# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:25:13 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 5-[(3-aminopropyl)amino]pentane-1-thiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNCCCCCS
#
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
 SS9  SS9  5-[(3-aminopropyl)amino]pentane-1-thiol  ligand  31  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SS9
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
 SS9  C2   C  CH2   0  -0.273  -5.6441  -0.3447  -0.0082
 SS9  C3   C  CH2   0  -0.453  -4.3387   0.4353   0.0236
 SS9  C4   C  CH2   0  -0.253  -3.1206  -0.4748   0.0094
 SS9  C6   C  CH2   0  -0.248  -0.7036  -0.5506   0.0144
 SS9  C7   C  CH2   0  -0.441   0.5693   0.2797   0.0615
 SS9  C8   C  CH2   0  -0.415   1.8276  -0.5766  -0.0050
 SS9  C9   C  CH2   0  -0.415   3.1050   0.2527   0.0608
 SS9  C10  C  CH2   0  -0.549   4.3482  -0.6186  -0.0282
 SS9  N1   N  NH2   0  -0.800  -6.7878   0.5572  -0.0049
 SS9  N5   N  NH1   0  -0.600  -1.8871   0.2864   0.0640
 SS9  S11  S  S2    0  -0.262   5.8332   0.4379   0.0747
 SS9  H1   H  HCH2  0   0.189  -5.6309  -1.0297  -0.8686
 SS9  H2   H  HCH2  0   0.213  -5.7037  -0.9759   0.8830
 SS9  H3   H  HCH2  0   0.214  -4.2982   1.1065  -0.8425
 SS9  H4   H  HCH2  0   0.219  -4.3137   1.0683   0.9149
 SS9  H5   H  HCH2  0   0.212  -3.1536  -1.1354   0.8826
 SS9  H6   H  HCH2  0   0.183  -3.1683  -1.1351  -0.8727
 SS9  H7   H  HCH2  0   0.183  -0.6824  -1.1983  -0.8784
 SS9  H8   H  HCH2  0   0.212  -0.7259  -1.2256   0.8766
 SS9  H9   H  HCH2  0   0.215   0.5716   0.9890  -0.7739
 SS9  H10  H  HCH2  0   0.217   0.5753   0.8789   0.9773
 SS9  H11  H  HCH2  0   0.218   1.8215  -1.3001   0.8171
 SS9  H12  H  HCH2  0   0.217   1.8221  -1.1632  -0.9302
 SS9  H13  H  HCH2  0   0.229   3.1107   0.9827  -0.7542
 SS9  H14  H  HCH2  0   0.229   3.1213   0.8241   0.9939
 SS9  H15  H  HCH2  0   0.261   4.3645  -1.3437   0.7859
 SS9  H16  H  HCH2  0   0.262   4.3621  -1.1657  -0.9714
 SS9  H17  H  HNH2  0   0.337  -6.8062   1.0692  -0.8788
 SS9  H18  H  HNH2  0   0.345  -7.6430   0.0161   0.0081
 SS9  H20  H  HNH1  0   0.334  -1.8652   0.9229  -0.7254
 SS9  H22  H  HSH1  0   0.221   6.7539  -0.5202  -0.0765

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
 SS9  S11  C10  single  1.825  0.020  1.825
 SS9  C9   C10  single  1.521  0.020  1.521
 SS9  C9   C8   single  1.524  0.020  1.524
 SS9  C2   N1   single  1.457  0.020  1.457
 SS9  C2   C3   single  1.521  0.020  1.521
 SS9  C7   C8   single  1.523  0.020  1.523
 SS9  C7   C6   single  1.521  0.020  1.521
 SS9  C4   C3   single  1.521  0.020  1.521
 SS9  C4   N5   single  1.450  0.020  1.450
 SS9  C6   N5   single  1.450  0.020  1.450
 SS9  C2   H1   single  0.970  0.020  1.090
 SS9  C2   H2   single  0.970  0.020  1.090
 SS9  C3   H3   single  0.970  0.020  1.090
 SS9  C3   H4   single  0.970  0.020  1.090
 SS9  C4   H5   single  0.970  0.020  1.090
 SS9  C4   H6   single  0.970  0.020  1.090
 SS9  C6   H7   single  0.970  0.020  1.090
 SS9  C6   H8   single  0.970  0.020  1.090
 SS9  C7   H9   single  0.970  0.020  1.090
 SS9  C7   H10  single  0.970  0.020  1.090
 SS9  C8   H11  single  0.970  0.020  1.090
 SS9  C8   H12  single  0.970  0.020  1.090
 SS9  C9   H13  single  0.970  0.020  1.090
 SS9  C9   H14  single  0.970  0.020  1.090
 SS9  C10  H15  single  0.970  0.020  1.090
 SS9  C10  H16  single  0.970  0.020  1.090
 SS9  N1   H17  single  0.890  0.020  1.040
 SS9  N1   H18  single  0.890  0.020  1.040
 SS9  N5   H20  single  0.890  0.020  1.040
 SS9  S11  H22  single  1.200  0.020  1.300

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
 SS9  H2   C2   H1   106.18  3.000
 SS9  H2   C2   N1   108.22  3.000
 SS9  H1   C2   N1   113.38  3.000
 SS9  H2   C2   C3   109.01  3.000
 SS9  H1   C2   C3   108.99  3.000
 SS9  N1   C2   C3   110.87  3.000
 SS9  H4   C3   H3   106.78  3.000
 SS9  H4   C3   C4   109.62  3.000
 SS9  H3   C3   C4   109.24  3.000
 SS9  H4   C3   C2   109.48  3.000
 SS9  H3   C3   C2   109.21  3.000
 SS9  C4   C3   C2   112.36  3.000
 SS9  H6   C4   H5   105.97  3.000
 SS9  H6   C4   N5   112.41  3.000
 SS9  H5   C4   N5   108.18  3.000
 SS9  H6   C4   C3   109.34  3.000
 SS9  H5   C4   C3   109.23  3.000
 SS9  N5   C4   C3   111.51  3.000
 SS9  H8   C6   H7   106.00  3.000
 SS9  H8   C6   N5   108.19  3.000
 SS9  H7   C6   N5   112.47  3.000
 SS9  H8   C6   C7   109.22  3.000
 SS9  H7   C6   C7   109.24  3.000
 SS9  N5   C6   C7   111.53  3.000
 SS9  H10  C7   H9   106.47  3.000
 SS9  H10  C7   C8   109.86  3.000
 SS9  H9   C7   C8   109.20  3.000
 SS9  H10  C7   C6   109.24  3.000
 SS9  H9   C7   C6   109.36  3.000
 SS9  C8   C7   C6   112.53  3.000
 SS9  H12  C8   H11  106.27  3.000
 SS9  H12  C8   C9   109.39  3.000
 SS9  H11  C8   C9   109.37  3.000
 SS9  H12  C8   C7   109.49  3.000
 SS9  H11  C8   C7   109.51  3.000
 SS9  C9   C8   C7   112.61  3.000
 SS9  H14  C9   H13  106.65  3.000
 SS9  H14  C9   C10  109.69  3.000
 SS9  H13  C9   C10  109.54  3.000
 SS9  H14  C9   C8   109.47  3.000
 SS9  H13  C9   C8   109.58  3.000
 SS9  C10  C9   C8   111.77  3.000
 SS9  H16  C10  H15  108.18  3.000
 SS9  H16  C10  S11  109.20  3.000
 SS9  H15  C10  S11  109.31  3.000
 SS9  H16  C10  C9   110.40  3.000
 SS9  H15  C10  C9   110.45  3.000
 SS9  S11  C10  C9   109.28  3.000
 SS9  H18  N1   H17  105.42  3.000
 SS9  H18  N1   C2   109.42  3.000
 SS9  H17  N1   C2   108.98  3.000
 SS9  H20  N5   C6   108.53  3.000
 SS9  H20  N5   C4   108.57  3.000
 SS9  C6   N5   C4   112.94  3.000
 SS9  H22  S11  C10   97.99  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
 SS9  Var_01  N5   C4   C3  C2  -178.98  30.0  1
 SS9  Var_02  C6   N5   C4  C3  -178.38  30.0  3
 SS9  Var_03  N1   C2   C3  C4  -179.52  30.0  1
 SS9  Var_04  C7   C6   N5  C4   179.51  30.0  1
 SS9  Var_05  C9   C8   C7  C6  -179.24  30.0  3
 SS9  Var_06  C10  C9   C8  C7  -179.14  30.0  1
 SS9  Var_07  S11  C10  C9  C8  -179.40  30.0  3
 SS9  Var_08  N5   C6   C7  C8  -179.36  30.0  3
 SS9  Var_09  H17  N1   C2  C3    67.27  30.0  3

