# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:31:38 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [4-amino-2-(cyclohexylamino)-1,3-thiazol-5-yl](naphthalen-2-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NC2CCCCC2)sc1C(=O)c3ccc4ccccc4c3
#
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
 O1Z  O1Z  '[4-amino-2-(cyclohexylamino)-1,3-thiazol-5-yl](naphthalen-2-yl)methanone'  ligand  46  25  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O1Z
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
 O1Z  C1    C  CR66  0   0.108  -4.9375   0.4227  -0.5233
 O1Z  S1    S  S2    0   0.150   0.2468   0.2905  -0.1588
 O1Z  C2    C  CR16  0  -0.303  -4.7277  -0.8589  -1.0871
 O1Z  N2    N  N     0  -0.481   2.1923  -1.2889   0.5186
 O1Z  C3    C  CR16  0  -0.286  -3.6125  -1.5847  -0.7816
 O1Z  N3    N  NH1   0  -0.650   2.8615   0.8439  -0.1232
 O1Z  O3    O  O     0  -0.485  -1.6388  -3.1018   0.6980
 O1Z  C4    C  CR16  0  -0.360  -2.8083   0.1790   0.6483
 O1Z  N4    N  NH2   0  -0.825   1.1426  -3.2572   1.1179
 O1Z  C5    C  CR66  0   0.139  -3.9638   0.9443   0.3657
 O1Z  C6    C  CR16  0  -0.309  -6.0874   1.1929  -0.8115
 O1Z  C7    C  CR16  0  -0.255  -6.2608   2.4243  -0.2391
 O1Z  C8    C  CR16  0  -0.257  -5.2942   2.9413   0.6490
 O1Z  C9    C  CR16  0  -0.311  -4.1717   2.2171   0.9461
 O1Z  C10   C  CR6   0  -0.028  -2.6225  -1.0572   0.0836
 O1Z  C11   C  C     0   0.360  -1.4424  -1.9106   0.4200
 O1Z  C12   C  CR5   0  -0.472  -0.1483  -1.3394   0.3849
 O1Z  C13   C  CR5   0   0.585   1.0565  -2.0018   0.6844
 O1Z  C14   C  CR5   0   0.363   1.9315  -0.0774   0.0910
 O1Z  C15   C  CH1   0  -0.068   4.2876   0.6073   0.0414
 O1Z  C16   C  CH2   0  -0.443   4.9666   1.8905   0.5106
 O1Z  C17   C  CH2   0  -0.439   6.4648   1.6699   0.6954
 O1Z  C18   C  CH2   0  -0.433   7.1107   1.1390  -0.5802
 O1Z  C19   C  CH2   0  -0.441   6.4230  -0.1378  -1.0546
 O1Z  C20   C  CH2   0  -0.426   4.9249   0.0814  -1.2442
 O1Z  H2    H  HCR6  0   0.258  -5.4708  -1.2642  -1.7630
 O1Z  H3    H  HCR6  0   0.259  -3.4722  -2.5672  -1.2132
 O1Z  HN3   H  HNH1  0   0.409   2.5799   1.7326  -0.5079
 O1Z  H4    H  HCR6  0   0.268  -2.0869   0.5843   1.3489
 O1Z  HN4   H  HNH2  0   0.401   2.0439  -3.6814   1.2510
 O1Z  HN4A  H  HNH2  0   0.413   0.3110  -3.8201   1.1786
 O1Z  H6    H  HCR6  0   0.258  -6.8308   0.7938  -1.4910
 O1Z  H7    H  HCR6  0   0.261  -7.1435   3.0079  -0.4662
 O1Z  H8    H  HCR6  0   0.261  -5.4453   3.9163   1.0932
 O1Z  H9    H  HCR6  0   0.258  -3.4270   2.6140   1.6253
 O1Z  H15   H  HCH1  0   0.248   4.4003  -0.1481   0.8229
 O1Z  H16   H  HCH2  0   0.222   4.8033   2.6806  -0.2323
 O1Z  H16A  H  HCH2  0   0.245   4.5098   2.2278   1.4439
 O1Z  H17   H  HCH2  0   0.236   6.9393   2.6042   1.0029
 O1Z  H17A  H  HCH2  0   0.217   6.6261   0.9552   1.5096
 O1Z  H18   H  HCH2  0   0.213   7.0378   1.8998  -1.3645
 O1Z  H18A  H  HCH2  0   0.232   8.1755   0.9582  -0.4173
 O1Z  H19   H  HCH2  0   0.234   6.8683  -0.4857  -1.9891
 O1Z  H19A  H  HCH2  0   0.216   6.5831  -0.9330  -0.3183
 O1Z  H20   H  HCH2  0   0.240   4.4329  -0.8472  -1.5432
 O1Z  H20A  H  HCH2  0   0.217   4.7578   0.8086  -2.0467

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
 O1Z  C2   C1    aromatic  1.416  0.020  1.416
 O1Z  C5   C1    aromatic  1.418  0.020  1.418
 O1Z  C1   C6    aromatic  1.414  0.020  1.414
 O1Z  C12  S1    aromatic  1.763  0.020  1.763
 O1Z  C14  S1    aromatic  1.742  0.020  1.742
 O1Z  C3   C2    aromatic  1.365  0.020  1.365
 O1Z  C2   H2    single    0.930  0.020  1.080
 O1Z  C13  N2    aromatic  1.351  0.020  1.351
 O1Z  N2   C14   aromatic  1.311  0.020  1.311
 O1Z  C10  C3    aromatic  1.417  0.020  1.417
 O1Z  C3   H3    single    0.930  0.020  1.080
 O1Z  C14  N3    single    1.326  0.020  1.326
 O1Z  N3   C15   single    1.455  0.020  1.455
 O1Z  N3   HN3   single    0.860  0.020  1.020
 O1Z  O3   C11   double    1.239  0.020  1.239
 O1Z  C10  C4    aromatic  1.372  0.020  1.372
 O1Z  C4   C5    aromatic  1.414  0.020  1.414
 O1Z  C4   H4    single    0.930  0.020  1.080
 O1Z  N4   C13   single    1.331  0.020  1.331
 O1Z  N4   HN4   single    0.860  0.020  1.020
 O1Z  N4   HN4A  single    0.860  0.020  1.020
 O1Z  C5   C9    aromatic  1.414  0.020  1.414
 O1Z  C6   C7    aromatic  1.369  0.020  1.369
 O1Z  C6   H6    single    0.930  0.020  1.080
 O1Z  C8   C7    aromatic  1.411  0.020  1.411
 O1Z  C7   H7    single    0.930  0.020  1.080
 O1Z  C9   C8    aromatic  1.369  0.020  1.369
 O1Z  C8   H8    single    0.930  0.020  1.080
 O1Z  C9   H9    single    0.930  0.020  1.080
 O1Z  C11  C10   single    1.495  0.020  1.495
 O1Z  C12  C11   single    1.415  0.020  1.415
 O1Z  C13  C12   aromatic  1.407  0.020  1.407
 O1Z  C15  C16   single    1.526  0.020  1.526
 O1Z  C15  C20   single    1.528  0.020  1.528
 O1Z  C15  H15   single    0.970  0.020  1.090
 O1Z  C16  C17   single    1.526  0.020  1.526
 O1Z  C16  H16   single    0.970  0.020  1.090
 O1Z  C16  H16A  single    0.970  0.020  1.090
 O1Z  C17  C18   single    1.525  0.020  1.525
 O1Z  C17  H17   single    0.970  0.020  1.090
 O1Z  C17  H17A  single    0.970  0.020  1.090
 O1Z  C19  C18   single    1.526  0.020  1.526
 O1Z  C18  H18   single    0.970  0.020  1.090
 O1Z  C18  H18A  single    0.970  0.020  1.090
 O1Z  C20  C19   single    1.526  0.020  1.526
 O1Z  C19  H19   single    0.970  0.020  1.090
 O1Z  C19  H19A  single    0.970  0.020  1.090
 O1Z  C20  H20   single    0.970  0.020  1.090
 O1Z  C20  H20A  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
 O1Z  C6    C1   C5   119.07  3.000
 O1Z  C6    C1   C2   122.18  3.000
 O1Z  C5    C1   C2   118.75  3.000
 O1Z  C14   S1   C12   88.70  3.000
 O1Z  H2    C2   C3   120.07  3.000
 O1Z  H2    C2   C1   119.05  3.000
 O1Z  C3    C2   C1   120.88  3.000
 O1Z  C14   N2   C13  111.12  3.000
 O1Z  H3    C3   C10  119.40  3.000
 O1Z  H3    C3   C2   119.96  3.000
 O1Z  C10   C3   C2   120.64  3.000
 O1Z  HN3   N3   C15  117.39  3.000
 O1Z  HN3   N3   C14  118.55  3.000
 O1Z  C15   N3   C14  123.78  3.000
 O1Z  H4    C4   C10  120.84  3.000
 O1Z  H4    C4   C5   118.06  3.000
 O1Z  C10   C4   C5   121.07  3.000
 O1Z  HN4A  N4   HN4  119.81  3.000
 O1Z  HN4A  N4   C13  119.60  3.000
 O1Z  HN4   N4   C13  119.95  3.000
 O1Z  C9    C5   C4   121.67  3.000
 O1Z  C9    C5   C1   119.17  3.000
 O1Z  C4    C5   C1   119.16  3.000
 O1Z  H6    C6   C7   120.44  3.000
 O1Z  H6    C6   C1   119.03  3.000
 O1Z  C7    C6   C1   120.53  3.000
 O1Z  H7    C7   C8   119.56  3.000
 O1Z  H7    C7   C6   120.04  3.000
 O1Z  C8    C7   C6   120.40  3.000
 O1Z  H8    C8   C9   120.15  3.000
 O1Z  H8    C8   C7   119.54  3.000
 O1Z  C9    C8   C7   120.31  3.000
 O1Z  H9    C9   C8   120.40  3.000
 O1Z  H9    C9   C5   119.08  3.000
 O1Z  C8    C9   C5   120.51  3.000
 O1Z  C11   C10  C4   121.93  3.000
 O1Z  C11   C10  C3   118.47  3.000
 O1Z  C4    C10  C3   119.49  3.000
 O1Z  C12   C11  C10  119.08  3.000
 O1Z  C12   C11  O3   122.59  3.000
 O1Z  C10   C11  O3   118.32  3.000
 O1Z  C13   C12  C11  126.00  3.000
 O1Z  C13   C12  S1   108.00  3.000
 O1Z  C11   C12  S1   125.86  3.000
 O1Z  C12   C13  N4   124.66  3.000
 O1Z  C12   C13  N2   116.44  3.000
 O1Z  N4    C13  N2   118.90  3.000
 O1Z  N3    C14  N2   123.71  3.000
 O1Z  N3    C14  S1   120.54  3.000
 O1Z  N2    C14  S1   115.74  3.000
 O1Z  H15   C15  C20  108.71  3.000
 O1Z  H15   C15  C16  108.39  3.000
 O1Z  C20   C15  C16  111.26  3.000
 O1Z  H15   C15  N3   107.12  3.000
 O1Z  C20   C15  N3   111.69  3.000
 O1Z  C16   C15  N3   109.52  3.000
 O1Z  H16A  C16  H16  107.10  3.000
 O1Z  H16A  C16  C17  110.60  3.000
 O1Z  H16   C16  C17  109.42  3.000
 O1Z  H16A  C16  C15  109.65  3.000
 O1Z  H16   C16  C15  109.35  3.000
 O1Z  C17   C16  C15  110.65  3.000
 O1Z  H17A  C17  H17  106.56  3.000
 O1Z  H17A  C17  C18  109.40  3.000
 O1Z  H17   C17  C18  110.45  3.000
 O1Z  H17A  C17  C16  109.21  3.000
 O1Z  H17   C17  C16  109.70  3.000
 O1Z  C18   C17  C16  111.40  3.000
 O1Z  H18A  C18  H18  106.66  3.000
 O1Z  H18A  C18  C19  110.32  3.000
 O1Z  H18   C18  C19  109.19  3.000
 O1Z  H18A  C18  C17  110.22  3.000
 O1Z  H18   C18  C17  109.20  3.000
 O1Z  C19   C18  C17  111.13  3.000
 O1Z  H19A  C19  H19  106.51  3.000
 O1Z  H19A  C19  C20  109.34  3.000
 O1Z  H19   C19  C20  109.87  3.000
 O1Z  H19A  C19  C18  109.43  3.000
 O1Z  H19   C19  C18  110.42  3.000
 O1Z  C20   C19  C18  111.16  3.000
 O1Z  H20A  C20  H20  107.15  3.000
 O1Z  H20A  C20  C19  109.64  3.000
 O1Z  H20   C20  C19  110.74  3.000
 O1Z  H20A  C20  C15  108.91  3.000
 O1Z  H20   C20  C15  109.57  3.000
 O1Z  C19   C20  C15  110.75  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
 O1Z  CONST_01  C10   C3   C2   C1     0.00   0.0  0
 O1Z  CONST_02  C10   C4   C5   C1     0.00   0.0  0
 O1Z  CONST_03  C8    C9   C5   C1     0.00   0.0  0
 O1Z  CONST_04  C8    C7   C6   C1     0.00   0.0  0
 O1Z  CONST_05  N2    C13  C12  S1     0.00   0.0  0
 O1Z  CONST_06  C13   N2   C14  S1     0.00   0.0  0
 O1Z  CONST_07  C4    C5   C1   C2     0.00   0.0  0
 O1Z  CONST_08  C9    C5   C1   C2   180.00   0.0  0
 O1Z  CONST_09  C7    C6   C1   C2   180.00   0.0  0
 O1Z  CONST_10  C4    C10  C3   C2     0.00   0.0  0
 O1Z  CONST_11  C12   S1   C14  N2     0.00   0.0  0
 O1Z  CONST_12  C5    C1   C2   C3     0.00   0.0  0
 O1Z  CONST_13  C6    C1   C2   C3   180.00   0.0  0
 O1Z  CONST_14  C5    C4   C10  C3     0.00   0.0  0
 O1Z  CONST_15  C6    C1   C5   C4   180.00   0.0  0
 O1Z  CONST_16  C8    C9   C5   C4   180.00   0.0  0
 O1Z  CONST_17  C7    C6   C1   C5     0.00   0.0  0
 O1Z  CONST_18  C7    C8   C9   C5     0.00   0.0  0
 O1Z  CONST_19  C9    C5   C1   C6     0.00   0.0  0
 O1Z  CONST_20  C9    C8   C7   C6     0.00   0.0  0
 O1Z  CONST_21  C10   C4   C5   C9   180.00   0.0  0
 O1Z  CONST_22  C14   N2   C13  C12    0.00   0.0  0
 O1Z  CONST_23  C14   S1   C12  C13    0.00   0.0  0
 O1Z  CONST_24  N4    C13  C12  S1   180.00   0.0  0
 O1Z  CONST_25  C11   C10  C3   C2   180.00   0.0  0
 O1Z  CONST_26  C11   C12  C13  N2   180.00   0.0  0
 O1Z  CONST_27  C12   S1   C14  N3   180.00   0.0  0
 O1Z  CONST_28  C13   N2   C14  N3   180.00   0.0  0
 O1Z  CONST_29  C14   N2   C13  N4   180.00   0.0  0
 O1Z  CONST_30  C11   C10  C4   C5   180.00   0.0  0
 O1Z  CONST_31  C14   S1   C12  C11  180.00   0.0  0
 O1Z  CONST_32  C15   N3   C14  S1   180.00   0.0  0
 O1Z  CONST_33  C15   N3   C14  N2     0.00   0.0  0
 O1Z  CONST_34  H3    C3   C2   C1   180.00   0.0  0
 O1Z  CONST_35  H4    C4   C5   C1   180.00   0.0  0
 O1Z  CONST_36  H9    C9   C5   C1   180.00   0.0  0
 O1Z  CONST_37  H7    C7   C6   C1   180.00   0.0  0
 O1Z  CONST_38  H6    C6   C1   C2     0.00   0.0  0
 O1Z  CONST_39  H2    C2   C1   C5   180.00   0.0  0
 O1Z  CONST_40  H8    C8   C9   C5   180.00   0.0  0
 O1Z  CONST_41  HN3   N3   C14  S1     0.00   0.0  0
 O1Z  CONST_42  HN4   N4   C13  N2     0.00   0.0  0
 O1Z  CONST_43  HN4A  N4   C13  N2   180.00   0.0  0
 O1Z  Var_01    C18   C17  C16  C15   55.76  30.0  1
 O1Z  Var_02    C18   C19  C20  C15  -55.85  30.0  1
 O1Z  Var_03    C19   C18  C17  C16  -55.59  30.0  1
 O1Z  Var_04    C20   C19  C18  C17   55.56  30.0  1
 O1Z  Var_05    C10   C11  C12  S1    -5.51  30.0  2
 O1Z  Var_06    C12   C11  C10  C3   134.93  30.0  3

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
 O1Z  chir_01  C15  N3  C16  C20  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
 O1Z  plan-1  S1    0.020
 O1Z  plan-1  N2    0.020
 O1Z  plan-1  N3    0.020
 O1Z  plan-1  N4    0.020
 O1Z  plan-1  C11   0.020
 O1Z  plan-1  C12   0.020
 O1Z  plan-1  C13   0.020
 O1Z  plan-1  C14   0.020
 O1Z  plan-2  C1    0.020
 O1Z  plan-2  C2    0.020
 O1Z  plan-2  C3    0.020
 O1Z  plan-2  C4    0.020
 O1Z  plan-2  C5    0.020
 O1Z  plan-2  C6    0.020
 O1Z  plan-2  C7    0.020
 O1Z  plan-2  C8    0.020
 O1Z  plan-2  C9    0.020
 O1Z  plan-2  C10   0.020
 O1Z  plan-2  C11   0.020
 O1Z  plan-2  H2    0.020
 O1Z  plan-2  H3    0.020
 O1Z  plan-2  H4    0.020
 O1Z  plan-2  H6    0.020
 O1Z  plan-2  H7    0.020
 O1Z  plan-2  H8    0.020
 O1Z  plan-2  H9    0.020
 O1Z  plan-3  N3    0.020
 O1Z  plan-3  C14   0.020
 O1Z  plan-3  C15   0.020
 O1Z  plan-3  HN3   0.020
 O1Z  plan-4  N4    0.020
 O1Z  plan-4  C13   0.020
 O1Z  plan-4  HN4   0.020
 O1Z  plan-4  HN4A  0.020
 O1Z  plan-5  O3    0.020
 O1Z  plan-5  C10   0.020
 O1Z  plan-5  C11   0.020
 O1Z  plan-5  C12   0.020

