# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 16:51:10 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-(2-amino-4-methyl-1,3-thiazol-5-yl)-N-(3-dioxaziridin-3-ylphenyl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)sc1c2ccnc(Nc3cccc(c3)n4oo4)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
 16X  16X  4-(2-amino-4-methyl-1,3-thiazol-5-yl)-N-(3-dioxaziridin-3-ylphenyl)pyrimidin-2-amine  ligand  35  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_16X
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
 16X  N7A   N  NH2   0  -0.812   7.0842  -0.0612  -0.1498
 16X  C3A   C  CR5   0   0.312   5.7613   0.1362  -0.1000
 16X  N2A   N  N     0  -0.445   5.1994   1.3155  -0.1116
 16X  C1A   C  CR5   0   0.361   3.8439   1.2306  -0.0929
 16X  C6A   C  CH3   0  -0.725   3.0672   2.5052  -0.0981
 16X  S4A   S  S2    0   0.170   4.6505  -1.1924  -0.0656
 16X  C5A   C  CR5   0  -0.349   3.3292  -0.0454  -0.0645
 16X  C4    C  CR6   0   0.305   1.9595  -0.4993  -0.0312
 16X  N3    N  N     0  -0.505   1.0012   0.4213  -0.0479
 16X  C5    C  CR16  0  -0.407   1.6266  -1.8637   0.0208
 16X  C6    C  CR16  0   0.004   0.2865  -2.1697   0.0519
 16X  N1    N  N     0  -0.480  -0.6773  -1.2523   0.0370
 16X  C2    C  CR6   0   0.603  -0.2636   0.0073  -0.0111
 16X  N7    N  NH1   0  -0.777  -1.1735   1.0264  -0.0262
 16X  C1B   C  CR6   0   0.380  -2.5570   1.0263   0.0172
 16X  C6B   C  CR16  0  -0.341  -3.1905   2.2735   0.0191
 16X  C2B   C  CR16  0  -0.359  -3.3553  -0.1206   0.0570
 16X  C3B   C  CR6   0   0.253  -4.7333   0.0110   0.0980
 16X  N7B   N  N     0   0.003  -5.4159  -1.2510   0.1380
 16X  O8B   O  OC2   0  -0.166  -6.5941  -1.1770   0.8876
 16X  O9B   O  OC2   0  -0.166  -6.6424  -1.1969  -0.5314
 16X  C4B   C  CR16  0  -0.281  -5.3705   1.2436   0.1004
 16X  C5B   C  CR16  0  -0.244  -4.5708   2.3741   0.0598
 16X  H7A1  H  HNH2  0   0.412   7.6808   0.7347   0.0078
 16X  H7A2  H  HNH2  0   0.416   7.4788  -0.9603   0.0678
 16X  H6A1  H  HCH3  0   0.253   2.4206   2.5745  -0.9717
 16X  H6A2  H  HCH3  0   0.253   2.4189   2.5815   0.7734
 16X  H6A3  H  HCH3  0   0.247   3.7541   3.3489  -0.1017
 16X  H5    H  HCR6  0   0.271   2.3673  -2.6500   0.0381
 16X  H6    H  HCR6  0   0.274  -0.0368  -3.2037   0.0926
 16X  H7    H  HNH1  0   0.411  -0.7416   1.9376  -0.0652
 16X  H6B   H  HCR6  0   0.279  -2.5919   3.1762  -0.0117
 16X  H2B   H  HCR6  0   0.305  -2.9132  -1.1040   0.0568
 16X  H5B   H  HCR6  0   0.272  -5.0276   3.3547   0.0602
 16X  H4B   H  HCR6  0   0.274  -6.4467   1.3364   0.1339

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
 16X  N7A  C3A   single    1.338  0.020  1.338
 16X  C3A  N2A   aromatic  1.306  0.020  1.306
 16X  C3A  S4A   aromatic  1.732  0.020  1.732
 16X  N2A  C1A   aromatic  1.358  0.020  1.358
 16X  C1A  C6A   single    1.493  0.020  1.493
 16X  C1A  C5A   aromatic  1.376  0.020  1.376
 16X  S4A  C5A   aromatic  1.750  0.020  1.750
 16X  C5A  C4    single    1.443  0.020  1.443
 16X  C4   N3    aromatic  1.329  0.020  1.329
 16X  C4   C5    aromatic  1.405  0.020  1.405
 16X  N3   C2    aromatic  1.331  0.020  1.331
 16X  C5   C6    aromatic  1.375  0.020  1.375
 16X  C6   N1    aromatic  1.331  0.020  1.331
 16X  N1   C2    aromatic  1.327  0.020  1.327
 16X  C2   N7    single    1.366  0.020  1.366
 16X  N7   C1B   single    1.384  0.020  1.384
 16X  C1B  C6B   aromatic  1.399  0.020  1.399
 16X  C1B  C2B   aromatic  1.398  0.020  1.398
 16X  C6B  C5B   aromatic  1.385  0.020  1.385
 16X  C2B  C3B   aromatic  1.385  0.020  1.385
 16X  C3B  N7B   single    1.435  0.020  1.435
 16X  C3B  C4B   aromatic  1.388  0.020  1.388
 16X  N7B  O8B   aromatic  1.398  0.020  1.398
 16X  N7B  O9B   aromatic  1.398  0.020  1.398
 16X  O8B  O9B   aromatic  1.420  0.020  1.420
 16X  C4B  C5B   aromatic  1.385  0.020  1.385
 16X  N7A  H7A1  single    0.890  0.020  1.040
 16X  N7A  H7A2  single    0.890  0.020  1.040
 16X  C6A  H6A1  single    0.970  0.020  1.090
 16X  C6A  H6A2  single    0.970  0.020  1.090
 16X  C6A  H6A3  single    0.970  0.020  1.090
 16X  C5   H5    single    0.930  0.020  1.080
 16X  C6   H6    single    0.930  0.020  1.080
 16X  N7   H7    single    0.860  0.020  1.020
 16X  C6B  H6B   single    0.930  0.020  1.080
 16X  C2B  H2B   single    0.930  0.020  1.080
 16X  C5B  H5B   single    0.930  0.020  1.080
 16X  C4B  H4B   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
 16X  H7A2  N7A  H7A1  116.11  3.000
 16X  H7A2  N7A  C3A   120.77  3.000
 16X  H7A1  N7A  C3A   117.59  3.000
 16X  S4A   C3A  N2A   114.63  3.000
 16X  S4A   C3A  N7A   121.43  3.000
 16X  N2A   C3A  N7A   123.91  3.000
 16X  C1A   N2A  C3A   111.88  3.000
 16X  C5A   C1A  C6A   126.67  3.000
 16X  C5A   C1A  N2A   115.56  3.000
 16X  C6A   C1A  N2A   117.76  3.000
 16X  H6A3  C6A  H6A2  108.92  3.000
 16X  H6A3  C6A  H6A1  108.84  3.000
 16X  H6A2  C6A  H6A1  106.50  3.000
 16X  H6A3  C6A  C1A   109.49  3.000
 16X  H6A2  C6A  C1A   111.52  3.000
 16X  H6A1  C6A  C1A   111.48  3.000
 16X  C5A   S4A  C3A    88.94  3.000
 16X  C4    C5A  S4A   120.70  3.000
 16X  C4    C5A  C1A   130.31  3.000
 16X  S4A   C5A  C1A   108.99  3.000
 16X  C5    C4   N3    120.14  3.000
 16X  C5    C4   C5A   122.07  3.000
 16X  N3    C4   C5A   117.79  3.000
 16X  C2    N3   C4    117.99  3.000
 16X  H5    C5   C6    120.39  3.000
 16X  H5    C5   C4    123.01  3.000
 16X  C6    C5   C4    116.60  3.000
 16X  H6    C6   N1    116.23  3.000
 16X  H6    C6   C5    120.25  3.000
 16X  N1    C6   C5    123.52  3.000
 16X  C2    N1   C6    115.41  3.000
 16X  N7    C2   N1    120.06  3.000
 16X  N7    C2   N3    113.61  3.000
 16X  N1    C2   N3    126.33  3.000
 16X  H7    N7   C1B   115.41  3.000
 16X  H7    N7   C2    112.89  3.000
 16X  C1B   N7   C2    131.70  3.000
 16X  C2B   C1B  C6B   118.22  3.000
 16X  C2B   C1B  N7    124.87  3.000
 16X  C6B   C1B  N7    116.91  3.000
 16X  H6B   C6B  C5B   119.41  3.000
 16X  H6B   C6B  C1B   119.51  3.000
 16X  C5B   C6B  C1B   121.08  3.000
 16X  H2B   C2B  C3B   119.64  3.000
 16X  H2B   C2B  C1B   120.94  3.000
 16X  C3B   C2B  C1B   119.41  3.000
 16X  C4B   C3B  N7B   124.23  3.000
 16X  C4B   C3B  C2B   122.78  3.000
 16X  N7B   C3B  C2B   112.99  3.000
 16X  O9B   N7B  O8B    61.02  3.000
 16X  O9B   N7B  C3B   111.70  3.000
 16X  O8B   N7B  C3B   111.66  3.000
 16X  O9B   O8B  N7B    59.48  3.000
 16X  O8B   O9B  N7B    59.49  3.000
 16X  H4B   C4B  C5B   120.37  3.000
 16X  H4B   C4B  C3B   122.26  3.000
 16X  C5B   C4B  C3B   117.37  3.000
 16X  H5B   C5B  C4B   119.73  3.000
 16X  H5B   C5B  C6B   119.13  3.000
 16X  C4B   C5B  C6B   121.14  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
 16X  CONST_01  C5A   C1A  N2A  C3A     0.00   0.0  0
 16X  CONST_02  C1A   C5A  S4A  C3A     0.00   0.0  0
 16X  CONST_03  C4    C5A  S4A  C3A   180.00   0.0  0
 16X  CONST_04  C5A   S4A  C3A  N2A     0.00   0.0  0
 16X  CONST_05  S4A   C5A  C1A  N2A     0.00   0.0  0
 16X  CONST_06  C4    C5A  C1A  N2A   180.00   0.0  0
 16X  CONST_07  S4A   C3A  N2A  C1A     0.00   0.0  0
 16X  CONST_08  N3    C4   C5A  C1A     0.00   0.0  0
 16X  CONST_09  C5    C4   C5A  C1A   180.00   0.0  0
 16X  CONST_10  N3    C4   C5A  S4A   180.00   0.0  0
 16X  CONST_11  C5    C4   C5A  S4A     0.00   0.0  0
 16X  CONST_12  C2    N3   C4   C5A   180.00   0.0  0
 16X  CONST_13  C6    C5   C4   C5A   180.00   0.0  0
 16X  CONST_14  N1    C2   N3   C4      0.00   0.0  0
 16X  CONST_15  N1    C6   C5   C4      0.00   0.0  0
 16X  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 16X  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 16X  CONST_18  C2    N3   C4   C5      0.00   0.0  0
 16X  CONST_19  C2    N1   C6   C5      0.00   0.0  0
 16X  CONST_20  C4B   C5B  C6B  C1B     0.00   0.0  0
 16X  CONST_21  N7B   C3B  C2B  C1B   180.00   0.0  0
 16X  CONST_22  C4B   C3B  C2B  C1B     0.00   0.0  0
 16X  CONST_23  C3B   C2B  C1B  C6B     0.00   0.0  0
 16X  CONST_24  C3B   C4B  C5B  C6B     0.00   0.0  0
 16X  CONST_25  C5B   C6B  C1B  C2B     0.00   0.0  0
 16X  CONST_28  C5B   C4B  C3B  C2B     0.00   0.0  0
 16X  CONST_30  C5B   C4B  C3B  N7B   180.00   0.0  0
 16X  CONST_33  C1A   N2A  C3A  N7A   180.00   0.0  0
 16X  CONST_34  C5A   S4A  C3A  N7A   180.00   0.0  0
 16X  CONST_35  C6A   C1A  N2A  C3A   180.00   0.0  0
 16X  CONST_36  S4A   C5A  C1A  C6A   180.00   0.0  0
 16X  CONST_37  C4    C5A  C1A  C6A     0.00   0.0  0
 16X  CONST_38  N7    C2   N3   C4    180.00   0.0  0
 16X  CONST_39  N7    C2   N1   C6    180.00   0.0  0
 16X  CONST_40  C5B   C6B  C1B  N7    180.00   0.0  0
 16X  CONST_41  C3B   C2B  C1B  N7    180.00   0.0  0
 16X  CONST_42  H5    C5   C4   C5A     0.00   0.0  0
 16X  CONST_43  H6    C6   C5   C4    180.00   0.0  0
 16X  CONST_44  H5B   C5B  C6B  C1B   180.00   0.0  0
 16X  CONST_45  H2B   C2B  C1B  C6B   180.00   0.0  0
 16X  CONST_46  H4B   C4B  C5B  C6B   180.00   0.0  0
 16X  CONST_47  H6B   C6B  C1B  C2B   180.00   0.0  0
 16X  CONST_48  H7A1  N7A  C3A  N2A     0.00   0.0  0
 16X  CONST_49  H7A2  N7A  C3A  N2A   180.00   0.0  0
 16X  Var_01    C1B   N7   C2   N3   -179.03  30.0  2
 16X  Var_02    C6B   C1B  N7   C2    178.37  30.0  2
 16X  Var_03    H6A1  C6A  C1A  N2A   119.62  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
 16X  plan-1  C3B   0.020
 16X  plan-1  N7B   0.020
 16X  plan-1  O8B   0.020
 16X  plan-1  O9B   0.020
 16X  plan-2  N7A   0.020
 16X  plan-2  C3A   0.020
 16X  plan-2  N2A   0.020
 16X  plan-2  C1A   0.020
 16X  plan-2  C6A   0.020
 16X  plan-2  S4A   0.020
 16X  plan-2  C5A   0.020
 16X  plan-2  C4    0.020
 16X  plan-3  C5A   0.020
 16X  plan-3  C4    0.020
 16X  plan-3  N3    0.020
 16X  plan-3  C5    0.020
 16X  plan-3  C6    0.020
 16X  plan-3  N1    0.020
 16X  plan-3  C2    0.020
 16X  plan-3  N7    0.020
 16X  plan-3  H5    0.020
 16X  plan-3  H6    0.020
 16X  plan-4  N7    0.020
 16X  plan-4  C1B   0.020
 16X  plan-4  C6B   0.020
 16X  plan-4  C2B   0.020
 16X  plan-4  C3B   0.020
 16X  plan-4  N7B   0.020
 16X  plan-4  C4B   0.020
 16X  plan-4  C5B   0.020
 16X  plan-4  H6B   0.020
 16X  plan-4  H2B   0.020
 16X  plan-4  H5B   0.020
 16X  plan-4  H4B   0.020
 16X  plan-5  N7A   0.020
 16X  plan-5  C3A   0.020
 16X  plan-5  H7A1  0.020
 16X  plan-5  H7A2  0.020

