# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:36:18 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2~{R},4~{S},6~{S})-4-[2,4-bis(fluoranyl)-5-pyrimidin-5-yl-phenyl]-6-(3,5-dimethyl-1,2-oxazol-4-yl)-1,3-thiazinan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(C)c1[C@@H]2C[C@H](N[C@@H](N)S2)c3cc(c(F)cc3F)c4cncnc4
#
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
 5QU  5QU  (2~{R},4~{S},6~{S})-4-[2,4-bis(fluoranyl)-5-pyrimidin-5-yl-phenyl]-6-(3,5-dimethyl-1,2-oxazol-4-yl)-1,3-thiazinan-2-amine  ligand  47  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5QU
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
 5QU  N14  N  NH2   0  -0.809  -1.9030   2.4874   2.5721
 5QU  C18  C  CR6   0   0.540   3.4362  -1.6706   0.2230
 5QU  C17  C  CR6   0  -0.136   3.1832  -0.3125   0.0722
 5QU  C16  C  CR16  0  -0.305   1.8593   0.1005   0.1880
 5QU  C15  C  CR6   0  -0.080   0.8116  -0.7793   0.4400
 5QU  C19  C  CR16  0  -0.552   2.4402  -2.5864   0.4785
 5QU  C20  C  CR6   0   0.528   1.1441  -2.1169   0.5820
 5QU  C23  C  CR6   0  -0.037   4.2517   0.6503  -0.2329
 5QU  C24  C  CR16  0  -0.035   4.1067   1.5868  -1.2515
 5QU  C12  C  CH1   0  -0.020  -1.9445   1.4375   1.5886
 5QU  C2   C  CR5   0   0.258  -5.0326   0.3215  -1.0564
 5QU  C3   C  CR5   0  -0.089  -3.7024  -0.1457  -0.8056
 5QU  C4   C  CR5   0   0.406  -3.8944  -1.4490  -0.4610
 5QU  O5   O  O     0  -0.351  -5.2070  -1.7172  -0.4775
 5QU  N6   N  N     0  -0.180  -5.9088  -0.6151  -0.8535
 5QU  C7   C  CH3   0  -0.797  -3.0288  -2.5994  -0.1006
 5QU  C8   C  CH1   0  -0.529  -2.4848   0.7050  -1.0044
 5QU  C9   C  CH2   0  -0.419  -1.1040   0.0596  -0.8865
 5QU  C10  C  CH1   0  -0.156  -0.6064  -0.2654   0.5301
 5QU  N11  N  NH1   0  -0.591  -0.6158   0.9175   1.3798
 5QU  S13  S  S2    0   0.018  -2.5293   2.2081   0.0443
 5QU  F21  F  F     0  -0.300   0.1839  -3.0162   0.8341
 5QU  F22  F  F     0  -0.296   4.6911  -2.1171   0.0994
 5QU  N25  N  N     0  -0.387   5.0428   2.4777  -1.5431
 5QU  C26  C  CR16  0   0.055   6.1474   2.4355  -0.8147
 5QU  N27  N  N     0  -0.388   6.3971   1.5966   0.1790
 5QU  C28  C  CR16  0  -0.031   5.4531   0.7130   0.4676
 5QU  H1   H  HNH2  0   0.362  -2.8464   2.7929   2.7775
 5QU  H2   H  HNH2  0   0.361  -1.5389   2.1168   3.4431
 5QU  H4   H  HCR6  0   0.279   1.6315   1.1558   0.0993
 5QU  H5   H  HCR6  0   0.307   2.6628  -3.6398   0.5875
 5QU  H6   H  HCR6  0   0.280   3.2051   1.6057  -1.8554
 5QU  H7   H  HCH1  0   0.225  -2.6576   0.6301   1.8328
 5QU  H8   H  HCH3  0   0.253  -4.8755   1.9829  -2.3846
 5QU  H9   H  HCH3  0   0.262  -6.5113   1.6633  -1.8006
 5QU  H10  H  HCH3  0   0.261  -5.3092   2.4130  -0.7394
 5QU  H11  H  HCH3  0   0.269  -2.7717  -2.5911   0.9593
 5QU  H12  H  HCH3  0   0.284  -3.5428  -3.5374  -0.3061
 5QU  H13  H  HCH3  0   0.265  -2.1075  -2.5967  -0.6758
 5QU  H14  H  HCH1  0   0.314  -2.5429   1.1130  -2.0182
 5QU  H15  H  HCH2  0   0.267  -1.0741  -0.8517  -1.4882
 5QU  H16  H  HCH2  0   0.268  -0.3948   0.7514  -1.3465
 5QU  H17  H  HCH1  0   0.262  -1.2411  -1.0495   0.9588
 5QU  H18  H  HNH1  0   0.363  -0.2284   0.6566   2.2824
 5QU  H20  H  HCR6  0   0.270   6.9210   3.1566  -1.0533
 5QU  H21  H  HCR6  0   0.278   5.6524   0.0430   1.2967
 5QU  C1   C  CH3   0  -0.743  -5.4599   1.6680  -1.5193

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
 5QU  N6   O5   aromatic  1.360  0.020  1.360
 5QU  N6   C2   aromatic  1.298  0.020  1.298
 5QU  O5   C4   aromatic  1.340  0.020  1.340
 5QU  C2   C1   single    1.487  0.020  1.487
 5QU  C2   C3   aromatic  1.432  0.020  1.432
 5QU  C4   C7   single    1.484  0.020  1.484
 5QU  C4   C3   aromatic  1.362  0.020  1.362
 5QU  C3   C8   single    1.499  0.020  1.499
 5QU  F21  C20  single    1.340  0.020  1.340
 5QU  C9   C8   single    1.529  0.020  1.529
 5QU  C9   C10  single    1.536  0.020  1.536
 5QU  C8   S13  single    1.833  0.020  1.833
 5QU  C20  C19  aromatic  1.382  0.020  1.382
 5QU  C20  C15  aromatic  1.386  0.020  1.386
 5QU  C19  C18  aromatic  1.377  0.020  1.377
 5QU  C10  C15  single    1.511  0.020  1.511
 5QU  C10  N11  single    1.457  0.020  1.457
 5QU  C15  C16  aromatic  1.391  0.020  1.391
 5QU  S13  C12  single    1.822  0.020  1.822
 5QU  C18  F22  single    1.338  0.020  1.338
 5QU  C18  C17  aromatic  1.390  0.020  1.390
 5QU  C12  N11  single    1.442  0.020  1.442
 5QU  C12  N14  single    1.439  0.020  1.439
 5QU  C16  C17  aromatic  1.392  0.020  1.392
 5QU  C17  C23  single    1.470  0.020  1.470
 5QU  C24  C23  aromatic  1.391  0.020  1.391
 5QU  C24  N25  aromatic  1.325  0.020  1.325
 5QU  C23  C28  aromatic  1.392  0.020  1.392
 5QU  N25  C26  aromatic  1.324  0.020  1.324
 5QU  C28  N27  aromatic  1.325  0.020  1.325
 5QU  C26  N27  aromatic  1.324  0.020  1.324
 5QU  N14  H1   single    0.890  0.020  1.040
 5QU  N14  H2   single    0.890  0.020  1.040
 5QU  C16  H4   single    0.930  0.020  1.080
 5QU  C19  H5   single    0.930  0.020  1.080
 5QU  C24  H6   single    0.930  0.020  1.080
 5QU  C12  H7   single    0.970  0.020  1.090
 5QU  C1   H8   single    0.970  0.020  1.090
 5QU  C1   H9   single    0.970  0.020  1.090
 5QU  C1   H10  single    0.970  0.020  1.090
 5QU  C7   H11  single    0.970  0.020  1.090
 5QU  C7   H12  single    0.970  0.020  1.090
 5QU  C7   H13  single    0.970  0.020  1.090
 5QU  C8   H14  single    0.970  0.020  1.090
 5QU  C9   H15  single    0.970  0.020  1.090
 5QU  C9   H16  single    0.970  0.020  1.090
 5QU  C10  H17  single    0.970  0.020  1.090
 5QU  N11  H18  single    0.890  0.020  1.040
 5QU  C26  H20  single    0.930  0.020  1.080
 5QU  C28  H21  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
 5QU  H2   N14  H1   105.69  3.000
 5QU  H2   N14  C12  109.31  3.000
 5QU  H1   N14  C12  109.38  3.000
 5QU  F22  C18  C19  118.27  3.000
 5QU  F22  C18  C17  119.14  3.000
 5QU  C19  C18  C17  122.58  3.000
 5QU  C23  C17  C16  120.95  3.000
 5QU  C23  C17  C18  122.01  3.000
 5QU  C16  C17  C18  117.02  3.000
 5QU  H4   C16  C15  118.20  3.000
 5QU  H4   C16  C17  118.84  3.000
 5QU  C15  C16  C17  122.94  3.000
 5QU  C10  C15  C20  123.19  3.000
 5QU  C10  C15  C16  120.16  3.000
 5QU  C20  C15  C16  116.64  3.000
 5QU  H5   C19  C20  121.06  3.000
 5QU  H5   C19  C18  121.16  3.000
 5QU  C20  C19  C18  117.78  3.000
 5QU  F21  C20  C19  117.27  3.000
 5QU  C19  C20  C15  123.04  3.000
 5QU  F21  C20  C15  119.69  3.000
 5QU  C28  C23  C24  115.35  3.000
 5QU  C28  C23  C17  123.52  3.000
 5QU  C24  C23  C17  121.12  3.000
 5QU  H6   C24  N25  116.92  3.000
 5QU  H6   C24  C23  120.38  3.000
 5QU  N25  C24  C23  122.69  3.000
 5QU  H7   C12  S13  106.82  3.000
 5QU  H7   C12  N11  111.30  3.000
 5QU  S13  C12  N11  108.99  3.000
 5QU  H7   C12  N14  113.63  3.000
 5QU  N11  C12  N14  109.60  3.000
 5QU  S13  C12  N14  106.25  3.000
 5QU  N6   C2   C3   111.35  3.000
 5QU  C3   C2   C1   128.10  3.000
 5QU  N6   C2   C1   120.53  3.000
 5QU  C8   C3   C4   133.75  3.000
 5QU  C8   C3   C2   123.11  3.000
 5QU  C4   C3   C2   103.04  3.000
 5QU  C7   C4   O5   114.79  3.000
 5QU  C7   C4   C3   136.15  3.000
 5QU  O5   C4   C3   109.06  3.000
 5QU  N6   O5   C4   110.30  3.000
 5QU  O5   N6   C2   106.24  3.000
 5QU  H13  C7   H12  107.60  3.000
 5QU  H13  C7   H11  108.34  3.000
 5QU  H12  C7   H11  107.52  3.000
 5QU  H13  C7   C4   111.36  3.000
 5QU  H12  C7   C4   110.28  3.000
 5QU  H11  C7   C4   111.57  3.000
 5QU  H14  C8   S13  102.89  3.000
 5QU  H14  C8   C9   106.07  3.000
 5QU  S13  C8   C9   108.90  3.000
 5QU  H14  C8   C3   106.94  3.000
 5QU  S13  C8   C3   111.71  3.000
 5QU  C9   C8   C3   118.95  3.000
 5QU  H16  C9   H15  106.18  3.000
 5QU  H16  C9   C10  108.18  3.000
 5QU  H15  C9   C10  108.82  3.000
 5QU  H16  C9   C8   106.65  3.000
 5QU  H15  C9   C8   109.54  3.000
 5QU  C10  C9   C8   116.94  3.000
 5QU  H17  C10  N11  110.43  3.000
 5QU  H17  C10  C9   108.93  3.000
 5QU  N11  C10  C9   111.34  3.000
 5QU  H17  C10  C15  108.87  3.000
 5QU  N11  C10  C15  108.49  3.000
 5QU  C9   C10  C15  108.72  3.000
 5QU  H18  N11  C10  107.89  3.000
 5QU  H18  N11  C12  108.37  3.000
 5QU  C10  N11  C12  112.54  3.000
 5QU  C8   S13  C12   97.49  3.000
 5QU  C26  N25  C24  116.55  3.000
 5QU  H20  C26  N27  116.87  3.000
 5QU  H20  C26  N25  116.95  3.000
 5QU  N27  C26  N25  126.19  3.000
 5QU  C28  N27  C26  116.85  3.000
 5QU  H21  C28  N27  116.59  3.000
 5QU  H21  C28  C23  121.03  3.000
 5QU  N27  C28  C23  122.37  3.000
 5QU  H10  C1   H9   108.77  3.000
 5QU  H10  C1   H8   107.25  3.000
 5QU  H9   C1   H8   108.29  3.000
 5QU  H10  C1   C2   110.91  3.000
 5QU  H9   C1   C2   110.74  3.000
 5QU  H8   C1   C2   110.77  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
 5QU  CONST_01  C15  C20  C19  C18    0.00   0.0  0
 5QU  CONST_02  C15  C16  C17  C18    0.00   0.0  0
 5QU  CONST_05  C20  C19  C18  C17    0.00   0.0  0
 5QU  CONST_06  C20  C15  C16  C17    0.00   0.0  0
 5QU  CONST_07  N25  C24  C23  C17  180.00   0.0  0
 5QU  CONST_08  N27  C28  C23  C17  180.00   0.0  0
 5QU  CONST_09  C19  C20  C15  C16    0.00   0.0  0
 5QU  CONST_10  C19  C18  C17  C16    0.00   0.0  0
 5QU  CONST_13  C23  C17  C16  C15  180.00   0.0  0
 5QU  CONST_14  C23  C17  C18  C19  180.00   0.0  0
 5QU  CONST_15  C26  N25  C24  C23    0.00   0.0  0
 5QU  CONST_16  C26  N27  C28  C23    0.00   0.0  0
 5QU  CONST_17  N27  C28  C23  C24    0.00   0.0  0
 5QU  CONST_18  N27  C26  N25  C24    0.00   0.0  0
 5QU  CONST_19  C4   O5   N6   C2     0.00   0.0  0
 5QU  CONST_20  O5   C4   C3   C2     0.00   0.0  0
 5QU  CONST_21  O5   N6   C2   C3     0.00   0.0  0
 5QU  CONST_22  N6   O5   C4   C3     0.00   0.0  0
 5QU  CONST_23  N6   C2   C3   C4     0.00   0.0  0
 5QU  CONST_24  C28  C23  C24  N25    0.00   0.0  0
 5QU  CONST_25  C28  N27  C26  N25    0.00   0.0  0
 5QU  CONST_26  C10  C15  C16  C17  180.00   0.0  0
 5QU  CONST_27  C10  C15  C20  C19  180.00   0.0  0
 5QU  CONST_28  C8   C3   C4   O5   180.00   0.0  0
 5QU  CONST_29  C8   C3   C2   N6   180.00   0.0  0
 5QU  CONST_30  F21  C20  C19  C18  180.00   0.0  0
 5QU  CONST_31  F21  C20  C15  C16  180.00   0.0  0
 5QU  CONST_32  F22  C18  C17  C16  180.00   0.0  0
 5QU  CONST_33  F22  C18  C19  C20  180.00   0.0  0
 5QU  CONST_34  F22  C18  C17  C23    0.00   0.0  0
 5QU  CONST_35  O5   N6   C2   C1   180.00   0.0  0
 5QU  CONST_36  C4   C3   C2   C1   180.00   0.0  0
 5QU  CONST_37  C8   C3   C2   C1     0.00   0.0  0
 5QU  CONST_38  C7   C4   C3   C2   180.00   0.0  0
 5QU  CONST_39  C7   C4   O5   N6   180.00   0.0  0
 5QU  CONST_40  C8   C3   C4   C7     0.00   0.0  0
 5QU  CONST_41  F21  C20  C15  C10    0.00   0.0  0
 5QU  CONST_42  H4   C16  C17  C18  180.00   0.0  0
 5QU  CONST_43  H5   C19  C18  C17  180.00   0.0  0
 5QU  CONST_44  H6   C24  C23  C17    0.00   0.0  0
 5QU  CONST_45  H21  C28  C23  C17    0.00   0.0  0
 5QU  CONST_46  H20  C26  N25  C24  180.00   0.0  0
 5QU  Var_01    H8   C1   C2   C3    48.93  30.0  2
 5QU  Var_02    H11  C7   C4   C3    84.69  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
 5QU  chir_01  C12  S13  N11  N14  negativ
 5QU  chir_02  C8   S13  C9   C3   negativ
 5QU  chir_03  C10  N11  C9   C15  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
 5QU  plan-1  C2   0.020
 5QU  plan-1  C3   0.020
 5QU  plan-1  C4   0.020
 5QU  plan-1  O5   0.020
 5QU  plan-1  N6   0.020
 5QU  plan-1  C7   0.020
 5QU  plan-1  C8   0.020
 5QU  plan-1  C1   0.020
 5QU  plan-2  C18  0.020
 5QU  plan-2  C17  0.020
 5QU  plan-2  C16  0.020
 5QU  plan-2  C15  0.020
 5QU  plan-2  C19  0.020
 5QU  plan-2  C20  0.020
 5QU  plan-2  C23  0.020
 5QU  plan-2  C10  0.020
 5QU  plan-2  F21  0.020
 5QU  plan-2  F22  0.020
 5QU  plan-2  H4   0.020
 5QU  plan-2  H5   0.020
 5QU  plan-3  C17  0.020
 5QU  plan-3  C23  0.020
 5QU  plan-3  C24  0.020
 5QU  plan-3  N25  0.020
 5QU  plan-3  C26  0.020
 5QU  plan-3  N27  0.020
 5QU  plan-3  C28  0.020
 5QU  plan-3  H6   0.020
 5QU  plan-3  H20  0.020
 5QU  plan-3  H21  0.020

