# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 09:34:45 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 2-azido-N-(2-sulfanylethyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCNC(=O)CN=[N+]=[N-]
#
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
 DA9  DA9  2-azido-N-(2-sulfanylethyl)ethanamide  ligand  18  10  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DA9
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
 DA9  N1   N  N      1   0.402  -3.7272  -0.2144   0.2389
 DA9  N2   N  N      0  -0.430  -3.2016   0.4305  -0.6527
 DA9  C3   C  CH2    0  -0.470  -1.9424   1.0789  -0.3324
 DA9  C4   C  C      0   0.514  -0.8209   0.0656  -0.1348
 DA9  O5   O  O      0  -0.315  -1.0542  -1.0569   0.2809
 DA9  N6   N  NH1    0  -0.666   0.4044   0.5346  -0.3985
 DA9  C7   C  CH2    0  -0.291   1.6130  -0.2323  -0.1848
 DA9  C8   C  CH2    0  -0.604   2.7758   0.7081   0.0870
 DA9  S9   S  S2     0  -0.234   4.2862  -0.2893   0.2930
 DA9  N10  N  N     -1  -0.195  -4.3164  -0.8200   0.9783
 DA9  H3   H  HCH2   0   0.271  -1.7286   1.7617  -1.1522
 DA9  H3A  H  HCH2   0   0.281  -2.0184   1.6773   0.5812
 DA9  HN6  H  HNH1   0   0.410   0.4932   1.4431  -0.8266
 DA9  H7   H  HCH2   0   0.291   1.4634  -0.8969   0.6660
 DA9  H7A  H  HCH2   0   0.238   1.8295  -0.8601  -1.0547
 DA9  H8   H  HCH2   0   0.301   2.9105   1.4002  -0.7452
 DA9  H8A  H  HCH2   0   0.275   2.5898   1.2861   0.9916
 DA9  HS9  H  HSH1   0   0.222   5.1085   0.7188   0.6002

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
 DA9  N1  N2   double  1.219  0.020  1.219
 DA9  N1  N10  double  1.123  0.020  1.123
 DA9  N2  C3   single  1.452  0.020  1.452
 DA9  C3  C4   single  1.524  0.020  1.524
 DA9  C3  H3   single  0.970  0.020  1.090
 DA9  C3  H3A  single  0.970  0.020  1.090
 DA9  C4  O5   double  1.220  0.020  1.220
 DA9  C4  N6   single  1.338  0.020  1.338
 DA9  N6  C7   single  1.447  0.020  1.447
 DA9  N6  HN6  single  0.860  0.020  1.020
 DA9  C7  C8   single  1.520  0.020  1.520
 DA9  C7  H7   single  0.970  0.020  1.090
 DA9  C7  H7A  single  0.970  0.020  1.090
 DA9  C8  S9   single  1.822  0.020  1.822
 DA9  C8  H8   single  0.970  0.020  1.090
 DA9  C8  H8A  single  0.970  0.020  1.090
 DA9  S9  HS9  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
 DA9  N10  N1  N2  173.18  3.000
 DA9  C3   N2  N1  116.66  3.000
 DA9  H3A  C3  H3  107.42  3.000
 DA9  H3A  C3  C4  107.83  3.000
 DA9  H3   C3  C4  111.74  3.000
 DA9  H3A  C3  N2  111.58  3.000
 DA9  H3   C3  N2  106.52  3.000
 DA9  C4   C3  N2  111.70  3.000
 DA9  N6   C4  O5  124.39  3.000
 DA9  N6   C4  C3  114.52  3.000
 DA9  O5   C4  C3  121.02  3.000
 DA9  HN6  N6  C7  117.82  3.000
 DA9  HN6  N6  C4  118.69  3.000
 DA9  C7   N6  C4  123.35  3.000
 DA9  H7A  C7  H7  107.33  3.000
 DA9  H7A  C7  C8  110.23  3.000
 DA9  H7   C7  C8  110.04  3.000
 DA9  H7A  C7  N6  110.59  3.000
 DA9  H7   C7  N6  108.89  3.000
 DA9  C8   C7  N6  109.72  3.000
 DA9  H8A  C8  H8  108.54  3.000
 DA9  H8A  C8  S9  109.76  3.000
 DA9  H8   C8  S9  109.35  3.000
 DA9  H8A  C8  C7  110.24  3.000
 DA9  H8   C8  C7  110.53  3.000
 DA9  S9   C8  C7  108.41  3.000
 DA9  HS9  S9  C8   97.07  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
 DA9  CONST_01  C7   N6  C4  C3   180.00   0.0  0
 DA9  CONST_02  C7   N6  C4  O5     0.00   0.0  0
 DA9  CONST_03  HN6  N6  C4  C3     0.00   0.0  0
 DA9  Var_01    C4   C3  N2  N1    69.18  30.0  3
 DA9  Var_02    O5   C4  C3  N2   -29.61  30.0  3
 DA9  Var_03    C8   C7  N6  C4  -152.35  30.0  3
 DA9  Var_04    S9   C8  C7  N6  -178.07  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
 DA9  plan-1  C3   0.020
 DA9  plan-1  C4   0.020
 DA9  plan-1  O5   0.020
 DA9  plan-1  N6   0.020
 DA9  plan-1  C7   0.020
 DA9  plan-1  HN6  0.020
 DA9  plan-2  N1   0.020
 DA9  plan-2  N2   0.020
 DA9  plan-2  C3   0.020
 DA9  plan-2  N10  0.020

