# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 12:50:06 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 8-fluoro-5-methyl-3-{[2-(piperidin-1-yl)ethyl]sulfanyl}-5H-[1,2,4]triazino[5,6-b]indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c2ccc(F)cc2c3nnc(SCCN4CCCCC4)nc13
#
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
 CJ7  CJ7  8-fluoro-5-methyl-3-{[2-(piperidin-1-yl)ethyl]sulfanyl}-5H-[1,2,4]triazino[5,6-b]indole  ligand  44  24  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CJ7
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
 CJ7  C5   C  CR16  0  -0.478  -4.3919   1.8401   0.3463
 CJ7  C4   C  CR6   0   0.531  -5.7652   1.7547   0.2741
 CJ7  N4   N  N     0  -0.213  -1.2071   1.0527   0.3268
 CJ7  C3   C  CR16  0  -0.411  -6.4393   0.5602   0.0438
 CJ7  C2   C  CR16  0  -0.288  -5.7319  -0.6203  -0.1225
 CJ7  C1   C  CR56  0   0.375  -4.3490  -0.5583  -0.0501
 CJ7  N2   N  NT    0  -0.420   5.1234   0.1728   0.1814
 CJ7  N3   N  N     0  -0.305  -0.0382   0.4413   0.2617
 CJ7  N1   N  N     0  -0.436  -1.0417  -1.6937  -0.1207
 CJ7  F    F  F     0  -0.316  -6.4920   2.8732   0.4325
 CJ7  C6   C  CR56  0   0.036  -3.6823   0.6583   0.1783
 CJ7  C7   C  CR56  0   0.092  -2.2834   0.3295   0.1746
 CJ7  C8   C  CR56  0   0.531  -2.1923  -1.0736  -0.0534
 CJ7  N    N  NR5   0  -0.612  -3.4273  -1.5921  -0.1797
 CJ7  C9   C  CR6   0   0.228  -0.0038  -0.8697   0.0455
 CJ7  S    S  S2    0   0.067   1.5475  -1.6666  -0.0437
 CJ7  C10  C  CH2   0  -0.561   2.7223  -0.2974   0.1579
 CJ7  C11  C  CH2   0  -0.267   4.1318  -0.8794   0.1002
 CJ7  C12  C  CH2   0  -0.281   6.3998  -0.3156   0.6797
 CJ7  C13  C  CH2   0  -0.435   7.3745   0.8320   0.8987
 CJ7  C14  C  CH2   0  -0.441   7.5701   1.6330  -0.3819
 CJ7  C15  C  CH2   0  -0.434   6.2187   2.0663  -0.9347
 CJ7  C16  C  CH2   0  -0.287   5.2942   0.8677  -1.0852
 CJ7  H1   H  HCR6  0   0.285  -3.8945   2.7839   0.5274
 CJ7  H2   H  HCR6  0   0.291  -7.5200   0.5562  -0.0038
 CJ7  H3   H  HCR6  0   0.291  -6.2577  -1.5478  -0.3045
 CJ7  H5   H  HCH3  0   0.266  -4.1666  -3.0905  -1.4427
 CJ7  H6   H  HCH3  0   0.277  -2.8534  -3.5717  -0.3589
 CJ7  H7   H  HCH3  0   0.265  -4.4796  -3.3330   0.2879
 CJ7  H8   H  HCH2  0   0.280   2.5473   0.4290  -0.6344
 CJ7  H9   H  HCH2  0   0.281   2.5543   0.1895   1.1169
 CJ7  H10  H  HCH2  0   0.210   4.2550  -1.4975  -0.8047
 CJ7  H11  H  HCH2  0   0.249   4.2649  -1.5486   0.9533
 CJ7  H12  H  HCH2  0   0.235   6.2290  -0.8391   1.6234
 CJ7  H13  H  HCH2  0   0.185   6.8497  -1.0474  -0.0151
 CJ7  H14  H  HCH2  0   0.215   6.9828   1.4838   1.6852
 CJ7  H15  H  HCH2  0   0.230   8.3261   0.4337   1.2575
 CJ7  H16  H  HCH2  0   0.231   8.2129   2.4975  -0.2024
 CJ7  H17  H  HCH2  0   0.210   8.0799   1.0097  -1.1245
 CJ7  H18  H  HCH2  0   0.215   5.7570   2.7936  -0.2602
 CJ7  H19  H  HCH2  0   0.230   6.3332   2.5562  -1.9042
 CJ7  H20  H  HCH2  0   0.188   5.7058   0.1878  -1.8534
 CJ7  H21  H  HCH2  0   0.235   4.3212   1.2010  -1.4502
 CJ7  C    C  CH3   0  -0.545  -3.7555  -2.9728  -0.4408

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
 CJ7  F    C4   single    1.343  0.020  1.343
 CJ7  C4   C5   aromatic  1.378  0.020  1.378
 CJ7  C4   C3   aromatic  1.391  0.020  1.391
 CJ7  C5   C6   aromatic  1.389  0.020  1.389
 CJ7  N4   N3   aromatic  1.321  0.020  1.321
 CJ7  N4   C7   aromatic  1.306  0.020  1.306
 CJ7  C3   C2   aromatic  1.386  0.020  1.386
 CJ7  C6   C7   aromatic  1.437  0.020  1.437
 CJ7  C6   C1   aromatic  1.406  0.020  1.406
 CJ7  N3   C9   aromatic  1.329  0.020  1.329
 CJ7  C7   C8   aromatic  1.424  0.020  1.424
 CJ7  C2   C1   aromatic  1.386  0.020  1.386
 CJ7  C1   N    aromatic  1.391  0.020  1.391
 CJ7  C9   N1   aromatic  1.336  0.020  1.336
 CJ7  C9   S    single    1.746  0.020  1.746
 CJ7  C8   N    aromatic  1.345  0.020  1.345
 CJ7  C8   N1   aromatic  1.309  0.020  1.309
 CJ7  N    C    single    1.443  0.020  1.443
 CJ7  S    C10  single    1.815  0.020  1.815
 CJ7  C11  C10  single    1.526  0.020  1.526
 CJ7  C11  N2   single    1.448  0.020  1.448
 CJ7  N2   C12  single    1.455  0.020  1.455
 CJ7  N2   C16  single    1.455  0.020  1.455
 CJ7  C12  C13  single    1.522  0.020  1.522
 CJ7  C16  C15  single    1.521  0.020  1.521
 CJ7  C13  C14  single    1.523  0.020  1.523
 CJ7  C15  C14  single    1.523  0.020  1.523
 CJ7  C5   H1   single    0.930  0.020  1.080
 CJ7  C3   H2   single    0.930  0.020  1.080
 CJ7  C2   H3   single    0.930  0.020  1.080
 CJ7  C    H5   single    0.970  0.020  1.090
 CJ7  C    H6   single    0.970  0.020  1.090
 CJ7  C    H7   single    0.970  0.020  1.090
 CJ7  C10  H8   single    0.970  0.020  1.090
 CJ7  C10  H9   single    0.970  0.020  1.090
 CJ7  C11  H10  single    0.970  0.020  1.090
 CJ7  C11  H11  single    0.970  0.020  1.090
 CJ7  C12  H12  single    0.970  0.020  1.090
 CJ7  C12  H13  single    0.970  0.020  1.090
 CJ7  C13  H14  single    0.970  0.020  1.090
 CJ7  C13  H15  single    0.970  0.020  1.090
 CJ7  C14  H16  single    0.970  0.020  1.090
 CJ7  C14  H17  single    0.970  0.020  1.090
 CJ7  C15  H18  single    0.970  0.020  1.090
 CJ7  C15  H19  single    0.970  0.020  1.090
 CJ7  C16  H20  single    0.970  0.020  1.090
 CJ7  C16  H21  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
 CJ7  H1   C5   C6   121.84  3.000
 CJ7  H1   C5   C4   121.40  3.000
 CJ7  C6   C5   C4   116.76  3.000
 CJ7  F    C4   C3   118.19  3.000
 CJ7  C3   C4   C5   123.02  3.000
 CJ7  F    C4   C5   118.78  3.000
 CJ7  C7   N4   N3   117.86  3.000
 CJ7  H2   C3   C2   120.09  3.000
 CJ7  H2   C3   C4   119.65  3.000
 CJ7  C2   C3   C4   120.27  3.000
 CJ7  H3   C2   C1   122.15  3.000
 CJ7  H3   C2   C3   120.16  3.000
 CJ7  C1   C2   C3   117.69  3.000
 CJ7  N    C1   C6   110.12  3.000
 CJ7  N    C1   C2   128.52  3.000
 CJ7  C6   C1   C2   121.36  3.000
 CJ7  C16  N2   C12  110.83  3.000
 CJ7  C16  N2   C11  112.25  3.000
 CJ7  C12  N2   C11  112.09  3.000
 CJ7  C9   N3   N4   119.18  3.000
 CJ7  C9   N1   C8   112.61  3.000
 CJ7  C7   C6   C1   105.26  3.000
 CJ7  C1   C6   C5   120.91  3.000
 CJ7  C7   C6   C5   133.83  3.000
 CJ7  C8   C7   C6   106.74  3.000
 CJ7  C8   C7   N4   120.77  3.000
 CJ7  C6   C7   N4   132.49  3.000
 CJ7  N    C8   C7   109.63  3.000
 CJ7  N    C8   N1   128.28  3.000
 CJ7  C7   C8   N1   122.09  3.000
 CJ7  C8   N    C    126.48  3.000
 CJ7  C    N    C1   125.26  3.000
 CJ7  C8   N    C1   108.24  3.000
 CJ7  S    C9   N1   113.73  3.000
 CJ7  S    C9   N3   118.78  3.000
 CJ7  N1   C9   N3   127.49  3.000
 CJ7  C10  S    C9   103.01  3.000
 CJ7  H9   C10  H8   108.52  3.000
 CJ7  H9   C10  C11  110.28  3.000
 CJ7  H8   C10  C11  112.05  3.000
 CJ7  H9   C10  S    109.59  3.000
 CJ7  H8   C10  S    108.56  3.000
 CJ7  C11  C10  S    107.81  3.000
 CJ7  H11  C11  H10  106.49  3.000
 CJ7  H11  C11  C10  108.46  3.000
 CJ7  H10  C11  C10  110.37  3.000
 CJ7  H11  C11  N2   108.53  3.000
 CJ7  H10  C11  N2   112.14  3.000
 CJ7  C10  C11  N2   110.68  3.000
 CJ7  H13  C12  H12  106.82  3.000
 CJ7  H13  C12  C13  109.22  3.000
 CJ7  H12  C12  C13  109.71  3.000
 CJ7  H13  C12  N2   111.37  3.000
 CJ7  H12  C12  N2   108.64  3.000
 CJ7  C13  C12  N2   110.99  3.000
 CJ7  H15  C13  H14  107.04  3.000
 CJ7  H15  C13  C14  110.86  3.000
 CJ7  H14  C13  C14  109.70  3.000
 CJ7  H15  C13  C12  109.29  3.000
 CJ7  H14  C13  C12  108.87  3.000
 CJ7  C14  C13  C12  110.97  3.000
 CJ7  H17  C14  H16  106.74  3.000
 CJ7  H17  C14  C15  109.20  3.000
 CJ7  H16  C14  C15  110.90  3.000
 CJ7  H17  C14  C13  109.30  3.000
 CJ7  H16  C14  C13  110.71  3.000
 CJ7  C15  C14  C13  109.92  3.000
 CJ7  H19  C15  H18  107.06  3.000
 CJ7  H19  C15  C16  109.22  3.000
 CJ7  H18  C15  C16  109.16  3.000
 CJ7  H19  C15  C14  110.90  3.000
 CJ7  H18  C15  C14  109.87  3.000
 CJ7  C16  C15  C14  110.55  3.000
 CJ7  H21  C16  H20  106.70  3.000
 CJ7  H21  C16  C15  109.53  3.000
 CJ7  H20  C16  C15  109.09  3.000
 CJ7  H21  C16  N2   109.41  3.000
 CJ7  H20  C16  N2   110.80  3.000
 CJ7  C15  C16  N2   111.20  3.000
 CJ7  H7   C    H6   108.64  3.000
 CJ7  H7   C    H5   109.20  3.000
 CJ7  H6   C    H5   108.86  3.000
 CJ7  H7   C    N    110.29  3.000
 CJ7  H6   C    N    108.98  3.000
 CJ7  H5   C    N    110.83  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
 CJ7  CONST_01  C2   C3   C4   C5     0.00   0.0  0
 CJ7  CONST_02  N4   C7   C6   C5     0.00   0.0  0
 CJ7  CONST_03  C8   C7   C6   C5   180.00   0.0  0
 CJ7  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 CJ7  CONST_05  N    C1   C6   C5   180.00   0.0  0
 CJ7  CONST_06  C7   C6   C5   C4   180.00   0.0  0
 CJ7  CONST_07  C1   C6   C5   C4     0.00   0.0  0
 CJ7  CONST_08  C1   C2   C3   C4     0.00   0.0  0
 CJ7  CONST_09  N1   C9   N3   N4     0.00   0.0  0
 CJ7  CONST_10  C1   C6   C7   N4   180.00   0.0  0
 CJ7  CONST_11  N    C8   C7   N4   180.00   0.0  0
 CJ7  CONST_12  N1   C8   C7   N4     0.00   0.0  0
 CJ7  CONST_13  C6   C5   C4   C3     0.00   0.0  0
 CJ7  CONST_14  C6   C1   C2   C3     0.00   0.0  0
 CJ7  CONST_15  N    C1   C2   C3   180.00   0.0  0
 CJ7  CONST_16  C7   C6   C1   C2   180.00   0.0  0
 CJ7  CONST_17  C8   N    C1   C2   180.00   0.0  0
 CJ7  CONST_18  C8   C7   C6   C1     0.00   0.0  0
 CJ7  CONST_19  C7   C8   N    C1     0.00   0.0  0
 CJ7  CONST_20  N1   C8   N    C1   180.00   0.0  0
 CJ7  CONST_21  C6   C7   N4   N3   180.00   0.0  0
 CJ7  CONST_22  C8   C7   N4   N3     0.00   0.0  0
 CJ7  CONST_23  C8   N1   C9   N3     0.00   0.0  0
 CJ7  CONST_24  C6   C7   C8   N1   180.00   0.0  0
 CJ7  CONST_25  N    C8   C7   C6     0.00   0.0  0
 CJ7  CONST_26  C8   N    C1   C6     0.00   0.0  0
 CJ7  CONST_27  C9   N3   N4   C7     0.00   0.0  0
 CJ7  CONST_28  N    C1   C6   C7     0.00   0.0  0
 CJ7  CONST_29  C9   N1   C8   C7     0.00   0.0  0
 CJ7  CONST_30  C9   N1   C8   N    180.00   0.0  0
 CJ7  CONST_31  S    C9   N3   N4   180.00   0.0  0
 CJ7  CONST_32  F    C4   C3   C2   180.00   0.0  0
 CJ7  CONST_33  C    N    C1   C2     0.00   0.0  0
 CJ7  CONST_34  C6   C1   N    C    180.00   0.0  0
 CJ7  CONST_35  C7   C8   N    C    180.00   0.0  0
 CJ7  CONST_36  N1   C8   N    C      0.00   0.0  0
 CJ7  CONST_37  C6   C5   C4   F    180.00   0.0  0
 CJ7  CONST_38  S    C9   N1   C8   180.00   0.0  0
 CJ7  CONST_39  H2   C3   C4   C5   180.00   0.0  0
 CJ7  CONST_40  H3   C2   C3   C4   180.00   0.0  0
 CJ7  CONST_41  H1   C5   C4   C3   180.00   0.0  0
 CJ7  Var_01    C14  C13  C12  N2   -56.59  30.0  1
 CJ7  Var_02    C14  C15  C16  N2    57.07  30.0  1
 CJ7  Var_03    C15  C16  N2   C12  -60.34  30.0  1
 CJ7  Var_04    C15  C14  C13  C12   53.02  30.0  1
 CJ7  Var_05    C16  N2   C12  C13   59.91  30.0  1
 CJ7  Var_06    C16  C15  C14  C13  -53.08  30.0  1
 CJ7  Var_07    C12  N2   C11  C10  156.13  30.0  3
 CJ7  Var_08    H5   C    N    C1    67.71  30.0  2
 CJ7  Var_09    S    C10  C11  N2   176.86  30.0  3
 CJ7  Var_10    C11  C10  S    C9   179.85  30.0  3

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
 CJ7  plan-1  C5  0.020
 CJ7  plan-1  C4  0.020
 CJ7  plan-1  N4  0.020
 CJ7  plan-1  C3  0.020
 CJ7  plan-1  C2  0.020
 CJ7  plan-1  C1  0.020
 CJ7  plan-1  N3  0.020
 CJ7  plan-1  N1  0.020
 CJ7  plan-1  F   0.020
 CJ7  plan-1  C6  0.020
 CJ7  plan-1  C7  0.020
 CJ7  plan-1  C8  0.020
 CJ7  plan-1  N   0.020
 CJ7  plan-1  C9  0.020
 CJ7  plan-1  S   0.020
 CJ7  plan-1  H1  0.020
 CJ7  plan-1  H2  0.020
 CJ7  plan-1  H3  0.020
 CJ7  plan-1  C   0.020

