# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 08:25:53 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNCCCCCC(=O)CS
#
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
 Q7Y  Q7Y  7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one  ligand  36  14  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Q7Y
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
 Q7Y  C10  C  CH2   0  -0.554  -2.7982   0.7217   0.0318
 Q7Y  C11  C  C     0   0.425  -4.1091  -0.0141   0.0886
 Q7Y  C13  C  CH2   0  -0.667  -5.3397   0.8358  -0.1065
 Q7Y  C02  C  CH2   0  -0.273   7.1915   0.3195   0.0082
 Q7Y  C03  C  CH2   0  -0.453   5.8761  -0.4440   0.0156
 Q7Y  C04  C  CH2   0  -0.253   4.6699   0.4820   0.0179
 Q7Y  C06  C  CH2   0  -0.248   2.2540   0.5894   0.0325
 Q7Y  C07  C  CH2   0  -0.442   0.9702  -0.2250   0.0522
 Q7Y  C08  C  CH2   0  -0.420  -0.2779   0.6480   0.0327
 Q7Y  C09  C  CH2   0  -0.416  -1.5650  -0.1670   0.0683
 Q7Y  N01  N  NH2   0  -0.800   8.3238  -0.5966  -0.0036
 Q7Y  N05  N  NH1   0  -0.600   3.4266  -0.2642   0.0531
 Q7Y  O12  O  O     0  -0.394  -4.1964  -1.2038   0.2812
 Q7Y  S14  S  S2    0  -0.230  -6.8224  -0.1949   0.0661
 Q7Y  H1   H  HCH2  0   0.268  -2.7966   1.3516  -0.8645
 Q7Y  H2   H  HCH2  0   0.275  -2.7878   1.4280   0.8707
 Q7Y  H3   H  HCH2  0   0.303  -5.3380   1.6483   0.6235
 Q7Y  H4   H  HCH2  0   0.306  -5.2997   1.2977  -1.0955
 Q7Y  H5   H  HCH2  0   0.189   7.1916   1.0243  -0.8360
 Q7Y  H6   H  HCH2  0   0.213   7.2542   0.9290   0.9143
 Q7Y  H7   H  HCH2  0   0.214   5.8313  -1.0940  -0.8663
 Q7Y  H8   H  HCH2  0   0.218   5.8374  -1.0976   0.8914
 Q7Y  H9   H  HCH2  0   0.212   4.7087   1.1228   0.9055
 Q7Y  H10  H  HCH2  0   0.183   4.7286   1.1611  -0.8491
 Q7Y  H11  H  HCH2  0   0.182   2.2413   1.2674  -0.8377
 Q7Y  H12  H  HCH2  0   0.211   2.2849   1.2346   0.9171
 Q7Y  H13  H  HCH2  0   0.214   0.9531  -0.8988  -0.8119
 Q7Y  H14  H  HCH2  0   0.216   0.9629  -0.8622   0.9422
 Q7Y  H15  H  HCH2  0   0.215  -0.2567   1.3330   0.8873
 Q7Y  H16  H  HCH2  0   0.215  -0.2686   1.2786  -0.8630
 Q7Y  H17  H  HCH2  0   0.226  -1.5782  -0.7847   0.9701
 Q7Y  H18  H  HCH2  0   0.226  -1.5822  -0.8569  -0.7801
 Q7Y  H19  H  HNH2  0   0.337   8.3402  -1.0893  -0.8886
 Q7Y  H20  H  HNH2  0   0.345   9.1851  -0.0658   0.0243
 Q7Y  H22  H  HNH1  0   0.333   3.3940  -0.8766  -0.7548
 Q7Y  H24  H  HSH1  0   0.224  -7.6992   0.7889  -0.1626

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
 Q7Y  N01  C02  single  1.457  0.020  1.457
 Q7Y  C02  C03  single  1.521  0.020  1.521
 Q7Y  C03  C04  single  1.521  0.020  1.521
 Q7Y  C04  N05  single  1.450  0.020  1.450
 Q7Y  O12  C11  double  1.208  0.020  1.208
 Q7Y  N05  C06  single  1.451  0.020  1.451
 Q7Y  S14  C13  single  1.814  0.020  1.814
 Q7Y  C11  C13  single  1.508  0.020  1.508
 Q7Y  C11  C10  single  1.504  0.020  1.504
 Q7Y  C09  C10  single  1.520  0.020  1.520
 Q7Y  C09  C08  single  1.524  0.020  1.524
 Q7Y  C06  C07  single  1.521  0.020  1.521
 Q7Y  C07  C08  single  1.523  0.020  1.523
 Q7Y  C10  H1   single  0.970  0.020  1.090
 Q7Y  C10  H2   single  0.970  0.020  1.090
 Q7Y  C13  H3   single  0.970  0.020  1.090
 Q7Y  C13  H4   single  0.970  0.020  1.090
 Q7Y  C02  H5   single  0.970  0.020  1.090
 Q7Y  C02  H6   single  0.970  0.020  1.090
 Q7Y  C03  H7   single  0.970  0.020  1.090
 Q7Y  C03  H8   single  0.970  0.020  1.090
 Q7Y  C04  H9   single  0.970  0.020  1.090
 Q7Y  C04  H10  single  0.970  0.020  1.090
 Q7Y  C06  H11  single  0.970  0.020  1.090
 Q7Y  C06  H12  single  0.970  0.020  1.090
 Q7Y  C07  H13  single  0.970  0.020  1.090
 Q7Y  C07  H14  single  0.970  0.020  1.090
 Q7Y  C08  H15  single  0.970  0.020  1.090
 Q7Y  C08  H16  single  0.970  0.020  1.090
 Q7Y  C09  H17  single  0.970  0.020  1.090
 Q7Y  C09  H18  single  0.970  0.020  1.090
 Q7Y  N01  H19  single  0.890  0.020  1.040
 Q7Y  N01  H20  single  0.890  0.020  1.040
 Q7Y  N05  H22  single  0.890  0.020  1.040
 Q7Y  S14  H24  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
 Q7Y  H2   C10  H1   104.80  3.000
 Q7Y  H2   C10  C09  110.51  3.000
 Q7Y  H1   C10  C09  110.76  3.000
 Q7Y  H2   C10  C11  107.12  3.000
 Q7Y  H1   C10  C11  108.26  3.000
 Q7Y  C09  C10  C11  114.83  3.000
 Q7Y  O12  C11  C13  121.09  3.000
 Q7Y  C13  C11  C10  115.50  3.000
 Q7Y  O12  C11  C10  123.40  3.000
 Q7Y  H4   C13  H3   106.89  3.000
 Q7Y  H4   C13  S14  110.88  3.000
 Q7Y  H3   C13  S14  111.13  3.000
 Q7Y  H4   C13  C11  108.99  3.000
 Q7Y  H3   C13  C11  109.36  3.000
 Q7Y  S14  C13  C11  109.54  3.000
 Q7Y  H6   C02  H5   106.18  3.000
 Q7Y  H6   C02  N01  108.22  3.000
 Q7Y  H5   C02  N01  113.38  3.000
 Q7Y  H6   C02  C03  108.98  3.000
 Q7Y  H5   C02  C03  109.00  3.000
 Q7Y  N01  C02  C03  110.90  3.000
 Q7Y  H8   C03  H7   106.76  3.000
 Q7Y  H8   C03  C04  109.56  3.000
 Q7Y  H7   C03  C04  109.26  3.000
 Q7Y  H8   C03  C02  109.54  3.000
 Q7Y  H7   C03  C02  109.21  3.000
 Q7Y  C04  C03  C02  112.36  3.000
 Q7Y  H10  C04  H9   105.95  3.000
 Q7Y  H10  C04  N05  112.42  3.000
 Q7Y  H9   C04  N05  108.16  3.000
 Q7Y  H10  C04  C03  109.36  3.000
 Q7Y  H9   C04  C03  109.23  3.000
 Q7Y  N05  C04  C03  111.51  3.000
 Q7Y  H12  C06  H11  105.99  3.000
 Q7Y  H12  C06  N05  108.20  3.000
 Q7Y  H11  C06  N05  112.47  3.000
 Q7Y  H12  C06  C07  109.19  3.000
 Q7Y  H11  C06  C07  109.25  3.000
 Q7Y  N05  C06  C07  111.54  3.000
 Q7Y  H14  C07  H13  106.44  3.000
 Q7Y  H14  C07  C08  109.79  3.000
 Q7Y  H13  C07  C08  109.24  3.000
 Q7Y  H14  C07  C06  109.15  3.000
 Q7Y  H13  C07  C06  109.40  3.000
 Q7Y  C08  C07  C06  112.62  3.000
 Q7Y  H16  C08  H15  106.12  3.000
 Q7Y  H16  C08  C09  109.52  3.000
 Q7Y  H15  C08  C09  109.42  3.000
 Q7Y  H16  C08  C07  109.48  3.000
 Q7Y  H15  C08  C07  109.42  3.000
 Q7Y  C09  C08  C07  112.66  3.000
 Q7Y  H18  C09  H17  106.45  3.000
 Q7Y  H18  C09  C08  109.42  3.000
 Q7Y  H17  C09  C08  109.37  3.000
 Q7Y  H18  C09  C10  109.72  3.000
 Q7Y  H17  C09  C10  109.89  3.000
 Q7Y  C08  C09  C10  111.83  3.000
 Q7Y  H20  N01  H19  105.39  3.000
 Q7Y  H20  N01  C02  109.36  3.000
 Q7Y  H19  N01  C02  109.00  3.000
 Q7Y  H22  N05  C06  108.54  3.000
 Q7Y  H22  N05  C04  108.60  3.000
 Q7Y  C06  N05  C04  112.95  3.000
 Q7Y  H24  S14  C13   95.83  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
 Q7Y  Var_01  S14  C13  C11  C10  -177.48  30.0  3
 Q7Y  Var_02  C07  C08  C09  C10  -179.34  30.0  3
 Q7Y  Var_03  C08  C09  C10  C11  -178.97  30.0  1
 Q7Y  Var_04  C09  C10  C11  C13  -173.23  30.0  3
 Q7Y  Var_05  N05  C04  C03  C02  -178.81  30.0  3
 Q7Y  Var_06  C06  N05  C04  C03  -178.98  30.0  3
 Q7Y  Var_07  N01  C02  C03  C04  -179.59  30.0  1
 Q7Y  Var_08  C07  C06  N05  C04   179.27  30.0  3
 Q7Y  Var_09  C09  C08  C07  C06  -179.36  30.0  3
 Q7Y  Var_10  N05  C06  C07  C08   179.94  30.0  1
 Q7Y  Var_11  H19  N01  C02  C03    67.22  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
 Q7Y  plan-1  C10  0.020
 Q7Y  plan-1  C11  0.020
 Q7Y  plan-1  C13  0.020
 Q7Y  plan-1  O12  0.020

