# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 08:20:32 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 2-[5-ethyl-2,4,6-tris(oxidanylidene)-1,3-diazinan-5-yl]ethyl selenocyanate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1(CC[Se]C#N)C(=O)NC(=O)NC1=O
#
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
 6JA  6JA  '2-[5-ethyl-2,4,6-tris(oxidanylidene)-1,3-diazinan-5-yl]ethyl selenocyanate'  ligand  27  16  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6JA
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
 6JA  C    C   CH3   0  -0.681   3.7801   1.7079   0.0420
 6JA  N    N   NS    0  -0.226  -4.4025  -1.7490  -0.2055
 6JA  C8   C   C     0   0.584   1.6684  -0.0664   1.2896
 6JA  N2   N   NH1   0  -0.611   2.3919  -1.2205   1.1498
 6JA  C7   C   C     0   0.677   2.7769  -1.8203  -0.0238
 6JA  O1   O   O     0  -0.515   3.4087  -2.8467  -0.0493
 6JA  N1   N   NH1   0  -0.619   2.3791  -1.1775  -1.1736
 6JA  C6   C   C     0   0.630   1.6610  -0.0172  -1.2663
 6JA  O    O   O     0  -0.389   1.3098   0.4114  -2.3400
 6JA  C2   C   CT    0  -0.467   1.3719   0.7226   0.0266
 6JA  C1   C   CH2   0  -0.420   2.2835   1.9817   0.0512
 6JA  C3   C   CH2   0  -0.479  -0.0930   1.1919   0.0424
 6JA  C4   C   CH2   0  -0.597  -1.0862   0.0406   0.0096
 6JA  SE   SE  SE    0   0.282  -2.9072   0.8056   0.1005
 6JA  C5   C   CSP   0  -0.083  -3.8013  -0.7702  -0.0888
 6JA  H1   H   HCH3  0   0.278   4.1084   1.1368   0.9113
 6JA  H2   H   HCH3  0   0.235   4.1044   1.1795  -0.8554
 6JA  H3   H   HCH3  0   0.250   4.3189   2.6543   0.0638
 6JA  H4   H   HNH1  0   0.436   2.6396  -1.7173   1.9983
 6JA  H5   H   HNH1  0   0.388   2.6145  -1.6453  -2.0410
 6JA  H6   H   HCH2  0   0.281   2.0154   2.5551   0.9399
 6JA  H7   H   HCH2  0   0.270   2.0129   2.5951  -0.8096
 6JA  H8   H   HCH2  0   0.283  -0.2316   1.7981   0.9391
 6JA  H9   H   HCH2  0   0.278  -0.2417   1.8509  -0.8140
 6JA  H10  H   HCH2  0   0.334  -1.0212  -0.5341  -0.9139
 6JA  H11  H   HCH2  0   0.296  -0.9724  -0.6317   0.8593
 6JA  O2   O   O     0  -0.416   1.3197   0.3210   2.3781

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
 6JA  N   C5   triple  1.155  0.020  1.155
 6JA  C5  SE   single  1.822  0.020  1.822
 6JA  C   C1   single  1.521  0.020  1.521
 6JA  SE  C4   single  1.977  0.020  1.977
 6JA  C1  C2   single  1.555  0.020  1.555
 6JA  C4  C3   single  1.521  0.020  1.521
 6JA  O2  C8   double  1.207  0.020  1.207
 6JA  C3  C2   single  1.538  0.020  1.538
 6JA  C2  C8   single  1.518  0.020  1.518
 6JA  C2  C6   single  1.517  0.020  1.517
 6JA  C8  N2   single  1.369  0.020  1.369
 6JA  O   C6   double  1.208  0.020  1.208
 6JA  C6  N1   single  1.368  0.020  1.368
 6JA  N2  C7   single  1.373  0.020  1.373
 6JA  N1  C7   single  1.376  0.020  1.376
 6JA  C7  O1   double  1.205  0.020  1.205
 6JA  C   H1   single  0.970  0.020  1.090
 6JA  C   H2   single  0.970  0.020  1.090
 6JA  C   H3   single  0.970  0.020  1.090
 6JA  N2  H4   single  0.860  0.020  1.020
 6JA  N1  H5   single  0.860  0.020  1.020
 6JA  C1  H6   single  0.970  0.020  1.090
 6JA  C1  H7   single  0.970  0.020  1.090
 6JA  C3  H8   single  0.970  0.020  1.090
 6JA  C3  H9   single  0.970  0.020  1.090
 6JA  C4  H10  single  0.970  0.020  1.090
 6JA  C4  H11  single  0.970  0.020  1.090

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
 6JA  H3   C   H2   106.88  3.000
 6JA  H3   C   H1   106.86  3.000
 6JA  H2   C   H1   108.22  3.000
 6JA  H3   C   C1   109.27  3.000
 6JA  H2   C   C1   112.62  3.000
 6JA  H1   C   C1   112.67  3.000
 6JA  C2   C8  N2   117.14  3.000
 6JA  N2   C8  O2   121.02  3.000
 6JA  C2   C8  O2   121.80  3.000
 6JA  H4   N2  C7   115.64  3.000
 6JA  H4   N2  C8   117.17  3.000
 6JA  C7   N2  C8   127.13  3.000
 6JA  N1   C7  O1   122.11  3.000
 6JA  O1   C7  N2   122.48  3.000
 6JA  N1   C7  N2   115.40  3.000
 6JA  H5   N1  C6   117.11  3.000
 6JA  H5   N1  C7   115.62  3.000
 6JA  C6   N1  C7   127.21  3.000
 6JA  C2   C6  O    121.93  3.000
 6JA  O    C6  N1   120.92  3.000
 6JA  C2   C6  N1   117.12  3.000
 6JA  C3   C2  C1   108.13  3.000
 6JA  C3   C2  C6   109.81  3.000
 6JA  C1   C2  C6   107.26  3.000
 6JA  C6   C2  C8   114.72  3.000
 6JA  C3   C2  C8   109.63  3.000
 6JA  C1   C2  C8   107.05  3.000
 6JA  H7   C1  H6   106.63  3.000
 6JA  H7   C1  C2   107.30  3.000
 6JA  H6   C1  C2   107.12  3.000
 6JA  H7   C1  C    109.90  3.000
 6JA  H6   C1  C    109.95  3.000
 6JA  C2   C1  C    115.53  3.000
 6JA  H9   C3  H8   106.99  3.000
 6JA  H9   C3  C4   110.58  3.000
 6JA  H8   C3  C4   110.81  3.000
 6JA  H9   C3  C2   107.82  3.000
 6JA  H8   C3  C2   107.39  3.000
 6JA  C4   C3  C2   113.00  3.000
 6JA  H11  C4  H10  109.23  3.000
 6JA  H11  C4  SE   107.40  3.000
 6JA  H10  C4  SE   107.33  3.000
 6JA  H11  C4  C3   112.46  3.000
 6JA  H10  C4  C3   112.25  3.000
 6JA  SE   C4  C3   107.91  3.000
 6JA  C5   SE  C4    96.46  3.000
 6JA  SE   C5  N    180.00  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
 6JA  CONST_01  N1  C7  N2  C8     0.00   0.0  0
 6JA  CONST_02  C6  N1  C7  N2     0.00   0.0  0
 6JA  CONST_03  C2  C8  N2  C7     0.00   0.0  0
 6JA  CONST_04  C7  N2  C8  O2   180.00   0.0  0
 6JA  CONST_05  O1  C7  N2  C8   180.00   0.0  0
 6JA  CONST_06  C6  N1  C7  O1   180.00   0.0  0
 6JA  CONST_07  H5  N1  C7  N2   180.00   0.0  0
 6JA  CONST_08  H4  N2  C7  N1   180.00   0.0  0
 6JA  Var_01    O   C6  N1  C7  -175.96  30.0  1
 6JA  Var_02    SE  C4  C3  C2   177.99  30.0  2
 6JA  Var_03    H1  C   C1  C2   -61.21  30.0  3

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
 6JA  chir_01  C2  C3  C8  C6  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
 6JA  plan-1  N1  0.020
 6JA  plan-1  C6  0.020
 6JA  plan-1  O   0.020
 6JA  plan-1  C2  0.020
 6JA  plan-2  C8  0.020
 6JA  plan-2  N2  0.020
 6JA  plan-2  C7  0.020
 6JA  plan-2  O1  0.020
 6JA  plan-2  N1  0.020
 6JA  plan-2  C6  0.020
 6JA  plan-2  C2  0.020
 6JA  plan-2  H4  0.020
 6JA  plan-2  H5  0.020
 6JA  plan-2  O2  0.020

