# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 07:59:27 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 6-bromo-13-thia-2,4,8,12,19-pentaazatricyclo[12.3.1.1~3,7~]nonadeca-1(18),3(19),4,6,14,16-hexaene 13,13-dioxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cnc2Nc3cccc(c3)[S](=O)(=O)NCCCNc1n2
#
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
 PY8  PY8  '6-bromo-13-thia-2,4,8,12,19-pentaazatricyclo[12.3.1.1~3,7~]nonadeca-1(18),3(19),4,6,14,16-hexaene 13,13-dioxide'  ligand  36  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PY8
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
 PY8  BR1   BR  BR    0   0.012   5.3039   3.7120  -5.2248
 PY8  C1    C   CR6   0  -0.305   4.0609   2.6350  -4.3151
 PY8  C2    C   CR16  0   0.003   2.7501   3.0333  -4.1783
 PY8  N3    N   N     0  -0.447   1.8291   2.3208  -3.5389
 PY8  C4    C   CR6   0   0.569   2.2590   1.1651  -3.0328
 PY8  N5    N   N     0  -0.481   3.4767   0.6714  -3.1434
 PY8  C6    C   CR6   0   0.627   4.4148   1.3798  -3.7670
 PY8  N7    N   NH1   0  -0.666   5.6353   0.8409  -3.8384
 PY8  C8    C   CH2   0  -0.271   5.9223  -0.5106  -3.3951
 PY8  C9    C   CH2   0  -0.405   6.0521  -0.6608  -1.8822
 PY8  C10   C   CH2   0  -0.256   6.2796  -2.1078  -1.4601
 PY8  N13   N   NC1   0  -0.728   5.1931  -3.0165  -1.8063
 PY8  S14   S   S     0   1.330   4.1180  -3.6493  -0.7690
 PY8  O14   O   OS    0  -0.495   4.7129  -3.7188   0.5583
 PY8  O15   O   OS    0  -0.705   3.6032  -4.8641  -1.3840
 PY8  C15   C   CR6   0  -0.181   2.7512  -2.5153  -0.6433
 PY8  C20   C   CR16  0  -0.275   2.6008  -1.5138  -1.5841
 PY8  C16   C   CR16  0  -0.307   1.8406  -2.7130   0.3859
 PY8  C17   C   CR16  0  -0.233   0.7445  -1.8659   0.4490
 PY8  C18   C   CR16  0  -0.304   0.5894  -0.8334  -0.4610
 PY8  C19   C   CR6   0   0.386   1.5261  -0.6267  -1.4772
 PY8  N21   N   NH1   0  -0.702   1.3274   0.4521  -2.3315
 PY8  H2    H   HCR6  0   0.305   2.4214   3.9767  -4.6012
 PY8  H21   H   HNH1  0   0.422   0.4423   0.9275  -2.2364
 PY8  H7    H   HNH1  0   0.382   6.3669   1.3392  -4.3164
 PY8  H8C1  H   HCH2  0   0.200   6.8567  -0.8042  -3.8741
 PY8  H8C2  H   HCH2  0   0.210   5.1479  -1.1782  -3.7809
 PY8  H9C1  H   HCH2  0   0.226   6.9053  -0.0738  -1.5332
 PY8  H9C2  H   HCH2  0   0.202   5.1657  -0.2671  -1.3828
 PY8  H101  H   HCH2  0   0.186   7.1855  -2.5000  -1.9259
 PY8  H102  H   HCH2  0   0.248   6.4435  -2.1544  -0.3847
 PY8  H13   H   HNC1  0   0.411   5.1519  -3.3963  -2.7416
 PY8  H20   H   HCR6  0   0.231   3.3210  -1.4038  -2.3757
 PY8  H16   H   HCR6  0   0.276   1.9717  -3.4961   1.1202
 PY8  H17   H   HCR6  0   0.264   0.0093  -1.9962   1.2317
 PY8  H18   H   HCR6  0   0.272  -0.2594  -0.1660  -0.3719

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
 PY8  BR1  C1    single    1.880  0.020  1.880
 PY8  C1   C2    aromatic  1.377  0.020  1.377
 PY8  C1   C6    single    1.415  0.020  1.415
 PY8  C2   N3    aromatic  1.328  0.020  1.328
 PY8  C2   H2    single    0.930  0.020  1.080
 PY8  N3   C4    single    1.333  0.020  1.333
 PY8  C4   N5    aromatic  1.319  0.020  1.319
 PY8  C4   N21   single    1.367  0.020  1.367
 PY8  N5   C6    aromatic  1.331  0.020  1.331
 PY8  C6   N7    single    1.336  0.020  1.336
 PY8  N7   C8    single    1.451  0.020  1.451
 PY8  N7   H7    single    0.860  0.020  1.020
 PY8  C8   C9    single    1.526  0.020  1.526
 PY8  C8   H8C1  single    0.970  0.020  1.090
 PY8  C8   H8C2  single    0.970  0.020  1.090
 PY8  C9   C10   single    1.524  0.020  1.524
 PY8  C9   H9C1  single    0.970  0.020  1.090
 PY8  C9   H9C2  single    0.970  0.020  1.090
 PY8  C10  N13   single    1.458  0.020  1.458
 PY8  C10  H101  single    0.970  0.020  1.090
 PY8  C10  H102  single    0.970  0.020  1.090
 PY8  N13  S14   single    1.622  0.020  1.622
 PY8  N13  H13   single    0.860  0.020  1.020
 PY8  S14  O14   double    1.456  0.020  1.456
 PY8  S14  O15   double    1.456  0.020  1.456
 PY8  S14  C15   single    1.780  0.020  1.780
 PY8  C15  C20   aromatic  1.382  0.020  1.382
 PY8  C15  C16   single    1.388  0.020  1.388
 PY8  C20  C19   aromatic  1.398  0.020  1.398
 PY8  C20  H20   single    0.930  0.020  1.080
 PY8  C16  C17   aromatic  1.387  0.020  1.387
 PY8  C16  H16   single    0.930  0.020  1.080
 PY8  C17  C18   aromatic  1.385  0.020  1.385
 PY8  C17  H17   single    0.930  0.020  1.080
 PY8  C18  C19   single    1.397  0.020  1.397
 PY8  C18  H18   single    0.930  0.020  1.080
 PY8  C19  N21   single    1.390  0.020  1.390
 PY8  N21  H21   single    0.860  0.020  1.020

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
 PY8  C6    C1   C2    117.16  3.000
 PY8  C6    C1   BR1   122.04  3.000
 PY8  C2    C1   BR1   120.79  3.000
 PY8  H2    C2   N3    116.36  3.000
 PY8  H2    C2   C1    120.09  3.000
 PY8  N3    C2   C1    123.55  3.000
 PY8  C4    N3   C2    115.10  3.000
 PY8  N21   C4   N5    118.50  3.000
 PY8  N21   C4   N3    115.30  3.000
 PY8  N5    C4   N3    126.20  3.000
 PY8  C6    N5   C4    119.41  3.000
 PY8  N7    C6   N5    117.02  3.000
 PY8  N7    C6   C1    124.45  3.000
 PY8  N5    C6   C1    118.53  3.000
 PY8  H7    N7   C8    117.56  3.000
 PY8  H7    N7   C6    119.33  3.000
 PY8  C8    N7   C6    122.69  3.000
 PY8  H8C2  C8   H8C1  106.72  3.000
 PY8  H8C2  C8   C9    110.50  3.000
 PY8  H8C1  C8   C9    109.65  3.000
 PY8  H8C2  C8   N7    108.72  3.000
 PY8  H8C1  C8   N7    106.62  3.000
 PY8  C9    C8   N7    114.29  3.000
 PY8  H9C2  C9   H9C1  107.12  3.000
 PY8  H9C2  C9   C10   109.70  3.000
 PY8  H9C1  C9   C10   107.75  3.000
 PY8  H9C2  C9   C8    110.45  3.000
 PY8  H9C1  C9   C8    109.28  3.000
 PY8  C10   C9   C8    112.37  3.000
 PY8  H102  C10  H101  106.33  3.000
 PY8  H102  C10  N13   108.67  3.000
 PY8  H101  C10  N13   107.05  3.000
 PY8  H102  C10  C9    109.66  3.000
 PY8  H101  C10  C9    110.29  3.000
 PY8  N13   C10  C9    114.49  3.000
 PY8  H13   N13  S14   114.73  3.000
 PY8  H13   N13  C10   118.97  3.000
 PY8  S14   N13  C10   125.81  3.000
 PY8  C15   S14  O15   106.85  3.000
 PY8  C15   S14  O14   106.24  3.000
 PY8  O15   S14  O14   119.32  3.000
 PY8  C15   S14  N13   107.79  3.000
 PY8  O15   S14  N13   106.84  3.000
 PY8  O14   S14  N13   109.31  3.000
 PY8  C16   C15  C20   122.44  3.000
 PY8  C16   C15  S14   117.72  3.000
 PY8  C20   C15  S14   119.79  3.000
 PY8  H20   C20  C19   120.41  3.000
 PY8  H20   C20  C15   120.14  3.000
 PY8  C19   C20  C15   119.44  3.000
 PY8  H16   C16  C17   120.48  3.000
 PY8  H16   C16  C15   121.80  3.000
 PY8  C17   C16  C15   117.72  3.000
 PY8  H17   C17  C18   119.28  3.000
 PY8  H17   C17  C16   119.78  3.000
 PY8  C18   C17  C16   120.93  3.000
 PY8  H18   C18  C19   119.59  3.000
 PY8  H18   C18  C17   119.54  3.000
 PY8  C19   C18  C17   120.86  3.000
 PY8  N21   C19  C18   117.76  3.000
 PY8  N21   C19  C20   123.74  3.000
 PY8  C18   C19  C20   118.50  3.000
 PY8  H21   N21  C19   115.66  3.000
 PY8  H21   N21  C4    113.60  3.000
 PY8  C19   N21  C4    128.51  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
 PY8  CONST_01  C4   N3   C2   C1      0.00   0.0  0
 PY8  CONST_02  C4   N5   C6   C1      0.00   0.0  0
 PY8  CONST_03  N5   C6   C1   C2      0.00   0.0  0
 PY8  CONST_04  N5   C4   N3   C2      0.00   0.0  0
 PY8  CONST_05  C6   C1   C2   N3      0.00   0.0  0
 PY8  CONST_06  C6   N5   C4   N3      0.00   0.0  0
 PY8  CONST_07  C18  C19  C20  C15     0.00   0.0  0
 PY8  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 PY8  CONST_09  C17  C16  C15  C20     0.00   0.0  0
 PY8  CONST_10  C17  C18  C19  C20     0.00   0.0  0
 PY8  CONST_11  C19  C20  C15  C16     0.00   0.0  0
 PY8  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 PY8  CONST_13  C8   N7   C6   C1    180.00   0.0  0
 PY8  CONST_14  C8   N7   C6   N5      0.00   0.0  0
 PY8  CONST_15  N3   C2   C1   BR1   180.00   0.0  0
 PY8  CONST_16  N5   C6   C1   BR1   180.00   0.0  0
 PY8  CONST_17  N7   C6   C1   BR1     0.00   0.0  0
 PY8  CONST_18  H2   C2   N3   C4    180.00   0.0  0
 PY8  CONST_19  H20  C20  C15  S14     0.00   0.0  0
 PY8  CONST_20  H16  C16  C15  S14     0.00   0.0  0
 PY8  CONST_21  H17  C17  C16  C15   180.00   0.0  0
 PY8  CONST_22  H18  C18  C19  C20   180.00   0.0  0
 PY8  CONST_23  H7   N7   C6   C1      0.00   0.0  0
 PY8  Var_01    C19  N21  C4   N3   -165.88  30.0  1
 PY8  Var_02    C20  C19  N21  C4    -27.34  30.0  1
 PY8  Var_03    C9   C8   N7   C6    -78.13  30.0  1
 PY8  Var_04    C10  C9   C8   N7    176.96  30.0  1
 PY8  Var_05    N13  C10  C9   C8    -61.98  30.0  1
 PY8  Var_06    S14  N13  C10  C9   -106.19  30.0  1
 PY8  Var_07    C15  S14  N13  C10    88.49  30.0  1
 PY8  Var_08    C20  C15  S14  N13    15.20  30.0  1

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
 PY8  plan-1  BR1  0.020
 PY8  plan-1  C1   0.020
 PY8  plan-1  C2   0.020
 PY8  plan-1  N3   0.020
 PY8  plan-1  C4   0.020
 PY8  plan-1  N5   0.020
 PY8  plan-1  C6   0.020
 PY8  plan-1  N7   0.020
 PY8  plan-1  N21  0.020
 PY8  plan-1  H2   0.020
 PY8  plan-2  S14  0.020
 PY8  plan-2  C15  0.020
 PY8  plan-2  C20  0.020
 PY8  plan-2  C16  0.020
 PY8  plan-2  C17  0.020
 PY8  plan-2  C18  0.020
 PY8  plan-2  C19  0.020
 PY8  plan-2  N21  0.020
 PY8  plan-2  H20  0.020
 PY8  plan-2  H16  0.020
 PY8  plan-2  H17  0.020
 PY8  plan-2  H18  0.020
 PY8  plan-3  C6   0.020
 PY8  plan-3  N7   0.020
 PY8  plan-3  C8   0.020
 PY8  plan-3  H7   0.020

