# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 06:28:15 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 5-[(~{E})-3-(furan-2-yl)prop-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/c2occc2)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
 5LL  5LL  5-[(~{E})-3-(furan-2-yl)prop-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_5LL
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
 5LL  C4   C  CR6   0   0.583   2.5274  -1.2679  -0.0690
 5LL  C5   C  CR6   0  -0.283   1.4191  -0.3053  -0.0181
 5LL  C6   C  CR6   0   0.564   1.7084   1.1261   0.0532
 5LL  N1   N  NR16  0  -0.718   3.0470   1.4598   0.0742
 5LL  N3   N  NR16  0  -0.723   3.7919  -0.7243  -0.0430
 5LL  CAA  C  CR15  0  -0.325  -4.7632  -1.0760  -0.0276
 5LL  CAB  C  CR15  0  -0.328  -5.7712  -0.0863   0.0272
 5LL  CAC  C  CR15  0   0.033  -5.1169   1.1056   0.0793
 5LL  OAD  O  O     0  -0.403  -3.7917   0.9222   0.0609
 5LL  CAE  C  CR5   0   0.380  -3.5636  -0.4123  -0.0046
 5LL  CAF  C  C1    0  -0.312  -2.2339  -0.9025  -0.0349
 5LL  CAG  C  C1    0  -0.236  -1.1009  -0.1517  -0.0051
 5LL  CAH  C  C1    0  -0.185   0.1523  -0.8164  -0.0401
 5LL  O4   O  O     0  -0.439   2.3892  -2.4737  -0.1308
 5LL  C2   C  CR6   0   0.690   4.1169   0.6051   0.0283
 5LL  O2   O  O     0  -0.458   5.2625   0.9942   0.0489
 5LL  O6   O  O     0  -0.437   0.8734   2.0084   0.0937
 5LL  H2   H  HNR6  0   0.430   3.2690   2.4465   0.1238
 5LL  H3   H  HNR6  0   0.430   4.5699  -1.3707  -0.0783
 5LL  H5   H  HCR5  0   0.281  -6.8386  -0.2310   0.0286
 5LL  H6   H  HCR5  0   0.296  -5.4648   2.1247   0.1318
 5LL  H7   H  H     0   0.301  -2.1543  -1.9833  -0.0855
 5LL  H9   H  H     0   0.289  -1.1507   0.9246   0.0448
 5LL  H11  H  H     0   0.285   0.0946  -1.8996  -0.0914
 5LL  H4   H  HCR5  0   0.283  -4.8922  -2.1455  -0.0768

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
 5LL  O2   C2   double    1.210  0.020  1.210
 5LL  N3   C2   single    1.370  0.020  1.370
 5LL  N3   C4   single    1.377  0.020  1.377
 5LL  C2   N1   single    1.370  0.020  1.370
 5LL  O4   C4   double    1.215  0.020  1.215
 5LL  C4   C5   single    1.469  0.020  1.469
 5LL  N1   C6   single    1.380  0.020  1.380
 5LL  C6   C5   single    1.462  0.020  1.462
 5LL  C6   O6   double    1.215  0.020  1.215
 5LL  C5   CAH  double    1.366  0.020  1.366
 5LL  CAH  CAG  single    1.419  0.020  1.419
 5LL  CAF  CAG  double    1.360  0.020  1.360
 5LL  CAF  CAE  single    1.417  0.020  1.417
 5LL  CAA  CAE  aromatic  1.371  0.020  1.371
 5LL  CAA  CAB  aromatic  1.414  0.020  1.414
 5LL  CAE  OAD  aromatic  1.356  0.020  1.356
 5LL  CAB  CAC  aromatic  1.361  0.020  1.361
 5LL  OAD  CAC  aromatic  1.338  0.020  1.338
 5LL  N1   H2   single    0.860  0.020  1.020
 5LL  N3   H3   single    0.860  0.020  1.020
 5LL  CAA  H4   single    0.930  0.020  1.080
 5LL  CAB  H5   single    0.930  0.020  1.080
 5LL  CAC  H6   single    0.930  0.020  1.080
 5LL  CAF  H7   single    0.930  0.020  1.080
 5LL  CAG  H9   single    0.930  0.020  1.080
 5LL  CAH  H11  single    0.930  0.020  1.080

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
 5LL  O4   C4   N3   119.82  3.000
 5LL  O4   C4   C5   124.48  3.000
 5LL  N3   C4   C5   115.70  3.000
 5LL  CAH  C5   C6   123.40  3.000
 5LL  CAH  C5   C4   117.00  3.000
 5LL  C6   C5   C4   119.60  3.000
 5LL  O6   C6   N1   119.37  3.000
 5LL  O6   C6   C5   125.20  3.000
 5LL  N1   C6   C5   115.43  3.000
 5LL  H2   N1   C2   115.99  3.000
 5LL  H2   N1   C6   116.69  3.000
 5LL  C2   N1   C6   127.32  3.000
 5LL  H3   N3   C2   116.04  3.000
 5LL  H3   N3   C4   116.95  3.000
 5LL  C2   N3   C4   127.01  3.000
 5LL  H4   CAA  CAE  125.84  3.000
 5LL  H4   CAA  CAB  127.64  3.000
 5LL  CAE  CAA  CAB  106.52  3.000
 5LL  H5   CAB  CAC  126.45  3.000
 5LL  H5   CAB  CAA  127.78  3.000
 5LL  CAC  CAB  CAA  105.77  3.000
 5LL  H6   CAC  OAD  116.73  3.000
 5LL  H6   CAC  CAB  132.43  3.000
 5LL  OAD  CAC  CAB  110.83  3.000
 5LL  CAE  OAD  CAC  107.59  3.000
 5LL  CAF  CAE  OAD  119.96  3.000
 5LL  OAD  CAE  CAA  109.28  3.000
 5LL  CAF  CAE  CAA  130.77  3.000
 5LL  H7   CAF  CAG  119.34  3.000
 5LL  H7   CAF  CAE  114.48  3.000
 5LL  CAG  CAF  CAE  126.18  3.000
 5LL  H9   CAG  CAH  120.62  3.000
 5LL  H9   CAG  CAF  120.90  3.000
 5LL  CAH  CAG  CAF  118.48  3.000
 5LL  H11  CAH  CAG  114.93  3.000
 5LL  H11  CAH  C5   115.03  3.000
 5LL  CAG  CAH  C5   130.04  3.000
 5LL  O2   C2   N3   122.51  3.000
 5LL  N3   C2   N1   114.93  3.000
 5LL  O2   C2   N1   122.56  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
 5LL  CONST_01  CAC  OAD  CAE  CAA     0.00   0.0  0
 5LL  CONST_02  OAD  CAC  CAB  CAA     0.00   0.0  0
 5LL  CONST_03  OAD  CAE  CAA  CAB     0.00   0.0  0
 5LL  CONST_04  CAE  OAD  CAC  CAB     0.00   0.0  0
 5LL  CONST_05  CAE  CAA  CAB  CAC     0.00   0.0  0
 5LL  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 5LL  CONST_07  C2   N3   C4   C5      0.00   0.0  0
 5LL  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 5LL  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 5LL  CONST_10  CAF  CAE  CAA  CAB   180.00   0.0  0
 5LL  CONST_11  CAF  CAE  OAD  CAC   180.00   0.0  0
 5LL  CONST_12  O2   C2   N3   C4    180.00   0.0  0
 5LL  CONST_13  O2   C2   N1   C6    180.00   0.0  0
 5LL  CONST_14  C2   N3   C4   O4    180.00   0.0  0
 5LL  CONST_15  O6   C6   N1   C2    180.00   0.0  0
 5LL  CONST_16  H6   CAC  CAB  CAA   180.00   0.0  0
 5LL  CONST_17  H4   CAA  CAB  CAC   180.00   0.0  0
 5LL  CONST_18  H5   CAB  CAC  OAD   180.00   0.0  0
 5LL  CONST_19  H3   N3   C4   C5    180.00   0.0  0
 5LL  CONST_20  H2   N1   C6   C5    180.00   0.0  0
 5LL  CONST_21  CAH  CAG  CAF  CAE   180.00   0.0  0
 5LL  CONST_22  H9   CAG  CAF  CAE     0.00   0.0  0
 5LL  CONST_23  H7   CAF  CAG  CAH     0.00   0.0  0
 5LL  Var_01    CAG  CAH  C5   C4   -179.92  30.0  2
 5LL  Var_02    CAG  CAF  CAE  CAA  -179.87  30.0  3
 5LL  Var_03    CAF  CAG  CAH  C5   -179.80  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
 5LL  plan-1  CAA  0.020
 5LL  plan-1  CAB  0.020
 5LL  plan-1  CAC  0.020
 5LL  plan-1  OAD  0.020
 5LL  plan-1  CAE  0.020
 5LL  plan-1  CAF  0.020
 5LL  plan-1  H5   0.020
 5LL  plan-1  H6   0.020
 5LL  plan-1  H4   0.020
 5LL  plan-2  CAE  0.020
 5LL  plan-2  CAF  0.020
 5LL  plan-2  CAG  0.020
 5LL  plan-2  CAH  0.020
 5LL  plan-2  H7   0.020
 5LL  plan-2  H9   0.020
 5LL  plan-3  C4   0.020
 5LL  plan-3  C5   0.020
 5LL  plan-3  C6   0.020
 5LL  plan-3  N1   0.020
 5LL  plan-3  N3   0.020
 5LL  plan-3  CAH  0.020
 5LL  plan-3  O4   0.020
 5LL  plan-3  C2   0.020
 5LL  plan-3  O2   0.020
 5LL  plan-3  O6   0.020
 5LL  plan-3  H2   0.020
 5LL  plan-3  H3   0.020

