# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:15:06 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 5-[[(2~{R})-2-methyl-1,4-diazepan-4-ium-1-yl]sulfonyl]isoquinoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[NH2+]CCCN1[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
 7K7  7K7  5-[[(2~{R})-2-methyl-1,4-diazepan-4-ium-1-yl]sulfonyl]isoquinoline  ligand  41  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7K7
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
 7K7  C2   C  CH2   0  -0.327   4.3840   0.5724  -0.1093
 7K7  O1   O  OS    0  -0.636   0.4232   0.7735  -2.1793
 7K7  C9   C  CR16  0  -0.275  -3.4266  -1.7300   0.3559
 7K7  C10  C  CR16  0  -0.253  -2.4664  -2.6000  -0.0747
 7K7  C4   C  CH1   0  -0.146   1.4830  -0.2745   1.3622
 7K7  C3   C  CH2   0  -0.304   2.9652  -0.4762   1.6717
 7K7  C8   C  CR66  0  -0.021  -3.1858  -0.3393   0.3489
 7K7  C7   C  CR66  0   0.303  -1.9507   0.1818  -0.1060
 7K7  C6   C  CR6   0  -0.256  -0.9734  -0.7596  -0.5347
 7K7  C5   C  CH3   0  -0.634   0.7900   0.3236   2.5757
 7K7  O    O  OS    0  -0.645   1.3799  -1.4214  -1.4640
 7K7  N    N  N     0  -0.585   1.2563   0.5399   0.1671
 7K7  N1   N  NT2   1  -0.664   3.8070  -0.6850   0.4598
 7K7  C1   C  CH2   0  -0.468   3.3709   1.4383  -0.8290
 7K7  C    C  CH2   0  -0.344   2.0825   1.7252  -0.0660
 7K7  C11  C  CR16  0  -0.230  -1.2273  -2.1070  -0.5213
 7K7  C12  C  CR16  0  -0.074  -4.1729   0.5689   0.7982
 7K7  N2   N  N     0  -0.400  -4.0174   1.8628   0.8210
 7K7  C13  C  CR16  0  -0.066  -2.8401   2.3552   0.3823
 7K7  C14  C  CR16  0  -0.386  -1.8070   1.5866  -0.0784
 7K7  H1   H  HCH2  0   0.296   4.8367   1.0976   0.7299
 7K7  H2   H  HCH2  0   0.312   5.1779   0.2712  -0.7886
 7K7  H4   H  HCR6  0   0.285  -2.6423  -3.6662  -0.0724
 7K7  H5   H  HCH1  0   0.297   1.0538  -1.2626   1.1825
 7K7  H6   H  HCH2  0   0.293   3.3866   0.3759   2.2029
 7K7  H7   H  HCH2  0   0.328   3.0764  -1.3497   2.3097
 7K7  H8   H  HCH3  0   0.253  -0.2863   0.3615   2.4167
 7K7  H9   H  HCH3  0   0.252   0.9819  -0.2846   3.4597
 7K7  H10  H  HCH3  0   0.243   1.1477   1.3337   2.7764
 7K7  H11  H  HNT2  0   0.459   3.2897  -1.2013  -0.2591
 7K7  H13  H  HCH2  0   0.289   3.8671   2.3883  -1.0345
 7K7  H14  H  HCH2  0   0.261   3.1383   1.0079  -1.8045
 7K7  H15  H  HCH2  0   0.299   1.5021   2.4713  -0.6057
 7K7  H16  H  HCH2  0   0.284   2.2890   2.1629   0.9128
 7K7  H17  H  HCR6  0   0.301  -0.4725  -2.8092  -0.8475
 7K7  H18  H  HCR6  0   0.280  -5.1215   0.1731   1.1487
 7K7  H19  H  HCR6  0   0.277  -2.7369   3.4331   0.4071
 7K7  H20  H  HCR6  0   0.270  -0.9099   2.0812  -0.4150
 7K7  H12  H  HNT2  0   0.484   4.5841  -1.2954   0.7131
 7K7  S    S  S     0   1.366   0.6025  -0.2256  -1.1387
 7K7  H3   H  HCR6  0   0.282  -4.3822  -2.0952   0.7106

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
 7K7  C3   C4   single    1.528  0.020  1.528
 7K7  C3   N1   single    1.490  0.020  1.490
 7K7  C5   C4   single    1.520  0.020  1.520
 7K7  C4   N    single    1.464  0.020  1.464
 7K7  N1   C2   single    1.496  0.020  1.496
 7K7  O    S    double    1.463  0.020  1.463
 7K7  N    S    single    1.649  0.020  1.649
 7K7  N    C    single    1.463  0.020  1.463
 7K7  C2   C1   single    1.515  0.020  1.515
 7K7  S    O1   double    1.454  0.020  1.454
 7K7  S    C6   single    1.770  0.020  1.770
 7K7  C    C1   single    1.525  0.020  1.525
 7K7  C6   C11  aromatic  1.371  0.020  1.371
 7K7  C6   C7   aromatic  1.423  0.020  1.423
 7K7  C11  C10  aromatic  1.406  0.020  1.406
 7K7  C7   C14  aromatic  1.412  0.020  1.412
 7K7  C7   C8   aromatic  1.416  0.020  1.416
 7K7  C10  C9   aromatic  1.365  0.020  1.365
 7K7  C14  C13  aromatic  1.368  0.020  1.368
 7K7  C9   C8   aromatic  1.411  0.020  1.411
 7K7  C8   C12  aromatic  1.415  0.020  1.415
 7K7  C13  N2   aromatic  1.349  0.020  1.349
 7K7  C12  N2   aromatic  1.303  0.020  1.303
 7K7  C2   H1   single    0.970  0.020  1.090
 7K7  C2   H2   single    0.970  0.020  1.090
 7K7  C9   H3   single    0.930  0.020  1.080
 7K7  C10  H4   single    0.930  0.020  1.080
 7K7  C4   H5   single    0.970  0.020  1.090
 7K7  C3   H6   single    0.970  0.020  1.090
 7K7  C3   H7   single    0.970  0.020  1.090
 7K7  C5   H8   single    0.970  0.020  1.090
 7K7  C5   H9   single    0.970  0.020  1.090
 7K7  C5   H10  single    0.970  0.020  1.090
 7K7  N1   H11  single    0.890  0.020  1.040
 7K7  C1   H13  single    0.970  0.020  1.090
 7K7  C1   H14  single    0.970  0.020  1.090
 7K7  C    H15  single    0.970  0.020  1.090
 7K7  C    H16  single    0.970  0.020  1.090
 7K7  C11  H17  single    0.930  0.020  1.080
 7K7  C12  H18  single    0.930  0.020  1.080
 7K7  C13  H19  single    0.930  0.020  1.080
 7K7  C14  H20  single    0.930  0.020  1.080
 7K7  N1   H12  single    0.890  0.020  1.040

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
 7K7  H2   C2   H1   108.15  3.000
 7K7  H2   C2   C1   110.48  3.000
 7K7  H1   C2   C1   111.64  3.000
 7K7  H2   C2   N1   106.64  3.000
 7K7  H1   C2   N1   105.82  3.000
 7K7  C1   C2   N1   113.79  3.000
 7K7  H3   C9   C8   118.98  3.000
 7K7  H3   C9   C10  120.60  3.000
 7K7  C8   C9   C10  120.42  3.000
 7K7  H4   C10  C11  119.34  3.000
 7K7  H4   C10  C9   120.90  3.000
 7K7  C11  C10  C9   119.76  3.000
 7K7  H5   C4   N    107.95  3.000
 7K7  H5   C4   C5   107.95  3.000
 7K7  N    C4   C5   111.23  3.000
 7K7  H5   C4   C3   107.17  3.000
 7K7  N    C4   C3   112.90  3.000
 7K7  C5   C4   C3   109.43  3.000
 7K7  H7   C3   H6   107.63  3.000
 7K7  H7   C3   N1   107.87  3.000
 7K7  H6   C3   N1   106.73  3.000
 7K7  H7   C3   C4   108.92  3.000
 7K7  H6   C3   C4   111.77  3.000
 7K7  N1   C3   C4   113.69  3.000
 7K7  C12  C8   C7   118.33  3.000
 7K7  C12  C8   C9   120.80  3.000
 7K7  C7   C8   C9   120.87  3.000
 7K7  C14  C7   C6   126.44  3.000
 7K7  C14  C7   C8   116.66  3.000
 7K7  C6   C7   C8   116.90  3.000
 7K7  C11  C6   S    117.69  3.000
 7K7  C11  C6   C7   121.33  3.000
 7K7  S    C6   C7   120.97  3.000
 7K7  H10  C5   H9   108.05  3.000
 7K7  H10  C5   H8   108.60  3.000
 7K7  H9   C5   H8   108.17  3.000
 7K7  H10  C5   C4   111.23  3.000
 7K7  H9   C5   C4   110.34  3.000
 7K7  H8   C5   C4   110.36  3.000
 7K7  C    N    S    118.28  3.000
 7K7  C    N    C4   119.55  3.000
 7K7  S    N    C4   116.72  3.000
 7K7  H12  N1   H11  104.91  3.000
 7K7  H12  N1   C3   108.19  3.000
 7K7  H11  N1   C3   110.84  3.000
 7K7  H12  N1   C2   107.67  3.000
 7K7  H11  N1   C2   110.56  3.000
 7K7  C3   N1   C2   114.17  3.000
 7K7  H14  C1   H13  105.78  3.000
 7K7  H14  C1   C    109.96  3.000
 7K7  H13  C1   C    108.34  3.000
 7K7  H14  C1   C2   109.99  3.000
 7K7  H13  C1   C2   106.44  3.000
 7K7  C    C1   C2   115.78  3.000
 7K7  H16  C    H15  105.70  3.000
 7K7  H16  C    C1   111.36  3.000
 7K7  H15  C    C1   109.35  3.000
 7K7  H16  C    N    106.78  3.000
 7K7  H15  C    N    109.46  3.000
 7K7  C1   C    N    113.85  3.000
 7K7  H17  C11  C6   120.39  3.000
 7K7  H17  C11  C10  118.89  3.000
 7K7  C6   C11  C10  120.71  3.000
 7K7  H18  C12  N2   117.41  3.000
 7K7  H18  C12  C8   118.56  3.000
 7K7  N2   C12  C8   124.03  3.000
 7K7  C13  N2   C12  117.43  3.000
 7K7  H19  C13  C14  119.68  3.000
 7K7  H19  C13  N2   116.03  3.000
 7K7  C14  C13  N2   124.29  3.000
 7K7  H20  C14  C13  118.41  3.000
 7K7  H20  C14  C7   122.33  3.000
 7K7  C13  C14  C7   119.26  3.000
 7K7  N    S    O    110.18  3.000
 7K7  N    S    C6   102.87  3.000
 7K7  O    S    C6   107.60  3.000
 7K7  C6   S    O1   109.99  3.000
 7K7  N    S    O1   107.26  3.000
 7K7  O    S    O1   117.92  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
 7K7  CONST_01  C6   C11  C10  C9     0.00   0.0  0
 7K7  CONST_02  C6   C7   C8   C9     0.00   0.0  0
 7K7  CONST_03  C14  C7   C8   C9   180.00   0.0  0
 7K7  CONST_04  N2   C12  C8   C9   180.00   0.0  0
 7K7  CONST_05  C7   C6   C11  C10    0.00   0.0  0
 7K7  CONST_06  C7   C8   C9   C10    0.00   0.0  0
 7K7  CONST_07  C12  C8   C9   C10  180.00   0.0  0
 7K7  CONST_08  C11  C6   C7   C8     0.00   0.0  0
 7K7  CONST_09  C13  C14  C7   C8     0.00   0.0  0
 7K7  CONST_10  C11  C10  C9   C8     0.00   0.0  0
 7K7  CONST_11  C13  N2   C12  C8     0.00   0.0  0
 7K7  CONST_12  N2   C13  C14  C7     0.00   0.0  0
 7K7  CONST_13  N2   C12  C8   C7     0.00   0.0  0
 7K7  CONST_14  C13  C14  C7   C6   180.00   0.0  0
 7K7  CONST_15  C12  C8   C7   C6   180.00   0.0  0
 7K7  CONST_16  C14  C7   C6   C11  180.00   0.0  0
 7K7  CONST_17  C14  C7   C8   C12    0.00   0.0  0
 7K7  CONST_18  C14  C13  N2   C12    0.00   0.0  0
 7K7  CONST_19  S    C6   C11  C10  180.00   0.0  0
 7K7  CONST_20  S    C6   C7   C8   180.00   0.0  0
 7K7  CONST_21  C14  C7   C6   S      0.00   0.0  0
 7K7  CONST_22  H17  C11  C10  C9   180.00   0.0  0
 7K7  CONST_23  H18  C12  C8   C9     0.00   0.0  0
 7K7  CONST_24  H20  C14  C7   C8   180.00   0.0  0
 7K7  CONST_25  H4   C10  C9   C8   180.00   0.0  0
 7K7  CONST_26  H19  C13  C14  C7   180.00   0.0  0
 7K7  CONST_27  H3   C9   C8   C7   180.00   0.0  0
 7K7  Var_01    N    S    C6   C7    62.34  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
 7K7  chir_01  C4  C3  C5  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
 7K7  plan-1  C9   0.020
 7K7  plan-1  C10  0.020
 7K7  plan-1  C8   0.020
 7K7  plan-1  C7   0.020
 7K7  plan-1  C6   0.020
 7K7  plan-1  C11  0.020
 7K7  plan-1  C12  0.020
 7K7  plan-1  N2   0.020
 7K7  plan-1  C13  0.020
 7K7  plan-1  C14  0.020
 7K7  plan-1  H4   0.020
 7K7  plan-1  H17  0.020
 7K7  plan-1  H18  0.020
 7K7  plan-1  H19  0.020
 7K7  plan-1  H20  0.020
 7K7  plan-1  S    0.020
 7K7  plan-1  H3   0.020

