# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 20:55:43 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: ~{N}-[3-[(5~{R})-3-azanyl-5-methyl-9,9-bis(oxidanylidene)-2,9$l^{6}-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(N=C(N)SCC12CC[S](=O)(=O)CC2)c3cc(NC(=O)c4cnc(OCF)cn4)ccc3F
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 C7O  C7O  ~{N}-[3-[(5~{R})-3-azanyl-5-methyl-9,9-bis(oxidanylidene)-2,9$l^{6}-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide  ligand  57  34  .  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_C7O
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
 C7O  C1   C  CH3   0  -0.678  -1.7174   1.4326   2.1822
 C7O  C2   C  CT    0   0.066  -2.3889   1.2194   0.8091
 C7O  C3   C  C     0   0.261  -4.4622   2.3500   1.1418
 C7O  C4   C  CH2   0  -0.595  -4.0687  -0.2861   1.9222
 C7O  C5   C  CT    0  -0.101  -3.1137  -0.1825   0.7315
 C7O  C6   C  CH2   0  -0.458  -2.0931  -1.3341   0.8400
 C7O  C7   C  CH2   0  -0.624  -2.7063  -2.7301   0.8367
 C7O  N1   N  N     0  -0.381  -3.2967   2.3352   0.6545
 C7O  N2   N  NH2   0  -0.810  -5.2319   3.4799   1.1027
 C7O  C8   C  CH2   0  -0.623  -4.6620  -1.6185  -0.7591
 C7O  C9   C  CH2   0  -0.444  -3.8750  -0.3219  -0.6011
 C7O  C10  C  CR6   0  -0.060  -1.3357   1.3395  -0.2999
 C7O  C11  C  CR16  0  -0.404  -0.0185   0.9535  -0.0666
 C7O  C12  C  CR6   0   0.413   0.9912   1.0471  -1.0234
 C7O  C13  C  C     0   0.539   3.4226   0.6565  -1.3142
 C7O  C14  C  CR6   0   0.056   4.5848   0.1297  -0.5373
 C7O  C15  C  CR16  0  -0.133   5.3989  -0.7690   1.3857
 C7O  C21  C  CR6   0   0.512  -1.5974   1.8437  -1.5724
 C7O  S2   S  S     0   1.221  -3.5816  -3.0376  -0.6882
 C7O  S1   S  S2    0   0.028  -5.3079   1.0332   1.9806
 C7O  C20  C  CR16  0  -0.398  -0.6166   1.9527  -2.5389
 C7O  C19  C  CR16  0  -0.312   0.6845   1.5585  -2.2817
 C7O  O3   O  O     0  -0.458   3.5665   1.0750  -2.4506
 C7O  C18  C  CR16  0  -0.043   5.8517   0.1111  -1.0915
 C7O  N5   N  N     0  -0.414   6.8981  -0.3387  -0.4060
 C7O  C16  C  CR6   0   0.496   6.6805  -0.7739   0.8096
 C7O  N4   N  N     0  -0.384   4.3784  -0.3155   0.7031
 C7O  O4   O  O2    0  -0.472   7.6824  -1.2450   1.5585
 C7O  C17  C  CH2   0   0.173   8.9641  -1.3035   1.0132
 C7O  F1   F  F     0  -0.360   9.5045  -0.0435   0.9766
 C7O  H1   H  HCH3  0   0.259  -1.1255   2.3472   2.1568
 C7O  H2   H  HCH3  0   0.251  -2.4736   1.5631   2.9550
 C7O  H3   H  HCH3  0   0.238  -1.0645   0.6225   2.5023
 C7O  H4   H  HCH2  0   0.301  -4.6527  -1.2052   1.9026
 C7O  H5   H  HCH2  0   0.309  -3.5156  -0.3018   2.8604
 C7O  H6   H  HCH2  0   0.278  -1.3823  -1.2687   0.0157
 C7O  H7   H  HCH2  0   0.279  -1.5041  -1.2527   1.7544
 C7O  H8   H  HCH2  0   0.332  -1.9311  -3.4962   0.9010
 C7O  H9   H  HCH2  0   0.303  -3.4115  -2.8955   1.6519
 C7O  H10  H  HNH2  0   0.387  -4.9111   4.1802   0.4511
 C7O  H11  H  HNH2  0   0.393  -6.2337   3.3666   1.1007
 C7O  H12  H  HCH2  0   0.298  -5.4350  -1.7533  -0.0017
 C7O  H13  H  HCH2  0   0.330  -5.1474  -1.6594  -1.7365
 C7O  H14  H  HNH1  0   0.424   2.3320   0.2397   0.3058
 C7O  H15  H  HCH2  0   0.284  -4.5875   0.4900  -0.7390
 C7O  H16  H  HCH2  0   0.270  -3.1707  -0.2551  -1.4306
 C7O  H17  H  HCR6  0   0.277   0.2502   0.5617   0.9058
 C7O  H18  H  HCR6  0   0.296   5.2316  -1.1344   2.3915
 C7O  H19  H  HCR6  0   0.278  -0.8780   2.3496  -3.5112
 C7O  H20  H  HCR6  0   0.288   1.4278   1.6512  -3.0553
 C7O  H21  H  HCR6  0   0.291   6.0374   0.4662  -2.0963
 C7O  H22  H  HCH2  0   0.239   9.5487  -1.9176   1.6924
 C7O  H23  H  HCH2  0   0.224   8.9598  -1.7104   0.0031
 C7O  O1   O  OS    0  -0.687  -2.6241  -2.9396  -1.7932
 C7O  O2   O  OS    0  -0.682  -4.3718  -4.2631  -0.5665
 C7O  F2   F  F     0  -0.307  -2.8303   2.2309  -1.9352
 C7O  N3   N  NH1   0  -0.765   2.2610   0.6149  -0.6318

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
 C7O  O2   S2   double    1.463  0.020  1.463
 C7O  O1   S2   double    1.465  0.020  1.465
 C7O  S2   C8   single    1.785  0.020  1.785
 C7O  S2   C7   single    1.785  0.020  1.785
 C7O  C8   C9   single    1.525  0.020  1.525
 C7O  C7   C6   single    1.525  0.020  1.525
 C7O  C9   C5   single    1.541  0.020  1.541
 C7O  C6   C5   single    1.542  0.020  1.542
 C7O  F2   C21  single    1.342  0.020  1.342
 C7O  C5   C4   single    1.530  0.020  1.530
 C7O  C5   C2   single    1.580  0.020  1.580
 C7O  C4   S1   single    1.811  0.020  1.811
 C7O  C1   C2   single    1.543  0.020  1.543
 C7O  C21  C20  aromatic  1.381  0.020  1.381
 C7O  C21  C10  aromatic  1.394  0.020  1.394
 C7O  C2   C10  single    1.534  0.020  1.534
 C7O  C2   N1   single    1.447  0.020  1.447
 C7O  C20  C19  aromatic  1.384  0.020  1.384
 C7O  C10  C11  aromatic  1.392  0.020  1.392
 C7O  S1   C3   single    1.776  0.020  1.776
 C7O  N1   C3   double    1.263  0.020  1.263
 C7O  C19  C12  aromatic  1.392  0.020  1.392
 C7O  C11  C12  aromatic  1.394  0.020  1.394
 C7O  C3   N2   single    1.368  0.020  1.368
 C7O  C12  N3   single    1.397  0.020  1.397
 C7O  N3   C13  single    1.348  0.020  1.348
 C7O  O3   C13  double    1.219  0.020  1.219
 C7O  C13  C14  single    1.494  0.020  1.494
 C7O  C14  C18  aromatic  1.383  0.020  1.383
 C7O  C14  N4   aromatic  1.334  0.020  1.334
 C7O  C18  N5   aromatic  1.329  0.020  1.329
 C7O  N4   C15  aromatic  1.309  0.020  1.309
 C7O  N5   C16  aromatic  1.309  0.020  1.309
 C7O  C15  C16  aromatic  1.405  0.020  1.405
 C7O  C16  O4   single    1.337  0.020  1.337
 C7O  O4   C17  single    1.394  0.020  1.394
 C7O  C17  F1   single    1.371  0.020  1.371
 C7O  C1   H1   single    0.970  0.020  1.090
 C7O  C1   H2   single    0.970  0.020  1.090
 C7O  C1   H3   single    0.970  0.020  1.090
 C7O  C4   H4   single    0.970  0.020  1.090
 C7O  C4   H5   single    0.970  0.020  1.090
 C7O  C6   H6   single    0.970  0.020  1.090
 C7O  C6   H7   single    0.970  0.020  1.090
 C7O  C7   H8   single    0.970  0.020  1.090
 C7O  C7   H9   single    0.970  0.020  1.090
 C7O  N2   H10  single    0.890  0.020  1.040
 C7O  N2   H11  single    0.890  0.020  1.040
 C7O  C8   H12  single    0.970  0.020  1.090
 C7O  C8   H13  single    0.970  0.020  1.090
 C7O  N3   H14  single    0.860  0.020  1.020
 C7O  C9   H15  single    0.970  0.020  1.090
 C7O  C9   H16  single    0.970  0.020  1.090
 C7O  C11  H17  single    0.930  0.020  1.080
 C7O  C15  H18  single    0.930  0.020  1.080
 C7O  C20  H19  single    0.930  0.020  1.080
 C7O  C19  H20  single    0.930  0.020  1.080
 C7O  C18  H21  single    0.930  0.020  1.080
 C7O  C17  H22  single    0.970  0.020  1.090
 C7O  C17  H23  single    0.970  0.020  1.090

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
 C7O  H3   C1   H2   107.28  3.000
 C7O  H3   C1   H1   107.80  3.000
 C7O  H2   C1   H1   107.05  3.000
 C7O  H3   C1   C2   114.82  3.000
 C7O  H2   C1   C2   110.23  3.000
 C7O  H1   C1   C2   109.36  3.000
 C7O  C10  C2   N1   107.04  3.000
 C7O  N1   C2   C5   113.03  3.000
 C7O  C10  C2   C5   110.42  3.000
 C7O  N1   C2   C1   105.16  3.000
 C7O  C10  C2   C1   109.49  3.000
 C7O  C5   C2   C1   111.46  3.000
 C7O  S1   C3   N2   110.98  3.000
 C7O  N2   C3   N1   121.19  3.000
 C7O  S1   C3   N1   127.80  3.000
 C7O  H5   C4   H4   106.00  3.000
 C7O  H5   C4   S1   109.28  3.000
 C7O  H4   C4   S1   104.39  3.000
 C7O  H5   C4   C5   110.75  3.000
 C7O  H4   C4   C5   112.20  3.000
 C7O  S1   C4   C5   113.76  3.000
 C7O  C9   C5   C6   108.67  3.000
 C7O  C6   C5   C4   107.92  3.000
 C7O  C9   C5   C4   111.01  3.000
 C7O  C4   C5   C2   107.95  3.000
 C7O  C6   C5   C2   110.82  3.000
 C7O  C9   C5   C2   110.45  3.000
 C7O  H7   C6   H6   106.10  3.000
 C7O  H7   C6   C7   106.69  3.000
 C7O  H6   C6   C7   108.38  3.000
 C7O  H7   C6   C5   111.14  3.000
 C7O  H6   C6   C5   109.47  3.000
 C7O  C7   C6   C5   114.67  3.000
 C7O  H9   C7   H8   107.99  3.000
 C7O  H9   C7   S2   107.18  3.000
 C7O  H8   C7   S2   106.12  3.000
 C7O  H9   C7   C6   113.41  3.000
 C7O  H8   C7   C6   110.90  3.000
 C7O  S2   C7   C6   110.90  3.000
 C7O  C3   N1   C2   123.14  3.000
 C7O  H11  N2   H10  113.12  3.000
 C7O  H11  N2   C3   117.80  3.000
 C7O  H10  N2   C3   114.39  3.000
 C7O  H13  C8   H12  107.57  3.000
 C7O  H13  C8   S2   105.95  3.000
 C7O  H12  C8   S2   107.65  3.000
 C7O  H13  C8   C9   110.73  3.000
 C7O  H12  C8   C9   113.51  3.000
 C7O  S2   C8   C9   111.07  3.000
 C7O  H16  C9   H15  106.30  3.000
 C7O  H16  C9   C8   107.86  3.000
 C7O  H15  C9   C8   106.45  3.000
 C7O  H16  C9   C5   109.47  3.000
 C7O  H15  C9   C5   111.42  3.000
 C7O  C8   C9   C5   114.93  3.000
 C7O  C21  C10  C11  115.53  3.000
 C7O  C11  C10  C2   120.44  3.000
 C7O  C21  C10  C2   124.03  3.000
 C7O  H17  C11  C12  117.46  3.000
 C7O  H17  C11  C10  119.07  3.000
 C7O  C12  C11  C10  123.48  3.000
 C7O  C19  C12  C11  119.03  3.000
 C7O  C11  C12  N3   116.43  3.000
 C7O  C19  C12  N3   124.54  3.000
 C7O  O3   C13  C14  120.92  3.000
 C7O  C14  C13  N3   113.35  3.000
 C7O  O3   C13  N3   125.74  3.000
 C7O  N4   C14  C18  120.65  3.000
 C7O  N4   C14  C13  118.74  3.000
 C7O  C18  C14  C13  120.60  3.000
 C7O  H18  C15  N4   118.73  3.000
 C7O  H18  C15  C16  121.36  3.000
 C7O  N4   C15  C16  119.90  3.000
 C7O  C20  C21  F2   116.13  3.000
 C7O  C20  C21  C10  122.29  3.000
 C7O  F2   C21  C10  121.57  3.000
 C7O  O2   S2   C8   110.02  3.000
 C7O  C8   S2   O1   108.20  3.000
 C7O  O2   S2   O1   118.14  3.000
 C7O  C8   S2   C7   101.17  3.000
 C7O  O1   S2   C7   108.20  3.000
 C7O  O2   S2   C7   109.76  3.000
 C7O  C4   S1   C3   101.49  3.000
 C7O  H19  C20  C19  119.91  3.000
 C7O  H19  C20  C21  119.08  3.000
 C7O  C19  C20  C21  121.01  3.000
 C7O  H20  C19  C20  119.41  3.000
 C7O  H20  C19  C12  121.92  3.000
 C7O  C20  C19  C12  118.67  3.000
 C7O  H21  C18  N5   117.06  3.000
 C7O  H21  C18  C14  121.67  3.000
 C7O  N5   C18  C14  121.27  3.000
 C7O  C16  N5   C18  117.41  3.000
 C7O  O4   C16  N5   120.85  3.000
 C7O  O4   C16  C15  117.08  3.000
 C7O  N5   C16  C15  122.08  3.000
 C7O  C15  N4   C14  118.68  3.000
 C7O  C17  O4   C16  119.00  3.000
 C7O  H23  C17  H22  111.77  3.000
 C7O  H23  C17  F1   108.67  3.000
 C7O  H22  C17  F1   108.91  3.000
 C7O  H23  C17  O4   112.02  3.000
 C7O  H22  C17  O4   105.89  3.000
 C7O  F1   C17  O4   109.52  3.000
 C7O  H14  N3   C13  114.83  3.000
 C7O  H14  N3   C12  115.97  3.000
 C7O  C13  N3   C12  129.17  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
 C7O  CONST_01  C19  C20  C21  C10     0.00   0.0  0
 C7O  CONST_02  C19  C12  C11  C10     0.00   0.0  0
 C7O  CONST_03  C20  C21  C10  C11     0.00   0.0  0
 C7O  CONST_04  C20  C19  C12  C11     0.00   0.0  0
 C7O  CONST_05  C21  C20  C19  C12     0.00   0.0  0
 C7O  CONST_06  C21  C10  C11  C12     0.00   0.0  0
 C7O  CONST_07  C16  N5   C18  C14     0.00   0.0  0
 C7O  CONST_08  C16  C15  N4   C14     0.00   0.0  0
 C7O  CONST_09  C18  C14  N4   C15     0.00   0.0  0
 C7O  CONST_10  C18  N5   C16  C15     0.00   0.0  0
 C7O  CONST_11  N4   C14  C18  N5      0.00   0.0  0
 C7O  CONST_12  N4   C15  C16  N5      0.00   0.0  0
 C7O  CONST_13  C20  C21  C10  C2    180.00   0.0  0
 C7O  CONST_14  C12  C11  C10  C2    180.00   0.0  0
 C7O  CONST_15  S1   C3   N1   C2      0.00   0.0  0
 C7O  CONST_16  F2   C21  C10  C2      0.00   0.0  0
 C7O  CONST_17  C20  C19  C12  N3    180.00   0.0  0
 C7O  CONST_18  C10  C11  C12  N3    180.00   0.0  0
 C7O  CONST_19  F2   C21  C10  C11   180.00   0.0  0
 C7O  CONST_20  N5   C18  C14  C13   180.00   0.0  0
 C7O  CONST_21  C15  N4   C14  C13   180.00   0.0  0
 C7O  CONST_22  C19  C20  C21  F2    180.00   0.0  0
 C7O  CONST_23  O4   C16  N5   C18   180.00   0.0  0
 C7O  CONST_24  O4   C16  C15  N4    180.00   0.0  0
 C7O  CONST_25  N2   C3   N1   C2    180.00   0.0  0
 C7O  CONST_26  H17  C11  C10  C2      0.00   0.0  0
 C7O  CONST_27  H19  C20  C21  C10   180.00   0.0  0
 C7O  CONST_28  H20  C19  C12  C11   180.00   0.0  0
 C7O  CONST_29  H18  C15  N4   C14   180.00   0.0  0
 C7O  CONST_30  H21  C18  N5   C16   180.00   0.0  0
 C7O  CONST_31  C14  C13  N3   C12   180.00   0.0  0
 C7O  CONST_32  C13  N3   C12  C11   180.00   0.0  0
 C7O  CONST_33  C19  C12  N3   C13     0.00   0.0  0
 C7O  CONST_34  H14  N3   C12  C11     0.00   0.0  0
 C7O  CONST_37  O3   C13  N3   C12     0.00   0.0  0
 C7O  Var_01    C8   C9   C5   C2   -177.58  30.0  1
 C7O  Var_02    C7   C6   C5   C2    177.43  30.0  1
 C7O  Var_03    S1   C4   C5   C2     58.24  30.0  3
 C7O  Var_04    C5   C4   S1   C3    -27.51  30.0  1
 C7O  Var_05    N1   C3   S1   C4     -0.48  30.0  1
 C7O  Var_06    S2   C8   C9   C5    -60.79  30.0  1
 C7O  Var_07    S2   C7   C6   C5     61.52  30.0  1
 C7O  Var_08    C8   S2   C7   C6    -52.84  30.0  1
 C7O  Var_09    C9   C8   S2   C7     52.47  30.0  1
 C7O  Var_10    C18  C14  C13  N3   -179.56  30.0  2
 C7O  Var_11    F1   C17  O4   C16    75.57  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
 C7O  chir_01  C2  C5  C10  N1  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
 C7O  plan-1  C13  0.020
 C7O  plan-1  C14  0.020
 C7O  plan-1  C15  0.020
 C7O  plan-1  C18  0.020
 C7O  plan-1  N5   0.020
 C7O  plan-1  C16  0.020
 C7O  plan-1  N4   0.020
 C7O  plan-1  O4   0.020
 C7O  plan-1  H18  0.020
 C7O  plan-1  H21  0.020
 C7O  plan-2  C2   0.020
 C7O  plan-2  C10  0.020
 C7O  plan-2  C11  0.020
 C7O  plan-2  C12  0.020
 C7O  plan-2  C21  0.020
 C7O  plan-2  C20  0.020
 C7O  plan-2  C19  0.020
 C7O  plan-2  H17  0.020
 C7O  plan-2  H19  0.020
 C7O  plan-2  H20  0.020
 C7O  plan-2  F2   0.020
 C7O  plan-2  N3   0.020
 C7O  plan-3  C12  0.020
 C7O  plan-3  C13  0.020
 C7O  plan-3  C14  0.020
 C7O  plan-3  O3   0.020
 C7O  plan-3  H14  0.020
 C7O  plan-3  N3   0.020
 C7O  plan-4  C2   0.020
 C7O  plan-4  C3   0.020
 C7O  plan-4  N1   0.020
 C7O  plan-4  N2   0.020
 C7O  plan-4  S1   0.020
 C7O  plan-4  H10  0.020
 C7O  plan-4  H11  0.020

