# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:05:53 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: [4-amino-2-(cyclohexylamino)-1,3-thiazol-5-yl](3-nitrophenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NC2CCCCC2)sc1C(=O)c3cccc(c3)[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
 Z68  Z68  '[4-amino-2-(cyclohexylamino)-1,3-thiazol-5-yl](3-nitrophenyl)methanone'  ligand  42  24  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Z68
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
 Z68  C1    C  CR16   0  -0.267   5.1413   0.6154  -0.6206
 Z68  N1    N  N      1   0.329   4.2606   2.3260   0.8975
 Z68  O1    O  O     -1  -0.374   5.2232   3.0064   0.6343
 Z68  S1    S  S2     0   0.156   0.0154   0.1733  -0.5061
 Z68  C2    C  CR6    0   0.275   4.1411   1.0292   0.2448
 Z68  N2    N  N      0  -0.480  -1.8779  -1.4758   0.1572
 Z68  O2    O  O      0  -0.375   3.3912   2.6556   1.6691
 Z68  C3    C  CR16   0  -0.310   3.0303   0.2436   0.5155
 Z68  N3    N  NH1    0  -0.650  -2.6259   0.5776  -0.6329
 Z68  O3    O  O      0  -0.478   2.0375  -3.0849   0.5401
 Z68  C4    C  CR6    0  -0.030   2.9243  -1.0013  -0.0893
 Z68  N4    N  NH2    0  -0.823  -0.7602  -3.3809   0.8299
 Z68  C5    C  CR16   0  -0.261   3.9366  -1.4418  -0.9396
 Z68  C6    C  CR16   0  -0.240   5.0268  -0.6317  -1.2143
 Z68  C7    C  C      0   0.365   1.7795  -1.9184   0.2176
 Z68  C8    C  CR5    0  -0.468   0.4647  -1.4192   0.1025
 Z68  C9    C  CR5    0   0.591  -0.7188  -2.1324   0.3764
 Z68  C10   C  CR5    0   0.365  -1.6589  -0.2700  -0.3090
 Z68  C11   C  CH1    0  -0.066  -4.0377   0.3104  -0.3896
 Z68  C12   C  CH2    0  -0.446  -4.8817   1.1008  -1.3833
 Z68  C13   C  CH2    0  -0.439  -6.3700   0.8608  -1.1448
 Z68  C14   C  CH2    0  -0.433  -6.7685   1.1836   0.2914
 Z68  C15   C  CH2    0  -0.441  -5.9164   0.3998   1.2836
 Z68  C16   C  CH2    0  -0.427  -4.4280   0.6415   1.0500
 Z68  H1    H  HCR6   0   0.303   5.9966   1.2408  -0.8306
 Z68  H3    H  HCR6   0   0.306   2.2712   0.5819   1.2074
 Z68  HN3   H  HNH1   0   0.410  -2.3729   1.5096  -0.9238
 Z68  H1N4  H  HNH2   0   0.404  -1.6448  -3.8268   0.9999
 Z68  H2N4  H  HNH2   0   0.415   0.0945  -3.8917   0.9744
 Z68  H5    H  HCR6   0   0.280   3.8656  -2.4188  -1.3995
 Z68  H6    H  HCR6   0   0.283   5.7993  -0.9733  -1.8891
 Z68  H11   H  HCH1   0   0.248  -4.1962  -0.7568  -0.5664
 Z68  H112  H  HCH2   0   0.223  -4.6629   2.1697  -1.2746
 Z68  H212  H  HCH2   0   0.246  -4.6093   0.8213  -2.4037
 Z68  H113  H  HCH2   0   0.236  -6.9528   1.4598  -1.8475
 Z68  H213  H  HCH2   0   0.217  -6.6066  -0.1862  -1.3610
 Z68  H114  H  HCH2   0   0.213  -6.6440   2.2569   0.4713
 Z68  H214  H  HCH2   0   0.232  -7.8275   0.9642   0.4455
 Z68  H115  H  HCH2   0   0.235  -6.1764   0.6715   2.3089
 Z68  H215  H  HCH2   0   0.216  -6.1308  -0.6697   1.1832
 Z68  H116  H  HCH2   0   0.240  -3.8318   0.0422   1.7418
 Z68  H216  H  HCH2   0   0.218  -4.1876   1.6917   1.2474

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
 Z68  C1   C2    aromatic  1.386  0.020  1.386
 Z68  C1   H1    single    0.930  0.020  1.080
 Z68  N1   O1    single    1.208  0.020  1.208
 Z68  N1   O2    double    1.208  0.020  1.208
 Z68  C2   N1    single    1.457  0.020  1.457
 Z68  N2   C10   aromatic  1.311  0.020  1.311
 Z68  C3   C2    aromatic  1.387  0.020  1.387
 Z68  C3   H3    single    0.930  0.020  1.080
 Z68  N3   C11   single    1.457  0.020  1.457
 Z68  N3   HN3   single    0.860  0.020  1.020
 Z68  O3   C7    double    1.237  0.020  1.237
 Z68  C4   C5    aromatic  1.393  0.020  1.393
 Z68  C4   C3    aromatic  1.388  0.020  1.388
 Z68  N4   C9    single    1.329  0.020  1.329
 Z68  N4   H1N4  single    0.860  0.020  1.020
 Z68  N4   H2N4  single    0.860  0.020  1.020
 Z68  C5   C6    aromatic  1.386  0.020  1.386
 Z68  C5   H5    single    0.930  0.020  1.080
 Z68  C6   C1    aromatic  1.386  0.020  1.386
 Z68  C6   H6    single    0.930  0.020  1.080
 Z68  C7   C4    single    1.499  0.020  1.499
 Z68  C8   C7    single    1.411  0.020  1.411
 Z68  C8   S1    aromatic  1.763  0.020  1.763
 Z68  C9   N2    aromatic  1.350  0.020  1.350
 Z68  C9   C8    aromatic  1.409  0.020  1.409
 Z68  C10  N3    single    1.326  0.020  1.326
 Z68  C10  S1    aromatic  1.743  0.020  1.743
 Z68  C11  C12   single    1.525  0.020  1.525
 Z68  C11  C16   single    1.528  0.020  1.528
 Z68  C11  H11   single    0.970  0.020  1.090
 Z68  C12  C13   single    1.526  0.020  1.526
 Z68  C12  H112  single    0.970  0.020  1.090
 Z68  C12  H212  single    0.970  0.020  1.090
 Z68  C13  C14   single    1.525  0.020  1.525
 Z68  C13  H113  single    0.970  0.020  1.090
 Z68  C13  H213  single    0.970  0.020  1.090
 Z68  C14  H114  single    0.970  0.020  1.090
 Z68  C14  H214  single    0.970  0.020  1.090
 Z68  C15  C14   single    1.525  0.020  1.525
 Z68  C15  H115  single    0.970  0.020  1.090
 Z68  C15  H215  single    0.970  0.020  1.090
 Z68  C16  C15   single    1.526  0.020  1.526
 Z68  C16  H116  single    0.970  0.020  1.090
 Z68  C16  H216  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
 Z68  H1    C1   C6    120.21  3.000
 Z68  C6    C1   C2    118.46  3.000
 Z68  H1    C1   C2    121.33  3.000
 Z68  O2    N1   C2    118.03  3.000
 Z68  C2    N1   O1    117.98  3.000
 Z68  O2    N1   O1    123.98  3.000
 Z68  C10   S1   C8     88.63  3.000
 Z68  C3    C2   N1    118.84  3.000
 Z68  C3    C2   C1    122.05  3.000
 Z68  N1    C2   C1    119.11  3.000
 Z68  C10   N2   C9    111.19  3.000
 Z68  H3    C3   C4    120.38  3.000
 Z68  C4    C3   C2    118.95  3.000
 Z68  H3    C3   C2    120.65  3.000
 Z68  HN3   N3   C11   117.43  3.000
 Z68  HN3   N3   C10   118.56  3.000
 Z68  C11   N3   C10   123.26  3.000
 Z68  C7    C4   C5    119.11  3.000
 Z68  C7    C4   C3    121.20  3.000
 Z68  C5    C4   C3    119.59  3.000
 Z68  H2N4  N4   H1N4  119.88  3.000
 Z68  H2N4  N4   C9    119.97  3.000
 Z68  H1N4  N4   C9    120.12  3.000
 Z68  H5    C5   C6    119.68  3.000
 Z68  H5    C5   C4    119.81  3.000
 Z68  C6    C5   C4    120.51  3.000
 Z68  H6    C6   C5    120.08  3.000
 Z68  H6    C6   C1    119.51  3.000
 Z68  C5    C6   C1    120.41  3.000
 Z68  C8    C7   C4    118.59  3.000
 Z68  C8    C7   O3    123.30  3.000
 Z68  C4    C7   O3    118.10  3.000
 Z68  C9    C8   C7    126.00  3.000
 Z68  C9    C8   S1    108.08  3.000
 Z68  C7    C8   S1    125.82  3.000
 Z68  C8    C9   N4    124.62  3.000
 Z68  C8    C9   N2    116.33  3.000
 Z68  N4    C9   N2    119.05  3.000
 Z68  N3    C10  N2    123.56  3.000
 Z68  N3    C10  S1    120.68  3.000
 Z68  N2    C10  S1    115.76  3.000
 Z68  H11   C11  C16   109.08  3.000
 Z68  H11   C11  C12   108.69  3.000
 Z68  C16   C11  C12   111.12  3.000
 Z68  H11   C11  N3    107.01  3.000
 Z68  C16   C11  N3    111.41  3.000
 Z68  C12   C11  N3    109.42  3.000
 Z68  H212  C12  H112  106.99  3.000
 Z68  H212  C12  C13   110.42  3.000
 Z68  H112  C12  C13   109.41  3.000
 Z68  H212  C12  C11   109.76  3.000
 Z68  H112  C12  C11   109.28  3.000
 Z68  C13   C12  C11   110.88  3.000
 Z68  H213  C13  H113  106.39  3.000
 Z68  H213  C13  C14   109.39  3.000
 Z68  H113  C13  C14   110.52  3.000
 Z68  H213  C13  C12   109.28  3.000
 Z68  H113  C13  C12   109.48  3.000
 Z68  C14   C13  C12   111.64  3.000
 Z68  H214  C14  H114  106.49  3.000
 Z68  H214  C14  C15   110.28  3.000
 Z68  H114  C14  C15   109.47  3.000
 Z68  C15   C14  C13   110.98  3.000
 Z68  H214  C14  C13   110.10  3.000
 Z68  H114  C14  C13   109.42  3.000
 Z68  H215  C15  H115  106.40  3.000
 Z68  H215  C15  C16   109.36  3.000
 Z68  H115  C15  C16   109.67  3.000
 Z68  C16   C15  C14   111.35  3.000
 Z68  H215  C15  C14   109.44  3.000
 Z68  H115  C15  C14   110.49  3.000
 Z68  H216  C16  H116  106.98  3.000
 Z68  H216  C16  C15   109.78  3.000
 Z68  H116  C16  C15   110.40  3.000
 Z68  H216  C16  C11   108.76  3.000
 Z68  H116  C16  C11   109.78  3.000
 Z68  C15   C16  C11   111.04  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
 Z68  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 Z68  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 Z68  CONST_03  N2    C9   C8   S1     0.00   0.0  0
 Z68  CONST_04  C9    N2   C10  S1     0.00   0.0  0
 Z68  CONST_05  C5    C6   C1   C2     0.00   0.0  0
 Z68  CONST_06  C5    C4   C3   C2     0.00   0.0  0
 Z68  CONST_07  C8    S1   C10  N2     0.00   0.0  0
 Z68  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 Z68  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 Z68  CONST_10  C10   N2   C9   C8     0.00   0.0  0
 Z68  CONST_11  C10   S1   C8   C9     0.00   0.0  0
 Z68  CONST_12  C6    C1   C2   N1   180.00   0.0  0
 Z68  CONST_13  C4    C3   C2   N1   180.00   0.0  0
 Z68  CONST_14  N4    C9   C8   S1   180.00   0.0  0
 Z68  CONST_15  C7    C4   C3   C2   180.00   0.0  0
 Z68  CONST_16  C7    C8   C9   N2   180.00   0.0  0
 Z68  CONST_17  C9    N2   C10  N3   180.00   0.0  0
 Z68  CONST_18  C8    S1   C10  N3   180.00   0.0  0
 Z68  CONST_19  C10   N2   C9   N4   180.00   0.0  0
 Z68  CONST_20  C7    C4   C5   C6   180.00   0.0  0
 Z68  CONST_21  C10   S1   C8   C7   180.00   0.0  0
 Z68  CONST_22  C11   N3   C10  S1   180.00   0.0  0
 Z68  CONST_23  C11   N3   C10  N2     0.00   0.0  0
 Z68  CONST_24  H3    C3   C2   C1   180.00   0.0  0
 Z68  CONST_25  H5    C5   C6   C1   180.00   0.0  0
 Z68  CONST_26  H6    C6   C1   C2   180.00   0.0  0
 Z68  CONST_27  H1    C1   C2   C3   180.00   0.0  0
 Z68  CONST_28  O1    N1   C2   C1     0.00   0.0  0
 Z68  CONST_29  O2    N1   C2   C1   180.00   0.0  0
 Z68  CONST_30  C3    C2   N1   O1   180.00   0.0  0
 Z68  CONST_31  C3    C2   N1   O2     0.00   0.0  0
 Z68  CONST_32  HN3   N3   C10  S1     0.00   0.0  0
 Z68  CONST_33  H1N4  N4   C9   N2     0.00   0.0  0
 Z68  CONST_34  H2N4  N4   C9   N2   180.00   0.0  0
 Z68  Var_01    C14   C13  C12  C11   55.59  30.0  1
 Z68  Var_02    C14   C15  C16  C11  -55.71  30.0  1
 Z68  Var_03    C15   C14  C13  C12  -55.28  30.0  1
 Z68  Var_04    C16   C15  C14  C13   55.24  30.0  1
 Z68  Var_05    C4    C7   C8   S1     5.42  30.0  2
 Z68  Var_06    C8    C7   C4   C3    52.38  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 Z68  chir_01  C11  N3  C12  C16  positiv

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
 Z68  plan-1  S1    0.020
 Z68  plan-1  N2    0.020
 Z68  plan-1  N3    0.020
 Z68  plan-1  N4    0.020
 Z68  plan-1  C7    0.020
 Z68  plan-1  C8    0.020
 Z68  plan-1  C9    0.020
 Z68  plan-1  C10   0.020
 Z68  plan-2  C1    0.020
 Z68  plan-2  N1    0.020
 Z68  plan-2  C2    0.020
 Z68  plan-2  C3    0.020
 Z68  plan-2  C4    0.020
 Z68  plan-2  C5    0.020
 Z68  plan-2  C6    0.020
 Z68  plan-2  C7    0.020
 Z68  plan-2  H1    0.020
 Z68  plan-2  H3    0.020
 Z68  plan-2  H5    0.020
 Z68  plan-2  H6    0.020
 Z68  plan-3  N1    0.020
 Z68  plan-3  O1    0.020
 Z68  plan-3  C2    0.020
 Z68  plan-3  O2    0.020
 Z68  plan-4  N3    0.020
 Z68  plan-4  C10   0.020
 Z68  plan-4  C11   0.020
 Z68  plan-4  HN3   0.020
 Z68  plan-5  N4    0.020
 Z68  plan-5  C9    0.020
 Z68  plan-5  H1N4  0.020
 Z68  plan-5  H2N4  0.020
 Z68  plan-6  O3    0.020
 Z68  plan-6  C4    0.020
 Z68  plan-6  C7    0.020
 Z68  plan-6  C8    0.020

