# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:41:25 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-{[3,5-bis(trifluoromethyl)benzyl]amino}-N-hydroxy-6-oxo-1,6-dihydropyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)C1=CN=C(NCc2cc(cc(c2)C(F)(F)F)C(F)(F)F)NC1=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
 NIH  NIH  2-{[3,5-bis(trifluoromethyl)benzyl]amino}-N-hydroxy-6-oxo-1,6-dihydropyrimidine-5-carboxamide  ligand  37  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NIH
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
 NIH  N1    N  NR16  0  -0.720   2.8557  -1.6250   0.4519
 NIH  C2    C  CR6   0   0.794   1.9353  -1.2654  -0.4729
 NIH  N3    N  N     0  -0.484   1.9797  -0.0953  -1.0790
 NIH  C4    C  CR16  0   0.005   2.9783   0.7164  -0.7344
 NIH  C5    C  CR6   0  -0.379   3.9548   0.4505   0.1977
 NIH  C6    C  CR6   0   0.596   3.9114  -0.8240   0.8598
 NIH  C7    C  C     0   0.529   4.9910   1.4815   0.4408
 NIH  N8    N  NH1   0  -0.410   5.8251   1.2274   1.4686
 NIH  O9    O  O     0  -0.486   5.0524   2.5046  -0.2265
 NIH  O10   O  OC    0  -0.488   4.6849  -1.2522   1.7098
 NIH  O11   O  OH1   0  -0.545   6.9252   2.0151   1.6389
 NIH  N12   N  NH1   0  -0.651   0.9740  -2.1355  -0.7708
 NIH  C13   C  CH2   0  -0.403  -0.1048  -1.8264  -1.6877
 NIH  C14   C  CR6   0   0.161  -1.1500  -0.9323  -1.0682
 NIH  C15   C  CR16  0  -0.312  -1.2001   0.4226  -1.3768
 NIH  C16   C  CR6   0  -0.153  -2.1532   1.2375  -0.7871
 NIH  C17   C  CR16  0  -0.332  -3.0702   0.7138   0.1168
 NIH  C18   C  CR6   0  -0.154  -3.0198  -0.6350   0.4230
 NIH  C19   C  CR16  0  -0.313  -2.0638  -1.4547  -0.1665
 NIH  C20   C  CT    0   1.061  -3.9842  -1.2467   1.3922
 NIH  F21   F  F     0  -0.299  -4.8701  -0.3669   1.8626
 NIH  F22   F  F     0  -0.311  -4.6777  -2.2452   0.8296
 NIH  F23   F  F     0  -0.312  -3.3485  -1.7720   2.4483
 NIH  C24   C  CT    0   1.060  -2.2428   2.6912  -1.1384
 NIH  F25   F  F     0  -0.312  -3.2813   2.9334  -1.9513
 NIH  F26   F  F     0  -0.309  -2.4202   3.4541  -0.0530
 NIH  F27   F  F     0  -0.300  -1.1482   3.1363  -1.7592
 NIH  H1    H  HNR6  0   0.432   2.7944  -2.5369   0.8888
 NIH  H4    H  HCR6  0   0.282   2.9970   1.6698  -1.2497
 NIH  H8    H  HNH1  0   0.418   5.8637   0.3134   1.9055
 NIH  H11   H  HOH1  0   0.476   6.6852   2.6717   2.3050
 NIH  H12   H  HNH1  0   0.424   0.9312  -3.0093  -0.2702
 NIH  H131  H  HCH2  0   0.286   0.2991  -1.3716  -2.5910
 NIH  H132  H  HCH2  0   0.300  -0.5497  -2.7774  -1.9755
 NIH  H15   H  HCR6  0   0.277  -0.4800   0.8252  -2.0754
 NIH  H17   H  HCR6  0   0.289  -3.8129   1.3535   0.5739
 NIH  H19   H  HCR6  0   0.284  -2.0272  -2.5117   0.0720

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
 NIH  N1   C2    aromatic  1.353  0.020  1.353
 NIH  N1   C6    aromatic  1.387  0.020  1.387
 NIH  N1   H1    single    0.860  0.020  1.020
 NIH  C2   N3    aromatic  1.319  0.020  1.319
 NIH  C2   N12   single    1.330  0.020  1.330
 NIH  N3   C4    aromatic  1.332  0.020  1.332
 NIH  C4   C5    aromatic  1.376  0.020  1.376
 NIH  C4   H4    single    0.930  0.020  1.080
 NIH  C5   C6    aromatic  1.437  0.020  1.437
 NIH  C5   C7    single    1.482  0.020  1.482
 NIH  C6   O10   double    1.227  0.020  1.227
 NIH  C7   N8    single    1.348  0.020  1.348
 NIH  C7   O9    double    1.223  0.020  1.223
 NIH  N8   O11   single    1.364  0.020  1.364
 NIH  N8   H8    single    0.890  0.020  1.040
 NIH  O11  H11   single    0.850  0.020  0.980
 NIH  N12  C13   single    1.449  0.020  1.449
 NIH  N12  H12   single    0.860  0.020  1.020
 NIH  C13  C14   single    1.509  0.020  1.509
 NIH  C13  H131  single    0.970  0.020  1.090
 NIH  C13  H132  single    0.970  0.020  1.090
 NIH  C14  C15   aromatic  1.391  0.020  1.391
 NIH  C14  C19   aromatic  1.386  0.020  1.386
 NIH  C15  C16   aromatic  1.386  0.020  1.386
 NIH  C15  H15   single    0.930  0.020  1.080
 NIH  C16  C17   aromatic  1.390  0.020  1.390
 NIH  C16  C24   single    1.498  0.020  1.498
 NIH  C17  C18   aromatic  1.384  0.020  1.384
 NIH  C17  H17   single    0.930  0.020  1.080
 NIH  C18  C19   aromatic  1.390  0.020  1.390
 NIH  C18  C20   single    1.498  0.020  1.498
 NIH  C19  H19   single    0.930  0.020  1.080
 NIH  C20  F21   single    1.334  0.020  1.334
 NIH  C20  F22   single    1.340  0.020  1.340
 NIH  C20  F23   single    1.340  0.020  1.340
 NIH  C24  F25   single    1.341  0.020  1.341
 NIH  C24  F26   single    1.339  0.020  1.339
 NIH  C24  F27   single    1.335  0.020  1.335

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
 NIH  H1    N1   C6    116.06  3.000
 NIH  H1    N1   C2    119.52  3.000
 NIH  C6    N1   C2    124.42  3.000
 NIH  N12   C2   N3    120.12  3.000
 NIH  N12   C2   N1    118.07  3.000
 NIH  N3    C2   N1    121.80  3.000
 NIH  C4    N3   C2    116.56  3.000
 NIH  H4    C4   C5    118.68  3.000
 NIH  H4    C4   N3    115.21  3.000
 NIH  C5    C4   N3    126.12  3.000
 NIH  C7    C5   C6    124.24  3.000
 NIH  C7    C5   C4    118.22  3.000
 NIH  C6    C5   C4    117.53  3.000
 NIH  O10   C6   C5    127.59  3.000
 NIH  O10   C6   N1    118.84  3.000
 NIH  C5    C6   N1    113.57  3.000
 NIH  O9    C7   N8    122.86  3.000
 NIH  O9    C7   C5    121.85  3.000
 NIH  N8    C7   C5    115.26  3.000
 NIH  H8    N8   O11   115.86  3.000
 NIH  H8    N8   C7    121.48  3.000
 NIH  O11   N8   C7    119.05  3.000
 NIH  H11   O11  N8    106.17  3.000
 NIH  H12   N12  C13   117.87  3.000
 NIH  H12   N12  C2    119.11  3.000
 NIH  C13   N12  C2    122.69  3.000
 NIH  H132  C13  H131  107.28  3.000
 NIH  H132  C13  C14   110.07  3.000
 NIH  H131  C13  C14   110.49  3.000
 NIH  H132  C13  N12   106.57  3.000
 NIH  H131  C13  N12   109.75  3.000
 NIH  C14   C13  N12   112.48  3.000
 NIH  C19   C14  C15   119.20  3.000
 NIH  C19   C14  C13   120.04  3.000
 NIH  C15   C14  C13   120.75  3.000
 NIH  H15   C15  C16   120.94  3.000
 NIH  H15   C15  C14   118.83  3.000
 NIH  C16   C15  C14   120.22  3.000
 NIH  C24   C16  C17   118.59  3.000
 NIH  C24   C16  C15   120.79  3.000
 NIH  C17   C16  C15   120.59  3.000
 NIH  H17   C17  C18   120.52  3.000
 NIH  H17   C17  C16   120.33  3.000
 NIH  C18   C17  C16   119.15  3.000
 NIH  C20   C18  C19   118.44  3.000
 NIH  C20   C18  C17   121.18  3.000
 NIH  C19   C18  C17   120.38  3.000
 NIH  H19   C19  C18   120.31  3.000
 NIH  H19   C19  C14   119.23  3.000
 NIH  C18   C19  C14   120.46  3.000
 NIH  F23   C20  F22   106.53  3.000
 NIH  F23   C20  F21   107.20  3.000
 NIH  F22   C20  F21   107.21  3.000
 NIH  F23   C20  C18   111.39  3.000
 NIH  F22   C20  C18   111.47  3.000
 NIH  F21   C20  C18   112.73  3.000
 NIH  F27   C24  F26   107.20  3.000
 NIH  F27   C24  F25   107.04  3.000
 NIH  F26   C24  F25   106.62  3.000
 NIH  F27   C24  C16   112.56  3.000
 NIH  F26   C24  C16   111.77  3.000
 NIH  F25   C24  C16   111.33  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
 NIH  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 NIH  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 NIH  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 NIH  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 NIH  CONST_05  C6   N1   C2   N3     0.00   0.0  0
 NIH  CONST_06  C6   C5   C4   N3     0.00   0.0  0
 NIH  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 NIH  CONST_08  C17  C18  C19  C14    0.00   0.0  0
 NIH  CONST_09  C18  C19  C14  C15    0.00   0.0  0
 NIH  CONST_10  C18  C17  C16  C15    0.00   0.0  0
 NIH  CONST_11  C19  C14  C15  C16    0.00   0.0  0
 NIH  CONST_12  C19  C18  C17  C16    0.00   0.0  0
 NIH  CONST_13  C7   C5   C6   N1   180.00   0.0  0
 NIH  CONST_14  O10  C6   N1   C2   180.00   0.0  0
 NIH  CONST_15  C7   C5   C4   N3   180.00   0.0  0
 NIH  CONST_16  N12  C2   N3   C4   180.00   0.0  0
 NIH  CONST_17  O10  C6   C5   C4   180.00   0.0  0
 NIH  CONST_18  N12  C2   N1   C6   180.00   0.0  0
 NIH  CONST_19  C16  C15  C14  C13  180.00   0.0  0
 NIH  CONST_20  C18  C19  C14  C13  180.00   0.0  0
 NIH  CONST_21  C24  C16  C15  C14  180.00   0.0  0
 NIH  CONST_22  C20  C18  C19  C14  180.00   0.0  0
 NIH  CONST_23  C20  C18  C17  C16  180.00   0.0  0
 NIH  CONST_24  C24  C16  C17  C18  180.00   0.0  0
 NIH  CONST_25  H4   C4   N3   C2   180.00   0.0  0
 NIH  CONST_26  H1   N1   C2   N3   180.00   0.0  0
 NIH  CONST_27  H19  C19  C14  C15  180.00   0.0  0
 NIH  CONST_28  H17  C17  C16  C15  180.00   0.0  0
 NIH  CONST_29  H15  C15  C16  C17  180.00   0.0  0
 NIH  CONST_30  N8   C7   C5   C6     0.00   0.0  0
 NIH  CONST_31  C13  N12  C2   N1   180.00   0.0  0
 NIH  CONST_32  C13  N12  C2   N3     0.00   0.0  0
 NIH  CONST_33  H12  N12  C2   N1     0.00   0.0  0
 NIH  CONST_34  O11  N8   C7   C5   180.00   0.0  0
 NIH  CONST_35  H8   N8   C7   C5     0.00   0.0  0
 NIH  CONST_36  O11  N8   C7   O9     0.00   0.0  0
 NIH  Var_01    C14  C13  N12  C2   -76.20  30.0  3
 NIH  Var_02    C15  C14  C13  N12  103.07  30.0  2
 NIH  Var_03    F25  C24  C16  C15  104.08  30.0  2
 NIH  Var_04    F21  C20  C18  C17    1.65  30.0  2

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
 NIH  plan-1  N1   0.020
 NIH  plan-1  C2   0.020
 NIH  plan-1  N3   0.020
 NIH  plan-1  C4   0.020
 NIH  plan-1  C5   0.020
 NIH  plan-1  C6   0.020
 NIH  plan-1  C7   0.020
 NIH  plan-1  N8   0.020
 NIH  plan-1  O9   0.020
 NIH  plan-1  O10  0.020
 NIH  plan-1  O11  0.020
 NIH  plan-1  N12  0.020
 NIH  plan-1  H1   0.020
 NIH  plan-1  H4   0.020
 NIH  plan-1  H8   0.020
 NIH  plan-2  C13  0.020
 NIH  plan-2  C14  0.020
 NIH  plan-2  C15  0.020
 NIH  plan-2  C16  0.020
 NIH  plan-2  C17  0.020
 NIH  plan-2  C18  0.020
 NIH  plan-2  C19  0.020
 NIH  plan-2  C20  0.020
 NIH  plan-2  C24  0.020
 NIH  plan-2  H15  0.020
 NIH  plan-2  H17  0.020
 NIH  plan-2  H19  0.020
 NIH  plan-3  C2   0.020
 NIH  plan-3  N12  0.020
 NIH  plan-3  C13  0.020
 NIH  plan-3  H12  0.020

