# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:38:08 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=S)NC(=C/C2=CNC(=O)C=C2)/C1=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
 42V  42V  5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one  ligand  25  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_42V
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
 42V  N    N  NR16  0  -0.652   3.4814  -0.8425  -0.2639
 42V  C    C  CH3   0  -0.525  -3.3532  -2.1092  -0.1840
 42V  O    O  O     0  -0.489   5.6827  -0.2947  -0.2925
 42V  C01  C  CR5   0   0.527  -1.2028  -0.8936  -0.0485
 42V  C02  C  CR5   0   0.281  -0.8174   0.5033   0.2028
 42V  C03  C  CR5   0   0.401  -3.0853   0.3412   0.2865
 42V  C04  C  C1    0  -0.363   0.3708   1.1380   0.2609
 42V  C05  C  CR6   0  -0.030   1.7394   0.7094   0.1082
 42V  C06  C  CR16  0  -0.139   2.7599   1.7032   0.2301
 42V  C07  C  CR16  0  -0.460   4.0765   1.4131   0.1050
 42V  C08  C  CR6   0   0.546   4.5225   0.0712  -0.1606
 42V  C09  C  CR16  0   0.018   2.1748  -0.5698  -0.1435
 42V  N01  N  NR5   0  -0.519  -2.5783  -0.9072   0.0187
 42V  N02  N  NR15  0  -0.681  -2.0313   1.1604   0.3904
 42V  S    S  S1    0  -0.324  -4.6762   0.7592   0.4481
 42V  H1   H  HNR6  0   0.431   3.7449  -1.8017  -0.4500
 42V  H2   H  HCH3  0   0.266  -4.4038  -1.8668  -0.0577
 42V  H3   H  HCH3  0   0.265  -3.1938  -2.4977  -1.1878
 42V  H4   H  HCH3  0   0.265  -3.0714  -2.8675   0.5434
 42V  H5   H  H     0   0.291   0.2846   2.2014   0.4642
 42V  H7   H  HCR6  0   0.283   2.4639   2.7261   0.4303
 42V  H8   H  HCR6  0   0.281   4.8284   2.1837   0.2006
 42V  H9   H  HCR6  0   0.333   1.5061  -1.4085  -0.2558
 42V  H6   H  HNR5  0   0.431  -2.1286   2.1439   0.5894
 42V  O01  O  O     0  -0.436  -0.5198  -1.8709  -0.2736

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
 42V  C    N01  single  1.444  0.020  1.444
 42V  S    C03  double  1.653  0.020  1.653
 42V  N01  C03  single  1.374  0.020  1.374
 42V  N01  C01  single  1.377  0.020  1.377
 42V  C03  N02  single  1.339  0.020  1.339
 42V  C01  O01  double  1.213  0.020  1.213
 42V  C01  C02  single  1.471  0.020  1.471
 42V  N02  C02  single  1.393  0.020  1.393
 42V  C07  C06  double  1.354  0.020  1.354
 42V  C07  C08  single  1.439  0.020  1.439
 42V  C06  C05  single  1.430  0.020  1.430
 42V  C02  C04  double  1.348  0.020  1.348
 42V  O    C08  double  1.224  0.020  1.224
 42V  C08  N    single  1.389  0.020  1.389
 42V  C05  C04  single  1.442  0.020  1.442
 42V  C05  C09  double  1.375  0.020  1.375
 42V  N    C09  single  1.340  0.020  1.340
 42V  N    H1   single  0.860  0.020  1.020
 42V  C    H2   single  0.970  0.020  1.090
 42V  C    H3   single  0.970  0.020  1.090
 42V  C    H4   single  0.970  0.020  1.090
 42V  C04  H5   single  0.930  0.020  1.080
 42V  C06  H7   single  0.930  0.020  1.080
 42V  C07  H8   single  0.930  0.020  1.080
 42V  C09  H9   single  0.930  0.020  1.080
 42V  N02  H6   single  0.860  0.020  1.020

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
 42V  H1   N    C09  117.59  3.000
 42V  H1   N    C08  116.24  3.000
 42V  C09  N    C08  126.17  3.000
 42V  H4   C    H3   109.27  3.000
 42V  H4   C    H2   109.18  3.000
 42V  H3   C    H2   109.20  3.000
 42V  H4   C    N01  110.32  3.000
 42V  H3   C    N01  110.36  3.000
 42V  H2   C    N01  108.48  3.000
 42V  O01  C01  N01  124.28  3.000
 42V  O01  C01  C02  130.48  3.000
 42V  N01  C01  C02  105.23  3.000
 42V  N02  C02  C04  122.69  3.000
 42V  C04  C02  C01  133.26  3.000
 42V  N02  C02  C01  104.05  3.000
 42V  S    C03  N02  126.54  3.000
 42V  N02  C03  N01  106.30  3.000
 42V  S    C03  N01  127.16  3.000
 42V  H5   C04  C05  112.71  3.000
 42V  H5   C04  C02  113.51  3.000
 42V  C05  C04  C02  133.78  3.000
 42V  C09  C05  C06  115.87  3.000
 42V  C09  C05  C04  126.62  3.000
 42V  C06  C05  C04  117.50  3.000
 42V  H7   C06  C07  119.01  3.000
 42V  H7   C06  C05  118.49  3.000
 42V  C07  C06  C05  122.50  3.000
 42V  H8   C07  C08  117.75  3.000
 42V  H8   C07  C06  121.03  3.000
 42V  C08  C07  C06  121.22  3.000
 42V  C07  C08  O    126.35  3.000
 42V  O    C08  N    120.39  3.000
 42V  C07  C08  N    113.26  3.000
 42V  H9   C09  C05  123.12  3.000
 42V  H9   C09  N    115.90  3.000
 42V  C05  C09  N    120.98  3.000
 42V  C03  N01  C01  111.66  3.000
 42V  C01  N01  C    122.49  3.000
 42V  C03  N01  C    125.85  3.000
 42V  H6   N02  C03  122.42  3.000
 42V  H6   N02  C02  124.82  3.000
 42V  C03  N02  C02  112.76  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
 42V  CONST_01  N02  C03  N01  C01    0.00   0.0  0
 42V  CONST_02  C03  N02  C02  C01    0.00   0.0  0
 42V  CONST_03  C03  N01  C01  C02    0.00   0.0  0
 42V  CONST_04  N01  C03  N02  C02    0.00   0.0  0
 42V  CONST_05  C09  N    C08  C07    0.00   0.0  0
 42V  CONST_06  N02  C02  C01  N01    0.00   0.0  0
 42V  CONST_07  N02  C03  N01  C    180.00   0.0  0
 42V  CONST_08  C02  C01  N01  C    180.00   0.0  0
 42V  CONST_09  C09  N    C08  O    180.00   0.0  0
 42V  CONST_10  S    C03  N01  C01  180.00   0.0  0
 42V  CONST_11  S    C03  N02  C02  180.00   0.0  0
 42V  CONST_12  O01  C01  N01  C03  180.00   0.0  0
 42V  CONST_13  H6   N02  C02  C01  180.00   0.0  0
 42V  CONST_14  H1   N    C08  C07  180.00   0.0  0
 42V  CONST_15  S    C03  N01  C      0.00   0.0  0
 42V  CONST_16  O01  C01  N01  C      0.00   0.0  0
 42V  Var_01    C05  C04  C02  C01   -0.37  30.0  2
 42V  Var_02    C06  C05  C04  C02  179.43  30.0  2
 42V  Var_03    H2   C    N01  C01  178.69  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
 42V  plan-1  C    0.020
 42V  plan-1  C01  0.020
 42V  plan-1  C02  0.020
 42V  plan-1  C03  0.020
 42V  plan-1  C04  0.020
 42V  plan-1  N01  0.020
 42V  plan-1  N02  0.020
 42V  plan-1  S    0.020
 42V  plan-1  H6   0.020
 42V  plan-1  O01  0.020
 42V  plan-2  N    0.020
 42V  plan-2  O    0.020
 42V  plan-2  C04  0.020
 42V  plan-2  C05  0.020
 42V  plan-2  C06  0.020
 42V  plan-2  C07  0.020
 42V  plan-2  C08  0.020
 42V  plan-2  C09  0.020
 42V  plan-2  H1   0.020
 42V  plan-2  H7   0.020
 42V  plan-2  H8   0.020
 42V  plan-2  H9   0.020

