# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 06:45:17 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 5-[(~{E})-3-thiophen-2-ylprop-2-enylidene]-1,3-diazinane-2,4,6-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)C(=C/C=C/c2sccc2)C(=O)N1
#
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
 5LM  5LM  5-[(~{E})-3-thiophen-2-ylprop-2-enylidene]-1,3-diazinane-2,4,6-trione  ligand  25  17  .  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_5LM
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
 5LM  CAQ  C  CR15  0  -0.210   4.4363  -1.3404  -0.0628
 5LM  CAP  C  CR15  0  -0.169   5.6302  -0.5912  -0.0486
 5LM  CAO  C  CR15  0  -0.441   5.3956   0.7550  -0.0214
 5LM  SAN  S  S2    0   0.250   3.7304   1.1231  -0.0133
 5LM  CAM  C  CR5   0  -0.172   3.3048  -0.5543  -0.0465
 5LM  CAL  C  C1    0  -0.206   1.9591  -1.0276  -0.0546
 5LM  CAK  C  C1    0  -0.255   0.8347  -0.2665  -0.0378
 5LM  CAJ  C  C1    0  -0.188  -0.4291  -0.9132  -0.0484
 5LM  CAE  C  CR6   0  -0.280  -1.6868  -0.3829  -0.0314
 5LM  CAF  C  CR6   0   0.584  -2.8104  -1.3298  -0.0508
 5LM  OAG  O  O     0  -0.438  -2.6903  -2.5384  -0.0850
 5LM  NAA  N  NR16  0  -0.723  -4.0657  -0.7662  -0.0272
 5LM  CAB  C  CR6   0   0.690  -4.3698   0.5697   0.0101
 5LM  OAH  O  O     0  -0.457  -5.5089   0.9768   0.0285
 5LM  NAC  N  NR16  0  -0.718  -3.2868   1.4091   0.0248
 5LM  CAD  C  CR6   0   0.566  -1.9540   1.0549   0.0064
 5LM  OAI  O  O     0  -0.436  -1.1044   1.9238   0.0225
 5LM  H1   H  HCR5  0   0.283   4.3946  -2.4204  -0.0844
 5LM  H2   H  HCR5  0   0.281   6.6202  -1.0225  -0.0580
 5LM  H3   H  HCR5  0   0.312   6.1244   1.5506  -0.0056
 5LM  H4   H  H     0   0.291   1.8586  -2.1087  -0.0751
 5LM  H6   H  H     0   0.287   0.8954   0.8116  -0.0168
 5LM  H8   H  H     0   0.286  -0.3862  -1.9981  -0.0730
 5LM  H11  H  HNR6  0   0.431  -4.8540  -1.4010  -0.0426
 5LM  H12  H  HNR6  0   0.431  -3.4938   2.3999   0.0521

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
 5LM  OAH  CAB  double    1.210  0.020  1.210
 5LM  CAB  NAA  single    1.371  0.020  1.371
 5LM  CAB  NAC  single    1.370  0.020  1.370
 5LM  NAA  CAF  single    1.376  0.020  1.376
 5LM  NAC  CAD  single    1.379  0.020  1.379
 5LM  OAG  CAF  double    1.215  0.020  1.215
 5LM  CAF  CAE  single    1.469  0.020  1.469
 5LM  CAD  CAE  single    1.463  0.020  1.463
 5LM  CAD  OAI  double    1.215  0.020  1.215
 5LM  CAE  CAJ  double    1.365  0.020  1.365
 5LM  CAJ  CAK  single    1.420  0.020  1.420
 5LM  CAL  CAK  double    1.358  0.020  1.358
 5LM  CAL  CAM  single    1.427  0.020  1.427
 5LM  CAQ  CAM  aromatic  1.378  0.020  1.378
 5LM  CAQ  CAP  aromatic  1.410  0.020  1.410
 5LM  CAM  SAN  aromatic  1.731  0.020  1.731
 5LM  CAP  CAO  aromatic  1.367  0.020  1.367
 5LM  SAN  CAO  aromatic  1.705  0.020  1.705
 5LM  CAQ  H1   single    0.930  0.020  1.080
 5LM  CAP  H2   single    0.930  0.020  1.080
 5LM  CAO  H3   single    0.930  0.020  1.080
 5LM  CAL  H4   single    0.930  0.020  1.080
 5LM  CAK  H6   single    0.930  0.020  1.080
 5LM  CAJ  H8   single    0.930  0.020  1.080
 5LM  NAA  H11  single    0.860  0.020  1.020
 5LM  NAC  H12  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
 5LM  H1   CAQ  CAM  122.58  3.000
 5LM  H1   CAQ  CAP  124.32  3.000
 5LM  CAM  CAQ  CAP  113.10  3.000
 5LM  H2   CAP  CAO  123.43  3.000
 5LM  H2   CAP  CAQ  124.34  3.000
 5LM  CAO  CAP  CAQ  112.23  3.000
 5LM  H3   CAO  SAN  120.02  3.000
 5LM  H3   CAO  CAP  127.63  3.000
 5LM  SAN  CAO  CAP  112.36  3.000
 5LM  CAM  SAN  CAO   91.76  3.000
 5LM  CAL  CAM  SAN  123.61  3.000
 5LM  SAN  CAM  CAQ  110.56  3.000
 5LM  CAL  CAM  CAQ  125.83  3.000
 5LM  H4   CAL  CAK  118.79  3.000
 5LM  H4   CAL  CAM  114.69  3.000
 5LM  CAK  CAL  CAM  126.52  3.000
 5LM  H6   CAK  CAJ  120.32  3.000
 5LM  H6   CAK  CAL  120.88  3.000
 5LM  CAJ  CAK  CAL  118.80  3.000
 5LM  H8   CAJ  CAE  115.14  3.000
 5LM  H8   CAJ  CAK  114.84  3.000
 5LM  CAE  CAJ  CAK  130.03  3.000
 5LM  CAD  CAE  CAF  119.61  3.000
 5LM  CAD  CAE  CAJ  123.39  3.000
 5LM  CAF  CAE  CAJ  117.00  3.000
 5LM  NAA  CAF  OAG  119.87  3.000
 5LM  OAG  CAF  CAE  124.45  3.000
 5LM  NAA  CAF  CAE  115.68  3.000
 5LM  H11  NAA  CAB  116.03  3.000
 5LM  H11  NAA  CAF  116.95  3.000
 5LM  CAB  NAA  CAF  127.01  3.000
 5LM  NAC  CAB  OAH  122.54  3.000
 5LM  NAC  CAB  NAA  114.96  3.000
 5LM  OAH  CAB  NAA  122.50  3.000
 5LM  H12  NAC  CAD  116.69  3.000
 5LM  H12  NAC  CAB  115.98  3.000
 5LM  CAD  NAC  CAB  127.33  3.000
 5LM  OAI  CAD  NAC  119.45  3.000
 5LM  OAI  CAD  CAE  125.13  3.000
 5LM  NAC  CAD  CAE  115.42  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
 5LM  CONST_01  CAO  SAN  CAM  CAQ    0.00   0.0  0
 5LM  CONST_02  SAN  CAO  CAP  CAQ    0.00   0.0  0
 5LM  CONST_03  SAN  CAM  CAQ  CAP    0.00   0.0  0
 5LM  CONST_04  CAM  SAN  CAO  CAP    0.00   0.0  0
 5LM  CONST_05  CAM  CAQ  CAP  CAO    0.00   0.0  0
 5LM  CONST_06  CAB  NAA  CAF  CAE    0.00   0.0  0
 5LM  CONST_07  NAC  CAB  NAA  CAF    0.00   0.0  0
 5LM  CONST_08  CAD  NAC  CAB  NAA    0.00   0.0  0
 5LM  CONST_09  CAL  CAM  CAQ  CAP  180.00   0.0  0
 5LM  CONST_10  CAL  CAM  SAN  CAO  180.00   0.0  0
 5LM  CONST_11  OAH  CAB  NAA  CAF  180.00   0.0  0
 5LM  CONST_12  CAB  NAA  CAF  OAG  180.00   0.0  0
 5LM  CONST_13  CAD  NAC  CAB  OAH  180.00   0.0  0
 5LM  CONST_14  H3   CAO  CAP  CAQ  180.00   0.0  0
 5LM  CONST_15  H1   CAQ  CAP  CAO  180.00   0.0  0
 5LM  CONST_16  H2   CAP  CAO  SAN  180.00   0.0  0
 5LM  CONST_17  H11  NAA  CAF  CAE  180.00   0.0  0
 5LM  CONST_18  H12  NAC  CAB  NAA  180.00   0.0  0
 5LM  CONST_19  CAJ  CAK  CAL  CAM  180.00   0.0  0
 5LM  CONST_20  H6   CAK  CAL  CAM    0.00   0.0  0
 5LM  CONST_21  H4   CAL  CAK  CAJ    0.00   0.0  0
 5LM  Var_01    CAK  CAL  CAM  CAQ  179.95  30.0  2
 5LM  Var_02    CAF  CAE  CAJ  CAK  179.95  30.0  2
 5LM  Var_03    CAE  CAJ  CAK  CAL  179.75  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
 5LM  plan-1  CAQ  0.020
 5LM  plan-1  CAP  0.020
 5LM  plan-1  CAO  0.020
 5LM  plan-1  SAN  0.020
 5LM  plan-1  CAM  0.020
 5LM  plan-1  CAL  0.020
 5LM  plan-1  H1   0.020
 5LM  plan-1  H2   0.020
 5LM  plan-1  H3   0.020
 5LM  plan-2  CAM  0.020
 5LM  plan-2  CAL  0.020
 5LM  plan-2  CAK  0.020
 5LM  plan-2  CAJ  0.020
 5LM  plan-2  H4   0.020
 5LM  plan-2  H6   0.020
 5LM  plan-3  CAJ  0.020
 5LM  plan-3  CAE  0.020
 5LM  plan-3  CAF  0.020
 5LM  plan-3  OAG  0.020
 5LM  plan-3  NAA  0.020
 5LM  plan-3  CAB  0.020
 5LM  plan-3  OAH  0.020
 5LM  plan-3  NAC  0.020
 5LM  plan-3  CAD  0.020
 5LM  plan-3  OAI  0.020
 5LM  plan-3  H11  0.020
 5LM  plan-3  H12  0.020

