# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:02:18 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: cis-tetrahydroimidazo[4,5-d]imidazole-2,5(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@@H]2NC(=O)N[C@@H]2N1
#
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
 GLL  GLL  cis-tetrahydroimidazo[4,5-d]imidazole-2,5(1H,3H)-dione  ligand  16  10  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GLL
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
 GLL  C1    C  CR5   0   0.647  -0.0309   0.2368  -1.8867
 GLL  O1    O  O     0  -0.507  -0.0490   0.8452  -2.9402
 GLL  N1    N  NR15  0  -0.671   1.0566   0.0438  -1.0797
 GLL  N2    N  NR15  0  -0.666  -1.0893  -0.3962  -1.2995
 GLL  C2    C  C     0   0.096   0.7744  -0.8705   0.0022
 GLL  C3    C  C     0   0.098  -0.7737  -0.8821   0.0078
 GLL  N1'   N  NR15  0  -0.666   1.0830  -0.3841   1.3112
 GLL  N2'   N  NR15  0  -0.671  -1.0692   0.0241   1.0928
 GLL  C1'   C  CR5   0   0.647   0.0153   0.2346   1.8985
 GLL  O1'   O  O     0  -0.507   0.0255   0.8442   2.9513
 GLL  HN1   H  HNR5  0   0.405   1.9813   0.0971  -1.4773
 GLL  HN2   H  HNR5  0   0.407  -2.0355  -0.1880  -1.5756
 GLL  H2    H  H     0   0.288   1.2203  -1.8496  -0.1742
 GLL  H3    H  H     0   0.288  -1.2049  -1.8684   0.1810
 GLL  HN1'  H  HNR5  0   0.407   2.0257  -0.1562   1.5840
 GLL  HN2'  H  HNR5  0   0.405  -1.9955   0.0668   1.4880

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
 GLL  C1   O1    double  1.217  0.020  1.217
 GLL  C1   N1    single  1.368  0.020  1.368
 GLL  C1   N2    single  1.366  0.020  1.366
 GLL  N1   C2    single  1.444  0.020  1.444
 GLL  N1   HN1   single  0.890  0.020  1.040
 GLL  N2   C3    single  1.430  0.020  1.430
 GLL  N2   HN2   single  0.890  0.020  1.040
 GLL  C2   C3    single  1.548  0.020  1.548
 GLL  C2   N1'   single  1.430  0.020  1.430
 GLL  C2   H2    single  0.970  0.020  1.090
 GLL  C3   N2'   single  1.444  0.020  1.444
 GLL  C3   H3    single  0.970  0.020  1.090
 GLL  N1'  C1'   single  1.367  0.020  1.367
 GLL  N1'  HN1'  single  0.890  0.020  1.040
 GLL  N2'  C1'   single  1.367  0.020  1.367
 GLL  N2'  HN2'  single  0.890  0.020  1.040
 GLL  C1'  O1'   double  1.217  0.020  1.217

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
 GLL  N2    C1   N1   107.28  3.000
 GLL  N2    C1   O1   126.33  3.000
 GLL  N1    C1   O1   126.39  3.000
 GLL  HN1   N1   C2   120.55  3.000
 GLL  HN1   N1   C1   119.28  3.000
 GLL  C2    N1   C1   112.09  3.000
 GLL  HN2   N2   C3   121.88  3.000
 GLL  HN2   N2   C1   120.94  3.000
 GLL  C3    N2   C1   112.30  3.000
 GLL  H2    C2   N1'  111.43  3.000
 GLL  H2    C2   C3   113.75  3.000
 GLL  N1'   C2   C3   102.42  3.000
 GLL  H2    C2   N1   111.55  3.000
 GLL  N1'   C2   N1   115.35  3.000
 GLL  C3    C2   N1   101.70  3.000
 GLL  H3    C3   N2'  111.55  3.000
 GLL  H3    C3   C2   113.76  3.000
 GLL  N2'   C3   C2   101.69  3.000
 GLL  H3    C3   N2   111.43  3.000
 GLL  N2'   C3   N2   115.37  3.000
 GLL  C2    C3   N2   102.41  3.000
 GLL  HN1'  N1'  C1'  120.82  3.000
 GLL  HN1'  N1'  C2   121.78  3.000
 GLL  C1'   N1'  C2   112.26  3.000
 GLL  HN2'  N2'  C1'  119.43  3.000
 GLL  HN2'  N2'  C3   120.61  3.000
 GLL  C1'   N2'  C3   112.15  3.000
 GLL  O1'   C1'  N2'  126.42  3.000
 GLL  O1'   C1'  N1'  126.31  3.000
 GLL  N2'   C1'  N1'  107.26  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
 GLL  CONST_01  C3   N2   C1   N1    0.00  0.0  0
 GLL  CONST_02  C2   N1   C1   N2    0.00  0.0  0
 GLL  CONST_03  N2'  C1'  N1'  C2    0.00  0.0  0
 GLL  CONST_04  N1'  C1'  N2'  C3    0.00  0.0  0
 GLL  CONST_05  C2   N1   C1   O1  180.00  0.0  0
 GLL  CONST_06  C3   N2   C1   O1  180.00  0.0  0
 GLL  CONST_07  O1'  C1'  N1'  C2  180.00  0.0  0
 GLL  CONST_08  O1'  C1'  N2'  C3  180.00  0.0  0

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
 GLL  chir_01  C2  N1  C3   N1'  positiv
 GLL  chir_02  C3  N2  N2'  C2   positiv

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
 GLL  plan-1  C1    0.020
 GLL  plan-1  O1    0.020
 GLL  plan-1  N1    0.020
 GLL  plan-1  N2    0.020
 GLL  plan-1  C2    0.020
 GLL  plan-1  C3    0.020
 GLL  plan-1  HN1   0.020
 GLL  plan-1  HN2   0.020
 GLL  plan-2  C2    0.020
 GLL  plan-2  C3    0.020
 GLL  plan-2  N1'   0.020
 GLL  plan-2  N2'   0.020
 GLL  plan-2  C1'   0.020
 GLL  plan-2  O1'   0.020
 GLL  plan-2  HN1'  0.020
 GLL  plan-2  HN2'  0.020

