# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 23:22:02 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: [4-amino-2-(cyclohexylamino)-1,3-thiazol-5-yl](pyridin-3-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NC2CCCCC2)sc1C(=O)c3cccnc3
#
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
 12Z  12Z  '[4-amino-2-(cyclohexylamino)-1,3-thiazol-5-yl](pyridin-3-yl)methanone'  ligand  39  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_12Z
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
 12Z  C1    C  CR5   0  -0.469   1.1970  -0.8194   0.0838
 12Z  C2    C  CR5   0   0.590   0.1403  -1.7499   0.0929
 12Z  N3    N  N     0  -0.480  -1.1059  -1.2435  -0.0305
 12Z  C4    C  CR5   0   0.364  -1.0765   0.0613  -0.1538
 12Z  S5    S  S2    0   0.154   0.5069   0.7890  -0.1262
 12Z  C6    C  C     0   0.358   2.5752  -1.1265   0.1392
 12Z  N7    N  NH2   0  -0.824   0.2926  -3.0647   0.2172
 12Z  N8    N  NH1   0  -0.653  -2.1606   0.8096  -0.3047
 12Z  O9    O  O     0  -0.480   3.0061  -2.2868   0.1764
 12Z  C10   C  CR16  0  -0.062   5.4917   1.9090   0.0069
 12Z  N11   N  N     0  -0.400   5.5876   0.8668  -0.8128
 12Z  C12   C  CR16  0  -0.074   4.6501  -0.0664  -0.7427
 12Z  C13   C  CR6   0  -0.125   3.5591  -0.0021   0.1221
 12Z  C14   C  CR16  0  -0.183   3.4759   1.0904   0.9777
 12Z  C15   C  CR16  0  -0.316   4.4624   2.0625   0.9222
 12Z  C16   C  CH2   0  -0.439  -5.8746   0.7292  -1.0311
 12Z  C17   C  CH2   0  -0.453  -4.4403   1.2486  -1.0190
 12Z  C18   C  CH1   0  -0.055  -3.5152   0.2739  -0.2982
 12Z  C19   C  CH2   0  -0.430  -4.0087  -0.0133   1.1189
 12Z  C20   C  CH2   0  -0.440  -5.4430  -0.5339   1.1006
 12Z  C21   C  CH2   0  -0.432  -6.3742   0.4343   0.3789
 12Z  HN7   H  HNH2  0   0.414   1.2157  -3.4579   0.2914
 12Z  HN7A  H  HNH2  0   0.403  -0.5113  -3.6675   0.2166
 12Z  HN8   H  HNH1  0   0.411  -2.0552   1.8122  -0.3289
 12Z  H12   H  HCR6  0   0.268   4.7556  -0.9092  -1.4171
 12Z  H14   H  HCR6  0   0.283   2.6709   1.1757   1.6971
 12Z  H15   H  HCR6  0   0.278   4.4388   2.9209   1.5786
 12Z  H16   H  HCH2  0   0.236  -6.5226   1.4586  -1.5215
 12Z  H16A  H  HCH2  0   0.217  -5.9217  -0.1829  -1.6345
 12Z  H17   H  HCH2  0   0.247  -4.0840   1.4121  -2.0389
 12Z  H17A  H  HCH2  0   0.224  -4.4110   2.2196  -0.5110
 12Z  H18   H  HCH1  0   0.244  -3.4959  -0.6647  -0.8600
 12Z  H19   H  HCH2  0   0.241  -3.3467  -0.7367   1.5997
 12Z  H19A  H  HCH2  0   0.217  -3.9577   0.9087   1.7078
 12Z  H20   H  HCH2  0   0.215  -5.4691  -1.5080   0.6006
 12Z  H20A  H  HCH2  0   0.234  -5.7859  -0.7039   2.1235
 12Z  H21   H  HCH2  0   0.213  -6.4295   1.3700   0.9450
 12Z  H21A  H  HCH2  0   0.232  -7.3887   0.0308   0.3423
 12Z  H10   H  HCR6  0   0.270   6.2741   2.6557  -0.0655

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
 12Z  C1   C2    aromatic  1.408  0.020  1.408
 12Z  C1   S5    aromatic  1.763  0.020  1.763
 12Z  C1   C6    single    1.413  0.020  1.413
 12Z  C2   N3    aromatic  1.351  0.020  1.351
 12Z  C2   N7    single    1.329  0.020  1.329
 12Z  N3   C4    aromatic  1.311  0.020  1.311
 12Z  C4   S5    aromatic  1.743  0.020  1.743
 12Z  C4   N8    single    1.326  0.020  1.326
 12Z  C6   O9    double    1.238  0.020  1.238
 12Z  C6   C13   single    1.494  0.020  1.494
 12Z  N8   C18   single    1.457  0.020  1.457
 12Z  C10  N11   aromatic  1.329  0.020  1.329
 12Z  C10  C15   aromatic  1.386  0.020  1.386
 12Z  N11  C12   aromatic  1.325  0.020  1.325
 12Z  C12  C13   aromatic  1.394  0.020  1.394
 12Z  C13  C14   aromatic  1.390  0.020  1.390
 12Z  C14  C15   aromatic  1.386  0.020  1.386
 12Z  C16  C17   single    1.525  0.020  1.525
 12Z  C16  C21   single    1.525  0.020  1.525
 12Z  C17  C18   single    1.525  0.020  1.525
 12Z  C18  C19   single    1.528  0.020  1.528
 12Z  C19  C20   single    1.526  0.020  1.526
 12Z  C20  C21   single    1.525  0.020  1.525
 12Z  N7   HN7   single    0.860  0.020  1.020
 12Z  N7   HN7A  single    0.860  0.020  1.020
 12Z  N8   HN8   single    0.860  0.020  1.020
 12Z  C10  H10   single    0.930  0.020  1.080
 12Z  C12  H12   single    0.930  0.020  1.080
 12Z  C14  H14   single    0.930  0.020  1.080
 12Z  C15  H15   single    0.930  0.020  1.080
 12Z  C16  H16   single    0.970  0.020  1.090
 12Z  C16  H16A  single    0.970  0.020  1.090
 12Z  C17  H17   single    0.970  0.020  1.090
 12Z  C17  H17A  single    0.970  0.020  1.090
 12Z  C18  H18   single    0.970  0.020  1.090
 12Z  C19  H19   single    0.970  0.020  1.090
 12Z  C19  H19A  single    0.970  0.020  1.090
 12Z  C20  H20   single    0.970  0.020  1.090
 12Z  C20  H20A  single    0.970  0.020  1.090
 12Z  C21  H21   single    0.970  0.020  1.090
 12Z  C21  H21A  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
 12Z  C6    C1   S5   125.79  3.000
 12Z  C6    C1   C2   126.02  3.000
 12Z  S5    C1   C2   108.05  3.000
 12Z  N7    C2   N3   119.02  3.000
 12Z  N7    C2   C1   124.62  3.000
 12Z  N3    C2   C1   116.36  3.000
 12Z  C4    N3   C2   111.16  3.000
 12Z  N8    C4   S5   120.59  3.000
 12Z  N8    C4   N3   123.65  3.000
 12Z  S5    C4   N3   115.76  3.000
 12Z  C4    S5   C1    88.66  3.000
 12Z  C13   C6   O9   118.44  3.000
 12Z  C13   C6   C1   118.57  3.000
 12Z  O9    C6   C1   122.97  3.000
 12Z  HN7A  N7   HN7  119.98  3.000
 12Z  HN7A  N7   C2   120.10  3.000
 12Z  HN7   N7   C2   119.91  3.000
 12Z  HN8   N8   C18  117.58  3.000
 12Z  HN8   N8   C4   118.58  3.000
 12Z  C18   N8   C4   123.52  3.000
 12Z  H10   C10  C15  120.26  3.000
 12Z  H10   C10  N11  116.54  3.000
 12Z  C15   C10  N11  123.20  3.000
 12Z  C12   N11  C10  117.94  3.000
 12Z  H12   C12  C13  119.86  3.000
 12Z  H12   C12  N11  116.47  3.000
 12Z  C13   C12  N11  123.67  3.000
 12Z  C14   C13  C12  117.71  3.000
 12Z  C14   C13  C6   123.02  3.000
 12Z  C12   C13  C6   119.20  3.000
 12Z  H14   C14  C15  120.02  3.000
 12Z  H14   C14  C13  121.01  3.000
 12Z  C15   C14  C13  118.94  3.000
 12Z  H15   C15  C14  121.13  3.000
 12Z  H15   C15  C10  120.35  3.000
 12Z  C14   C15  C10  118.51  3.000
 12Z  H16A  C16  H16  106.47  3.000
 12Z  H16A  C16  C21  109.54  3.000
 12Z  H16   C16  C21  110.49  3.000
 12Z  H16A  C16  C17  109.18  3.000
 12Z  H16   C16  C17  109.52  3.000
 12Z  C21   C16  C17  111.51  3.000
 12Z  H17A  C17  H17  106.94  3.000
 12Z  H17A  C17  C18  109.32  3.000
 12Z  H17   C17  C18  109.81  3.000
 12Z  H17A  C17  C16  109.29  3.000
 12Z  H17   C17  C16  110.50  3.000
 12Z  C18   C17  C16  110.89  3.000
 12Z  H18   C18  C19  108.70  3.000
 12Z  H18   C18  C17  108.44  3.000
 12Z  C19   C18  C17  111.26  3.000
 12Z  H18   C18  N8   107.26  3.000
 12Z  C19   C18  N8   111.94  3.000
 12Z  C17   C18  N8   109.08  3.000
 12Z  H19A  C19  H19  107.02  3.000
 12Z  H19A  C19  C20  109.72  3.000
 12Z  H19   C19  C20  110.43  3.000
 12Z  H19A  C19  C18  108.99  3.000
 12Z  H19   C19  C18  109.70  3.000
 12Z  C20   C19  C18  110.89  3.000
 12Z  H20A  C20  H20  106.35  3.000
 12Z  H20A  C20  C21  110.51  3.000
 12Z  H20   C20  C21  109.52  3.000
 12Z  H20A  C20  C19  109.69  3.000
 12Z  H20   C20  C19  109.35  3.000
 12Z  C21   C20  C19  111.29  3.000
 12Z  H21A  C21  H21  106.63  3.000
 12Z  H21A  C21  C20  110.39  3.000
 12Z  H21   C21  C20  109.19  3.000
 12Z  H21A  C21  C16  110.16  3.000
 12Z  H21   C21  C16  109.23  3.000
 12Z  C20   C21  C16  111.12  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
 12Z  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 12Z  CONST_02  N3    C4   S5   C1      0.00   0.0  0
 12Z  CONST_03  C4    S5   C1   C2      0.00   0.0  0
 12Z  CONST_04  S5    C4   N3   C2      0.00   0.0  0
 12Z  CONST_05  S5    C1   C2   N3      0.00   0.0  0
 12Z  CONST_06  C13   C12  N11  C10     0.00   0.0  0
 12Z  CONST_07  C13   C14  C15  C10     0.00   0.0  0
 12Z  CONST_08  C14   C15  C10  N11     0.00   0.0  0
 12Z  CONST_09  C14   C13  C12  N11     0.00   0.0  0
 12Z  CONST_10  C15   C10  N11  C12     0.00   0.0  0
 12Z  CONST_11  C15   C14  C13  C12     0.00   0.0  0
 12Z  CONST_12  N8    C4   S5   C1    180.00   0.0  0
 12Z  CONST_13  N8    C4   N3   C2    180.00   0.0  0
 12Z  CONST_14  C6    C1   C2   N3    180.00   0.0  0
 12Z  CONST_15  N7    C2   N3   C4    180.00   0.0  0
 12Z  CONST_16  C6    C1   S5   C4    180.00   0.0  0
 12Z  CONST_17  N7    C2   C1   S5    180.00   0.0  0
 12Z  CONST_18  N11   C12  C13  C6    180.00   0.0  0
 12Z  CONST_19  C15   C14  C13  C6    180.00   0.0  0
 12Z  CONST_20  C18   N8   C4   N3      0.00   0.0  0
 12Z  CONST_21  C18   N8   C4   S5    180.00   0.0  0
 12Z  CONST_22  H12   C12  N11  C10   180.00   0.0  0
 12Z  CONST_23  H14   C14  C15  C10   180.00   0.0  0
 12Z  CONST_24  H15   C15  C10  N11   180.00   0.0  0
 12Z  CONST_25  H10   C10  N11  C12   180.00   0.0  0
 12Z  CONST_26  HN7   N7   C2   C1      0.00   0.0  0
 12Z  CONST_27  HN7A  N7   C2   C1    180.00   0.0  0
 12Z  CONST_28  HN8   N8   C4   N3    180.00   0.0  0
 12Z  Var_01    C19   C20  C21  C16    55.39  30.0  1
 12Z  Var_02    C20   C21  C16  C17   -55.32  30.0  1
 12Z  Var_03    C21   C16  C17  C18    55.47  30.0  1
 12Z  Var_04    C21   C20  C19  C18   -55.70  30.0  1
 12Z  Var_05    C12   C13  C6   C1   -132.30  30.0  2
 12Z  Var_06    C13   C6   C1   C2   -179.88  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
 12Z  chir_01  C18  N8  C17  C19  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
 12Z  plan-1  C1    0.020
 12Z  plan-1  C2    0.020
 12Z  plan-1  N3    0.020
 12Z  plan-1  C4    0.020
 12Z  plan-1  S5    0.020
 12Z  plan-1  C6    0.020
 12Z  plan-1  N7    0.020
 12Z  plan-1  N8    0.020
 12Z  plan-2  C6    0.020
 12Z  plan-2  C10   0.020
 12Z  plan-2  N11   0.020
 12Z  plan-2  C12   0.020
 12Z  plan-2  C13   0.020
 12Z  plan-2  C14   0.020
 12Z  plan-2  C15   0.020
 12Z  plan-2  H12   0.020
 12Z  plan-2  H14   0.020
 12Z  plan-2  H15   0.020
 12Z  plan-2  H10   0.020
 12Z  plan-3  C2    0.020
 12Z  plan-3  N7    0.020
 12Z  plan-3  HN7   0.020
 12Z  plan-3  HN7A  0.020
 12Z  plan-4  C4    0.020
 12Z  plan-4  N8    0.020
 12Z  plan-4  C18   0.020
 12Z  plan-4  HN8   0.020
 12Z  plan-5  C1    0.020
 12Z  plan-5  C6    0.020
 12Z  plan-5  O9    0.020
 12Z  plan-5  C13   0.020

