# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 09:16:35 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-(2,4-dimethyl-1,3-thiazol-5-yl)-N-(3-nitrophenyl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(c(C)n1)c2ccnc(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
 16K  16K  4-(2,4-dimethyl-1,3-thiazol-5-yl)-N-(3-nitrophenyl)pyrimidin-2-amine  ligand  36  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_16K
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
 16K  S     S  S2     0   0.231  -4.9441   0.7052   0.3100
 16K  C1    C  CR5    0  -0.343  -3.4141  -0.0396  -0.0014
 16K  N1    N  N      0  -0.495  -1.0411   0.0907  -0.0064
 16K  O1    O  O      0  -0.377   5.2923  -2.6471  -0.0603
 16K  C2    C  CR6    0   0.306  -2.1919   0.7479  -0.0390
 16K  N2    N  N      0  -0.470   0.1671   2.1267  -0.1107
 16K  O2    O  O     -1  -0.375   6.9328  -1.2901  -0.1734
 16K  C3    C  CR6    0   0.610   0.0835   0.8044  -0.0540
 16K  N3    N  NH1    0  -0.780   1.2175   0.0443  -0.0313
 16K  C4    C  CR16   0   0.008  -0.9905   2.7777  -0.1366
 16K  N4    N  N      1   0.328   5.7500  -1.5307  -0.1261
 16K  C5    C  CR16   0  -0.396  -2.2142   2.1466  -0.1089
 16K  N5    N  N      0  -0.392  -4.8934  -1.8026  -0.0777
 16K  C6    C  CR6    0   0.397   2.5562   0.3904  -0.1018
 16K  C7    C  CR16   0  -0.394   3.4681  -0.6684  -0.0811
 16K  C8    C  CR6    0   0.272   4.8231  -0.4055  -0.1501
 16K  C9    C  CR16   0  -0.291   5.3285   0.8824  -0.2424
 16K  C10   C  CR16   0  -0.240   4.4151   1.9217  -0.2626
 16K  C11   C  CR16   0  -0.291   3.0482   1.6968  -0.1930
 16K  C12   C  CR5    0   0.353  -3.5968  -1.3899  -0.1840
 16K  C13   C  CR5    0   0.074  -5.7093  -0.8279   0.1784
 16K  C14   C  CH3    0  -0.724  -7.1816  -0.9750   0.3257
 16K  C15   C  CH3    0  -0.726  -2.5559  -2.4154  -0.4835
 16K  HN3   H  HNH1   0   0.415   1.0265  -0.9453   0.0222
 16K  H4    H  HCR6   0   0.280  -0.9326   3.8588  -0.1864
 16K  H5    H  HCR6   0   0.276  -3.1286   2.7206  -0.1513
 16K  H7    H  HCR6   0   0.307   3.1082  -1.6860  -0.0108
 16K  H9    H  HCR6   0   0.294   6.3888   1.0761  -0.2983
 16K  H10   H  HCR6   0   0.277   4.7729   2.9397  -0.3353
 16K  H11   H  HCR6   0   0.304   2.3665   2.5305  -0.2088
 16K  H14   H  HCH3   0   0.274  -7.6918  -0.6761  -0.5915
 16K  H14A  H  HCH3   0   0.270  -7.4283  -2.0145   0.5295
 16K  H14B  H  HCH3   0   0.264  -7.5693  -0.3569   1.1340
 16K  H15   H  HCH3   0   0.254  -2.0122  -2.6958   0.4197
 16K  H15A  H  HCH3   0   0.248  -3.0312  -3.3098  -0.8816
 16K  H15B  H  HCH3   0   0.253  -1.8182  -2.0545  -1.1954

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
 16K  S    C13   aromatic  1.719  0.020  1.719
 16K  C1   S     aromatic  1.730  0.020  1.730
 16K  C1   C12   aromatic  1.375  0.020  1.375
 16K  N1   C2    aromatic  1.326  0.020  1.326
 16K  C2   C1    single    1.454  0.020  1.454
 16K  N2   C3    aromatic  1.326  0.020  1.326
 16K  N2   C4    aromatic  1.328  0.020  1.328
 16K  C3   N1    aromatic  1.333  0.020  1.333
 16K  N3   C3    single    1.365  0.020  1.365
 16K  N3   C6    single    1.385  0.020  1.385
 16K  N3   HN3   single    0.860  0.020  1.020
 16K  C4   C5    aromatic  1.377  0.020  1.377
 16K  C4   H4    single    0.930  0.020  1.080
 16K  N4   O1    double    1.208  0.020  1.208
 16K  N4   O2    single    1.208  0.020  1.208
 16K  C5   C2    aromatic  1.401  0.020  1.401
 16K  C5   H5    single    0.930  0.020  1.080
 16K  N5   C13   aromatic  1.297  0.020  1.297
 16K  C6   C7    aromatic  1.397  0.020  1.397
 16K  C7   C8    aromatic  1.382  0.020  1.382
 16K  C7   H7    single    0.930  0.020  1.080
 16K  C8   N4    single    1.458  0.020  1.458
 16K  C9   C8    aromatic  1.387  0.020  1.387
 16K  C9   H9    single    0.930  0.020  1.080
 16K  C10  C9    aromatic  1.384  0.020  1.384
 16K  C10  H10   single    0.930  0.020  1.080
 16K  C11  C6    aromatic  1.399  0.020  1.399
 16K  C11  C10   aromatic  1.387  0.020  1.387
 16K  C11  H11   single    0.930  0.020  1.080
 16K  C12  N5    aromatic  1.365  0.020  1.365
 16K  C13  C14   single    1.487  0.020  1.487
 16K  C14  H14   single    0.970  0.020  1.090
 16K  C14  H14A  single    0.970  0.020  1.090
 16K  C14  H14B  single    0.970  0.020  1.090
 16K  C15  C12   single    1.492  0.020  1.492
 16K  C15  H15   single    0.970  0.020  1.090
 16K  C15  H15A  single    0.970  0.020  1.090
 16K  C15  H15B  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
 16K  C13   S    C1     89.76  3.000
 16K  C12   C1   C2    129.80  3.000
 16K  C2    C1   S     120.98  3.000
 16K  C12   C1   S     109.22  3.000
 16K  C3    N1   C2    117.79  3.000
 16K  C5    C2   N1    120.67  3.000
 16K  C5    C2   C1    121.91  3.000
 16K  N1    C2   C1    117.42  3.000
 16K  C4    N2   C3    115.76  3.000
 16K  N3    C3   N2    120.23  3.000
 16K  N3    C3   N1    113.71  3.000
 16K  N2    C3   N1    126.06  3.000
 16K  HN3   N3   C6    115.52  3.000
 16K  HN3   N3   C3    112.93  3.000
 16K  C6    N3   C3    131.53  3.000
 16K  H4    C4   C5    120.37  3.000
 16K  H4    C4   N2    116.31  3.000
 16K  C5    C4   N2    123.32  3.000
 16K  C8    N4   O2    117.91  3.000
 16K  C8    N4   O1    118.24  3.000
 16K  O2    N4   O1    123.85  3.000
 16K  H5    C5   C4    120.51  3.000
 16K  H5    C5   C2    123.09  3.000
 16K  C4    C5   C2    116.40  3.000
 16K  C13   N5   C12   112.70  3.000
 16K  C11   C6   C7    118.62  3.000
 16K  C11   C6   N3    125.23  3.000
 16K  C7    C6   N3    116.15  3.000
 16K  H7    C7   C8    120.56  3.000
 16K  H7    C7   C6    119.78  3.000
 16K  C8    C7   C6    119.66  3.000
 16K  C9    C8   C7    122.50  3.000
 16K  C9    C8   N4    119.09  3.000
 16K  C7    C8   N4    118.40  3.000
 16K  H9    C9   C10   120.85  3.000
 16K  C10   C9   C8    117.26  3.000
 16K  H9    C9   C8    121.88  3.000
 16K  H10   C10  C11   118.82  3.000
 16K  C11   C10  C9    121.87  3.000
 16K  H10   C10  C9    119.32  3.000
 16K  H11   C11  C10   119.84  3.000
 16K  H11   C11  C6    120.08  3.000
 16K  C10   C11  C6    120.08  3.000
 16K  C15   C12  N5    118.08  3.000
 16K  C15   C12  C1    127.53  3.000
 16K  N5    C12  C1    114.39  3.000
 16K  C14   C13  N5    124.63  3.000
 16K  C14   C13  S     121.43  3.000
 16K  N5    C13  S     113.93  3.000
 16K  H14B  C14  H14A  108.82  3.000
 16K  H14B  C14  H14   107.57  3.000
 16K  H14A  C14  H14   108.25  3.000
 16K  H14B  C14  C13   111.71  3.000
 16K  H14A  C14  C13   109.73  3.000
 16K  H14   C14  C13   110.65  3.000
 16K  H15B  C15  H15A  109.26  3.000
 16K  H15B  C15  H15   106.82  3.000
 16K  H15A  C15  H15   108.01  3.000
 16K  H15B  C15  C12   112.15  3.000
 16K  H15A  C15  C12   109.49  3.000
 16K  H15   C15  C12   111.00  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
 16K  CONST_01  C12  N5   C13  S       0.00   0.0  0
 16K  CONST_02  N5   C12  C1   S       0.00   0.0  0
 16K  CONST_03  N1   C2   C1   S     180.00   0.0  0
 16K  CONST_04  C5   C2   C1   S       0.00   0.0  0
 16K  CONST_05  N5   C13  S    C1      0.00   0.0  0
 16K  CONST_06  C13  N5   C12  C1      0.00   0.0  0
 16K  CONST_07  C3   N1   C2   C1    180.00   0.0  0
 16K  CONST_08  C4   C5   C2   C1    180.00   0.0  0
 16K  CONST_09  C12  C1   C2   N1      0.00   0.0  0
 16K  CONST_10  C4   C5   C2   N1      0.00   0.0  0
 16K  CONST_11  C4   N2   C3   N1      0.00   0.0  0
 16K  CONST_12  N2   C3   N1   C2      0.00   0.0  0
 16K  CONST_13  C13  S    C1   C2    180.00   0.0  0
 16K  CONST_14  N5   C12  C1   C2    180.00   0.0  0
 16K  CONST_15  N2   C4   C5   C2      0.00   0.0  0
 16K  CONST_16  C5   C4   N2   C3      0.00   0.0  0
 16K  CONST_17  C5   C2   N1   C3      0.00   0.0  0
 16K  CONST_18  C12  C1   C2   C5    180.00   0.0  0
 16K  CONST_19  C9   C8   C7   C6      0.00   0.0  0
 16K  CONST_20  C9   C10  C11  C6      0.00   0.0  0
 16K  CONST_21  C10  C11  C6   C7      0.00   0.0  0
 16K  CONST_22  C10  C9   C8   C7      0.00   0.0  0
 16K  CONST_23  C11  C6   C7   C8      0.00   0.0  0
 16K  CONST_24  C11  C10  C9   C8      0.00   0.0  0
 16K  CONST_25  C13  S    C1   C12     0.00   0.0  0
 16K  CONST_26  C15  C12  C1   S     180.00   0.0  0
 16K  CONST_27  C14  C13  S    C1    180.00   0.0  0
 16K  CONST_28  N3   C3   N1   C2    180.00   0.0  0
 16K  CONST_29  C15  C12  C1   C2      0.00   0.0  0
 16K  CONST_30  C4   N2   C3   N3    180.00   0.0  0
 16K  CONST_31  C8   C7   C6   N3    180.00   0.0  0
 16K  CONST_32  C10  C11  C6   N3    180.00   0.0  0
 16K  CONST_33  C6   C7   C8   N4    180.00   0.0  0
 16K  CONST_34  C10  C9   C8   N4    180.00   0.0  0
 16K  CONST_35  C14  C13  N5   C12   180.00   0.0  0
 16K  CONST_36  C15  C12  N5   C13   180.00   0.0  0
 16K  CONST_37  H5   C5   C2   C1      0.00   0.0  0
 16K  CONST_38  H4   C4   C5   C2    180.00   0.0  0
 16K  CONST_39  H10  C10  C11  C6    180.00   0.0  0
 16K  CONST_40  H11  C11  C6   C7    180.00   0.0  0
 16K  CONST_41  H9   C9   C8   C7    180.00   0.0  0
 16K  CONST_42  H7   C7   C8   C9    180.00   0.0  0
 16K  CONST_43  C7   C8   N4   O1      0.00   0.0  0
 16K  CONST_44  C9   C8   N4   O1    180.00   0.0  0
 16K  CONST_45  C7   C8   N4   O2    180.00   0.0  0
 16K  CONST_46  C9   C8   N4   O2      0.00   0.0  0
 16K  Var_01    C6   N3   C3   N1    177.90  30.0  2
 16K  Var_02    C7   C6   N3   C3   -178.52  30.0  2
 16K  Var_03    H14  C14  C13  S      78.75  30.0  2
 16K  Var_04    H15  C15  C12  C1     78.95  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
 16K  plan-1  S    0.020
 16K  plan-1  C1   0.020
 16K  plan-1  C2   0.020
 16K  plan-1  N5   0.020
 16K  plan-1  C12  0.020
 16K  plan-1  C13  0.020
 16K  plan-1  C14  0.020
 16K  plan-1  C15  0.020
 16K  plan-2  C1   0.020
 16K  plan-2  N1   0.020
 16K  plan-2  C2   0.020
 16K  plan-2  N2   0.020
 16K  plan-2  C3   0.020
 16K  plan-2  N3   0.020
 16K  plan-2  C4   0.020
 16K  plan-2  C5   0.020
 16K  plan-2  H4   0.020
 16K  plan-2  H5   0.020
 16K  plan-3  N3   0.020
 16K  plan-3  N4   0.020
 16K  plan-3  C6   0.020
 16K  plan-3  C7   0.020
 16K  plan-3  C8   0.020
 16K  plan-3  C9   0.020
 16K  plan-3  C10  0.020
 16K  plan-3  C11  0.020
 16K  plan-3  H7   0.020
 16K  plan-3  H9   0.020
 16K  plan-3  H10  0.020
 16K  plan-3  H11  0.020
 16K  plan-4  O1   0.020
 16K  plan-4  O2   0.020
 16K  plan-4  N4   0.020
 16K  plan-4  C8   0.020

