK3  CONST_07  C5    C4   C5A  S4A     0.00   0.0  0
 CK3  CONST_08  C5A   S4A  C3A  N2A     0.00   0.0  0
 CK3  CONST_09  C4    C5A  C1A  N2A   180.00   0.0  0
 CK3  CONST_10  N3    C4   C5A  C1A     0.00   0.0  0
 CK3  CONST_11  C5    C4   C5A  C1A   180.00   0.0  0
 CK3  CONST_12  C2    N3   C4   C5A   180.00   0.0  0
 CK3  CONST_13  C6    C5   C4   C5A   180.00   0.0  0
 CK3  CONST_14  N1    C2   N3   C4      0.00   0.0  0
 CK3  CONST_15  N1    C6   C5   C4      0.00   0.0  0
 CK3  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 CK3  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 CK3  CONST_18  C2    N3   C4   C5      0.00   0.0  0
 CK3  CONST_19  C2    N1   C6   C5      0.00   0.0  0
 CK3  CONST_20  C5A   S4A  C3A  C7A   180.00   0.0  0
 CK3  CONST_21  C1A   N2A  C3A  C7A   180.00   0.0  0
 CK3  CONST_22  C6A   C1A  N2A  C3A   180.00   0.0  0
 CK3  CONST_23  C6A   C1A  C5A  S4A   180.00   0.0  0
 CK3  CONST_24  C4    C5A  C1A  C6A     0.00   0.0  0
 CK3  CONST_25  N7    C2   N3   C4    180.00   0.0  0
 CK3  CONST_26  N7    C2   N1   C6    180.00   0.0  0
 CK3  CONST_27  H5    C5   C4   C5A     0.00   0.0  0
 CK3  CONST_28  H6    C6   C5   C4    180.00   0.0  0
 CK3  CONST_29  C8    N7   C2   N3    180.00   0.0  0
 CK3  CONST_30  C8    N7   C2   N1      0.00   0.0  0
 CK3  CONST_31  HN7   N7   C2   N3      0.00   0.0  0
 CK3  CONST_32  N9    C8   N7   C2    180.00   0.0  0
 CK3  CONST_33  H8    C8   N7   C2      0.00   0.0  0
 CK3  CONST_34  O10   N9   C8   N7      0.00   0.0  0
 CK3  Var_01    H7A1  C7A  C3A  S4A    71.91  30.0  2
 CK3  Var_02    H6A1  C6A  C1A  N2A  -120.45  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
 CK3  plan-1  C7A  0.020
 CK3  plan-1  C3A  0.020
 CK3  plan-1  S4A  0.020
 CK3  plan-1  N2A  0.020
 CK3  plan-1  C1A  0.020
 CK3  plan-1  C6A  0.020
 CK3  plan-1  C5A  0.020
 CK3  plan-1  C4   0.020
 CK3  plan-2  C5A  0.020
 CK3  plan-2  C4   0.020
 CK3  plan-2  N3   0.020
 CK3  plan-2  C5   0.020
 CK3  plan-2  C6   0.020
 CK3  plan-2  N1   0.020
 CK3  plan-2  C2   0.020
 CK3  plan-2  N7   0.020
 CK3  plan-2  H5   0.020
 CK3  plan-2  H6   0.020
 CK3  plan-3  C2   0.020
 CK3  plan-3  N7   0.020
 CK3  plan-3  C8   0.020
 CK3  plan-3  N9   0.020
 CK3  plan-3  O10  0.020
 CK3  plan-3  HN7  0.020
 CK3  plan-3  H8   0.020

