# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 08:25:32 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2Z,5E)-2-imino-5-(pyridin-2-ylmethylidene)-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=C1NC(=O)C(\S1)=C/c2ccccn2
#
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
 C53  C53  (2Z,5E)-2-imino-5-(pyridin-2-ylmethylidene)-1,3-thiazolidin-4-one  ligand  21  14  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C53
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
 C53  C2    C  CR16  0  -0.316  -2.7262  -1.1863  -0.4180
 C53  C3    C  CR16  0  -0.154  -3.9954  -0.6378  -0.5094
 C53  C4    C  CR16  0  -0.319  -4.2409   0.5764   0.1117
 C53  C5    C  CR16  0  -0.082  -3.1997   1.1820   0.8029
 C53  N1    N  N     0  -0.396  -1.9798   0.6725   0.8851
 C53  C1    C  CR6   0   0.205  -1.7413  -0.4843   0.2730
 C53  C6    C  C1    0  -0.245  -0.3956  -1.0712   0.3926
 C53  C7    C  CR5   0  -0.259   0.7686  -0.4621   0.1571
 C53  S1    S  S2    0   0.147   2.3217  -1.2321   0.4594
 C53  C8    C  CR5   0   0.603   0.9757   0.8822  -0.4570
 C53  O1    O  O     0  -0.404   0.1174   1.6187  -0.8770
 C53  N2    N  NR15  0  -0.657   2.3151   1.1428  -0.5235
 C53  C9    C  CR5   0   0.287   3.2154   0.1863  -0.1141
 C53  N3    N  N     0  -0.596   4.4608   0.3512  -0.1674
 C53  H2    H  HCR6  0   0.275  -2.4965  -2.1383  -0.8780
 C53  H3    H  HCR6  0   0.277  -4.7773  -1.1527  -1.0513
 C53  H4    H  HCR6  0   0.274  -5.2163   1.0414   0.0773
 C53  H5    H  HCR6  0   0.265  -3.3639   2.1219   1.3182
 C53  H6C1  H  H     0   0.301  -0.3699  -2.1081   0.7140
 C53  H3N1  H  H     0   0.364   4.9807  -0.4513   0.1658
 C53  H2N   H  HNR5  0   0.431   2.6574   2.0069  -0.9233

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
 C53  C2  C3    aromatic  1.386  0.020  1.386
 C53  C2  C1    aromatic  1.393  0.020  1.393
 C53  C2  H2    single    0.930  0.020  1.080
 C53  C3  C4    aromatic  1.386  0.020  1.386
 C53  C3  H3    single    0.930  0.020  1.080
 C53  C4  C5    aromatic  1.389  0.020  1.389
 C53  C4  H4    single    0.930  0.020  1.080
 C53  C5  H5    single    0.930  0.020  1.080
 C53  C5  N1    aromatic  1.324  0.020  1.324
 C53  N1  C1    aromatic  1.330  0.020  1.330
 C53  C1  C6    single    1.473  0.020  1.473
 C53  C6  H6C1  single    0.930  0.020  1.080
 C53  C6  C7    double    1.335  0.020  1.335
 C53  C7  S1    single    1.760  0.020  1.760
 C53  C7  C8    single    1.492  0.020  1.492
 C53  S1  C9    single    1.772  0.020  1.772
 C53  C8  O1    double    1.206  0.020  1.206
 C53  C8  N2    single    1.366  0.020  1.366
 C53  N2  H2N   single    0.860  0.020  1.020
 C53  N2  C9    single    1.376  0.020  1.376
 C53  C9  N3    double    1.257  0.020  1.257
 C53  N3  H3N1  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
 C53  H2    C2  C1  120.27  3.000
 C53  H2    C2  C3  120.98  3.000
 C53  C1    C2  C3  118.74  3.000
 C53  H3    C3  C4  120.90  3.000
 C53  H3    C3  C2  120.44  3.000
 C53  C4    C3  C2  118.66  3.000
 C53  H4    C4  C5  120.32  3.000
 C53  H4    C4  C3  121.50  3.000
 C53  C5    C4  C3  118.18  3.000
 C53  H5    C5  N1  116.32  3.000
 C53  N1    C5  C4  123.62  3.000
 C53  H5    C5  C4  120.06  3.000
 C53  C1    N1  C5  118.10  3.000
 C53  C6    C1  N1  118.22  3.000
 C53  C6    C1  C2  119.04  3.000
 C53  N1    C1  C2  122.66  3.000
 C53  H6C1  C6  C7  117.86  3.000
 C53  C7    C6  C1  126.91  3.000
 C53  H6C1  C6  C1  115.22  3.000
 C53  C8    C7  S1  110.02  3.000
 C53  C8    C7  C6  127.21  3.000
 C53  S1    C7  C6  122.67  3.000
 C53  C9    S1  C7   92.25  3.000
 C53  N2    C8  O1  124.34  3.000
 C53  N2    C8  C7  109.14  3.000
 C53  O1    C8  C7  126.47  3.000
 C53  H2N   N2  C9  119.34  3.000
 C53  C9    N2  C8  119.64  3.000
 C53  H2N   N2  C8  120.92  3.000
 C53  N3    C9  N2  122.98  3.000
 C53  N3    C9  S1  128.19  3.000
 C53  N2    C9  S1  108.83  3.000
 C53  H3N1  N3  C9  112.99  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
 C53  CONST_01  C5    C4  C3  C2    0.00   0.0  0
 C53  CONST_02  C5    N1  C1  C2    0.00   0.0  0
 C53  CONST_03  N1    C1  C2  C3    0.00   0.0  0
 C53  CONST_04  N1    C5  C4  C3    0.00   0.0  0
 C53  CONST_05  C1    C2  C3  C4    0.00   0.0  0
 C53  CONST_06  C1    N1  C5  C4    0.00   0.0  0
 C53  CONST_07  C9    N2  C8  C7    0.00   0.0  0
 C53  CONST_08  C8    N2  C9  S1    0.00   0.0  0
 C53  CONST_09  C6    C1  C2  C3  180.00   0.0  0
 C53  CONST_10  C6    C1  N1  C5  180.00   0.0  0
 C53  CONST_11  N3    C9  N2  C8  180.00   0.0  0
 C53  CONST_12  C9    N2  C8  O1  180.00   0.0  0
 C53  CONST_13  H4    C4  C3  C2  180.00   0.0  0
 C53  CONST_14  H5    C5  C4  C3  180.00   0.0  0
 C53  CONST_15  H2    C2  C3  C4  180.00   0.0  0
 C53  CONST_16  H3    C3  C4  C5  180.00   0.0  0
 C53  CONST_17  H2N   N2  C8  C7  180.00   0.0  0
 C53  CONST_18  H3N1  N3  C9  S1    0.00   0.0  0
 C53  Var_01    C7    C6  C1  C2  131.98  30.0  2
 C53  Var_02    S1    C7  C6  C1  174.96  30.0  2

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
 C53  plan-1  C6    0.020
 C53  plan-1  C7    0.020
 C53  plan-1  S1    0.020
 C53  plan-1  C8    0.020
 C53  plan-1  O1    0.020
 C53  plan-1  N2    0.020
 C53  plan-1  C9    0.020
 C53  plan-1  N3    0.020
 C53  plan-1  H3N1  0.020
 C53  plan-1  H2N   0.020
 C53  plan-2  C2    0.020
 C53  plan-2  C3    0.020
 C53  plan-2  C4    0.020
 C53  plan-2  C5    0.020
 C53  plan-2  N1    0.020
 C53  plan-2  C1    0.020
 C53  plan-2  C6    0.020
 C53  plan-2  H2    0.020
 C53  plan-2  H3    0.020
 C53  plan-2  H4    0.020
 C53  plan-2  H5    0.020

