# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:17:44 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N-{4-[(pyrimidin-2-yl)oxy]phenyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc(Oc2ncccn2)cc1
#
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
 O0S  O0S  N-{4-[(pyrimidin-2-yl)oxy]phenyl}acetamide  ligand  28  17  .  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_O0S
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
 O0S  N1   N  N     0  -0.426  -4.0065   0.8725   0.0039
 O0S  C4   C  CR16  0  -0.296   0.0847   0.6782  -1.4968
 O0S  C5   C  CR6   0   0.338  -0.5115   0.9051  -0.2686
 O0S  C6   C  CR6   0   0.582  -2.7856   0.3715  -0.0664
 O0S  C7   C  CR16  0  -0.015  -4.9837  -0.0092   0.1660
 O0S  C8   C  CR16  0  -0.364  -4.7495  -1.3729   0.2489
 O0S  C10  C  CR16  0  -0.294   0.2244   0.7936   0.8956
 O0S  C    C  CH3   0  -0.783   5.8191  -0.7667  -0.1587
 O0S  O    O  O     0  -0.473   4.2995  -0.2064   1.5957
 O0S  C1   C  C     0   0.514   4.4853  -0.3385   0.3984
 O0S  C11  C  CR16  0  -0.317   1.5684   0.4505   0.8479
 O0S  C2   C  CR6   0   0.373   2.1834   0.2134  -0.3828
 O0S  C3   C  CR16  0  -0.348   1.4241   0.3376  -1.5494
 O0S  C9   C  CR16  0  -0.003  -3.4282  -1.7674   0.1498
 O0S  N2   N  N     0  -0.444  -2.4364  -0.8976  -0.0072
 O0S  O1   O  O2    0  -0.499  -1.8323   1.3026  -0.2139
 O0S  H1   H  HCR6  0   0.277  -0.4862   0.7724  -2.4116
 O0S  H2   H  HCR6  0   0.286  -5.9897   0.3895   0.2288
 O0S  H3   H  HCR6  0   0.285  -5.5507  -2.0840   0.3799
 O0S  H4   H  HCR6  0   0.275  -0.2421   0.9788   1.8549
 O0S  H5   H  HNH1  0   0.417   3.8091  -0.2894  -1.4986
 O0S  H6   H  HCH3  0   0.255   5.9145  -0.6165  -1.2323
 O0S  H7   H  HCH3  0   0.270   6.6157  -0.2207   0.3433
 O0S  H8   H  HCH3  0   0.276   5.9665  -1.8275   0.0493
 O0S  H9   H  HCR6  0   0.287   2.1202   0.3684   1.7690
 O0S  H10  H  HCR6  0   0.278   1.8849   0.1622  -2.5142
 O0S  H11  H  HCR6  0   0.285  -3.1512  -2.8141   0.1973
 O0S  N    N  NH1   0  -0.735   3.5255  -0.1420  -0.5425

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
 O0S  N2   C9   aromatic  1.328  0.020  1.328
 O0S  N2   C6   aromatic  1.318  0.020  1.318
 O0S  O1   C6   single    1.341  0.020  1.341
 O0S  O1   C5   single    1.380  0.020  1.380
 O0S  C10  C5   aromatic  1.382  0.020  1.382
 O0S  C10  C11  aromatic  1.388  0.020  1.388
 O0S  C9   C8   aromatic  1.383  0.020  1.383
 O0S  C6   N1   aromatic  1.322  0.020  1.322
 O0S  C5   C4   aromatic  1.384  0.020  1.384
 O0S  C11  C2   aromatic  1.396  0.020  1.396
 O0S  C4   C3   aromatic  1.383  0.020  1.383
 O0S  C8   C7   aromatic  1.386  0.020  1.386
 O0S  N1   C7   aromatic  1.326  0.020  1.326
 O0S  C2   N    single    1.397  0.020  1.397
 O0S  C2   C3   aromatic  1.398  0.020  1.398
 O0S  N    C1   single    1.358  0.020  1.358
 O0S  C1   C    single    1.508  0.020  1.508
 O0S  C1   O    double    1.219  0.020  1.219
 O0S  C4   H1   single    0.930  0.020  1.080
 O0S  C7   H2   single    0.930  0.020  1.080
 O0S  C8   H3   single    0.930  0.020  1.080
 O0S  C10  H4   single    0.930  0.020  1.080
 O0S  N    H5   single    0.860  0.020  1.020
 O0S  C    H6   single    0.970  0.020  1.090
 O0S  C    H7   single    0.970  0.020  1.090
 O0S  C    H8   single    0.970  0.020  1.090
 O0S  C11  H9   single    0.930  0.020  1.080
 O0S  C3   H10  single    0.930  0.020  1.080
 O0S  C9   H11  single    0.930  0.020  1.080

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
 O0S  C7   N1   C6   115.80  3.000
 O0S  H1   C4   C3   120.00  3.000
 O0S  H1   C4   C5   120.56  3.000
 O0S  C3   C4   C5   119.43  3.000
 O0S  O1   C5   C10  119.96  3.000
 O0S  C10  C5   C4   120.33  3.000
 O0S  O1   C5   C4   119.64  3.000
 O0S  O1   C6   N2   119.04  3.000
 O0S  O1   C6   N1   113.54  3.000
 O0S  N2   C6   N1   127.41  3.000
 O0S  H2   C7   C8   121.01  3.000
 O0S  H2   C7   N1   116.52  3.000
 O0S  C8   C7   N1   122.47  3.000
 O0S  H3   C8   C9   122.02  3.000
 O0S  H3   C8   C7   122.01  3.000
 O0S  C9   C8   C7   115.97  3.000
 O0S  H4   C10  C11  119.34  3.000
 O0S  H4   C10  C5   120.21  3.000
 O0S  C11  C10  C5   120.44  3.000
 O0S  H8   C    H7   107.51  3.000
 O0S  H8   C    H6   108.08  3.000
 O0S  H7   C    H6   108.76  3.000
 O0S  H8   C    C1   108.98  3.000
 O0S  H7   C    C1   109.56  3.000
 O0S  H6   C    C1   113.76  3.000
 O0S  O    C1   C    121.91  3.000
 O0S  O    C1   N    123.86  3.000
 O0S  C    C1   N    114.22  3.000
 O0S  H9   C11  C2   121.02  3.000
 O0S  H9   C11  C10  119.05  3.000
 O0S  C2   C11  C10  119.93  3.000
 O0S  C3   C2   C11  118.78  3.000
 O0S  C3   C2   N    116.68  3.000
 O0S  C11  C2   N    124.54  3.000
 O0S  H10  C3   C2   119.86  3.000
 O0S  H10  C3   C4   119.06  3.000
 O0S  C2   C3   C4   121.09  3.000
 O0S  H11  C9   N2   116.53  3.000
 O0S  H11  C9   C8   121.12  3.000
 O0S  N2   C9   C8   122.35  3.000
 O0S  C9   N2   C6   115.99  3.000
 O0S  C6   O1   C5   118.99  3.000
 O0S  H5   N    C2   114.57  3.000
 O0S  H5   N    C1   115.91  3.000
 O0S  C2   N    C1   129.51  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
 O0S  CONST_01  C9   N2   C6   N1     0.00   0.0  0
 O0S  CONST_02  C9   C8   C7   N1     0.00   0.0  0
 O0S  CONST_03  C11  C10  C5   C4     0.00   0.0  0
 O0S  CONST_04  C11  C2   C3   C4     0.00   0.0  0
 O0S  CONST_05  C2   C11  C10  C5     0.00   0.0  0
 O0S  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 O0S  CONST_07  C8   C9   N2   C6     0.00   0.0  0
 O0S  CONST_08  C8   C7   N1   C6     0.00   0.0  0
 O0S  CONST_09  N2   C9   C8   C7     0.00   0.0  0
 O0S  CONST_10  N2   C6   N1   C7     0.00   0.0  0
 O0S  CONST_11  C3   C4   C5   C10    0.00   0.0  0
 O0S  CONST_12  C3   C2   C11  C10    0.00   0.0  0
 O0S  CONST_13  N    C2   C3   C4   180.00   0.0  0
 O0S  CONST_14  O1   C6   N1   C7   180.00   0.0  0
 O0S  CONST_15  N    C2   C11  C10  180.00   0.0  0
 O0S  CONST_16  O1   C5   C10  C11  180.00   0.0  0
 O0S  CONST_17  O1   C5   C4   C3   180.00   0.0  0
 O0S  CONST_18  O1   C6   N2   C9   180.00   0.0  0
 O0S  CONST_19  H3   C8   C7   N1   180.00   0.0  0
 O0S  CONST_20  H4   C10  C5   C4   180.00   0.0  0
 O0S  CONST_21  H9   C11  C10  C5   180.00   0.0  0
 O0S  CONST_22  H10  C3   C4   C5   180.00   0.0  0
 O0S  CONST_23  H11  C9   N2   C6   180.00   0.0  0
 O0S  CONST_24  H2   C7   N1   C6   180.00   0.0  0
 O0S  CONST_25  H1   C4   C5   C10  180.00   0.0  0
 O0S  CONST_26  C11  C2   N    C1     0.00   0.0  0
 O0S  CONST_27  C3   C2   N    C1   180.00   0.0  0
 O0S  CONST_28  H5   N    C2   C11  180.00   0.0  0
 O0S  CONST_29  C2   N    C1   C    180.00   0.0  0
 O0S  CONST_30  C2   N    C1   O      0.00   0.0  0
 O0S  Var_01    N2   C6   O1   C5    -1.47  30.0  2
 O0S  Var_02    C10  C5   O1   C6   -89.08  30.0  2
 O0S  Var_03    H6   C    C1   N     14.87  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
 O0S  plan-1  C4   0.020
 O0S  plan-1  C5   0.020
 O0S  plan-1  C10  0.020
 O0S  plan-1  C11  0.020
 O0S  plan-1  C2   0.020
 O0S  plan-1  C3   0.020
 O0S  plan-1  O1   0.020
 O0S  plan-1  H1   0.020
 O0S  plan-1  H4   0.020
 O0S  plan-1  H9   0.020
 O0S  plan-1  H10  0.020
 O0S  plan-1  N    0.020
 O0S  plan-2  N1   0.020
 O0S  plan-2  C6   0.020
 O0S  plan-2  C7   0.020
 O0S  plan-2  C8   0.020
 O0S  plan-2  C9   0.020
 O0S  plan-2  N2   0.020
 O0S  plan-2  O1   0.020
 O0S  plan-2  H2   0.020
 O0S  plan-2  H3   0.020
 O0S  plan-2  H11  0.020
 O0S  plan-3  C    0.020
 O0S  plan-3  O    0.020
 O0S  plan-3  C1   0.020
 O0S  plan-3  C2   0.020
 O0S  plan-3  H5   0.020
 O0S  plan-3  N    0.020

