# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 20:25:34 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N~4~-[4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-yl]-N~1~,N~1~-dimethyl-2-nitrobenzene-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc(Nc2nccc(n2)c3sc(C)nc3C)cc1[N+]([O-])=O
#
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
 19K  19K  N~4~-[4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-yl]-N~1~,N~1~-dimethyl-2-nitrobenzene-1,4-diamine  ligand  44  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_19K
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
 19K  S     S  S2     0   0.230  -5.8196   0.7977   0.0705
 19K  C1    C  CH3    0  -0.725  -8.1101  -0.8076   0.1350
 19K  N1    N  N      0  -0.391  -5.8268  -1.7399   0.1118
 19K  O1    O  O      0  -0.383   4.4968  -2.7924  -0.4761
 19K  C2    C  CR5    0   0.077  -6.6262  -0.7188   0.1141
 19K  N2    N  N      0  -0.472  -0.6299   2.0045  -0.0208
 19K  C3    C  CR5    0   0.351  -4.5114  -1.3797   0.0738
 19K  N3    N  NH1    0  -0.781   0.3329  -0.1204   0.0300
 19K  C4    C  CH3    0  -0.726  -3.4850  -2.4630   0.0686
 19K  N4    N  NT     0  -0.478   5.9025   0.7503   0.2257
 19K  C5    C  CR5    0  -0.343  -4.2953  -0.0211   0.0465
 19K  N5    N  N      1   0.330   4.7572  -1.8873   0.2842
 19K  C6    C  CR6    0   0.311  -3.0447   0.7199   0.0171
 19K  N6    N  N      0  -0.499  -1.9210   0.0175   0.0299
 19K  C7    C  CR16   0  -0.398  -3.0098   2.1202  -0.0179
 19K  C8    C  CR16   0   0.006  -1.7613   2.7011  -0.0350
 19K  C9    C  CR6    0   0.609  -0.7679   0.6855   0.0113
 19K  C10   C  CR6    0   0.380   1.6858   0.1760   0.0599
 19K  C11   C  CR16   0  -0.294   2.2366   1.4597   0.0009
 19K  C12   C  CR16   0  -0.272   3.6087   1.6322   0.0576
 19K  C13   C  CR6    0   0.277   4.5033   0.5719   0.1815
 19K  C14   C  CH3    0  -0.536   6.4228   1.6624  -0.7754
 19K  C15   C  CH3    0  -0.527   6.3964   1.0657   1.5567
 19K  C16   C  CR6    0   0.218   3.9241  -0.6988   0.2134
 19K  C17   C  CR16   0  -0.390   2.5595  -0.9081   0.1424
 19K  H1    H  HCH3   0   0.272  -8.5310  -0.5228  -0.8303
 19K  H1A   H  HCH3   0   0.269  -8.4116  -1.8294   0.3534
 19K  H1B   H  HCH3   0   0.268  -8.5383  -0.1468   0.8878
 19K  HN3   H  HNH1   0   0.414   0.1006  -1.1021   0.0600
 19K  H4    H  HCH3   0   0.253  -2.8332  -2.3954  -0.8004
 19K  H4A   H  HCH3   0   0.253  -2.8415  -2.4087   0.9457
 19K  H4B   H  HCH3   0   0.248  -3.9822  -3.4309   0.0612
 19K  H7    H  HCR6   0   0.275  -3.8981   2.7349  -0.0316
 19K  H8    H  HCR6   0   0.279  -1.6603   3.7799  -0.0616
 19K  H11   H  HCR6   0   0.300   1.5949   2.3214  -0.0808
 19K  H12   H  HCR6   0   0.271   3.9961   2.6418   0.0028
 19K  H14   H  HCH3   0   0.244   7.5104   1.5790  -0.7937
 19K  H14A  H  HCH3   0   0.245   6.0502   1.3908  -1.7623
 19K  H14B  H  HCH3   0   0.206   6.1801   2.7179  -0.5929
 19K  H15   H  HCH3   0   0.207   6.1250   2.0804   1.8796
 19K  H15A  H  HCH3   0   0.246   6.0052   0.3618   2.2873
 19K  H15B  H  HCH3   0   0.235   7.4847   0.9904   1.5665
 19K  H17   H  HCR6   0   0.299   2.1674  -1.9173   0.1669
 19K  O2    O  O     -1  -0.360   5.6489  -1.9165   1.0947

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
 19K  S    C2    aromatic  1.718  0.020  1.718
 19K  C1   H1    single    0.970  0.020  1.090
 19K  C1   H1A   single    0.970  0.020  1.090
 19K  C1   H1B   single    0.970  0.020  1.090
 19K  N1   C2    aromatic  1.297  0.020  1.297
 19K  O1   N5    double    1.210  0.020  1.210
 19K  C2   C1    single    1.487  0.020  1.487
 19K  N2   C9    aromatic  1.327  0.020  1.327
 19K  C3   N1    aromatic  1.364  0.020  1.364
 19K  C3   C5    aromatic  1.376  0.020  1.376
 19K  N3   C10   single    1.385  0.020  1.385
 19K  N3   HN3   single    0.860  0.020  1.020
 19K  C4   C3    single    1.492  0.020  1.492
 19K  C4   H4    single    0.970  0.020  1.090
 19K  C4   H4A   single    0.970  0.020  1.090
 19K  C4   H4B   single    0.970  0.020  1.090
 19K  N4   C14   single    1.451  0.020  1.451
 19K  N4   C15   single    1.454  0.020  1.454
 19K  C5   S     aromatic  1.730  0.020  1.730
 19K  C6   C5    single    1.454  0.020  1.454
 19K  C6   N6    aromatic  1.325  0.020  1.325
 19K  C7   C6    aromatic  1.401  0.020  1.401
 19K  C7   H7    single    0.930  0.020  1.080
 19K  C8   N2    aromatic  1.329  0.020  1.329
 19K  C8   C7    aromatic  1.377  0.020  1.377
 19K  C8   H8    single    0.930  0.020  1.080
 19K  C9   N3    single    1.364  0.020  1.364
 19K  C9   N6    aromatic  1.333  0.020  1.333
 19K  C10  C17   aromatic  1.395  0.020  1.395
 19K  C10  C11   aromatic  1.398  0.020  1.398
 19K  C11  C12   aromatic  1.384  0.020  1.384
 19K  C11  H11   single    0.930  0.020  1.080
 19K  C12  C13   aromatic  1.393  0.020  1.393
 19K  C12  H12   single    0.930  0.020  1.080
 19K  C13  N4    single    1.411  0.020  1.411
 19K  C14  H14   single    0.970  0.020  1.090
 19K  C14  H14A  single    0.970  0.020  1.090
 19K  C14  H14B  single    0.970  0.020  1.090
 19K  C15  H15   single    0.970  0.020  1.090
 19K  C15  H15A  single    0.970  0.020  1.090
 19K  C15  H15B  single    0.970  0.020  1.090
 19K  C16  N5    single    1.453  0.020  1.453
 19K  C16  C13   aromatic  1.397  0.020  1.397
 19K  C17  C16   aromatic  1.382  0.020  1.382
 19K  C17  H17   single    0.930  0.020  1.080
 19K  N5   O2    single    1.205  0.020  1.205

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
 19K  C5    S    C2     89.79  3.000
 19K  H1B   C1   H1A   108.79  3.000
 19K  H1B   C1   H1    107.54  3.000
 19K  H1A   C1   H1    108.42  3.000
 19K  H1B   C1   C2    111.46  3.000
 19K  H1A   C1   C2    109.62  3.000
 19K  H1    C1   C2    110.92  3.000
 19K  C3    N1   C2    112.74  3.000
 19K  N1    C2   C1    124.63  3.000
 19K  C1    C2   S     121.44  3.000
 19K  N1    C2   S     113.92  3.000
 19K  C9    N2   C8    115.65  3.000
 19K  C5    C3   C4    127.50  3.000
 19K  C4    C3   N1    118.13  3.000
 19K  C5    C3   N1    114.37  3.000
 19K  HN3   N3   C10   115.61  3.000
 19K  HN3   N3   C9    112.91  3.000
 19K  C10   N3   C9    131.44  3.000
 19K  H4B   C4   H4A   108.66  3.000
 19K  H4B   C4   H4    108.87  3.000
 19K  H4A   C4   H4    106.62  3.000
 19K  H4B   C4   C3    109.36  3.000
 19K  H4A   C4   C3    111.55  3.000
 19K  H4    C4   C3    111.69  3.000
 19K  C15   N4   C14   111.92  3.000
 19K  C15   N4   C13   113.13  3.000
 19K  C14   N4   C13   114.43  3.000
 19K  C6    C5   C3    129.69  3.000
 19K  C6    C5   S     121.12  3.000
 19K  C3    C5   S     109.18  3.000
 19K  O2    N5   C16   118.47  3.000
 19K  O2    N5   O1    124.29  3.000
 19K  C16   N5   O1    117.23  3.000
 19K  C7    C6   N6    120.58  3.000
 19K  C7    C6   C5    122.09  3.000
 19K  N6    C6   C5    117.33  3.000
 19K  C9    N6   C6    117.89  3.000
 19K  H7    C7   C8    120.35  3.000
 19K  C8    C7   C6    116.39  3.000
 19K  H7    C7   C6    123.26  3.000
 19K  H8    C8   C7    120.30  3.000
 19K  H8    C8   N2    116.28  3.000
 19K  C7    C8   N2    123.42  3.000
 19K  N6    C9   N3    113.69  3.000
 19K  N6    C9   N2    126.07  3.000
 19K  N3    C9   N2    120.24  3.000
 19K  C17   C10  C11   118.00  3.000
 19K  C11   C10  N3    125.47  3.000
 19K  C17   C10  N3    116.54  3.000
 19K  H11   C11  C12   119.60  3.000
 19K  H11   C11  C10   120.19  3.000
 19K  C12   C11  C10   120.21  3.000
 19K  H12   C12  C13   118.98  3.000
 19K  H12   C12  C11   117.96  3.000
 19K  C13   C12  C11   123.06  3.000
 19K  C16   C13  C12   115.36  3.000
 19K  C16   C13  N4    121.70  3.000
 19K  C12   C13  N4    122.91  3.000
 19K  H14B  C14  H14A  108.33  3.000
 19K  H14B  C14  H14   107.25  3.000
 19K  H14A  C14  H14   107.86  3.000
 19K  H14B  C14  N4    114.22  3.000
 19K  H14A  C14  N4    110.23  3.000
 19K  H14   C14  N4    108.73  3.000
 19K  H15B  C15  H15A  107.95  3.000
 19K  H15B  C15  H15   107.90  3.000
 19K  H15A  C15  H15   108.15  3.000
 19K  H15B  C15  N4    109.39  3.000
 19K  H15A  C15  N4    110.63  3.000
 19K  H15   C15  N4    112.66  3.000
 19K  C17   C16  C13   123.08  3.000
 19K  C17   C16  N5    116.40  3.000
 19K  C13   C16  N5    120.49  3.000
 19K  H17   C17  C16   119.82  3.000
 19K  H17   C17  C10   119.92  3.000
 19K  C16   C17  C10   120.25  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
 19K  CONST_01  C3   N1   C2   S       0.00   0.0  0
 19K  CONST_02  N1   C3   C5   S       0.00   0.0  0
 19K  CONST_03  N6   C6   C5   S     180.00   0.0  0
 19K  CONST_04  C7   C6   C5   S       0.00   0.0  0
 19K  CONST_05  C5   S    C2   N1      0.00   0.0  0
 19K  CONST_06  C6   C5   C3   N1    180.00   0.0  0
 19K  CONST_07  C3   C5   S    C2      0.00   0.0  0
 19K  CONST_08  C6   C5   S    C2    180.00   0.0  0
 19K  CONST_09  C5   C3   N1   C2      0.00   0.0  0
 19K  CONST_10  C6   N6   C9   N2      0.00   0.0  0
 19K  CONST_11  C6   C7   C8   N2      0.00   0.0  0
 19K  CONST_12  N6   C6   C5   C3      0.00   0.0  0
 19K  CONST_13  C7   C6   C5   C3    180.00   0.0  0
 19K  CONST_14  C9   N6   C6   C5    180.00   0.0  0
 19K  CONST_15  C8   C7   C6   C5    180.00   0.0  0
 19K  CONST_16  C8   C7   C6   N6      0.00   0.0  0
 19K  CONST_17  C8   N2   C9   N6      0.00   0.0  0
 19K  CONST_18  C9   N6   C6   C7      0.00   0.0  0
 19K  CONST_19  C9   N2   C8   C7      0.00   0.0  0
 19K  CONST_20  C13  C16  C17  C10     0.00   0.0  0
 19K  CONST_21  C13  C12  C11  C10     0.00   0.0  0
 19K  CONST_22  C16  C17  C10  C11     0.00   0.0  0
 19K  CONST_23  C16  C13  C12  C11     0.00   0.0  0
 19K  CONST_24  C17  C10  C11  C12     0.00   0.0  0
 19K  CONST_25  C17  C16  C13  C12     0.00   0.0  0
 19K  CONST_26  C4   C3   C5   S     180.00   0.0  0
 19K  CONST_27  C5   S    C2   C1    180.00   0.0  0
 19K  CONST_28  C3   N1   C2   C1    180.00   0.0  0
 19K  CONST_29  C4   C3   N1   C2    180.00   0.0  0
 19K  CONST_30  C16  C17  C10  N3    180.00   0.0  0
 19K  CONST_31  C12  C11  C10  N3    180.00   0.0  0
 19K  CONST_32  C8   N2   C9   N3    180.00   0.0  0
 19K  CONST_33  C6   N6   C9   N3    180.00   0.0  0
 19K  CONST_34  C6   C5   C3   C4      0.00   0.0  0
 19K  CONST_35  C11  C12  C13  N4    180.00   0.0  0
 19K  CONST_36  C17  C16  C13  N4    180.00   0.0  0
 19K  CONST_37  C12  C13  C16  N5    180.00   0.0  0
 19K  CONST_38  C10  C17  C16  N5    180.00   0.0  0
 19K  CONST_39  H7   C7   C8   N2    180.00   0.0  0
 19K  CONST_40  H8   C8   C7   C6    180.00   0.0  0
 19K  CONST_41  H12  C12  C11  C10   180.00   0.0  0
 19K  CONST_42  H17  C17  C10  C11   180.00   0.0  0
 19K  CONST_43  H11  C11  C12  C13   180.00   0.0  0
 19K  Var_01    C10  N3   C9   N2      2.11  30.0  2
 19K  Var_02    C17  C10  N3   C9    176.78  30.0  2
 19K  Var_03    H1   C1   C2   S      71.11  30.0  2
 19K  Var_04    H4   C4   C3   N1    122.63  30.0  2
 19K  Var_05    H14  C14  N4   C13  -168.67  30.0  3
 19K  Var_06    H15  C15  N4   C13   -71.43  30.0  3

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
 19K  plan-1  S    0.020
 19K  plan-1  C1   0.020
 19K  plan-1  N1   0.020
 19K  plan-1  C2   0.020
 19K  plan-1  C3   0.020
 19K  plan-1  C4   0.020
 19K  plan-1  C5   0.020
 19K  plan-1  C6   0.020
 19K  plan-2  N2   0.020
 19K  plan-2  N3   0.020
 19K  plan-2  C5   0.020
 19K  plan-2  C6   0.020
 19K  plan-2  N6   0.020
 19K  plan-2  C7   0.020
 19K  plan-2  C8   0.020
 19K  plan-2  C9   0.020
 19K  plan-2  H7   0.020
 19K  plan-2  H8   0.020
 19K  plan-3  N3   0.020
 19K  plan-3  N4   0.020
 19K  plan-3  N5   0.020
 19K  plan-3  C10  0.020
 19K  plan-3  C11  0.020
 19K  plan-3  C12  0.020
 19K  plan-3  C13  0.020
 19K  plan-3  C16  0.020
 19K  plan-3  C17  0.020
 19K  plan-3  H11  0.020
 19K  plan-3  H12  0.020
 19K  plan-3  H17  0.020
 19K  plan-4  N4   0.020
 19K  plan-4  C13  0.020
 19K  plan-4  C14  0.020
 19K  plan-4  C15  0.020
 19K  plan-5  O1   0.020
 19K  plan-5  N5   0.020
 19K  plan-5  C16  0.020
 19K  plan-5  O2   0.020

