# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:29:18 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-(5-methyl-1,2-oxazol-3-yl)-N'-[(3S)-4,4,4-trifluoro-3-hydroxy-3-(5-methylfuran-2-yl)butyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(NC(=O)NCC[C@](O)(c2oc(C)cc2)C(F)(F)F)c1
#
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
 N5S  N5S  N-(5-methyl-1,2-oxazol-3-yl)-N'-[(3S)-4,4,4-trifluoro-3-hydroxy-3-(5-methylfuran-2-yl)butyl]urea  ligand  40  24  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N5S
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
 N5S  N1   N  NH1   0  -0.773   3.5372   0.7183   0.6234
 N5S  C4   C  CR5   0   0.322  -2.9785   0.7851  -0.3537
 N5S  C5   C  CT    0  -0.072  -2.0291  -0.3590  -0.5629
 N5S  C6   C  CH2   0  -0.481  -0.7071  -0.1664   0.1985
 N5S  C7   C  CH2   0  -0.287   0.0026   1.1409  -0.1593
 N5S  C8   C  C     0   0.751   2.3793   0.5980  -0.1142
 N5S  C10  C  CR15  0  -0.521   5.1591  -0.5312  -0.8738
 N5S  C13  C  CT    0   1.039  -2.7108  -1.6597  -0.1054
 N5S  N    N  NH1   0  -0.678   1.3164   1.2253   0.4326
 N5S  C    C  CH3   0  -0.753  -4.2529   3.0713   2.0828
 N5S  O    O  O     0  -0.431  -3.0818   1.3183   0.8839
 N5S  C1   C  CR5   0   0.348  -3.9712   2.3371   0.8286
 N5S  C11  C  CR5   0   0.439   6.4714  -0.7771  -0.6462
 N5S  C12  C  CH3   0  -0.748   7.5008  -1.4947  -1.4312
 N5S  C2   C  CR15  0  -0.372  -4.4344   2.4605  -0.4395
 N5S  C3   C  CR15  0  -0.345  -3.7901   1.4464  -1.2115
 N5S  C9   C  CR5   0   0.496   4.7575   0.1911   0.2828
 N5S  F    F  F     0  -0.301  -3.8398  -1.8853  -0.7797
 N5S  F1   F  F     0  -0.305  -1.9269  -2.7273  -0.2857
 N5S  F2   F  F     0  -0.303  -3.0261  -1.6123   1.1926
 N5S  N2   N  N     0  -0.233   5.7534   0.3538   1.1138
 N5S  O1   O  OH1   0  -0.658  -1.8289  -0.5612  -1.9339
 N5S  O2   O  O     0  -0.511   2.3302  -0.0090  -1.1718
 N5S  O3   O  O     0  -0.342   6.8296  -0.2554   0.5271
 N5S  H1   H  HNH1  0   0.412   3.5122   1.2292   1.4936
 N5S  H2   H  HCH2  0   0.260  -0.8769  -0.1844   1.2766
 N5S  H3   H  HCH2  0   0.272  -0.0484  -1.0034  -0.0389
 N5S  H4   H  HCH2  0   0.239   0.1002   1.2601  -1.2387
 N5S  H5   H  HCH2  0   0.270  -0.5641   1.9974   0.2027
 N5S  H6   H  HCR5  0   0.287   4.5803  -0.8240  -1.7290
 N5S  H7   H  HNH1  0   0.406   1.3873   1.6432   1.3465
 N5S  H8   H  HCH3  0   0.256  -3.3480   3.5078   2.5088
 N5S  H9   H  HCH3  0   0.259  -4.9540   3.8782   1.8818
 N5S  H10  H  HCH3  0   0.257  -4.6949   2.4223   2.8411
 N5S  H11  H  HCH3  0   0.269   8.3812  -0.8726  -1.5943
 N5S  H12  H  HCH3  0   0.270   7.8239  -2.4008  -0.9170
 N5S  H13  H  HCH3  0   0.268   7.0948  -1.7782  -2.3989
 N5S  H14  H  HCR5  0   0.262  -5.1523   3.1871  -0.7849
 N5S  H15  H  HCR5  0   0.269  -3.9234   1.2454  -2.2620
 N5S  H16  H  HOH1  0   0.465  -1.4632   0.2376  -2.3293

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
 N5S  C12  C11  single    1.480  0.020  1.480
 N5S  O3   C11  aromatic  1.333  0.020  1.333
 N5S  O3   N2   aromatic  1.369  0.020  1.369
 N5S  C11  C10  aromatic  1.354  0.020  1.354
 N5S  N2   C9   aromatic  1.307  0.020  1.307
 N5S  C10  C9   aromatic  1.422  0.020  1.422
 N5S  C9   N1   single    1.372  0.020  1.372
 N5S  N1   C8   single    1.378  0.020  1.378
 N5S  O2   C8   double    1.220  0.020  1.220
 N5S  C8   N    single    1.350  0.020  1.350
 N5S  N    C7   single    1.443  0.020  1.443
 N5S  C7   C6   single    1.530  0.020  1.530
 N5S  C2   C3   aromatic  1.428  0.020  1.428
 N5S  C2   C1   aromatic  1.356  0.020  1.356
 N5S  C3   C4   aromatic  1.353  0.020  1.353
 N5S  C6   C5   single    1.538  0.020  1.538
 N5S  C1   C    single    1.480  0.020  1.480
 N5S  C1   O    aromatic  1.354  0.020  1.354
 N5S  C4   O    aromatic  1.352  0.020  1.352
 N5S  C4   C5   single    1.501  0.020  1.501
 N5S  C5   O1   single    1.400  0.020  1.400
 N5S  C5   C13  single    1.538  0.020  1.538
 N5S  F1   C13  single    1.337  0.020  1.337
 N5S  C13  F    single    1.334  0.020  1.334
 N5S  C13  F2   single    1.337  0.020  1.337
 N5S  N1   H1   single    0.860  0.020  1.020
 N5S  C6   H2   single    0.970  0.020  1.090
 N5S  C6   H3   single    0.970  0.020  1.090
 N5S  C7   H4   single    0.970  0.020  1.090
 N5S  C7   H5   single    0.970  0.020  1.090
 N5S  C10  H6   single    0.930  0.020  1.080
 N5S  N    H7   single    0.860  0.020  1.020
 N5S  C    H8   single    0.970  0.020  1.090
 N5S  C    H9   single    0.970  0.020  1.090
 N5S  C    H10  single    0.970  0.020  1.090
 N5S  C12  H11  single    0.970  0.020  1.090
 N5S  C12  H12  single    0.970  0.020  1.090
 N5S  C12  H13  single    0.970  0.020  1.090
 N5S  C2   H14  single    0.930  0.020  1.080
 N5S  C3   H15  single    0.930  0.020  1.080
 N5S  O1   H16  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
 N5S  H1   N1   C9   115.50  3.000
 N5S  H1   N1   C8   119.00  3.000
 N5S  C9   N1   C8   125.50  3.000
 N5S  C3   C4   O    109.99  3.000
 N5S  O    C4   C5   118.45  3.000
 N5S  C3   C4   C5   131.55  3.000
 N5S  O1   C5   C13  103.44  3.000
 N5S  C13  C5   C6   109.86  3.000
 N5S  O1   C5   C6   112.34  3.000
 N5S  C13  C5   C4   108.83  3.000
 N5S  O1   C5   C4   109.69  3.000
 N5S  C6   C5   C4   112.29  3.000
 N5S  H3   C6   H2   107.23  3.000
 N5S  H3   C6   C7   108.93  3.000
 N5S  H2   C6   C7   108.50  3.000
 N5S  H3   C6   C5   108.37  3.000
 N5S  H2   C6   C5   110.69  3.000
 N5S  C7   C6   C5   112.95  3.000
 N5S  H5   C7   H4   106.84  3.000
 N5S  H5   C7   N    106.94  3.000
 N5S  H4   C7   N    108.55  3.000
 N5S  H5   C7   C6   110.67  3.000
 N5S  H4   C7   C6   111.49  3.000
 N5S  N    C7   C6   112.10  3.000
 N5S  O2   C8   N    123.40  3.000
 N5S  N    C8   N1   113.84  3.000
 N5S  O2   C8   N1   122.76  3.000
 N5S  H6   C10  C9   129.39  3.000
 N5S  H6   C10  C11  127.36  3.000
 N5S  C9   C10  C11  103.25  3.000
 N5S  F2   C13  F1   107.32  3.000
 N5S  F2   C13  F    107.29  3.000
 N5S  F1   C13  F    107.04  3.000
 N5S  F2   C13  C5   111.31  3.000
 N5S  F    C13  C5   111.57  3.000
 N5S  F1   C13  C5   112.05  3.000
 N5S  H7   N    C8   120.32  3.000
 N5S  H7   N    C7   117.41  3.000
 N5S  C8   N    C7   121.56  3.000
 N5S  H10  C    H9   107.96  3.000
 N5S  H10  C    H8   107.60  3.000
 N5S  H9   C    H8   108.05  3.000
 N5S  H10  C    C1   111.76  3.000
 N5S  H9   C    C1   109.52  3.000
 N5S  H8   C    C1   111.80  3.000
 N5S  C1   O    C4   108.04  3.000
 N5S  C2   C1   O    109.34  3.000
 N5S  O    C1   C    117.63  3.000
 N5S  C2   C1   C    133.02  3.000
 N5S  O3   C11  C12  118.02  3.000
 N5S  O3   C11  C10  109.70  3.000
 N5S  C12  C11  C10  132.28  3.000
 N5S  H13  C12  H12  108.28  3.000
 N5S  H13  C12  H11  108.50  3.000
 N5S  H12  C12  H11  107.77  3.000
 N5S  H13  C12  C11  109.81  3.000
 N5S  H12  C12  C11  111.02  3.000
 N5S  H11  C12  C11  111.36  3.000
 N5S  H14  C2   C3   127.28  3.000
 N5S  H14  C2   C1   126.05  3.000
 N5S  C3   C2   C1   106.67  3.000
 N5S  H15  C3   C2   127.12  3.000
 N5S  H15  C3   C4   126.93  3.000
 N5S  C2   C3   C4   105.95  3.000
 N5S  N2   C9   C10  111.42  3.000
 N5S  C10  C9   N1   130.42  3.000
 N5S  N2   C9   N1   118.16  3.000
 N5S  O3   N2   C9   105.73  3.000
 N5S  H16  O1   C5   109.66  3.000
 N5S  N2   O3   C11  109.89  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
 N5S  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 N5S  CONST_02  C2   C1   O    C4      0.00   0.0  0
 N5S  CONST_03  N2   O3   C11  C10     0.00   0.0  0
 N5S  CONST_04  O3   N2   C9   C10     0.00   0.0  0
 N5S  CONST_05  C3   C2   C1   O       0.00   0.0  0
 N5S  CONST_06  C2   C3   C4   O       0.00   0.0  0
 N5S  CONST_07  C3   C4   O    C1      0.00   0.0  0
 N5S  CONST_08  C9   N2   O3   C11     0.00   0.0  0
 N5S  CONST_09  N2   C9   C10  C11     0.00   0.0  0
 N5S  CONST_10  O3   C11  C10  C9      0.00   0.0  0
 N5S  CONST_11  O3   N2   C9   N1    180.00   0.0  0
 N5S  CONST_12  C11  C10  C9   N1    180.00   0.0  0
 N5S  CONST_13  C    C1   O    C4    180.00   0.0  0
 N5S  CONST_14  C2   C3   C4   C5    180.00   0.0  0
 N5S  CONST_15  C1   O    C4   C5    180.00   0.0  0
 N5S  CONST_16  C3   C2   C1   C     180.00   0.0  0
 N5S  CONST_17  N2   O3   C11  C12   180.00   0.0  0
 N5S  CONST_18  C9   C10  C11  C12   180.00   0.0  0
 N5S  CONST_19  H14  C2   C3   C4    180.00   0.0  0
 N5S  CONST_20  H15  C3   C4   O     180.00   0.0  0
 N5S  CONST_21  H6   C10  C9   N2    180.00   0.0  0
 N5S  CONST_22  N2   C9   N1   C8    180.00   0.0  0
 N5S  CONST_23  C10  C9   N1   C8      0.00   0.0  0
 N5S  CONST_24  H1   N1   C9   C10   180.00   0.0  0
 N5S  CONST_25  O2   C8   N1   C9      0.00   0.0  0
 N5S  CONST_26  C9   N1   C8   N     180.00   0.0  0
 N5S  CONST_27  O2   C8   N    C7      0.00   0.0  0
 N5S  CONST_28  C7   N    C8   N1    180.00   0.0  0
 N5S  CONST_29  H7   N    C8   O2    180.00   0.0  0
 N5S  Var_01    H11  C12  C11  C10   126.38  30.0  2
 N5S  Var_02    H8   C    C1   O      58.33  30.0  2
 N5S  Var_03    N    C7   C6   C5   -172.65  30.0  2
 N5S  Var_04    C8   N    C7   C6     80.23  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
 N5S  chir_01  C5  C4  O1  C13  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
 N5S  plan-1  C4   0.020
 N5S  plan-1  C5   0.020
 N5S  plan-1  C    0.020
 N5S  plan-1  O    0.020
 N5S  plan-1  C1   0.020
 N5S  plan-1  C2   0.020
 N5S  plan-1  C3   0.020
 N5S  plan-1  H14  0.020
 N5S  plan-1  H15  0.020
 N5S  plan-2  N1   0.020
 N5S  plan-2  C10  0.020
 N5S  plan-2  C11  0.020
 N5S  plan-2  C12  0.020
 N5S  plan-2  C9   0.020
 N5S  plan-2  N2   0.020
 N5S  plan-2  O3   0.020
 N5S  plan-2  H6   0.020
 N5S  plan-3  N1   0.020
 N5S  plan-3  C7   0.020
 N5S  plan-3  C8   0.020
 N5S  plan-3  N    0.020
 N5S  plan-3  C9   0.020
 N5S  plan-3  O2   0.020
 N5S  plan-3  H1   0.020
 N5S  plan-3  H7   0.020

