# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 10:19:51 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 4-(3,3-dimethylbutanoylamino)-3,5-bis(fluoranyl)-~{N}-(1,3-thiazol-2-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)CC(=O)Nc1c(F)cc(cc1F)C(=O)Nc2sccn2
#
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
 9Y2  9Y2  4-(3,3-dimethylbutanoylamino)-3,5-bis(fluoranyl)-~{N}-(1,3-thiazol-2-yl)benzamide  ligand  41  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9Y2
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
 9Y2  C10  C  CR6   0   0.580   1.0293   0.4425   0.7727
 9Y2  C13  C  CR6   0  -0.018  -1.2353   0.2533   0.0560
 9Y2  C15  C  CR6   0   0.564   0.5469  -0.3724  -1.3937
 9Y2  C17  C  C     0   0.567  -2.6781   0.4376   0.3701
 9Y2  C20  C  CR5   0   0.296  -4.9022  -0.3769  -0.1154
 9Y2  C22  C  CR15  0  -0.020  -6.9703  -1.0072  -0.4273
 9Y2  C01  C  CH3   0  -0.634   5.9229  -0.6482   2.0124
 9Y2  C02  C  CT    0  -0.102   5.9998  -0.2697   0.5333
 9Y2  C03  C  CH3   0  -0.646   5.6342   1.2049   0.3593
 9Y2  C04  C  CH3   0  -0.636   7.4271  -0.4968   0.0323
 9Y2  C05  C  CH2   0  -0.536   5.0751  -1.1656  -0.3242
 9Y2  C06  C  C     0   0.534   3.6197  -1.1060   0.0618
 9Y2  C09  C  CR6   0  -0.005   1.5017  -0.0597  -0.4352
 9Y2  C12  C  CR16  0  -0.459  -0.3126   0.6056   1.0351
 9Y2  C14  C  CR16  0  -0.473  -0.8064  -0.2222  -1.1786
 9Y2  C23  C  CR15  0  -0.512  -7.2106   0.0043   0.4400
 9Y2  F11  F  F     0  -0.291   1.9182   0.7949   1.6990
 9Y2  F16  F  F     0  -0.291   0.9715  -0.8300  -2.5715
 9Y2  N08  N  NH1   0  -0.716   2.8640  -0.2423  -0.6777
 9Y2  N19  N  NH1   0  -0.706  -3.5352  -0.3965  -0.2714
 9Y2  N21  N  N     0  -0.421  -5.6578  -1.2210  -0.7414
 9Y2  O07  O  O     0  -0.462   3.1349  -1.7601   0.9651
 9Y2  O18  O  O     0  -0.441  -3.0719   1.2703   1.1655
 9Y2  S24  S  S2    0   0.236  -5.7272   0.7432   0.9100
 9Y2  H1   H  HCR5  0   0.274  -7.7292  -1.6355  -0.8706
 9Y2  H2   H  HCH3  0   0.228   4.9418  -0.4405   2.4397
 9Y2  H3   H  HCH3  0   0.224   6.1377  -1.7075   2.1641
 9Y2  H4   H  HCH3  0   0.224   6.6569  -0.0754   2.5826
 9Y2  H5   H  HCH3  0   0.231   6.3478   1.8398   0.8874
 9Y2  H6   H  HCH3  0   0.225   5.6488   1.4983  -0.6934
 9Y2  H7   H  HCH3  0   0.227   4.6436   1.4315   0.7562
 9Y2  H8   H  HCH3  0   0.227   7.7267  -1.5412   0.1456
 9Y2  H9   H  HCH3  0   0.226   7.5270  -0.2334  -1.0228
 9Y2  H10  H  HCH3  0   0.230   8.1358   0.1133   0.5954
 9Y2  H11  H  HCH2  0   0.256   5.1991  -0.8877  -1.3749
 9Y2  H12  H  HCH2  0   0.267   5.3971  -2.2047  -0.2250
 9Y2  H13  H  HCR6  0   0.297  -0.6321   0.9987   1.9907
 9Y2  H14  H  HCR6  0   0.297  -1.4944  -0.4628  -1.9784
 9Y2  H15  H  HCR5  0   0.305  -8.1569   0.3480   0.8255
 9Y2  H16  H  HNH1  0   0.418   3.2678   0.1870  -1.4961
 9Y2  H17  H  HNH1  0   0.437  -3.1847  -1.1445  -0.8538

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
 9Y2  C04  C02  single    1.530  0.020  1.530
 9Y2  C01  C02  single    1.529  0.020  1.529
 9Y2  C02  C03  single    1.529  0.020  1.529
 9Y2  C02  C05  single    1.547  0.020  1.547
 9Y2  C05  C06  single    1.507  0.020  1.507
 9Y2  N08  C06  single    1.365  0.020  1.365
 9Y2  N08  C09  single    1.396  0.020  1.396
 9Y2  C06  O07  double    1.216  0.020  1.216
 9Y2  F11  C10  single    1.331  0.020  1.331
 9Y2  C09  C10  aromatic  1.391  0.020  1.391
 9Y2  C09  C15  aromatic  1.389  0.020  1.389
 9Y2  F16  C15  single    1.333  0.020  1.333
 9Y2  C10  C12  aromatic  1.377  0.020  1.377
 9Y2  C15  C14  aromatic  1.379  0.020  1.379
 9Y2  C12  C13  aromatic  1.391  0.020  1.391
 9Y2  C14  C13  aromatic  1.391  0.020  1.391
 9Y2  C13  C17  single    1.488  0.020  1.488
 9Y2  C17  O18  double    1.217  0.020  1.217
 9Y2  C17  N19  single    1.357  0.020  1.357
 9Y2  N19  C20  single    1.376  0.020  1.376
 9Y2  C20  N21  aromatic  1.294  0.020  1.294
 9Y2  C20  S24  aromatic  1.728  0.020  1.728
 9Y2  N21  C22  aromatic  1.366  0.020  1.366
 9Y2  S24  C23  aromatic  1.723  0.020  1.723
 9Y2  C22  C23  aromatic  1.354  0.020  1.354
 9Y2  C22  H1   single    0.930  0.020  1.080
 9Y2  C01  H2   single    0.970  0.020  1.090
 9Y2  C01  H3   single    0.970  0.020  1.090
 9Y2  C01  H4   single    0.970  0.020  1.090
 9Y2  C03  H5   single    0.970  0.020  1.090
 9Y2  C03  H6   single    0.970  0.020  1.090
 9Y2  C03  H7   single    0.970  0.020  1.090
 9Y2  C04  H8   single    0.970  0.020  1.090
 9Y2  C04  H9   single    0.970  0.020  1.090
 9Y2  C04  H10  single    0.970  0.020  1.090
 9Y2  C05  H11  single    0.970  0.020  1.090
 9Y2  C05  H12  single    0.970  0.020  1.090
 9Y2  C12  H13  single    0.930  0.020  1.080
 9Y2  C14  H14  single    0.930  0.020  1.080
 9Y2  C23  H15  single    0.930  0.020  1.080
 9Y2  N08  H16  single    0.860  0.020  1.020
 9Y2  N19  H17  single    0.860  0.020  1.020

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
 9Y2  F11  C10  C12  119.13  3.000
 9Y2  C12  C10  C09  122.63  3.000
 9Y2  F11  C10  C09  118.23  3.000
 9Y2  C14  C13  C12  120.46  3.000
 9Y2  C14  C13  C17  121.92  3.000
 9Y2  C12  C13  C17  117.60  3.000
 9Y2  F16  C15  C14  119.21  3.000
 9Y2  C14  C15  C09  122.87  3.000
 9Y2  F16  C15  C09  117.92  3.000
 9Y2  O18  C17  N19  121.67  3.000
 9Y2  N19  C17  C13  115.87  3.000
 9Y2  O18  C17  C13  122.45  3.000
 9Y2  S24  C20  N21  115.53  3.000
 9Y2  S24  C20  N19  123.42  3.000
 9Y2  N21  C20  N19  121.06  3.000
 9Y2  H1   C22  N21  119.31  3.000
 9Y2  H1   C22  C23  124.93  3.000
 9Y2  N21  C22  C23  115.76  3.000
 9Y2  H4   C01  H3   107.72  3.000
 9Y2  H4   C01  H2   107.48  3.000
 9Y2  H3   C01  H2   107.91  3.000
 9Y2  H4   C01  C02  109.98  3.000
 9Y2  H3   C01  C02  111.40  3.000
 9Y2  H2   C01  C02  112.17  3.000
 9Y2  C05  C02  C04  106.87  3.000
 9Y2  C05  C02  C03  110.64  3.000
 9Y2  C04  C02  C03  109.21  3.000
 9Y2  C05  C02  C01  111.28  3.000
 9Y2  C03  C02  C01  109.68  3.000
 9Y2  C04  C02  C01  109.09  3.000
 9Y2  H7   C03  H6   107.87  3.000
 9Y2  H7   C03  H5   107.26  3.000
 9Y2  H6   C03  H5   107.52  3.000
 9Y2  H7   C03  C02  112.09  3.000
 9Y2  H6   C03  C02  111.43  3.000
 9Y2  H5   C03  C02  110.46  3.000
 9Y2  H10  C04  H9   107.71  3.000
 9Y2  H10  C04  H8   107.63  3.000
 9Y2  H9   C04  H8   107.80  3.000
 9Y2  H10  C04  C02  110.72  3.000
 9Y2  H9   C04  C02  111.46  3.000
 9Y2  H8   C04  C02  111.34  3.000
 9Y2  H12  C05  H11  107.19  3.000
 9Y2  H12  C05  C06  107.41  3.000
 9Y2  H11  C05  C06  110.22  3.000
 9Y2  H12  C05  C02  108.92  3.000
 9Y2  H11  C05  C02  108.51  3.000
 9Y2  C06  C05  C02  114.35  3.000
 9Y2  O07  C06  N08  121.46  3.000
 9Y2  O07  C06  C05  123.65  3.000
 9Y2  N08  C06  C05  114.89  3.000
 9Y2  N08  C09  C15  121.45  3.000
 9Y2  C15  C09  C10  116.57  3.000
 9Y2  N08  C09  C10  121.98  3.000
 9Y2  H13  C12  C13  121.21  3.000
 9Y2  H13  C12  C10  119.95  3.000
 9Y2  C13  C12  C10  118.84  3.000
 9Y2  H14  C14  C15  118.99  3.000
 9Y2  H14  C14  C13  122.42  3.000
 9Y2  C15  C14  C13  118.59  3.000
 9Y2  H15  C23  S24  121.44  3.000
 9Y2  H15  C23  C22  128.53  3.000
 9Y2  S24  C23  C22  110.03  3.000
 9Y2  H16  N08  C09  118.43  3.000
 9Y2  H16  N08  C06  119.16  3.000
 9Y2  C09  N08  C06  121.93  3.000
 9Y2  H17  N19  C20  114.86  3.000
 9Y2  H17  N19  C17  120.54  3.000
 9Y2  C20  N19  C17  124.41  3.000
 9Y2  C22  N21  C20  110.34  3.000
 9Y2  C23  S24  C20   88.35  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
 9Y2  CONST_01  C14  C15  C09  C10    0.00   0.0  0
 9Y2  CONST_02  C14  C13  C12  C10    0.00   0.0  0
 9Y2  CONST_03  C09  C10  C12  C13    0.00   0.0  0
 9Y2  CONST_04  C09  C15  C14  C13    0.00   0.0  0
 9Y2  CONST_05  C12  C10  C09  C15    0.00   0.0  0
 9Y2  CONST_06  C12  C13  C14  C15    0.00   0.0  0
 9Y2  CONST_07  C23  C22  N21  C20    0.00   0.0  0
 9Y2  CONST_08  C22  C23  S24  C20    0.00   0.0  0
 9Y2  CONST_09  S24  C20  N21  C22    0.00   0.0  0
 9Y2  CONST_10  N21  C20  S24  C23    0.00   0.0  0
 9Y2  CONST_11  S24  C23  C22  N21    0.00   0.0  0
 9Y2  CONST_12  F16  C15  C09  C10  180.00   0.0  0
 9Y2  CONST_13  C17  C13  C12  C10  180.00   0.0  0
 9Y2  CONST_14  F11  C10  C12  C13  180.00   0.0  0
 9Y2  CONST_15  F16  C15  C14  C13  180.00   0.0  0
 9Y2  CONST_16  F11  C10  C09  C15  180.00   0.0  0
 9Y2  CONST_17  C17  C13  C14  C15  180.00   0.0  0
 9Y2  CONST_18  N19  C20  N21  C22  180.00   0.0  0
 9Y2  CONST_19  N08  C09  C10  C12  180.00   0.0  0
 9Y2  CONST_20  N08  C09  C15  C14  180.00   0.0  0
 9Y2  CONST_21  N19  C20  S24  C23  180.00   0.0  0
 9Y2  CONST_22  H1   C22  N21  C20  180.00   0.0  0
 9Y2  CONST_23  H15  C23  S24  C20  180.00   0.0  0
 9Y2  CONST_24  H13  C12  C10  C09  180.00   0.0  0
 9Y2  CONST_25  H14  C14  C15  C09  180.00   0.0  0
 9Y2  CONST_26  C20  N19  C17  C13  180.00   0.0  0
 9Y2  CONST_29  N21  C20  N19  C17  180.00   0.0  0
 9Y2  CONST_30  S24  C20  N19  C17    0.00   0.0  0
 9Y2  CONST_32  H17  N19  C20  N21    0.00   0.0  0
 9Y2  CONST_33  O18  C17  N19  C20    0.00   0.0  0
 9Y2  CONST_34  C09  N08  C06  C05  180.00   0.0  0
 9Y2  CONST_35  O07  C06  N08  C09    0.00   0.0  0
 9Y2  Var_01    O18  C17  C13  C12   26.85  30.0  2
 9Y2  Var_02    C06  C05  C02  C01   59.07  30.0  3
 9Y2  Var_03    N08  C06  C05  C02   96.33  30.0  3
 9Y2  Var_04    H8   C04  C02  C01   59.84  30.0  3
 9Y2  Var_05    H5   C03  C02  C01   62.38  30.0  3
 9Y2  Var_06    H2   C01  C02  C03   56.49  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
 9Y2  plan-1  C20  0.020
 9Y2  plan-1  C22  0.020
 9Y2  plan-1  C23  0.020
 9Y2  plan-1  N19  0.020
 9Y2  plan-1  N21  0.020
 9Y2  plan-1  S24  0.020
 9Y2  plan-1  H1   0.020
 9Y2  plan-1  H15  0.020
 9Y2  plan-2  C10  0.020
 9Y2  plan-2  C13  0.020
 9Y2  plan-2  C15  0.020
 9Y2  plan-2  C17  0.020
 9Y2  plan-2  C09  0.020
 9Y2  plan-2  C12  0.020
 9Y2  plan-2  C14  0.020
 9Y2  plan-2  F11  0.020
 9Y2  plan-2  F16  0.020
 9Y2  plan-2  N08  0.020
 9Y2  plan-2  H13  0.020
 9Y2  plan-2  H14  0.020
 9Y2  plan-3  C13  0.020
 9Y2  plan-3  C17  0.020
 9Y2  plan-3  C20  0.020
 9Y2  plan-3  N19  0.020
 9Y2  plan-3  O18  0.020
 9Y2  plan-3  H17  0.020
 9Y2  plan-4  C05  0.020
 9Y2  plan-4  C06  0.020
 9Y2  plan-4  C09  0.020
 9Y2  plan-4  N08  0.020
 9Y2  plan-4  O07  0.020
 9Y2  plan-4  H16  0.020

