# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:45:05 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (4~{S},6~{S})-4-[2,4-bis(fluoranyl)-5-pyrimidin-5-yl-phenyl]-6-(3,5-dimethyl-1,2-oxazol-4-yl)-4-methyl-5,6-dihydro-1,3-thiazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(C)c1[C@@H]2C[C@](C)(N=C(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
 5QV  5QV  (4~{S},6~{S})-4-[2,4-bis(fluoranyl)-5-pyrimidin-5-yl-phenyl]-6-(3,5-dimethyl-1,2-oxazol-4-yl)-4-methyl-5,6-dihydro-1,3-thiazin-2-amine  ligand  48  29  .  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_5QV
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
 5QV  N14  N  NH2   0  -0.805   0.3487   3.6251  -0.5314
 5QV  C18  C  CR6   0  -0.124  -2.7159  -0.6001  -0.3090
 5QV  C17  C  CR16  0  -0.334  -1.6212   0.0902  -0.8266
 5QV  C16  C  CR6   0  -0.067  -0.5089  -0.5318  -1.3821
 5QV  C15  C  CH3   0  -0.637   0.8087   0.0540  -3.4382
 5QV  C19  C  CR6   0   0.535  -2.6772  -1.9836  -0.3684
 5QV  C20  C  CR16  0  -0.552  -1.6117  -2.6625  -0.9185
 5QV  C21  C  CR6   0   0.539  -0.5557  -1.9227  -1.4133
 5QV  C24  C  CR6   0  -0.037  -3.8291   0.1330   0.3108
 5QV  C12  C  C     0   0.280   0.6676   2.3123  -0.6882
 5QV  C27  C  CR16  0   0.055  -5.8021   1.5348   1.4341
 5QV  C2   C  CR5   0   0.255   4.4561   0.3647   0.8665
 5QV  C3   C  CR5   0  -0.081   3.2015  -0.3124   0.9596
 5QV  C4   C  CR5   0   0.410   3.4535  -1.3364   1.8162
 5QV  O5   O  O     0  -0.346   4.7300  -1.2838   2.1998
 5QV  N6   N  N     0  -0.178   5.3492  -0.2205   1.6082
 5QV  C7   C  CH3   0  -0.751   2.6234  -2.4382   2.3527
 5QV  C8   C  CH1   0  -0.539   1.9110  -0.0143   0.2812
 5QV  C9   C  CH2   0  -0.414   1.9849  -0.1053  -1.2326
 5QV  C10  C  CT    0  -0.001   0.6698   0.2832  -1.9289
 5QV  N11  N  N     0  -0.403   0.4150   1.6996  -1.7703
 5QV  S13  S  S2    0   0.048   1.3317   1.6413   0.8180
 5QV  F22  F  F     0  -0.303   0.4648  -2.6180  -1.9368
 5QV  F23  F  F     0  -0.297  -3.6901  -2.6926   0.1422
 5QV  C25  C  CR16  0  -0.033  -3.5916   1.1530   1.2268
 5QV  N26  N  N     0  -0.386  -4.5663   1.8550   1.7851
 5QV  N28  N  N     0  -0.388  -6.1506   0.5863   0.5782
 5QV  C29  C  CR16  0  -0.032  -5.1689  -0.1068   0.0202
 5QV  H1   H  HNH2  0   0.392   0.0992   4.1149  -1.3770
 5QV  H2   H  HNH2  0   0.397   0.8740   4.1765   0.1279
 5QV  H4   H  HCR6  0   0.282  -1.6570   1.1702  -0.8116
 5QV  H5   H  HCH3  0   0.231   1.0245  -0.9828  -3.6865
 5QV  H6   H  HCH3  0   0.237  -0.1081   0.3490  -3.9486
 5QV  H7   H  HCH3  0   0.236   1.6234   0.6685  -3.8238
 5QV  H8   H  HCR6  0   0.306  -1.5935  -3.7440  -0.9517
 5QV  H10  H  HCR6  0   0.270  -6.6047   2.1046   1.8887
 5QV  H11  H  HCH3  0   0.258   4.1283   2.3934   0.2984
 5QV  H12  H  HCH3  0   0.265   5.8273   1.8947   0.3031
 5QV  H13  H  HCH3  0   0.259   4.7509   1.3767  -0.9925
 5QV  H14  H  HCH3  0   0.276   2.9557  -3.4025   1.9664
 5QV  H15  H  HCH3  0   0.275   2.6748  -2.4769   3.4408
 5QV  H16  H  HCH3  0   0.259   1.5812  -2.3087   2.0703
 5QV  H17  H  HCH1  0   0.300   1.1617  -0.7230   0.6388
 5QV  H18  H  HCH2  0   0.265   2.7678   0.5493  -1.6229
 5QV  H19  H  HCH2  0   0.273   2.2823  -1.1231  -1.4841
 5QV  H22  H  HCR6  0   0.273  -2.5764   1.3997   1.5229
 5QV  H23  H  HCR6  0   0.278  -5.4583  -0.8664  -0.6977
 5QV  C1   C  CH3   0  -0.750   4.8120   1.5742   0.0778

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
 5QV  O5   N6   aromatic  1.365  0.020  1.365
 5QV  O5   C4   aromatic  1.334  0.020  1.334
 5QV  N6   C2   aromatic  1.300  0.020  1.300
 5QV  C4   C7   single    1.480  0.020  1.480
 5QV  C4   C3   aromatic  1.359  0.020  1.359
 5QV  C2   C1   single    1.487  0.020  1.487
 5QV  C2   C3   aromatic  1.429  0.020  1.429
 5QV  C3   C8   single    1.488  0.020  1.488
 5QV  F22  C21  single    1.341  0.020  1.341
 5QV  C9   C8   single    1.518  0.020  1.518
 5QV  C9   C10  single    1.538  0.020  1.538
 5QV  C8   S13  single    1.834  0.020  1.834
 5QV  C21  C20  aromatic  1.381  0.020  1.381
 5QV  C21  C16  aromatic  1.392  0.020  1.392
 5QV  C20  C19  aromatic  1.378  0.020  1.378
 5QV  C15  C10  single    1.533  0.020  1.533
 5QV  C10  C16  single    1.534  0.020  1.534
 5QV  C10  N11  single    1.448  0.020  1.448
 5QV  C16  C17  aromatic  1.390  0.020  1.390
 5QV  S13  C12  single    1.778  0.020  1.778
 5QV  C19  F23  single    1.338  0.020  1.338
 5QV  C19  C18  aromatic  1.385  0.020  1.385
 5QV  N11  C12  double    1.269  0.020  1.269
 5QV  C12  N14  single    1.360  0.020  1.360
 5QV  C17  C18  aromatic  1.394  0.020  1.394
 5QV  C18  C24  single    1.470  0.020  1.470
 5QV  C25  C24  aromatic  1.391  0.020  1.391
 5QV  C25  N26  aromatic  1.325  0.020  1.325
 5QV  C24  C29  aromatic  1.392  0.020  1.392
 5QV  N26  C27  aromatic  1.324  0.020  1.324
 5QV  C29  N28  aromatic  1.325  0.020  1.325
 5QV  C27  N28  aromatic  1.324  0.020  1.324
 5QV  N14  H1   single    0.890  0.020  1.040
 5QV  N14  H2   single    0.890  0.020  1.040
 5QV  C17  H4   single    0.930  0.020  1.080
 5QV  C15  H5   single    0.970  0.020  1.090
 5QV  C15  H6   single    0.970  0.020  1.090
 5QV  C15  H7   single    0.970  0.020  1.090
 5QV  C20  H8   single    0.930  0.020  1.080
 5QV  C27  H10  single    0.930  0.020  1.080
 5QV  C1   H11  single    0.970  0.020  1.090
 5QV  C1   H12  single    0.970  0.020  1.090
 5QV  C1   H13  single    0.970  0.020  1.090
 5QV  C7   H14  single    0.970  0.020  1.090
 5QV  C7   H15  single    0.970  0.020  1.090
 5QV  C7   H16  single    0.970  0.020  1.090
 5QV  C8   H17  single    0.970  0.020  1.090
 5QV  C9   H18  single    0.970  0.020  1.090
 5QV  C9   H19  single    0.970  0.020  1.090
 5QV  C25  H22  single    0.930  0.020  1.080
 5QV  C29  H23  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
 5QV  H2   N14  H1   114.33  3.000
 5QV  H2   N14  C12  118.79  3.000
 5QV  H1   N14  C12  115.47  3.000
 5QV  C24  C18  C19  122.50  3.000
 5QV  C24  C18  C17  120.29  3.000
 5QV  C19  C18  C17  117.17  3.000
 5QV  H4   C17  C16  118.63  3.000
 5QV  H4   C17  C18  117.63  3.000
 5QV  C16  C17  C18  123.73  3.000
 5QV  C10  C16  C21  123.28  3.000
 5QV  C10  C16  C17  121.31  3.000
 5QV  C21  C16  C17  115.41  3.000
 5QV  H7   C15  H6   108.07  3.000
 5QV  H7   C15  H5   107.95  3.000
 5QV  H6   C15  H5   108.54  3.000
 5QV  H7   C15  C10  109.35  3.000
 5QV  H6   C15  C10  110.14  3.000
 5QV  H5   C15  C10  112.66  3.000
 5QV  F23  C19  C20  118.48  3.000
 5QV  F23  C19  C18  119.46  3.000
 5QV  C20  C19  C18  122.06  3.000
 5QV  H8   C20  C21  120.77  3.000
 5QV  H8   C20  C19  121.17  3.000
 5QV  C21  C20  C19  118.06  3.000
 5QV  F22  C21  C20  116.35  3.000
 5QV  C20  C21  C16  123.57  3.000
 5QV  F22  C21  C16  120.08  3.000
 5QV  C29  C24  C25  115.35  3.000
 5QV  C29  C24  C18  123.71  3.000
 5QV  C25  C24  C18  120.93  3.000
 5QV  S13  C12  N11  127.93  3.000
 5QV  N11  C12  N14  121.18  3.000
 5QV  S13  C12  N14  110.75  3.000
 5QV  H10  C27  N28  116.91  3.000
 5QV  H10  C27  N26  116.92  3.000
 5QV  N28  C27  N26  126.17  3.000
 5QV  N6   C2   C3   110.66  3.000
 5QV  C3   C2   C1   129.06  3.000
 5QV  N6   C2   C1   120.28  3.000
 5QV  C8   C3   C4   126.82  3.000
 5QV  C8   C3   C2   129.56  3.000
 5QV  C4   C3   C2   103.61  3.000
 5QV  C7   C4   O5   117.50  3.000
 5QV  C7   C4   C3   133.27  3.000
 5QV  O5   C4   C3   109.22  3.000
 5QV  N6   O5   C4   109.88  3.000
 5QV  O5   N6   C2   106.64  3.000
 5QV  H16  C7   H15  107.98  3.000
 5QV  H16  C7   H14  107.78  3.000
 5QV  H15  C7   H14  107.93  3.000
 5QV  H16  C7   C4   110.77  3.000
 5QV  H15  C7   C4   111.21  3.000
 5QV  H14  C7   C4   111.03  3.000
 5QV  H17  C8   S13  105.86  3.000
 5QV  H17  C8   C9   108.73  3.000
 5QV  S13  C8   C9   111.18  3.000
 5QV  H17  C8   C3   108.41  3.000
 5QV  S13  C8   C3   108.74  3.000
 5QV  C9   C8   C3   113.60  3.000
 5QV  H19  C9   H18  106.35  3.000
 5QV  H19  C9   C10  111.40  3.000
 5QV  H18  C9   C10  107.43  3.000
 5QV  H19  C9   C8   107.42  3.000
 5QV  H18  C9   C8   110.80  3.000
 5QV  C10  C9   C8   113.25  3.000
 5QV  N11  C10  C9   110.37  3.000
 5QV  N11  C10  C15  105.67  3.000
 5QV  C9   C10  C15  109.30  3.000
 5QV  N11  C10  C16  110.21  3.000
 5QV  C15  C10  C16  109.95  3.000
 5QV  C9   C10  C16  111.19  3.000
 5QV  C10  N11  C12  122.06  3.000
 5QV  C8   S13  C12  102.16  3.000
 5QV  H22  C25  N26  116.91  3.000
 5QV  H22  C25  C24  120.38  3.000
 5QV  N26  C25  C24  122.71  3.000
 5QV  C25  N26  C27  116.55  3.000
 5QV  C29  N28  C27  116.87  3.000
 5QV  H23  C29  N28  116.58  3.000
 5QV  H23  C29  C24  121.06  3.000
 5QV  N28  C29  C24  122.35  3.000
 5QV  H13  C1   H12  108.00  3.000
 5QV  H13  C1   H11  107.44  3.000
 5QV  H12  C1   H11  108.80  3.000
 5QV  H13  C1   C2   111.09  3.000
 5QV  H12  C1   C2   110.67  3.000
 5QV  H11  C1   C2   110.73  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
 5QV  CONST_01  C21  C20  C19  C18    0.00   0.0  0
 5QV  CONST_02  C21  C16  C17  C18    0.00   0.0  0
 5QV  CONST_03  N26  C25  C24  C18  180.00   0.0  0
 5QV  CONST_04  N28  C29  C24  C18  180.00   0.0  0
 5QV  CONST_05  C20  C21  C16  C17    0.00   0.0  0
 5QV  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 5QV  CONST_09  C19  C20  C21  C16    0.00   0.0  0
 5QV  CONST_10  C19  C18  C17  C16    0.00   0.0  0
 5QV  CONST_11  C24  C18  C17  C16  180.00   0.0  0
 5QV  CONST_14  C24  C18  C19  C20  180.00   0.0  0
 5QV  CONST_15  C27  N26  C25  C24    0.00   0.0  0
 5QV  CONST_16  C27  N28  C29  C24    0.00   0.0  0
 5QV  CONST_17  C4   O5   N6   C2     0.00   0.0  0
 5QV  CONST_18  O5   C4   C3   C2     0.00   0.0  0
 5QV  CONST_19  N6   O5   C4   C3     0.00   0.0  0
 5QV  CONST_20  O5   N6   C2   C3     0.00   0.0  0
 5QV  CONST_21  N6   C2   C3   C4     0.00   0.0  0
 5QV  CONST_22  N28  C29  C24  C25    0.00   0.0  0
 5QV  CONST_23  N28  C27  N26  C25    0.00   0.0  0
 5QV  CONST_24  C29  C24  C25  N26    0.00   0.0  0
 5QV  CONST_25  C29  N28  C27  N26    0.00   0.0  0
 5QV  CONST_26  C10  C16  C17  C18  180.00   0.0  0
 5QV  CONST_27  C10  C16  C21  C20  180.00   0.0  0
 5QV  CONST_28  C8   C3   C4   O5   180.00   0.0  0
 5QV  CONST_29  C8   C3   C2   N6   180.00   0.0  0
 5QV  CONST_30  S13  C12  N11  C10    0.00   0.0  0
 5QV  CONST_31  F22  C21  C16  C17  180.00   0.0  0
 5QV  CONST_32  F23  C19  C18  C17  180.00   0.0  0
 5QV  CONST_33  F22  C21  C20  C19  180.00   0.0  0
 5QV  CONST_34  F23  C19  C20  C21  180.00   0.0  0
 5QV  CONST_35  F23  C19  C18  C24    0.00   0.0  0
 5QV  CONST_36  O5   N6   C2   C1   180.00   0.0  0
 5QV  CONST_37  C4   C3   C2   C1   180.00   0.0  0
 5QV  CONST_38  C8   C3   C2   C1     0.00   0.0  0
 5QV  CONST_39  C7   C4   C3   C2   180.00   0.0  0
 5QV  CONST_40  C7   C4   O5   N6   180.00   0.0  0
 5QV  CONST_41  C8   C3   C4   C7     0.00   0.0  0
 5QV  CONST_42  F22  C21  C16  C10    0.00   0.0  0
 5QV  CONST_43  C10  N11  C12  N14  180.00   0.0  0
 5QV  CONST_44  H8   C20  C19  C18  180.00   0.0  0
 5QV  CONST_45  H22  C25  C24  C18    0.00   0.0  0
 5QV  CONST_46  H23  C29  C24  C18    0.00   0.0  0
 5QV  CONST_47  H4   C17  C18  C19  180.00   0.0  0
 5QV  CONST_48  H10  C27  N26  C25  180.00   0.0  0
 5QV  CONST_49  H1   N14  C12  N11    0.00   0.0  0
 5QV  Var_01    N11  C12  S13  C8    12.76  30.0  1
 5QV  Var_02    H14  C7   C4   C3   111.91  30.0  2
 5QV  Var_03    H11  C1   C2   C3    53.59  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
 5QV  chir_01  C8   C3  C9   S13  positiv
 5QV  chir_02  C10  C9  N11  C16  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
 5QV  plan-1  C2   0.020
 5QV  plan-1  C3   0.020
 5QV  plan-1  C4   0.020
 5QV  plan-1  O5   0.020
 5QV  plan-1  N6   0.020
 5QV  plan-1  C7   0.020
 5QV  plan-1  C8   0.020
 5QV  plan-1  C1   0.020
 5QV  plan-2  C18  0.020
 5QV  plan-2  C17  0.020
 5QV  plan-2  C16  0.020
 5QV  plan-2  C19  0.020
 5QV  plan-2  C20  0.020
 5QV  plan-2  C21  0.020
 5QV  plan-2  C24  0.020
 5QV  plan-2  C10  0.020
 5QV  plan-2  F22  0.020
 5QV  plan-2  F23  0.020
 5QV  plan-2  H4   0.020
 5QV  plan-2  H8   0.020
 5QV  plan-3  N14  0.020
 5QV  plan-3  C12  0.020
 5QV  plan-3  C10  0.020
 5QV  plan-3  N11  0.020
 5QV  plan-3  S13  0.020
 5QV  plan-3  H1   0.020
 5QV  plan-3  H2   0.020
 5QV  plan-4  C18  0.020
 5QV  plan-4  C24  0.020
 5QV  plan-4  C27  0.020
 5QV  plan-4  C25  0.020
 5QV  plan-4  N26  0.020
 5QV  plan-4  N28  0.020
 5QV  plan-4  C29  0.020
 5QV  plan-4  H10  0.020
 5QV  plan-4  H22  0.020
 5QV  plan-4  H23  0.020

