# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:10:57 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-{3-[(3R)-5-amino-3-methyl-3,6-dihydro-2H-1,4-oxazin-3-yl]phenyl}-5-chloropyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(COCC(=N1)N)c2cccc(NC(=O)c3ccc(Cl)cn3)c2
#
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
 52K  52K  N-{3-[(3R)-5-amino-3-methyl-3,6-dihydro-2H-1,4-oxazin-3-yl]phenyl}-5-chloropyridine-2-carboxamide  ligand  41  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_52K
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
 52K  C1   C   CH2   0  -0.170   4.8297   0.2399  -0.7513
 52K  C2   C   CT    0  -0.031   3.9696   0.1216   0.5121
 52K  C5   C   CH2   0  -0.249   5.2603  -2.0337  -0.8285
 52K  C6   C   C     0   0.365   4.0611  -2.1862   0.0777
 52K  C8   C   CH3   0  -0.632   4.7858   0.4750   1.7623
 52K  C11  C   CR16  0  -0.324   3.0291   2.4616   0.2862
 52K  C12  C   CR6   0   0.425   0.4217   1.5018   0.1062
 52K  C16  C   C     0   0.539  -2.0501   1.4851  -0.1362
 52K  C18  C   CR6   0   0.129  -3.1764   0.4910  -0.1806
 52K  C21  C   CR16  0  -0.021  -3.8283  -1.6980  -0.0836
 52K  C23  C   CR6   0  -0.109  -5.1614  -1.3395  -0.2534
 52K  CL   CL  CL    0  -0.095  -6.3721  -2.5612  -0.2891
 52K  N19  N   N     0  -0.439  -2.8681  -0.7944  -0.0501
 52K  C22  C   CR16  0  -0.090  -5.4979  -0.0046  -0.3916
 52K  C20  C   CR16  0  -0.298  -4.4794   0.9335  -0.3539
 52K  O17  O   O     0  -0.457  -2.2668   2.6800  -0.2434
 52K  N15  N   NH1   0  -0.762  -0.8423   0.9124   0.0279
 52K  C10  C   CR16  0  -0.443   1.4981   0.6255   0.2720
 52K  C14  C   CR16  0  -0.335   0.6575   2.8729   0.0296
 52K  C13  C   CR16  0  -0.233   1.9653   3.3318   0.1207
 52K  C9   C   CR6   0   0.150   2.8011   1.0860   0.3644
 52K  N4   N   N     0  -0.429   3.4690  -1.2294   0.6737
 52K  N7   N   NH2   0  -0.816   3.6508  -3.4722   0.2481
 52K  O3   O   O2    0  -0.474   5.8250  -0.7567  -0.7523
 52K  H1   H   HCH2  0   0.221   4.1920   0.1569  -1.6440
 52K  H2   H   HCH2  0   0.241   5.3394   1.2035  -0.7972
 52K  H3   H   HCH2  0   0.270   6.0284  -2.7578  -0.5474
 52K  H4   H   HCH2  0   0.242   4.9466  -2.2745  -1.8561
 52K  H5   H   HCH3  0   0.223   5.1771   1.4918   1.7230
 52K  H6   H   HCH3  0   0.234   4.1659   0.3877   2.6551
 52K  H7   H   HCH3  0   0.234   5.6297  -0.2065   1.8681
 52K  H8   H   HCR6  0   0.247   4.0328   2.8614   0.3577
 52K  H9   H   HCR6  0   0.296  -3.5431  -2.7375   0.0263
 52K  H10  H   HCR6  0   0.304  -6.5264   0.2999  -0.5262
 52K  H11  H   HCR6  0   0.290  -4.6998   1.9858  -0.4592
 52K  H12  H   HNH1  0   0.422  -0.8657  -0.0979   0.0967
 52K  H13  H   HCR6  0   0.266   1.3176  -0.4406   0.3359
 52K  H14  H   HCR6  0   0.276  -0.1481   3.5770  -0.0955
 52K  H15  H   HCR6  0   0.256   2.1498   4.3969   0.0615
 52K  H16  H   HNH2  0   0.383   2.7241  -3.6069   0.6196
 52K  H17  H   HNH2  0   0.393   3.9299  -4.1593  -0.4326

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
 52K  CL   C23  single    1.720  0.020  1.720
 52K  C23  C21  aromatic  1.391  0.020  1.391
 52K  C23  C22  aromatic  1.384  0.020  1.384
 52K  C21  N19  aromatic  1.319  0.020  1.319
 52K  C22  C20  aromatic  1.385  0.020  1.385
 52K  N19  C18  aromatic  1.328  0.020  1.328
 52K  C20  C18  aromatic  1.387  0.020  1.387
 52K  C18  C16  single    1.503  0.020  1.503
 52K  C16  N15  single    1.347  0.020  1.347
 52K  C16  O17  double    1.219  0.020  1.219
 52K  N15  C12  single    1.397  0.020  1.397
 52K  N7   C6   single    1.361  0.020  1.361
 52K  C12  C10  aromatic  1.398  0.020  1.398
 52K  C12  C14  aromatic  1.393  0.020  1.393
 52K  C10  C9   aromatic  1.385  0.020  1.385
 52K  C6   N4   double    1.273  0.020  1.273
 52K  C6   C5   single    1.511  0.020  1.511
 52K  N4   C2   single    1.450  0.020  1.450
 52K  C14  C13  aromatic  1.389  0.020  1.389
 52K  C5   O3   single    1.398  0.020  1.398
 52K  C9   C2   single    1.522  0.020  1.522
 52K  C9   C11  aromatic  1.397  0.020  1.397
 52K  C2   C8   single    1.534  0.020  1.534
 52K  C2   C1   single    1.533  0.020  1.533
 52K  C13  C11  aromatic  1.384  0.020  1.384
 52K  O3   C1   single    1.409  0.020  1.409
 52K  C1   H1   single    0.970  0.020  1.090
 52K  C1   H2   single    0.970  0.020  1.090
 52K  C5   H3   single    0.970  0.020  1.090
 52K  C5   H4   single    0.970  0.020  1.090
 52K  C8   H5   single    0.970  0.020  1.090
 52K  C8   H6   single    0.970  0.020  1.090
 52K  C8   H7   single    0.970  0.020  1.090
 52K  C11  H8   single    0.930  0.020  1.080
 52K  C21  H9   single    0.930  0.020  1.080
 52K  C22  H10  single    0.930  0.020  1.080
 52K  C20  H11  single    0.930  0.020  1.080
 52K  N15  H12  single    0.860  0.020  1.020
 52K  C10  H13  single    0.930  0.020  1.080
 52K  C14  H14  single    0.930  0.020  1.080
 52K  C13  H15  single    0.930  0.020  1.080
 52K  N7   H16  single    0.890  0.020  1.040
 52K  N7   H17  single    0.890  0.020  1.040

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
 52K  H2   C1   H1   107.65  3.000
 52K  H2   C1   O3   107.14  3.000
 52K  H1   C1   O3   110.83  3.000
 52K  H2   C1   C2   111.40  3.000
 52K  H1   C1   C2   109.74  3.000
 52K  O3   C1   C2   110.03  3.000
 52K  N4   C2   C9   109.64  3.000
 52K  C9   C2   C8   109.97  3.000
 52K  N4   C2   C8   107.91  3.000
 52K  C8   C2   C1   110.81  3.000
 52K  C9   C2   C1   107.56  3.000
 52K  N4   C2   C1   110.95  3.000
 52K  H4   C5   H3   107.19  3.000
 52K  H4   C5   O3   111.44  3.000
 52K  H3   C5   O3   107.90  3.000
 52K  H4   C5   C6   108.16  3.000
 52K  H3   C5   C6   109.69  3.000
 52K  O3   C5   C6   112.33  3.000
 52K  N7   C6   N4   120.76  3.000
 52K  N4   C6   C5   125.03  3.000
 52K  N7   C6   C5   114.20  3.000
 52K  H7   C8   H6   108.10  3.000
 52K  H7   C8   H5   107.99  3.000
 52K  H6   C8   H5   107.95  3.000
 52K  H7   C8   C2   110.30  3.000
 52K  H6   C8   C2   110.26  3.000
 52K  H5   C8   C2   112.11  3.000
 52K  H8   C11  C9   120.76  3.000
 52K  H8   C11  C13  119.22  3.000
 52K  C9   C11  C13  120.03  3.000
 52K  C14  C12  C10  119.55  3.000
 52K  C14  C12  N15  124.42  3.000
 52K  C10  C12  N15  116.03  3.000
 52K  N15  C16  O17  125.94  3.000
 52K  O17  C16  C18  120.83  3.000
 52K  N15  C16  C18  113.23  3.000
 52K  C20  C18  N19  122.62  3.000
 52K  C20  C18  C16  119.78  3.000
 52K  N19  C18  C16  117.60  3.000
 52K  H9   C21  N19  117.58  3.000
 52K  H9   C21  C23  120.79  3.000
 52K  N19  C21  C23  121.62  3.000
 52K  C22  C23  CL   120.79  3.000
 52K  C22  C23  C21  119.60  3.000
 52K  CL   C23  C21  119.61  3.000
 52K  C21  N19  C18  119.44  3.000
 52K  H10  C22  C20  120.81  3.000
 52K  H10  C22  C23  121.04  3.000
 52K  C20  C22  C23  118.16  3.000
 52K  H11  C20  C22  120.47  3.000
 52K  H11  C20  C18  120.97  3.000
 52K  C22  C20  C18  118.56  3.000
 52K  H12  N15  C16  114.31  3.000
 52K  H12  N15  C12  115.98  3.000
 52K  C16  N15  C12  129.71  3.000
 52K  H13  C10  C9   118.69  3.000
 52K  H13  C10  C12  119.72  3.000
 52K  C9   C10  C12  121.59  3.000
 52K  H14  C14  C13  119.72  3.000
 52K  H14  C14  C12  121.53  3.000
 52K  C13  C14  C12  118.74  3.000
 52K  H15  C13  C14  118.81  3.000
 52K  H15  C13  C11  119.61  3.000
 52K  C14  C13  C11  121.58  3.000
 52K  C10  C9   C11  118.51  3.000
 52K  C11  C9   C2   120.27  3.000
 52K  C10  C9   C2   121.20  3.000
 52K  C6   N4   C2   119.18  3.000
 52K  H17  N7   H16  114.40  3.000
 52K  H17  N7   C6   118.48  3.000
 52K  H16  N7   C6   116.74  3.000
 52K  C5   O3   C1   111.15  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
 52K  CONST_01  C12  C10  C9   C11    0.00   0.0  0
 52K  CONST_02  C12  C14  C13  C11    0.00   0.0  0
 52K  CONST_03  C23  C21  N19  C18    0.00   0.0  0
 52K  CONST_04  C23  C22  C20  C18    0.00   0.0  0
 52K  CONST_05  C20  C22  C23  C21    0.00   0.0  0
 52K  CONST_06  C20  C18  N19  C21    0.00   0.0  0
 52K  CONST_07  C22  C23  C21  N19    0.00   0.0  0
 52K  CONST_08  C22  C20  C18  N19    0.00   0.0  0
 52K  CONST_09  C13  C14  C12  C10    0.00   0.0  0
 52K  CONST_10  C13  C11  C9   C10    0.00   0.0  0
 52K  CONST_11  C9   C10  C12  C14    0.00   0.0  0
 52K  CONST_12  C9   C11  C13  C14    0.00   0.0  0
 52K  CONST_13  C12  C10  C9   C2   180.00   0.0  0
 52K  CONST_14  C13  C11  C9   C2   180.00   0.0  0
 52K  CONST_15  C5   C6   N4   C2     0.00   0.0  0
 52K  CONST_16  C21  N19  C18  C16  180.00   0.0  0
 52K  CONST_17  C22  C20  C18  C16  180.00   0.0  0
 52K  CONST_18  N19  C21  C23  CL   180.00   0.0  0
 52K  CONST_19  C20  C22  C23  CL   180.00   0.0  0
 52K  CONST_20  C9   C10  C12  N15  180.00   0.0  0
 52K  CONST_21  C13  C14  C12  N15  180.00   0.0  0
 52K  CONST_22  N7   C6   N4   C2   180.00   0.0  0
 52K  CONST_23  H13  C10  C9   C2     0.00   0.0  0
 52K  CONST_24  H8   C11  C9   C2     0.00   0.0  0
 52K  CONST_25  H14  C14  C13  C11  180.00   0.0  0
 52K  CONST_26  H15  C13  C14  C12  180.00   0.0  0
 52K  CONST_27  H9   C21  N19  C18  180.00   0.0  0
 52K  CONST_28  H10  C22  C20  C18  180.00   0.0  0
 52K  CONST_29  H11  C20  C22  C23  180.00   0.0  0
 52K  CONST_30  C18  C16  N15  C12  180.00   0.0  0
 52K  CONST_31  C10  C12  N15  C16  180.00   0.0  0
 52K  CONST_32  C14  C12  N15  C16    0.00   0.0  0
 52K  CONST_33  H12  N15  C12  C10    0.00   0.0  0
 52K  CONST_36  O17  C16  N15  C12    0.00   0.0  0
 52K  Var_01    C6   C5   O3   C1   -43.38  30.0  1
 52K  Var_02    O3   C5   C6   N4    11.55  30.0  1
 52K  Var_03    H1   C1   O3   C5   -56.94  30.0  1
 52K  Var_04    N15  C16  C18  N19    0.38  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
 52K  chir_01  C2  C9  N4  C1  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
 52K  plan-1  C2   0.020
 52K  plan-1  C11  0.020
 52K  plan-1  C12  0.020
 52K  plan-1  N15  0.020
 52K  plan-1  C10  0.020
 52K  plan-1  C14  0.020
 52K  plan-1  C13  0.020
 52K  plan-1  C9   0.020
 52K  plan-1  H8   0.020
 52K  plan-1  H13  0.020
 52K  plan-1  H14  0.020
 52K  plan-1  H15  0.020
 52K  plan-2  C16  0.020
 52K  plan-2  C18  0.020
 52K  plan-2  C21  0.020
 52K  plan-2  C23  0.020
 52K  plan-2  CL   0.020
 52K  plan-2  N19  0.020
 52K  plan-2  C22  0.020
 52K  plan-2  C20  0.020
 52K  plan-2  H9   0.020
 52K  plan-2  H10  0.020
 52K  plan-2  H11  0.020
 52K  plan-3  C12  0.020
 52K  plan-3  C16  0.020
 52K  plan-3  C18  0.020
 52K  plan-3  O17  0.020
 52K  plan-3  N15  0.020
 52K  plan-3  H12  0.020
 52K  plan-4  C2   0.020
 52K  plan-4  C5   0.020
 52K  plan-4  C6   0.020
 52K  plan-4  N4   0.020
 52K  plan-4  N7   0.020
 52K  plan-4  H16  0.020
 52K  plan-4  H17  0.020

