# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:19:27 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (5~{R})-5-[3-[(3-chloranylquinolin-8-yl)amino]phenyl]-5-methyl-2,6-dihydro-1,4-oxazin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(COCC(=N1)N)c2cccc(Nc3cccc4cc(Cl)cnc34)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
 5T8  5T8  (5~{R})-5-[3-[(3-chloranylquinolin-8-yl)amino]phenyl]-5-methyl-2,6-dihydro-1,4-oxazin-3-amine  ligand  45  26  .  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_5T8
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
 5T8  C4   C   CH2   0  -0.242   5.6565   2.1906   0.5304
 5T8  C6   C   CH2   0  -0.171   5.0778   0.0081   1.0334
 5T8  C7   C   CR16  0  -0.236   2.0817  -3.0844   0.7139
 5T8  C8   C   CR16  0  -0.342   0.8168  -2.5242   0.6110
 5T8  C10  C   CR16  0  -0.431   1.8396  -0.4727  -0.1290
 5T8  C13  C   CH3   0  -0.638   5.2540  -0.9405  -1.2994
 5T8  C17  C   CR16  0  -0.362  -2.0298  -2.3160  -0.7050
 5T8  C20  C   CR66  0   0.135  -2.8919  -0.1972   0.0683
 5T8  C21  C   CR66  0   0.088  -4.2079  -0.6448  -0.1923
 5T8  C22  C   CR16  0  -0.140  -5.2624   0.2535   0.0791
 5T8  C24  C   CR16  0  -0.043  -3.6188   1.8555   0.7846
 5T8  C1   C   CT    0  -0.032   4.3538  -0.2031  -0.3008
 5T8  N2   N   N     0  -0.427   3.9776   1.0658  -0.8942
 5T8  C3   C   C     0   0.360   4.5581   2.1304  -0.5056
 5T8  O5   O   O2    0  -0.475   6.1373   0.9213   0.8674
 5T8  C9   C   CR6   0   0.402   0.6880  -1.2059   0.1758
 5T8  C11  C   CR6   0   0.150   3.1053  -1.0273  -0.0141
 5T8  C12  C   CR16  0  -0.333   3.2185  -2.3544   0.4061
 5T8  N14  N   NH2   0  -0.817   4.1660   3.3477  -0.9703
 5T8  N15  N   NH1   0  -0.793  -0.5349  -0.5513   0.0835
 5T8  C16  C   CR6   0   0.353  -1.7753  -1.0625  -0.1815
 5T8  C18  C   CR16  0  -0.244  -3.3460  -2.7419  -0.9538
 5T8  C19  C   CR16  0  -0.352  -4.4274  -1.9414  -0.7027
 5T8  C23  C   CR6   0  -0.118  -4.9637   1.4920   0.5655
 5T8  N25  N   N     0  -0.435  -2.6338   1.0376   0.5442
 5T8  CL2  CL  CL    0  -0.110  -6.2039   2.6367   0.9228
 5T8  H1   H   HCH2  0   0.266   6.4960   2.7723   0.1417
 5T8  H2   H   HCH2  0   0.243   5.2730   2.7255   1.4121
 5T8  H3   H   HCH2  0   0.220   4.3665   0.3725   1.7892
 5T8  H4   H   HCH2  0   0.243   5.5082  -0.9234   1.4040
 5T8  H6   H   HCR6  0   0.272  -0.0478  -3.1058   0.8988
 5T8  H7   H   HCR6  0   0.260   1.7407   0.5509  -0.4683
 5T8  H8   H   HCH3  0   0.224   5.5477  -1.9245  -0.9343
 5T8  H9   H   HCH3  0   0.234   4.7329  -1.0747  -2.2476
 5T8  H10  H   HCH3  0   0.234   6.1630  -0.3700  -1.4910
 5T8  H11  H   HCR6  0   0.278  -1.2180  -2.9852  -0.9508
 5T8  H12  H   HCR6  0   0.294  -6.2862  -0.0487  -0.1015
 5T8  H13  H   HCR6  0   0.287  -3.3776   2.8412   1.1667
 5T8  H14  H   HCR6  0   0.246   4.1880  -2.8266   0.5032
 5T8  H15  H   HNH2  0   0.382   3.5523   3.3505  -1.7693
 5T8  H16  H   HNH2  0   0.391   4.8244   4.1086  -0.9478
 5T8  H17  H   HNH1  0   0.401  -0.5204   0.4463   0.2377
 5T8  H18  H   HCR6  0   0.263  -3.4952  -3.7326  -1.3635
 5T8  H19  H   HCR6  0   0.259  -5.4362  -2.2814  -0.8955
 5T8  H5   H   HCR6  0   0.254   2.1787  -4.1075   1.0542

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
 5T8  CL2  C23  single    1.725  0.020  1.725
 5T8  C23  C24  aromatic  1.410  0.020  1.410
 5T8  C23  C22  aromatic  1.364  0.020  1.364
 5T8  C24  N25  aromatic  1.303  0.020  1.303
 5T8  C22  C21  aromatic  1.412  0.020  1.412
 5T8  N25  C20  aromatic  1.348  0.020  1.348
 5T8  C21  C20  aromatic  1.414  0.020  1.414
 5T8  C21  C19  aromatic  1.411  0.020  1.411
 5T8  C20  C16  aromatic  1.435  0.020  1.435
 5T8  C19  C18  aromatic  1.369  0.020  1.369
 5T8  C16  N15  single    1.368  0.020  1.368
 5T8  C16  C17  aromatic  1.382  0.020  1.382
 5T8  C18  C17  aromatic  1.406  0.020  1.406
 5T8  N15  C9   single    1.390  0.020  1.390
 5T8  N14  C3   single    1.361  0.020  1.361
 5T8  C9   C10  aromatic  1.399  0.020  1.399
 5T8  C9   C8   aromatic  1.394  0.020  1.394
 5T8  C10  C11  aromatic  1.387  0.020  1.387
 5T8  C3   N2   double    1.273  0.020  1.273
 5T8  C3   C4   single    1.511  0.020  1.511
 5T8  C8   C7   aromatic  1.387  0.020  1.387
 5T8  N2   C1   single    1.450  0.020  1.450
 5T8  C4   O5   single    1.399  0.020  1.399
 5T8  C11  C1   single    1.523  0.020  1.523
 5T8  C11  C12  aromatic  1.397  0.020  1.397
 5T8  C7   C12  aromatic  1.386  0.020  1.386
 5T8  C1   C13  single    1.533  0.020  1.533
 5T8  C1   C6   single    1.533  0.020  1.533
 5T8  O5   C6   single    1.409  0.020  1.409
 5T8  C4   H1   single    0.970  0.020  1.090
 5T8  C4   H2   single    0.970  0.020  1.090
 5T8  C6   H3   single    0.970  0.020  1.090
 5T8  C6   H4   single    0.970  0.020  1.090
 5T8  C7   H5   single    0.930  0.020  1.080
 5T8  C8   H6   single    0.930  0.020  1.080
 5T8  C10  H7   single    0.930  0.020  1.080
 5T8  C13  H8   single    0.970  0.020  1.090
 5T8  C13  H9   single    0.970  0.020  1.090
 5T8  C13  H10  single    0.970  0.020  1.090
 5T8  C17  H11  single    0.930  0.020  1.080
 5T8  C22  H12  single    0.930  0.020  1.080
 5T8  C24  H13  single    0.930  0.020  1.080
 5T8  C12  H14  single    0.930  0.020  1.080
 5T8  N14  H15  single    0.890  0.020  1.040
 5T8  N14  H16  single    0.890  0.020  1.040
 5T8  N15  H17  single    0.860  0.020  1.020
 5T8  C18  H18  single    0.930  0.020  1.080
 5T8  C19  H19  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
 5T8  H2   C4   H1   107.10  3.000
 5T8  H2   C4   O5   111.59  3.000
 5T8  H1   C4   O5   107.74  3.000
 5T8  H2   C4   C3   108.39  3.000
 5T8  H1   C4   C3   109.62  3.000
 5T8  O5   C4   C3   112.27  3.000
 5T8  H4   C6   H3   107.73  3.000
 5T8  H4   C6   O5   107.27  3.000
 5T8  H3   C6   O5   110.64  3.000
 5T8  H4   C6   C1   111.38  3.000
 5T8  H3   C6   C1   109.78  3.000
 5T8  O5   C6   C1   110.00  3.000
 5T8  H5   C7   C12  119.62  3.000
 5T8  H5   C7   C8   119.12  3.000
 5T8  C12  C7   C8   121.26  3.000
 5T8  H6   C8   C9   121.19  3.000
 5T8  H6   C8   C7   119.49  3.000
 5T8  C9   C8   C7   119.29  3.000
 5T8  H7   C10  C11  119.17  3.000
 5T8  H7   C10  C9   119.25  3.000
 5T8  C11  C10  C9   121.58  3.000
 5T8  H10  C13  H9   108.07  3.000
 5T8  H10  C13  H8   107.85  3.000
 5T8  H9   C13  H8   107.99  3.000
 5T8  H10  C13  C1   110.63  3.000
 5T8  H9   C13  C1   110.18  3.000
 5T8  H8   C13  C1   111.98  3.000
 5T8  H11  C17  C18  118.40  3.000
 5T8  H11  C17  C16  120.63  3.000
 5T8  C18  C17  C16  120.95  3.000
 5T8  N25  C20  C16  117.71  3.000
 5T8  C16  C20  C21  120.09  3.000
 5T8  N25  C20  C21  122.21  3.000
 5T8  C19  C21  C22  122.56  3.000
 5T8  C19  C21  C20  120.16  3.000
 5T8  C22  C21  C20  117.28  3.000
 5T8  H12  C22  C23  121.34  3.000
 5T8  H12  C22  C21  119.79  3.000
 5T8  C23  C22  C21  118.87  3.000
 5T8  H13  C24  N25  117.88  3.000
 5T8  H13  C24  C23  120.08  3.000
 5T8  N25  C24  C23  122.04  3.000
 5T8  C11  C1   N2   109.74  3.000
 5T8  C11  C1   C13  110.09  3.000
 5T8  N2   C1   C13  107.85  3.000
 5T8  C13  C1   C6   110.85  3.000
 5T8  C11  C1   C6   107.33  3.000
 5T8  N2   C1   C6   110.99  3.000
 5T8  C3   N2   C1   119.23  3.000
 5T8  N14  C3   N2   120.82  3.000
 5T8  N2   C3   C4   125.03  3.000
 5T8  N14  C3   C4   114.08  3.000
 5T8  C6   O5   C4   110.99  3.000
 5T8  N15  C9   C10  117.58  3.000
 5T8  C10  C9   C8   119.18  3.000
 5T8  N15  C9   C8   123.17  3.000
 5T8  C12  C11  C1   120.29  3.000
 5T8  C12  C11  C10  118.62  3.000
 5T8  C1   C11  C10  121.07  3.000
 5T8  H14  C12  C11  120.93  3.000
 5T8  H14  C12  C7   119.01  3.000
 5T8  C11  C12  C7   120.06  3.000
 5T8  H16  N14  H15  114.47  3.000
 5T8  H16  N14  C3   118.69  3.000
 5T8  H15  N14  C3   116.67  3.000
 5T8  H17  N15  C16  114.33  3.000
 5T8  H17  N15  C9   116.27  3.000
 5T8  C16  N15  C9   129.40  3.000
 5T8  N15  C16  C20  116.53  3.000
 5T8  N15  C16  C17  125.42  3.000
 5T8  C20  C16  C17  118.01  3.000
 5T8  H18  C18  C19  119.72  3.000
 5T8  H18  C18  C17  118.26  3.000
 5T8  C19  C18  C17  122.02  3.000
 5T8  H19  C19  C18  121.35  3.000
 5T8  H19  C19  C21  119.90  3.000
 5T8  C18  C19  C21  118.75  3.000
 5T8  CL2  C23  C24  118.84  3.000
 5T8  C24  C23  C22  119.89  3.000
 5T8  CL2  C23  C22  121.27  3.000
 5T8  C24  N25  C20  119.70  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
 5T8  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 5T8  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 5T8  CONST_03  C11  C10  C9   C8     0.00   0.0  0
 5T8  CONST_04  C11  C12  C7   C8     0.00   0.0  0
 5T8  CONST_05  N25  C20  C16  C17  180.00   0.0  0
 5T8  CONST_06  C21  C20  C16  C17    0.00   0.0  0
 5T8  CONST_07  C21  C19  C18  C17    0.00   0.0  0
 5T8  CONST_08  C23  C24  N25  C20    0.00   0.0  0
 5T8  CONST_09  C23  C22  C21  C20    0.00   0.0  0
 5T8  CONST_10  C18  C19  C21  C20    0.00   0.0  0
 5T8  CONST_11  C18  C17  C16  C20    0.00   0.0  0
 5T8  CONST_12  C24  C23  C22  C21    0.00   0.0  0
 5T8  CONST_13  C24  N25  C20  C21    0.00   0.0  0
 5T8  CONST_14  N25  C24  C23  C22    0.00   0.0  0
 5T8  CONST_15  N25  C20  C21  C22    0.00   0.0  0
 5T8  CONST_16  C16  C20  C21  C22  180.00   0.0  0
 5T8  CONST_17  C18  C19  C21  C22  180.00   0.0  0
 5T8  CONST_18  C16  C20  N25  C24  180.00   0.0  0
 5T8  CONST_19  C12  C11  C10  C9     0.00   0.0  0
 5T8  CONST_20  C12  C7   C8   C9     0.00   0.0  0
 5T8  CONST_21  C19  C21  C20  C16    0.00   0.0  0
 5T8  CONST_22  C19  C18  C17  C16    0.00   0.0  0
 5T8  CONST_23  C23  C22  C21  C19  180.00   0.0  0
 5T8  CONST_24  N25  C20  C21  C19  180.00   0.0  0
 5T8  CONST_25  C1   C11  C12  C7   180.00   0.0  0
 5T8  CONST_26  C9   C10  C11  C1   180.00   0.0  0
 5T8  CONST_27  C1   N2   C3   C4     0.00   0.0  0
 5T8  CONST_28  N15  C9   C8   C7   180.00   0.0  0
 5T8  CONST_29  CL2  C23  C22  C21  180.00   0.0  0
 5T8  CONST_30  N15  C16  C20  C21  180.00   0.0  0
 5T8  CONST_31  N15  C9   C10  C11  180.00   0.0  0
 5T8  CONST_32  N25  C20  C16  N15    0.00   0.0  0
 5T8  CONST_33  C18  C17  C16  N15  180.00   0.0  0
 5T8  CONST_34  CL2  C23  C24  N25  180.00   0.0  0
 5T8  CONST_35  N14  C3   N2   C1   180.00   0.0  0
 5T8  CONST_36  H7   C10  C9   C8   180.00   0.0  0
 5T8  CONST_37  H14  C12  C7   C8   180.00   0.0  0
 5T8  CONST_38  H6   C8   C9   C10  180.00   0.0  0
 5T8  CONST_39  H19  C19  C18  C17  180.00   0.0  0
 5T8  CONST_40  H13  C24  N25  C20  180.00   0.0  0
 5T8  CONST_41  H12  C22  C21  C20  180.00   0.0  0
 5T8  CONST_42  H11  C17  C16  C20  180.00   0.0  0
 5T8  CONST_43  H18  C18  C19  C21  180.00   0.0  0
 5T8  CONST_44  H5   C7   C8   C9   180.00   0.0  0
 5T8  CONST_45  H15  N14  C3   C4   180.00   0.0  0
 5T8  Var_01    C1   C6   O5   C4    65.08  30.0  1
 5T8  Var_02    C3   C4   O5   C6   -43.43  30.0  1
 5T8  Var_03    O5   C4   C3   N2    10.13  30.0  1
 5T8  Var_04    C16  N15  C9   C8   -30.63  30.0  1
 5T8  Var_05    C9   N15  C16  C17  -15.18  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
 5T8  chir_01  C1  C11  N2  C6  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
 5T8  plan-1  C7   0.020
 5T8  plan-1  C8   0.020
 5T8  plan-1  C10  0.020
 5T8  plan-1  C1   0.020
 5T8  plan-1  C9   0.020
 5T8  plan-1  C11  0.020
 5T8  plan-1  C12  0.020
 5T8  plan-1  N15  0.020
 5T8  plan-1  H6   0.020
 5T8  plan-1  H7   0.020
 5T8  plan-1  H14  0.020
 5T8  plan-1  H5   0.020
 5T8  plan-2  C4   0.020
 5T8  plan-2  C1   0.020
 5T8  plan-2  N2   0.020
 5T8  plan-2  C3   0.020
 5T8  plan-2  N14  0.020
 5T8  plan-2  H15  0.020
 5T8  plan-2  H16  0.020
 5T8  plan-3  C17  0.020
 5T8  plan-3  C20  0.020
 5T8  plan-3  C21  0.020
 5T8  plan-3  C22  0.020
 5T8  plan-3  C24  0.020
 5T8  plan-3  N15  0.020
 5T8  plan-3  C16  0.020
 5T8  plan-3  C18  0.020
 5T8  plan-3  C19  0.020
 5T8  plan-3  C23  0.020
 5T8  plan-3  N25  0.020
 5T8  plan-3  CL2  0.020
 5T8  plan-3  H11  0.020
 5T8  plan-3  H12  0.020
 5T8  plan-3  H13  0.020
 5T8  plan-3  H18  0.020
 5T8  plan-3  H19  0.020

