# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 14:55:44 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-(2-amino-4-methyl-1,3-thiazol-5-yl)-N-(3-nitrophenyl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)sc1c2ccnc(Nc3cccc(c3)[N+]([O-])=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
 CK7  CK7  4-(2-amino-4-methyl-1,3-thiazol-5-yl)-N-(3-nitrophenyl)pyrimidin-2-amine  ligand  35  23  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CK7
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
 CK7  N7A   N  NH2    0  -0.813   7.0416  -0.0794  -0.2056
 CK7  C3A   C  CR5    0   0.317   5.7227   0.1272  -0.1525
 CK7  N2A   N  N      0  -0.446   5.1641   1.3043  -0.2596
 CK7  C1A   C  CR5    0   0.362   3.8097   1.2275  -0.2091
 CK7  C6A   C  CH3    0  -0.726   3.0371   2.4994  -0.3231
 CK7  S4A   S  S2     0   0.168   4.6081  -1.1877   0.0226
 CK7  C5A   C  CR5    0  -0.349   3.2905  -0.0383  -0.0577
 CK7  C4    C  CR6    0   0.306   1.9210  -0.4812   0.0349
 CK7  N3    N  N      0  -0.504   0.9635   0.4357  -0.0655
 CK7  C5    C  CR16   0  -0.407   1.5845  -1.8330   0.2241
 CK7  C6    C  CR16   0   0.006   0.2447  -2.1311   0.2965
 CK7  N1    N  N      0  -0.483  -0.7173  -1.2159   0.2008
 CK7  C2    C  CR6    0   0.607  -0.3006   0.0309   0.0254
 CK7  N7    N  NH1    0  -0.779  -1.2099   1.0470  -0.0816
 CK7  C1B   C  CR6    0   0.389  -2.5920   1.0486  -0.0419
 CK7  C6B   C  CR16   0  -0.330  -3.2261   2.2890  -0.2006
 CK7  C2B   C  CR16   0  -0.365  -3.3816  -0.0855   0.1441
 CK7  C3B   C  CR6    0   0.289  -4.7610   0.0587   0.1628
 CK7  N7B   N  N      1   0.330  -5.5700  -1.1402   0.3566
 CK7  O8B   O  O     -1  -0.378  -6.7718  -1.0147   0.3828
 CK7  O9B   O  O      0  -0.378  -5.0033  -2.2000   0.4825
 CK7  C4B   C  CR16   0  -0.300  -5.4013   1.2757   0.0075
 CK7  C5B   C  CR16   0  -0.240  -4.6028   2.3950  -0.1756
 CK7  H7A1  H  HNH2   0   0.413   7.6505   0.7215  -0.1706
 CK7  H7A2  H  HNH2   0   0.417   7.4439  -0.9652   0.0473
 CK7  H6A1  H  HCH3   0   0.253   2.4345   2.5141  -1.2311
 CK7  H6A2  H  HCH3   0   0.254   2.3468   2.6285   0.5081
 CK7  H6A3  H  HCH3   0   0.247   3.7251   3.3417  -0.3491
 CK7  H5    H  HCR6   0   0.271   2.3233  -2.6163   0.3123
 CK7  H6    H  HCR6   0   0.275  -0.0808  -3.1550   0.4403
 CK7  HN7   H  HNH1   0   0.413  -0.7773   1.9477  -0.2216
 CK7  H6B   H  HCR6   0   0.287  -2.6270   3.1795  -0.3479
 CK7  H2B   H  HCR6   0   0.322  -2.9194  -1.0497   0.2707
 CK7  H4B   H  HCR6   0   0.294  -6.4768   1.3640   0.0248
 CK7  H5B   H  HCR6   0   0.279  -5.0625   3.3654  -0.3021

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
 CK7  N7A  C3A   single    1.336  0.020  1.336
 CK7  N7A  H7A1  single    0.890  0.020  1.040
 CK7  N7A  H7A2  single    0.890  0.020  1.040
 CK7  C3A  N2A   aromatic  1.307  0.020  1.307
 CK7  C3A  S4A   aromatic  1.733  0.020  1.733
 CK7  N2A  C1A   aromatic  1.358  0.020  1.358
 CK7  C1A  C6A   single    1.492  0.020  1.492
 CK7  C1A  C5A   aromatic  1.376  0.020  1.376
 CK7  C6A  H6A1  single    0.970  0.020  1.090
 CK7  C6A  H6A2  single    0.970  0.020  1.090
 CK7  C6A  H6A3  single    0.970  0.020  1.090
 CK7  S4A  C5A   aromatic  1.750  0.020  1.750
 CK7  C5A  C4    single    1.442  0.020  1.442
 CK7  C4   N3    aromatic  1.329  0.020  1.329
 CK7  C4   C5    aromatic  1.406  0.020  1.406
 CK7  N3   C2    aromatic  1.330  0.020  1.330
 CK7  C5   C6    aromatic  1.374  0.020  1.374
 CK7  C5   H5    single    0.930  0.020  1.080
 CK7  C6   N1    aromatic  1.331  0.020  1.331
 CK7  C6   H6    single    0.930  0.020  1.080
 CK7  N1   C2    aromatic  1.326  0.020  1.326
 CK7  C2   N7    single    1.368  0.020  1.368
 CK7  N7   C1B   single    1.383  0.020  1.383
 CK7  N7   HN7   single    0.860  0.020  1.020
 CK7  C1B  C6B   aromatic  1.402  0.020  1.402
 CK7  C1B  C2B   aromatic  1.394  0.020  1.394
 CK7  C6B  C5B   aromatic  1.381  0.020  1.381
 CK7  C6B  H6B   single    0.930  0.020  1.080
 CK7  C2B  C3B   aromatic  1.387  0.020  1.387
 CK7  C2B  H2B   single    0.930  0.020  1.080
 CK7  C3B  N7B   single    1.459  0.020  1.459
 CK7  C3B  C4B   aromatic  1.384  0.020  1.384
 CK7  N7B  O8B   single    1.209  0.020  1.209
 CK7  N7B  O9B   double    1.208  0.020  1.208
 CK7  C4B  C5B   aromatic  1.387  0.020  1.387
 CK7  C4B  H4B   single    0.930  0.020  1.080
 CK7  C5B  H5B   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
 CK7  H7A2  N7A  H7A1  116.76  3.000
 CK7  H7A2  N7A  C3A   121.43  3.000
 CK7  H7A1  N7A  C3A   118.21  3.000
 CK7  S4A   C3A  N2A   114.63  3.000
 CK7  S4A   C3A  N7A   121.44  3.000
 CK7  N2A   C3A  N7A   123.90  3.000
 CK7  C1A   N2A  C3A   111.86  3.000
 CK7  C5A   C1A  C6A   126.65  3.000
 CK7  C5A   C1A  N2A   115.62  3.000
 CK7  C6A   C1A  N2A   117.73  3.000
 CK7  H6A3  C6A  H6A2  109.12  3.000
 CK7  H6A3  C6A  H6A1  108.62  3.000
 CK7  H6A2  C6A  H6A1  106.50  3.000
 CK7  H6A3  C6A  C1A   109.53  3.000
 CK7  H6A2  C6A  C1A   111.79  3.000
 CK7  H6A1  C6A  C1A   111.18  3.000
 CK7  C5A   S4A  C3A    88.93  3.000
 CK7  C4    C5A  S4A   120.68  3.000
 CK7  C4    C5A  C1A   130.36  3.000
 CK7  S4A   C5A  C1A   108.96  3.000
 CK7  C5    C4   N3    120.06  3.000
 CK7  C5    C4   C5A   122.08  3.000
 CK7  N3    C4   C5A   117.86  3.000
 CK7  C2    N3   C4    117.99  3.000
 CK7  H5    C5   C6    120.34  3.000
 CK7  H5    C5   C4    122.99  3.000
 CK7  C6    C5   C4    116.68  3.000
 CK7  H6    C6   N1    116.23  3.000
 CK7  H6    C6   C5    120.30  3.000
 CK7  N1    C6   C5    123.47  3.000
 CK7  C2    N1   C6    115.39  3.000
 CK7  N7    C2   N1    120.00  3.000
 CK7  N7    C2   N3    113.59  3.000
 CK7  N1    C2   N3    126.41  3.000
 CK7  HN7   N7   C1B   115.56  3.000
 CK7  HN7   N7   C2    112.90  3.000
 CK7  C1B   N7   C2    131.54  3.000
 CK7  C2B   C1B  C6B   118.59  3.000
 CK7  C2B   C1B  N7    124.68  3.000
 CK7  C6B   C1B  N7    116.73  3.000
 CK7  H6B   C6B  C5B   119.38  3.000
 CK7  H6B   C6B  C1B   119.50  3.000
 CK7  C5B   C6B  C1B   121.11  3.000
 CK7  H2B   C2B  C3B   121.23  3.000
 CK7  H2B   C2B  C1B   120.06  3.000
 CK7  C3B   C2B  C1B   118.71  3.000
 CK7  C4B   C3B  N7B   118.74  3.000
 CK7  C4B   C3B  C2B   123.37  3.000
 CK7  N7B   C3B  C2B   117.88  3.000
 CK7  O9B   N7B  O8B   123.72  3.000
 CK7  O9B   N7B  C3B   118.32  3.000
 CK7  O8B   N7B  C3B   117.96  3.000
 CK7  H4B   C4B  C5B   120.65  3.000
 CK7  H4B   C4B  C3B   122.09  3.000
 CK7  C5B   C4B  C3B   117.26  3.000
 CK7  H5B   C5B  C4B   119.66  3.000
 CK7  H5B   C5B  C6B   119.39  3.000
 CK7  C4B   C5B  C6B   120.95  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
 CK7  CONST_01  C5A   C1A  N2A  C3A     0.00   0.0  0
 CK7  CONST_02  C1A   C5A  S4A  C3A     0.00   0.0  0
 CK7  CONST_03  C4    C5A  S4A  C3A   180.00   0.0  0
 CK7  CONST_04  C5A   S4A  C3A  N2A     0.00   0.0  0
 CK7  CONST_05  S4A   C5A  C1A  N2A     0.00   0.0  0
 CK7  CONST_06  C4    C5A  C1A  N2A   180.00   0.0  0
 CK7  CONST_07  S4A   C3A  N2A  C1A     0.00   0.0  0
 CK7  CONST_08  N3    C4   C5A  C1A     0.00   0.0  0
 CK7  CONST_09  C5    C4   C5A  C1A   180.00   0.0  0
 CK7  CONST_10  N3    C4   C5A  S4A   180.00   0.0  0
 CK7  CONST_11  C5    C4   C5A  S4A     0.00   0.0  0
 CK7  CONST_12  C2    N3   C4   C5A   180.00   0.0  0
 CK7  CONST_13  C6    C5   C4   C5A   180.00   0.0  0
 CK7  CONST_14  N1    C2   N3   C4      0.00   0.0  0
 CK7  CONST_15  N1    C6   C5   C4      0.00   0.0  0
 CK7  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 CK7  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 CK7  CONST_18  C2    N3   C4   C5      0.00   0.0  0
 CK7  CONST_19  C2    N1   C6   C5      0.00   0.0  0
 CK7  CONST_20  C4B   C5B  C6B  C1B     0.00   0.0  0
 CK7  CONST_21  C4B   C3B  C2B  C1B     0.00   0.0  0
 CK7  CONST_22  C3B   C2B  C1B  C6B     0.00   0.0  0
 CK7  CONST_23  C3B   C4B  C5B  C6B     0.00   0.0  0
 CK7  CONST_24  C5B   C6B  C1B  C2B     0.00   0.0  0
 CK7  CONST_25  C5B   C4B  C3B  C2B     0.00   0.0  0
 CK7  CONST_26  C1A   N2A  C3A  N7A   180.00   0.0  0
 CK7  CONST_27  C5A   S4A  C3A  N7A   180.00   0.0  0
 CK7  CONST_28  C6A   C1A  N2A  C3A   180.00   0.0  0
 CK7  CONST_29  S4A   C5A  C1A  C6A   180.00   0.0  0
 CK7  CONST_30  C4    C5A  C1A  C6A     0.00   0.0  0
 CK7  CONST_31  N7    C2   N3   C4    180.00   0.0  0
 CK7  CONST_32  N7    C2   N1   C6    180.00   0.0  0
 CK7  CONST_33  C5B   C6B  C1B  N7    180.00   0.0  0
 CK7  CONST_34  C3B   C2B  C1B  N7    180.00   0.0  0
 CK7  CONST_35  N7B   C3B  C2B  C1B   180.00   0.0  0
 CK7  CONST_36  C5B   C4B  C3B  N7B   180.00   0.0  0
 CK7  CONST_37  H5    C5   C4   C5A     0.00   0.0  0
 CK7  CONST_38  H6    C6   C5   C4    180.00   0.0  0
 CK7  CONST_39  H5B   C5B  C6B  C1B   180.00   0.0  0
 CK7  CONST_40  H2B   C2B  C1B  C6B   180.00   0.0  0
 CK7  CONST_41  H4B   C4B  C5B  C6B   180.00   0.0  0
 CK7  CONST_42  H6B   C6B  C1B  C2B   180.00   0.0  0
 CK7  CONST_43  O8B   N7B  C3B  C2B   180.00   0.0  0
 CK7  CONST_44  O9B   N7B  C3B  C2B     0.00   0.0  0
 CK7  CONST_45  C4B   C3B  N7B  O8B     0.00   0.0  0
 CK7  CONST_46  C4B   C3B  N7B  O9B   180.00   0.0  0
 CK7  CONST_47  H7A1  N7A  C3A  N2A     0.00   0.0  0
 CK7  CONST_48  H7A2  N7A  C3A  N2A   180.00   0.0  0
 CK7  Var_01    C1B   N7   C2   N3    179.94  30.0  2
 CK7  Var_02    C6B   C1B  N7   C2   -179.34  30.0  2
 CK7  Var_03    H6A1  C6A  C1A  N2A   115.23  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
 CK7  plan-1  N7A   0.020
 CK7  plan-1  C3A   0.020
 CK7  plan-1  N2A   0.020
 CK7  plan-1  C1A   0.020
 CK7  plan-1  C6A   0.020
 CK7  plan-1  S4A   0.020
 CK7  plan-1  C5A   0.020
 CK7  plan-1  C4    0.020
 CK7  plan-2  C5A   0.020
 CK7  plan-2  C4    0.020
 CK7  plan-2  N3    0.020
 CK7  plan-2  C5    0.020
 CK7  plan-2  C6    0.020
 CK7  plan-2  N1    0.020
 CK7  plan-2  C2    0.020
 CK7  plan-2  N7    0.020
 CK7  plan-2  H5    0.020
 CK7  plan-2  H6    0.020
 CK7  plan-3  N7    0.020
 CK7  plan-3  C1B   0.020
 CK7  plan-3  C6B   0.020
 CK7  plan-3  C2B   0.020
 CK7  plan-3  C3B   0.020
 CK7  plan-3  N7B   0.020
 CK7  plan-3  C4B   0.020
 CK7  plan-3  C5B   0.020
 CK7  plan-3  H6B   0.020
 CK7  plan-3  H2B   0.020
 CK7  plan-3  H4B   0.020
 CK7  plan-3  H5B   0.020
 CK7  plan-4  N7A   0.020
 CK7  plan-4  C3A   0.020
 CK7  plan-4  H7A1  0.020
 CK7  plan-4  H7A2  0.020
 CK7  plan-5  C3B   0.020
 CK7  plan-5  N7B   0.020
 CK7  plan-5  O8B   0.020
 CK7  plan-5  O9B   0.020

