# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:55:12 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: 5-[[(2~{S})-2-methyl-1,4-diazepan-1-yl]sulfonyl]isoquinoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CNCCCN1[S](=O)(=O)c2cccc3cnccc23
#
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
 9K6  9K6  5-[[(2~{S})-2-methyl-1,4-diazepan-1-yl]sulfonyl]isoquinoline  ligand  40  21  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9K6
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
 9K6  C6   C  CR6   0  -0.275  -0.5121  -1.1293   0.3277
 9K6  C4   C  CH2   0  -0.407   1.7132   2.6096   0.5166
 9K6  C2   C  CH2   0  -0.249   1.2369   0.4159  -1.9348
 9K6  C8   C  CR66  0  -0.028  -2.6103  -0.3762  -0.6249
 9K6  C10  C  CR16  0  -0.080  -2.5827   1.9658   0.7458
 9K6  C13  C  CR16  0  -0.250  -1.7541  -2.5528  -1.1864
 9K6  C1   C  CH3   0  -0.661   2.7350  -1.5267  -1.3403
 9K6  S    S  S     0   1.404   0.9773  -0.9154   1.2885
 9K6  O    O  OS    0  -0.647   1.5892  -2.2347   1.3720
 9K6  N    N  N     0  -0.581   1.9490   0.0942   0.4480
 9K6  C5   C  CH2   0  -0.315   2.4219   1.3596   1.0198
 9K6  C3   C  CH2   0  -0.317   1.4801   2.6727  -0.9904
 9K6  N1   N  NH1   0  -0.574   0.5999   1.6080  -1.4364
 9K6  C    C  CH1   0  -0.116   2.2965  -0.1188  -0.9644
 9K6  C14  C  CR16  0  -0.248  -0.6534  -2.3180  -0.3438
 9K6  C12  C  CR16  0  -0.287  -2.7088  -1.5889  -1.3382
 9K6  C9   C  CR16  0  -0.083  -3.6173   0.6118  -0.7459
 9K6  N2   N  N     0  -0.405  -3.6157   1.7401  -0.0955
 9K6  C11  C  CR16  0  -0.373  -1.5432   1.1020   0.9369
 9K6  C7   C  CR66  0   0.324  -1.5141  -0.1231   0.2354
 9K6  H2   H  HCH2  0   0.228   2.3162   3.4676   0.8280
 9K6  H3   H  HCH2  0   0.222   0.4624  -0.3369  -2.1076
 9K6  H4   H  HCH2  0   0.207   1.7548   0.5544  -2.8980
 9K6  H5   H  HCR6  0   0.268  -2.6088   2.9033   1.2882
 9K6  H6   H  HCR6  0   0.278  -1.8280  -3.4960  -1.7095
 9K6  H7   H  HCH3  0   0.240   3.1162  -1.4980  -2.3614
 9K6  H8   H  HCH3  0   0.245   3.5370  -1.8794  -0.6948
 9K6  H9   H  HCH3  0   0.228   1.9264  -2.2537  -1.3187
 9K6  H10  H  HCH2  0   0.251   3.4848   1.4156   0.7708
 9K6  H11  H  HCH2  0   0.269   2.3701   1.3157   2.1046
 9K6  H12  H  HCH2  0   0.242   1.0024   3.6280  -1.2139
 9K6  H13  H  HCH2  0   0.200   2.4389   2.6861  -1.5310
 9K6  H14  H  HNH1  0   0.353  -0.0682   1.9486  -2.1103
 9K6  H16  H  HCH1  0   0.262   3.1853   0.5040  -1.0884
 9K6  H17  H  HCR6  0   0.296   0.0912  -3.0946  -0.2434
 9K6  H18  H  HCR6  0   0.274  -3.5565  -1.7488  -1.9931
 9K6  H19  H  HCR6  0   0.272  -4.4501   0.4220  -1.4173
 9K6  H20  H  HCR6  0   0.265  -0.7683   1.3680   1.6353
 9K6  H1   H  HCH2  0   0.224   0.7458   2.7154   1.0095
 9K6  O1   O  OS    0  -0.658   0.6468  -0.2608   2.5489

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
 9K6  N2   C9   aromatic  1.302  0.020  1.302
 9K6  N2   C10  aromatic  1.351  0.020  1.351
 9K6  C9   C8   aromatic  1.416  0.020  1.416
 9K6  C10  C11  aromatic  1.365  0.020  1.365
 9K6  C8   C12  aromatic  1.410  0.020  1.410
 9K6  C8   C7   aromatic  1.416  0.020  1.416
 9K6  C12  C13  aromatic  1.365  0.020  1.365
 9K6  C11  C7   aromatic  1.412  0.020  1.412
 9K6  C7   C6   aromatic  1.423  0.020  1.423
 9K6  C13  C14  aromatic  1.406  0.020  1.406
 9K6  C1   C    single    1.522  0.020  1.522
 9K6  C6   C14  aromatic  1.373  0.020  1.373
 9K6  C6   S    single    1.785  0.020  1.785
 9K6  O    S    double    1.457  0.020  1.457
 9K6  C    C2   single    1.533  0.020  1.533
 9K6  C    N    single    1.470  0.020  1.470
 9K6  S    N    single    1.634  0.020  1.634
 9K6  S    O1   double    1.458  0.020  1.458
 9K6  C2   N1   single    1.441  0.020  1.441
 9K6  N    C5   single    1.467  0.020  1.467
 9K6  N1   C3   single    1.452  0.020  1.452
 9K6  C5   C4   single    1.522  0.020  1.522
 9K6  C3   C4   single    1.526  0.020  1.526
 9K6  C4   H1   single    0.970  0.020  1.090
 9K6  C4   H2   single    0.970  0.020  1.090
 9K6  C2   H3   single    0.970  0.020  1.090
 9K6  C2   H4   single    0.970  0.020  1.090
 9K6  C10  H5   single    0.930  0.020  1.080
 9K6  C13  H6   single    0.930  0.020  1.080
 9K6  C1   H7   single    0.970  0.020  1.090
 9K6  C1   H8   single    0.970  0.020  1.090
 9K6  C1   H9   single    0.970  0.020  1.090
 9K6  C5   H10  single    0.970  0.020  1.090
 9K6  C5   H11  single    0.970  0.020  1.090
 9K6  C3   H12  single    0.970  0.020  1.090
 9K6  C3   H13  single    0.970  0.020  1.090
 9K6  N1   H14  single    0.890  0.020  1.040
 9K6  C    H16  single    0.970  0.020  1.090
 9K6  C14  H17  single    0.930  0.020  1.080
 9K6  C12  H18  single    0.930  0.020  1.080
 9K6  C9   H19  single    0.930  0.020  1.080
 9K6  C11  H20  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
 9K6  C7   C6   C14  120.54  3.000
 9K6  C14  C6   S    116.93  3.000
 9K6  C7   C6   S    122.52  3.000
 9K6  H2   C4   H1   106.50  3.000
 9K6  H2   C4   C3   109.44  3.000
 9K6  H1   C4   C3   107.86  3.000
 9K6  H2   C4   C5   107.06  3.000
 9K6  H1   C4   C5   110.07  3.000
 9K6  C3   C4   C5   115.56  3.000
 9K6  H4   C2   H3   106.33  3.000
 9K6  H4   C2   C    105.79  3.000
 9K6  H3   C2   C    110.45  3.000
 9K6  H4   C2   N1   113.96  3.000
 9K6  H3   C2   N1   108.12  3.000
 9K6  C    C2   N1   112.04  3.000
 9K6  C7   C8   C9   118.53  3.000
 9K6  C7   C8   C12  120.99  3.000
 9K6  C9   C8   C12  120.47  3.000
 9K6  H5   C10  C11  119.72  3.000
 9K6  H5   C10  N2   115.97  3.000
 9K6  C11  C10  N2   124.31  3.000
 9K6  H6   C13  C12  120.96  3.000
 9K6  H6   C13  C14  119.29  3.000
 9K6  C12  C13  C14  119.75  3.000
 9K6  H9   C1   H8   108.63  3.000
 9K6  H9   C1   H7   107.23  3.000
 9K6  H8   C1   H7   107.84  3.000
 9K6  H9   C1   C    113.53  3.000
 9K6  H8   C1   C    111.45  3.000
 9K6  H7   C1   C    107.93  3.000
 9K6  N    S    O    109.83  3.000
 9K6  N    S    O1   107.58  3.000
 9K6  O    S    O1   116.88  3.000
 9K6  O1   S    C6   109.26  3.000
 9K6  N    S    C6   107.06  3.000
 9K6  O    S    C6   105.83  3.000
 9K6  C    N    C5   115.05  3.000
 9K6  C5   N    S    121.62  3.000
 9K6  C    N    S    123.04  3.000
 9K6  H11  C5   H10  106.01  3.000
 9K6  H11  C5   N    109.80  3.000
 9K6  H10  C5   N    105.60  3.000
 9K6  H11  C5   C4   109.93  3.000
 9K6  H10  C5   C4   109.59  3.000
 9K6  N    C5   C4   115.43  3.000
 9K6  H13  C3   H12  105.67  3.000
 9K6  H13  C3   N1   112.72  3.000
 9K6  H12  C3   N1   108.29  3.000
 9K6  H13  C3   C4   110.63  3.000
 9K6  H12  C3   C4   107.78  3.000
 9K6  N1   C3   C4   111.44  3.000
 9K6  H14  N1   C3   111.06  3.000
 9K6  H14  N1   C2   109.96  3.000
 9K6  C3   N1   C2   116.43  3.000
 9K6  H16  C    N    102.63  3.000
 9K6  H16  C    C1   105.37  3.000
 9K6  N    C    C1   116.08  3.000
 9K6  H16  C    C2   106.96  3.000
 9K6  N    C    C2   113.22  3.000
 9K6  C1   C    C2   111.44  3.000
 9K6  H17  C14  C13  118.37  3.000
 9K6  H17  C14  C6   120.40  3.000
 9K6  C13  C14  C6   121.23  3.000
 9K6  H18  C12  C13  120.68  3.000
 9K6  H18  C12  C8   119.17  3.000
 9K6  C13  C12  C8   120.14  3.000
 9K6  H19  C9   N2   117.45  3.000
 9K6  H19  C9   C8   118.43  3.000
 9K6  N2   C9   C8   124.12  3.000
 9K6  C9   N2   C10  117.17  3.000
 9K6  H20  C11  C7   121.46  3.000
 9K6  H20  C11  C10  118.86  3.000
 9K6  C7   C11  C10  119.68  3.000
 9K6  C11  C7   C8   116.16  3.000
 9K6  C11  C7   C6   126.57  3.000
 9K6  C8   C7   C6   117.26  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
 9K6  CONST_01  C9   C8   C7   C6   180.00   0.0  0
 9K6  CONST_02  C12  C8   C7   C6     0.00   0.0  0
 9K6  CONST_03  C10  C11  C7   C6   180.00   0.0  0
 9K6  CONST_04  C12  C13  C14  C6     0.00   0.0  0
 9K6  CONST_05  C10  N2   C9   C8     0.00   0.0  0
 9K6  CONST_06  C14  C13  C12  C8     0.00   0.0  0
 9K6  CONST_07  C10  C11  C7   C8     0.00   0.0  0
 9K6  CONST_08  C14  C6   C7   C8     0.00   0.0  0
 9K6  CONST_09  C9   C8   C12  C13  180.00   0.0  0
 9K6  CONST_10  C7   C8   C12  C13    0.00   0.0  0
 9K6  CONST_11  C7   C6   C14  C13    0.00   0.0  0
 9K6  CONST_12  C11  C7   C6   C14  180.00   0.0  0
 9K6  CONST_13  N2   C9   C8   C12  180.00   0.0  0
 9K6  CONST_14  C11  C7   C8   C12  180.00   0.0  0
 9K6  CONST_15  C11  C10  N2   C9     0.00   0.0  0
 9K6  CONST_16  C11  C7   C8   C9     0.00   0.0  0
 9K6  CONST_17  C7   C8   C9   N2     0.00   0.0  0
 9K6  CONST_18  C7   C11  C10  N2     0.00   0.0  0
 9K6  CONST_19  S    C6   C7   C8   180.00   0.0  0
 9K6  CONST_20  S    C6   C14  C13  180.00   0.0  0
 9K6  CONST_21  C11  C7   C6   S      0.00   0.0  0
 9K6  CONST_22  H20  C11  C7   C6     0.00   0.0  0
 9K6  CONST_23  H6   C13  C14  C6   180.00   0.0  0
 9K6  CONST_24  H19  C9   N2   C10  180.00   0.0  0
 9K6  CONST_25  H18  C12  C13  C14  180.00   0.0  0
 9K6  CONST_26  H17  C14  C13  C12  180.00   0.0  0
 9K6  CONST_27  H5   C10  N2   C9   180.00   0.0  0
 9K6  Var_01    C7   C6   S    N    -74.96  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
 9K6  chir_01  C  C1  C2  N  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
 9K6  plan-1  C6   0.020
 9K6  plan-1  C8   0.020
 9K6  plan-1  C10  0.020
 9K6  plan-1  C13  0.020
 9K6  plan-1  S    0.020
 9K6  plan-1  C14  0.020
 9K6  plan-1  C12  0.020
 9K6  plan-1  C9   0.020
 9K6  plan-1  N2   0.020
 9K6  plan-1  C11  0.020
 9K6  plan-1  C7   0.020
 9K6  plan-1  H5   0.020
 9K6  plan-1  H6   0.020
 9K6  plan-1  H17  0.020
 9K6  plan-1  H18  0.020
 9K6  plan-1  H19  0.020
 9K6  plan-1  H20  0.020

