# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 21:41:35 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: ~{N}-[3-[(4~{S},5~{S})-2-azanyl-4-methyl-5-phenyl-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(N=C(N)SC[C@H]1c2ccccc2)c3cc(NC(=O)c4cnc(OCF)cn4)ccc3F
#
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
 C7X  C7X  ~{N}-[3-[(4~{S},5~{S})-2-azanyl-4-methyl-5-phenyl-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide  ligand  54  33  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C7X
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
 C7X  C1   C  CR16  0  -0.317  -0.0115   2.7515   0.8115
 C7X  C2   C  CR16  0  -0.396  -1.3387   3.1305   0.9394
 C7X  C3   C  CR6   0   0.515  -2.3352   2.4044   0.3242
 C7X  C4   C  CR6   0  -0.053  -2.0753   1.2772  -0.4476
 C7X  C5   C  CR16  0  -0.413  -0.7405   0.9193  -0.5663
 C7X  C6   C  CT    0   0.053  -3.1722   0.4660  -1.1505
 C7X  C7   C  CH1   0  -0.351  -4.2199  -0.0032  -0.1046
 C7X  O1   O  O2    0  -0.471   7.0614  -1.4986  -1.0484
 C7X  C8   C  CH2   0  -0.553  -5.2225  -0.9795  -0.7160
 C7X  N3   N  N     0  -0.383   3.7260  -0.3523  -0.7651
 C7X  C9   C  C     0   0.278  -2.9744  -1.7643  -2.0546
 C7X  C10  C  C     0   0.538   2.7611   1.6252   0.2813
 C7X  C11  C  CR6   0   0.055   3.9356   0.7810  -0.0932
 C7X  C12  C  CR16  0  -0.134   4.7568  -1.0957  -1.0789
 C7X  C13  C  CR6   0   0.495   6.0502  -0.6948  -0.7036
 C7X  C14  C  CR16  0  -0.043   5.2163   1.1644   0.2611
 C7X  C15  C  CH3   0  -0.638  -3.8498   1.3697  -2.1977
 C7X  F1   F  F     0  -0.360   8.5861  -1.3067   0.6079
 C7X  C17  C  CH2   0   0.172   8.3641  -1.1163  -0.7323
 C7X  N4   N  N     0  -0.414   6.2706   0.4152  -0.0451
 C7X  O    O  O     0  -0.461   2.9118   2.6585   0.9124
 C7X  C    C  CR6   0   0.422   0.2921   1.6259   0.0508
 C7X  F    F  F     0  -0.318  -3.6022   2.8323   0.5018
 C7X  N    N  N     0  -0.411  -2.5238  -0.5944  -1.8825
 C7X  S    S  S2    0   0.008  -4.4505  -2.4733  -1.3745
 C7X  C16  C  CR6   0   0.185  -3.6657  -0.5230   1.2005
 C7X  C22  C  CR16  0  -0.300  -2.5810  -1.3939   1.2909
 C7X  C21  C  CR16  0  -0.240  -2.1440  -1.8586   2.5241
 C7X  C20  C  CR16  0  -0.275  -2.7846  -1.4691   3.6923
 C7X  C19  C  CR16  0  -0.241  -3.8666  -0.6030   3.6169
 C7X  C18  C  CR16  0  -0.319  -4.2954  -0.1356   2.3824
 C7X  H1   H  HCR6  0   0.285   0.7521   3.3302   1.3033
 C7X  H2   H  HCR6  0   0.276  -1.5982   4.0018   1.5269
 C7X  H3   H  HCR6  0   0.277  -0.5047   0.0482  -1.1634
 C7X  H4   H  HCH1  0   0.281  -4.8258   0.8701   0.1412
 C7X  H5   H  HNH2  0   0.390  -1.3418  -2.4419  -3.0220
 C7X  H6   H  HNH2  0   0.395  -2.5050  -3.6377  -2.7379
 C7X  H7   H  HNH1  0   0.422   1.6496   0.2602  -0.6628
 C7X  H8   H  HCH2  0   0.302  -5.9274  -1.3177   0.0427
 C7X  H9   H  HCH2  0   0.293  -5.8018  -0.5031  -1.5062
 C7X  H10  H  HCR6  0   0.296   4.5889  -2.0150  -1.6267
 C7X  H11  H  HCR6  0   0.290   5.4044   2.0821   0.8021
 C7X  H12  H  HCH3  0   0.243  -3.1025   1.7672  -2.8842
 C7X  H13  H  HCH3  0   0.238  -4.5690   0.8033  -2.7903
 C7X  H14  H  HCH3  0   0.234  -4.3766   2.2065  -1.7421
 C7X  H15  H  HCH2  0   0.239   9.0147  -1.7807  -1.2943
 C7X  H16  H  HCH2  0   0.224   8.5511  -0.0702  -0.9709
 C7X  H17  H  HCR6  0   0.254  -2.0506  -1.7066   0.4034
 C7X  H18  H  HCR6  0   0.251  -1.2958  -2.5299   2.5693
 C7X  H19  H  HCR6  0   0.252  -2.4413  -1.8328   4.6522
 C7X  H20  H  HCR6  0   0.251  -4.3753  -0.2865   4.5186
 C7X  H21  H  HCR6  0   0.246  -5.1372   0.5462   2.3379
 C7X  N1   N  NH2   0  -0.805  -2.3116  -2.6552  -2.8465
 C7X  N2   N  NH1   0  -0.762   1.5839   1.1250  -0.1403

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
 C7X  C21  C20  aromatic  1.388  0.020  1.388
 C7X  C21  C22  aromatic  1.388  0.020  1.388
 C7X  C20  C19  aromatic  1.388  0.020  1.388
 C7X  C22  C16  aromatic  1.394  0.020  1.394
 C7X  C19  C18  aromatic  1.388  0.020  1.388
 C7X  C16  C18  aromatic  1.394  0.020  1.394
 C7X  C16  C7   single    1.510  0.020  1.510
 C7X  C7   C8   single    1.527  0.020  1.527
 C7X  C7   C6   single    1.553  0.020  1.553
 C7X  F    C3   single    1.349  0.020  1.349
 C7X  C8   S    single    1.806  0.020  1.806
 C7X  C15  C6   single    1.540  0.020  1.540
 C7X  C6   C4   single    1.535  0.020  1.535
 C7X  C6   N    single    1.442  0.020  1.442
 C7X  C3   C4   aromatic  1.391  0.020  1.391
 C7X  C3   C2   aromatic  1.378  0.020  1.378
 C7X  S    C9   single    1.773  0.020  1.773
 C7X  C4   C5   aromatic  1.387  0.020  1.387
 C7X  C2   C1   aromatic  1.386  0.020  1.386
 C7X  N    C9   double    1.265  0.020  1.265
 C7X  C9   N1   single    1.364  0.020  1.364
 C7X  C5   C    aromatic  1.395  0.020  1.395
 C7X  C1   C    aromatic  1.392  0.020  1.392
 C7X  C    N2   single    1.399  0.020  1.399
 C7X  N2   C10  single    1.347  0.020  1.347
 C7X  O    C10  double    1.220  0.020  1.220
 C7X  C10  C11  single    1.494  0.020  1.494
 C7X  C11  C14  aromatic  1.383  0.020  1.383
 C7X  C11  N3   aromatic  1.334  0.020  1.334
 C7X  C14  N4   aromatic  1.329  0.020  1.329
 C7X  N3   C12  aromatic  1.309  0.020  1.309
 C7X  N4   C13  aromatic  1.309  0.020  1.309
 C7X  C12  C13  aromatic  1.405  0.020  1.405
 C7X  C13  O1   single    1.337  0.020  1.337
 C7X  O1   C17  single    1.394  0.020  1.394
 C7X  C17  F1   single    1.372  0.020  1.372
 C7X  C1   H1   single    0.930  0.020  1.080
 C7X  C2   H2   single    0.930  0.020  1.080
 C7X  C5   H3   single    0.930  0.020  1.080
 C7X  C7   H4   single    0.970  0.020  1.090
 C7X  N1   H5   single    0.890  0.020  1.040
 C7X  N1   H6   single    0.890  0.020  1.040
 C7X  N2   H7   single    0.860  0.020  1.020
 C7X  C8   H8   single    0.970  0.020  1.090
 C7X  C8   H9   single    0.970  0.020  1.090
 C7X  C12  H10  single    0.930  0.020  1.080
 C7X  C14  H11  single    0.930  0.020  1.080
 C7X  C15  H12  single    0.970  0.020  1.090
 C7X  C15  H13  single    0.970  0.020  1.090
 C7X  C15  H14  single    0.970  0.020  1.090
 C7X  C17  H15  single    0.970  0.020  1.090
 C7X  C17  H16  single    0.970  0.020  1.090
 C7X  C22  H17  single    0.930  0.020  1.080
 C7X  C21  H18  single    0.930  0.020  1.080
 C7X  C20  H19  single    0.930  0.020  1.080
 C7X  C19  H20  single    0.930  0.020  1.080
 C7X  C18  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
 C7X  H1   C1   C    121.96  3.000
 C7X  H1   C1   C2   119.33  3.000
 C7X  C    C1   C2   118.71  3.000
 C7X  H2   C2   C3   119.54  3.000
 C7X  H2   C2   C1   119.98  3.000
 C7X  C3   C2   C1   120.48  3.000
 C7X  F    C3   C4   120.38  3.000
 C7X  C4   C3   C2   122.67  3.000
 C7X  F    C3   C2   116.96  3.000
 C7X  C6   C4   C5   120.82  3.000
 C7X  C5   C4   C3   115.88  3.000
 C7X  C6   C4   C3   123.30  3.000
 C7X  H3   C5   C    119.38  3.000
 C7X  H3   C5   C4   117.68  3.000
 C7X  C    C5   C4   122.94  3.000
 C7X  N    C6   C15  106.50  3.000
 C7X  N    C6   C7   115.02  3.000
 C7X  C15  C6   C7   109.77  3.000
 C7X  N    C6   C4   107.44  3.000
 C7X  C15  C6   C4   108.40  3.000
 C7X  C7   C6   C4   109.48  3.000
 C7X  H4   C7   C16  106.54  3.000
 C7X  H4   C7   C8   103.73  3.000
 C7X  C16  C7   C8   111.53  3.000
 C7X  H4   C7   C6   106.53  3.000
 C7X  C8   C7   C6   111.50  3.000
 C7X  C16  C7   C6   116.00  3.000
 C7X  C17  O1   C13  118.91  3.000
 C7X  H9   C8   H8   107.26  3.000
 C7X  H9   C8   S    108.94  3.000
 C7X  H8   C8   S    105.89  3.000
 C7X  H9   C8   C7   111.10  3.000
 C7X  H8   C8   C7   110.14  3.000
 C7X  S    C8   C7   113.22  3.000
 C7X  C12  N3   C11  118.65  3.000
 C7X  S    C9   N    127.88  3.000
 C7X  N    C9   N1   120.65  3.000
 C7X  S    C9   N1   111.47  3.000
 C7X  O    C10  C11  120.74  3.000
 C7X  C11  C10  N2   113.50  3.000
 C7X  O    C10  N2   125.76  3.000
 C7X  C14  C11  C10  120.47  3.000
 C7X  C14  C11  N3   120.66  3.000
 C7X  C10  C11  N3   118.87  3.000
 C7X  H10  C12  C13  121.32  3.000
 C7X  H10  C12  N3   118.76  3.000
 C7X  C13  C12  N3   119.92  3.000
 C7X  N4   C13  C12  122.08  3.000
 C7X  C12  C13  O1   117.12  3.000
 C7X  N4   C13  O1   120.80  3.000
 C7X  H11  C14  N4   117.09  3.000
 C7X  H11  C14  C11  121.62  3.000
 C7X  N4   C14  C11  121.29  3.000
 C7X  H14  C15  H13  107.91  3.000
 C7X  H14  C15  H12  108.36  3.000
 C7X  H13  C15  H12  107.42  3.000
 C7X  H14  C15  C6   112.29  3.000
 C7X  H13  C15  C6   110.78  3.000
 C7X  H12  C15  C6   109.91  3.000
 C7X  H16  C17  H15  111.79  3.000
 C7X  H16  C17  F1   108.64  3.000
 C7X  H15  C17  F1   108.87  3.000
 C7X  H16  C17  O1   111.97  3.000
 C7X  H15  C17  O1   105.94  3.000
 C7X  F1   C17  O1   109.56  3.000
 C7X  C14  N4   C13  117.39  3.000
 C7X  N2   C    C5   116.22  3.000
 C7X  N2   C    C1   124.45  3.000
 C7X  C5   C    C1   119.33  3.000
 C7X  C9   N    C6   126.06  3.000
 C7X  C9   S    C8    99.49  3.000
 C7X  C18  C16  C22  118.04  3.000
 C7X  C18  C16  C7   118.11  3.000
 C7X  C22  C16  C7   123.83  3.000
 C7X  H17  C22  C21  118.57  3.000
 C7X  H17  C22  C16  120.64  3.000
 C7X  C21  C22  C16  120.77  3.000
 C7X  H18  C21  C20  120.03  3.000
 C7X  H18  C21  C22  119.42  3.000
 C7X  C20  C21  C22  120.55  3.000
 C7X  H19  C20  C19  120.34  3.000
 C7X  H19  C20  C21  120.37  3.000
 C7X  C19  C20  C21  119.29  3.000
 C7X  H20  C19  C18  119.82  3.000
 C7X  H20  C19  C20  120.23  3.000
 C7X  C18  C19  C20  119.95  3.000
 C7X  H21  C18  C19  119.22  3.000
 C7X  H21  C18  C16  119.38  3.000
 C7X  C19  C18  C16  121.40  3.000
 C7X  H6   N1   H5   114.19  3.000
 C7X  H6   N1   C9   118.77  3.000
 C7X  H5   N1   C9   115.49  3.000
 C7X  H7   N2   C    115.88  3.000
 C7X  H7   N2   C10  114.96  3.000
 C7X  C    N2   C10  129.16  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
 C7X  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 C7X  CONST_02  C4   C5   C    C1      0.00   0.0  0
 C7X  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 C7X  CONST_04  C5   C    C1   C2      0.00   0.0  0
 C7X  CONST_05  C    C5   C4   C3      0.00   0.0  0
 C7X  CONST_06  C    C1   C2   C3      0.00   0.0  0
 C7X  CONST_07  N4   C14  C11  N3      0.00   0.0  0
 C7X  CONST_08  N4   C13  C12  N3      0.00   0.0  0
 C7X  CONST_09  C13  N4   C14  C11     0.00   0.0  0
 C7X  CONST_10  C13  C12  N3   C11     0.00   0.0  0
 C7X  CONST_11  C14  C11  N3   C12     0.00   0.0  0
 C7X  CONST_12  C14  N4   C13  C12     0.00   0.0  0
 C7X  CONST_13  C20  C21  C22  C16     0.00   0.0  0
 C7X  CONST_14  C20  C19  C18  C16     0.00   0.0  0
 C7X  CONST_15  C19  C20  C21  C22     0.00   0.0  0
 C7X  CONST_16  C19  C18  C16  C22     0.00   0.0  0
 C7X  CONST_17  C18  C19  C20  C21     0.00   0.0  0
 C7X  CONST_18  C18  C16  C22  C21     0.00   0.0  0
 C7X  CONST_19  C6   C4   C3   C2    180.00   0.0  0
 C7X  CONST_20  C    C5   C4   C6    180.00   0.0  0
 C7X  CONST_21  C21  C22  C16  C7    180.00   0.0  0
 C7X  CONST_22  C19  C18  C16  C7    180.00   0.0  0
 C7X  CONST_23  S    C9   N    C6      0.00   0.0  0
 C7X  CONST_24  F    C3   C2   C1    180.00   0.0  0
 C7X  CONST_25  N2   C    C1   C2    180.00   0.0  0
 C7X  CONST_26  N2   C    C5   C4    180.00   0.0  0
 C7X  CONST_27  F    C3   C4   C5    180.00   0.0  0
 C7X  CONST_28  F    C3   C4   C6      0.00   0.0  0
 C7X  CONST_29  C14  N4   C13  O1    180.00   0.0  0
 C7X  CONST_30  N3   C12  C13  O1    180.00   0.0  0
 C7X  CONST_31  N4   C14  C11  C10   180.00   0.0  0
 C7X  CONST_32  C12  N3   C11  C10   180.00   0.0  0
 C7X  CONST_33  N1   C9   N    C6    180.00   0.0  0
 C7X  CONST_34  H3   C5   C    C1    180.00   0.0  0
 C7X  CONST_35  H1   C1   C2   C3    180.00   0.0  0
 C7X  CONST_36  H2   C2   C3   C4    180.00   0.0  0
 C7X  CONST_37  H17  C22  C16  C7      0.00   0.0  0
 C7X  CONST_38  H21  C18  C16  C7      0.00   0.0  0
 C7X  CONST_39  H11  C14  C11  N3    180.00   0.0  0
 C7X  CONST_40  H10  C12  N3   C11   180.00   0.0  0
 C7X  CONST_41  H18  C21  C22  C16   180.00   0.0  0
 C7X  CONST_42  H20  C19  C18  C16   180.00   0.0  0
 C7X  CONST_43  H19  C20  C21  C22   180.00   0.0  0
 C7X  CONST_44  C    N2   C10  C11   180.00   0.0  0
 C7X  CONST_45  C10  N2   C    C1      0.00   0.0  0
 C7X  CONST_46  C10  N2   C    C5    180.00   0.0  0
 C7X  CONST_47  H7   N2   C    C1    180.00   0.0  0
 C7X  CONST_50  C    N2   C10  O       0.00   0.0  0
 C7X  Var_01    N    C9   S    C8     11.32  30.0  1
 C7X  Var_02    H8   C8   S    C9   -158.85  30.0  1
 C7X  Var_03    C14  C11  C10  N2    179.62  30.0  2
 C7X  Var_04    N4   C13  O1   C17    -1.99  30.0  2
 C7X  Var_05    F1   C17  O1   C13    75.40  30.0  3

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
 C7X  chir_01  C6  C7  C4  N    negativ
 C7X  chir_02  C7  C6  C8  C16  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
 C7X  plan-1  C1   0.020
 C7X  plan-1  C2   0.020
 C7X  plan-1  C3   0.020
 C7X  plan-1  C4   0.020
 C7X  plan-1  C5   0.020
 C7X  plan-1  C6   0.020
 C7X  plan-1  C    0.020
 C7X  plan-1  F    0.020
 C7X  plan-1  H1   0.020
 C7X  plan-1  H2   0.020
 C7X  plan-1  H3   0.020
 C7X  plan-1  N2   0.020
 C7X  plan-2  O1   0.020
 C7X  plan-2  N3   0.020
 C7X  plan-2  C10  0.020
 C7X  plan-2  C11  0.020
 C7X  plan-2  C12  0.020
 C7X  plan-2  C13  0.020
 C7X  plan-2  C14  0.020
 C7X  plan-2  N4   0.020
 C7X  plan-2  H10  0.020
 C7X  plan-2  H11  0.020
 C7X  plan-3  C7   0.020
 C7X  plan-3  C16  0.020
 C7X  plan-3  C22  0.020
 C7X  plan-3  C21  0.020
 C7X  plan-3  C20  0.020
 C7X  plan-3  C19  0.020
 C7X  plan-3  C18  0.020
 C7X  plan-3  H17  0.020
 C7X  plan-3  H18  0.020
 C7X  plan-3  H19  0.020
 C7X  plan-3  H20  0.020
 C7X  plan-3  H21  0.020
 C7X  plan-4  C10  0.020
 C7X  plan-4  C11  0.020
 C7X  plan-4  O    0.020
 C7X  plan-4  C    0.020
 C7X  plan-4  H7   0.020
 C7X  plan-4  N2   0.020
 C7X  plan-5  C6   0.020
 C7X  plan-5  C9   0.020
 C7X  plan-5  N    0.020
 C7X  plan-5  S    0.020
 C7X  plan-5  H5   0.020
 C7X  plan-5  H6   0.020
 C7X  plan-5  N1   0.020

