# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 18:22:22 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-[(4,4-difluoro-1-phenylcyclohexyl)amino]-N-hydroxypyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1cnc(NC2(CCC(F)(F)CC2)c3ccccc3)nc1
#
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
 AH7  AH7  2-[(4,4-difluoro-1-phenylcyclohexyl)amino]-N-hydroxypyrimidine-5-carboxamide  ligand  43  25  .  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_AH7
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
 AH7  C10  C  CT    0   0.033   1.7205  -0.2272   0.1832
 AH7  C11  C  CR6   0   0.221   1.3933  -1.7156   0.0942
 AH7  C12  C  CR16  0  -0.338   1.7055  -2.4884  -1.0194
 AH7  C13  C  CR16  0  -0.238   1.4509  -3.8550  -1.0355
 AH7  C14  C  CR16  0  -0.273   0.8794  -4.4761   0.0642
 AH7  C15  C  CR16  0  -0.243   0.5656  -3.7153   1.1833
 AH7  C16  C  CR16  0  -0.300   0.8222  -2.3530   1.1952
 AH7  C17  C  CH2   0  -0.465   1.9931   0.4206  -1.1847
 AH7  C18  C  CH2   0  -0.559   2.4011   1.8843  -1.0557
 AH7  C19  C  CT    0   0.771   3.6210   2.0260  -0.1783
 AH7  C22  C  CH2   0  -0.575   3.4620   1.3752   1.1738
 AH7  C23  C  CH2   0  -0.472   2.9915  -0.0730   1.0426
 AH7  C25  C  CR16  0   0.021  -2.3013  -0.0155  -0.8976
 AH7  C05  C  CR6   0  -0.242  -3.2497   0.5875  -0.0756
 AH7  C06  C  CR16  0  -0.014  -2.7339   1.1889   1.0726
 AH7  C08  C  CR6   0   0.622  -0.6384   0.5224   0.5326
 AH7  F20  F  F     0  -0.358   4.7050   1.4698  -0.8191
 AH7  F21  F  F     0  -0.354   3.9421   3.3499  -0.0253
 AH7  N03  N  NH1   0  -0.394  -5.5445   0.8707   0.5143
 AH7  N07  N  N     0  -0.453  -1.4569   1.1639   1.3826
 AH7  N09  N  NH1   0  -0.681   0.6564   0.4830   0.8819
 AH7  N24  N  N     0  -0.436  -1.0177  -0.0593  -0.6101
 AH7  O01  O  O     0  -0.464  -5.0165   0.3894  -1.6345
 AH7  O04  O  OH1   0  -0.538  -6.8793   0.7462   0.2628
 AH7  H1   H  HCR6  0   0.247   2.1450  -2.0411  -1.8996
 AH7  H2   H  HCR6  0   0.254   1.7004  -4.4319  -1.9170
 AH7  H3   H  HCR6  0   0.253   0.6791  -5.5397   0.0505
 AH7  H4   H  HCR6  0   0.253   0.1187  -4.1826   2.0513
 AH7  H5   H  HCR6  0   0.245   0.5637  -1.7811   2.0782
 AH7  H6   H  HCH2  0   0.248   2.7970  -0.1222  -1.6844
 AH7  H7   H  HCH2  0   0.274   1.1156   0.3368  -1.8235
 AH7  H8   H  HCH2  0   0.272   2.6077   2.3017  -2.0442
 AH7  H9   H  HCH2  0   0.259   1.5894   2.4737  -0.6233
 AH7  H10  H  HCH2  0   0.279   4.4089   1.4054   1.7175
 AH7  H11  H  HCH2  0   0.258   2.7522   1.9664   1.7575
 AH7  H12  H  HCH2  0   0.270   2.8220  -0.4890   2.0387
 AH7  H13  H  HCH2  0   0.266   3.7773  -0.6808   0.5896
 AH7  H14  H  HCR6  0   0.276  -2.6035  -0.4850  -1.8274
 AH7  H15  H  HCR6  0   0.274  -3.3736   1.7313   1.7619
 AH7  H16  H  HNH1  0   0.417  -5.3043   0.7114   1.4823
 AH7  H17  H  HNH1  0   0.401   0.8637   0.8934   1.7788
 AH7  H18  H  HOH1  0   0.479  -7.2051   1.6439   0.1199
 AH7  C02  C  C     0   0.508  -4.6721   0.5914  -0.4834

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
 AH7  O04  N03  single    1.364  0.020  1.364
 AH7  C14  C15  aromatic  1.389  0.020  1.389
 AH7  C14  C13  aromatic  1.386  0.020  1.386
 AH7  N03  C02  single    1.355  0.020  1.355
 AH7  C15  C16  aromatic  1.386  0.020  1.386
 AH7  O01  C02  double    1.218  0.020  1.218
 AH7  C02  C05  single    1.480  0.020  1.480
 AH7  C13  C12  aromatic  1.390  0.020  1.390
 AH7  C25  C05  aromatic  1.392  0.020  1.392
 AH7  C25  N24  aromatic  1.316  0.020  1.316
 AH7  C05  C06  aromatic  1.395  0.020  1.395
 AH7  C16  C11  aromatic  1.395  0.020  1.395
 AH7  C12  C11  aromatic  1.391  0.020  1.391
 AH7  N24  C08  aromatic  1.337  0.020  1.337
 AH7  C11  C10  single    1.527  0.020  1.527
 AH7  C06  N07  aromatic  1.314  0.020  1.314
 AH7  C08  N07  aromatic  1.343  0.020  1.343
 AH7  C08  N09  single    1.342  0.020  1.342
 AH7  C10  N09  single    1.458  0.020  1.458
 AH7  C10  C23  single    1.542  0.020  1.542
 AH7  C10  C17  single    1.538  0.020  1.538
 AH7  C23  C22  single    1.528  0.020  1.528
 AH7  C17  C18  single    1.525  0.020  1.525
 AH7  C22  C19  single    1.509  0.020  1.509
 AH7  C18  C19  single    1.509  0.020  1.509
 AH7  C19  F20  single    1.377  0.020  1.377
 AH7  C19  F21  single    1.371  0.020  1.371
 AH7  C12  H1   single    0.930  0.020  1.080
 AH7  C13  H2   single    0.930  0.020  1.080
 AH7  C14  H3   single    0.930  0.020  1.080
 AH7  C15  H4   single    0.930  0.020  1.080
 AH7  C16  H5   single    0.930  0.020  1.080
 AH7  C17  H6   single    0.970  0.020  1.090
 AH7  C17  H7   single    0.970  0.020  1.090
 AH7  C18  H8   single    0.970  0.020  1.090
 AH7  C18  H9   single    0.970  0.020  1.090
 AH7  C22  H10  single    0.970  0.020  1.090
 AH7  C22  H11  single    0.970  0.020  1.090
 AH7  C23  H12  single    0.970  0.020  1.090
 AH7  C23  H13  single    0.970  0.020  1.090
 AH7  C25  H14  single    0.930  0.020  1.080
 AH7  C06  H15  single    0.930  0.020  1.080
 AH7  N03  H16  single    0.890  0.020  1.040
 AH7  N09  H17  single    0.860  0.020  1.020
 AH7  O04  H18  single    0.850  0.020  0.980

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
 AH7  N09  C10  C23  106.61  3.000
 AH7  C23  C10  C17  107.91  3.000
 AH7  N09  C10  C17  110.52  3.000
 AH7  C17  C10  C11  113.38  3.000
 AH7  C23  C10  C11  107.86  3.000
 AH7  N09  C10  C11  110.27  3.000
 AH7  C16  C11  C12  118.04  3.000
 AH7  C12  C11  C10  122.70  3.000
 AH7  C16  C11  C10  119.16  3.000
 AH7  H1   C12  C13  118.15  3.000
 AH7  H1   C12  C11  120.89  3.000
 AH7  C13  C12  C11  120.95  3.000
 AH7  H2   C13  C14  120.15  3.000
 AH7  H2   C13  C12  119.41  3.000
 AH7  C14  C13  C12  120.45  3.000
 AH7  H3   C14  C15  120.44  3.000
 AH7  H3   C14  C13  120.43  3.000
 AH7  C15  C14  C13  119.13  3.000
 AH7  H4   C15  C16  119.59  3.000
 AH7  H4   C15  C14  120.19  3.000
 AH7  C16  C15  C14  120.22  3.000
 AH7  H5   C16  C15  118.79  3.000
 AH7  H5   C16  C11  120.00  3.000
 AH7  C15  C16  C11  121.20  3.000
 AH7  H7   C17  H6   106.66  3.000
 AH7  H7   C17  C18  109.83  3.000
 AH7  H6   C17  C18  108.61  3.000
 AH7  H7   C17  C10  110.28  3.000
 AH7  H6   C17  C10  109.17  3.000
 AH7  C18  C17  C10  112.12  3.000
 AH7  H9   C18  H8   107.00  3.000
 AH7  H9   C18  C19  108.65  3.000
 AH7  H8   C18  C19  109.71  3.000
 AH7  H9   C18  C17  110.65  3.000
 AH7  H8   C18  C17  109.92  3.000
 AH7  C19  C18  C17  110.83  3.000
 AH7  F21  C19  F20  104.93  3.000
 AH7  F21  C19  C22  109.95  3.000
 AH7  F20  C19  C22  109.01  3.000
 AH7  F21  C19  C18  110.18  3.000
 AH7  F20  C19  C18  109.14  3.000
 AH7  C22  C19  C18  113.28  3.000
 AH7  H11  C22  H10  106.40  3.000
 AH7  H11  C22  C23  111.01  3.000
 AH7  H10  C22  C23  109.62  3.000
 AH7  H11  C22  C19  108.29  3.000
 AH7  H10  C22  C19  110.04  3.000
 AH7  C23  C22  C19  111.35  3.000
 AH7  H13  C23  H12  106.13  3.000
 AH7  H13  C23  C22  109.97  3.000
 AH7  H12  C23  C22  109.28  3.000
 AH7  H13  C23  C10  107.84  3.000
 AH7  H12  C23  C10  110.01  3.000
 AH7  C22  C23  C10  113.35  3.000
 AH7  H14  C25  N24  116.40  3.000
 AH7  H14  C25  C05  120.25  3.000
 AH7  N24  C25  C05  123.35  3.000
 AH7  C06  C05  C02  125.53  3.000
 AH7  C06  C05  C25  114.88  3.000
 AH7  C02  C05  C25  119.54  3.000
 AH7  H15  C06  N07  115.61  3.000
 AH7  H15  C06  C05  121.34  3.000
 AH7  N07  C06  C05  123.04  3.000
 AH7  N24  C08  N09  118.91  3.000
 AH7  N09  C08  N07  115.94  3.000
 AH7  N24  C08  N07  125.15  3.000
 AH7  H16  N03  O04  113.27  3.000
 AH7  H16  N03  C02  121.35  3.000
 AH7  O04  N03  C02  118.40  3.000
 AH7  C08  N07  C06  116.86  3.000
 AH7  H17  N09  C08  114.72  3.000
 AH7  H17  N09  C10  118.34  3.000
 AH7  C08  N09  C10  126.44  3.000
 AH7  C08  N24  C25  116.67  3.000
 AH7  H18  O04  N03  105.82  3.000
 AH7  O01  C02  N03  123.23  3.000
 AH7  O01  C02  C05  122.12  3.000
 AH7  N03  C02  C05  114.62  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
 AH7  CONST_01  C14  C15  C16  C11    0.00   0.0  0
 AH7  CONST_02  C14  C13  C12  C11    0.00   0.0  0
 AH7  CONST_03  C15  C14  C13  C12    0.00   0.0  0
 AH7  CONST_04  C15  C16  C11  C12    0.00   0.0  0
 AH7  CONST_05  C16  C15  C14  C13    0.00   0.0  0
 AH7  CONST_06  C16  C11  C12  C13    0.00   0.0  0
 AH7  CONST_07  N07  C06  C05  C25    0.00   0.0  0
 AH7  CONST_08  N07  C08  N24  C25    0.00   0.0  0
 AH7  CONST_09  C08  N24  C25  C05    0.00   0.0  0
 AH7  CONST_10  C08  N07  C06  C05    0.00   0.0  0
 AH7  CONST_11  N24  C25  C05  C06    0.00   0.0  0
 AH7  CONST_12  N24  C08  N07  C06    0.00   0.0  0
 AH7  CONST_13  C15  C16  C11  C10  180.00   0.0  0
 AH7  CONST_14  C13  C12  C11  C10  180.00   0.0  0
 AH7  CONST_15  N09  C08  N24  C25  180.00   0.0  0
 AH7  CONST_16  N24  C25  C05  C02  180.00   0.0  0
 AH7  CONST_17  N07  C06  C05  C02  180.00   0.0  0
 AH7  CONST_18  N09  C08  N07  C06  180.00   0.0  0
 AH7  CONST_19  N24  C08  N09  C10    0.00   0.0  0
 AH7  CONST_20  N07  C08  N09  C10  180.00   0.0  0
 AH7  CONST_21  H5   C16  C11  C10    0.00   0.0  0
 AH7  CONST_22  H1   C12  C11  C10    0.00   0.0  0
 AH7  CONST_23  H4   C15  C16  C11  180.00   0.0  0
 AH7  CONST_24  H2   C13  C12  C11  180.00   0.0  0
 AH7  CONST_25  H3   C14  C13  C12  180.00   0.0  0
 AH7  CONST_26  H15  C06  C05  C25  180.00   0.0  0
 AH7  CONST_27  H14  C25  C05  C06  180.00   0.0  0
 AH7  CONST_28  H17  N09  C08  N07    0.00   0.0  0
 AH7  CONST_29  O04  N03  C02  C05  180.00   0.0  0
 AH7  CONST_31  O04  N03  C02  O01    0.00   0.0  0
 AH7  Var_01    C19  C22  C23  C10  -53.07  30.0  1
 AH7  Var_02    C19  C18  C17  C10   57.28  30.0  1
 AH7  Var_03    C22  C19  C18  C17  -53.82  30.0  1
 AH7  Var_04    C23  C22  C19  C18   51.58  30.0  1
 AH7  Var_05    N03  C02  C05  C25  163.28  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
 AH7  chir_01  C10  C11  C23  C17  negativ

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
 AH7  plan-1  C10  0.020
 AH7  plan-1  C11  0.020
 AH7  plan-1  C12  0.020
 AH7  plan-1  C13  0.020
 AH7  plan-1  C14  0.020
 AH7  plan-1  C15  0.020
 AH7  plan-1  C16  0.020
 AH7  plan-1  H1   0.020
 AH7  plan-1  H2   0.020
 AH7  plan-1  H3   0.020
 AH7  plan-1  H4   0.020
 AH7  plan-1  H5   0.020
 AH7  plan-2  C25  0.020
 AH7  plan-2  C05  0.020
 AH7  plan-2  C06  0.020
 AH7  plan-2  C08  0.020
 AH7  plan-2  N07  0.020
 AH7  plan-2  N09  0.020
 AH7  plan-2  N24  0.020
 AH7  plan-2  H14  0.020
 AH7  plan-2  H15  0.020
 AH7  plan-2  C02  0.020
 AH7  plan-3  C10  0.020
 AH7  plan-3  C08  0.020
 AH7  plan-3  N09  0.020
 AH7  plan-3  H17  0.020
 AH7  plan-4  C05  0.020
 AH7  plan-4  N03  0.020
 AH7  plan-4  O01  0.020
 AH7  plan-4  O04  0.020
 AH7  plan-4  H16  0.020
 AH7  plan-4  C02  0.020

