# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 17:32:11 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: 1,6-dimethylpyrimido[5,4-e][1,2,4]triazine-5,7(1H,6H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1N=CN=C2C(=O)N(C)C(=O)N=C12
#
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
 TOF  TOF  1,6-dimethylpyrimido[5,4-e][1,2,4]triazine-5,7(1H,6H)-dione  ligand  21  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TOF
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
 TOF  C1    C  CR6   0   0.586  -1.1197  -1.1838   0.0579
 TOF  O1    O  O     0  -0.420  -1.5410  -2.3158   0.1249
 TOF  C2    C  CR66  0   0.045   0.3345  -0.8910   0.0321
 TOF  O2    O  O     0  -0.458  -2.2385   2.1652   0.0647
 TOF  N3    N  N     0  -0.334   1.1867  -1.8600   0.0361
 TOF  C4    C  CR16  0   0.048   2.4885  -1.5089   0.0107
 TOF  N5    N  N     0  -0.170   2.9331  -0.2883  -0.0128
 TOF  N6    N  NR6   0  -0.291   2.0599   0.6912  -0.0147
 TOF  C7    C  CR66  0   0.584   0.7182   0.4858   0.0067
 TOF  N8    N  N     0  -0.527  -0.0962   1.4936   0.0102
 TOF  C9    C  CR6   0   0.619  -1.4370   1.2562   0.0262
 TOF  N10   N  NR6   0  -0.584  -1.9163  -0.0741  -0.0076
 TOF  C11   C  CH3   0  -0.521   2.5840   2.0483  -0.0376
 TOF  C12   C  CH3   0  -0.528  -3.3602  -0.2793  -0.0118
 TOF  H4    H  HCR6  0   0.313   3.2295  -2.2938   0.0118
 TOF  H11   H  HCH3  0   0.285   3.6655   1.9862  -0.0572
 TOF  H11A  H  HCH3  0   0.282   2.2184   2.5670  -0.9208
 TOF  H11B  H  HCH3  0   0.282   2.2516   2.5832   0.8491
 TOF  H12   H  HCH3  0   0.261  -3.7481  -0.3239   1.0055
 TOF  H12A  H  HCH3  0   0.266  -3.8420   0.5360  -0.5383
 TOF  H12B  H  HCH3  0   0.262  -3.5924  -1.2107  -0.5175

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
 TOF  C1   O1    double  1.210  0.020  1.210
 TOF  C1   C2    single  1.484  0.020  1.484
 TOF  C1   N10   single  1.368  0.020  1.368
 TOF  C2   N3    double  1.290  0.020  1.290
 TOF  C2   C7    single  1.429  0.020  1.429
 TOF  O2   C9    double  1.212  0.020  1.212
 TOF  N3   C4    single  1.349  0.020  1.349
 TOF  C4   N5    double  1.299  0.020  1.299
 TOF  N5   N6    single  1.312  0.020  1.312
 TOF  N6   C7    single  1.357  0.020  1.357
 TOF  N6   C11   single  1.455  0.020  1.455
 TOF  C7   N8    double  1.296  0.020  1.296
 TOF  N8   C9    single  1.362  0.020  1.362
 TOF  C9   N10   single  1.414  0.020  1.414
 TOF  N10  C12   single  1.458  0.020  1.458
 TOF  C4   H4    single  0.930  0.020  1.080
 TOF  C11  H11   single  0.970  0.020  1.090
 TOF  C11  H11A  single  0.970  0.020  1.090
 TOF  C11  H11B  single  0.970  0.020  1.090
 TOF  C12  H12   single  0.970  0.020  1.090
 TOF  C12  H12A  single  0.970  0.020  1.090
 TOF  C12  H12B  single  0.970  0.020  1.090

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
 TOF  N10   C1   C2    114.20  3.000
 TOF  N10   C1   O1    123.99  3.000
 TOF  C2    C1   O1    121.80  3.000
 TOF  C7    C2   N3    123.10  3.000
 TOF  C7    C2   C1    116.96  3.000
 TOF  N3    C2   C1    119.94  3.000
 TOF  C4    N3   C2    116.23  3.000
 TOF  H4    C4   N5    116.63  3.000
 TOF  H4    C4   N3    118.25  3.000
 TOF  N5    C4   N3    125.11  3.000
 TOF  N6    N5   C4    118.26  3.000
 TOF  C11   N6   C7    119.83  3.000
 TOF  C11   N6   N5    117.16  3.000
 TOF  C7    N6   N5    123.01  3.000
 TOF  N8    C7   N6    120.23  3.000
 TOF  N8    C7   C2    125.48  3.000
 TOF  N6    C7   C2    114.29  3.000
 TOF  C9    N8   C7    118.90  3.000
 TOF  N10   C9   N8    119.82  3.000
 TOF  N10   C9   O2    118.81  3.000
 TOF  N8    C9   O2    121.37  3.000
 TOF  C12   N10  C9    117.89  3.000
 TOF  C12   N10  C1    117.56  3.000
 TOF  C9    N10  C1    124.38  3.000
 TOF  H11B  C11  H11A  108.95  3.000
 TOF  H11B  C11  H11   110.37  3.000
 TOF  H11A  C11  H11   110.37  3.000
 TOF  H11B  C11  N6    109.62  3.000
 TOF  H11A  C11  N6    109.67  3.000
 TOF  H11   C11  N6    107.85  3.000
 TOF  H12B  C12  H12A  108.92  3.000
 TOF  H12B  C12  H12   108.90  3.000
 TOF  H12A  C12  H12   109.03  3.000
 TOF  H12B  C12  N10   109.51  3.000
 TOF  H12A  C12  N10   109.62  3.000
 TOF  H12   C12  N10   110.82  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
 TOF  CONST_01  N8   C9   N10  C1    0.00   0.0  0
 TOF  CONST_02  C9   N10  C1   C2    0.00   0.0  0
 TOF  CONST_03  N5   C4   N3   C2    0.00   0.0  0
 TOF  CONST_04  N5   N6   C7   C2    0.00   0.0  0
 TOF  CONST_05  C9   N8   C7   C2    0.00   0.0  0
 TOF  CONST_06  N6   N5   C4   N3    0.00   0.0  0
 TOF  CONST_07  N8   C7   N6   N5  180.00   0.0  0
 TOF  CONST_08  C9   N8   C7   N6  180.00   0.0  0
 TOF  CONST_09  N10  C9   N8   C7    0.00   0.0  0
 TOF  CONST_10  O2   C9   N10  C1  180.00   0.0  0
 TOF  CONST_11  C9   N10  C1   O1  180.00   0.0  0
 TOF  CONST_12  C12  N10  C1   C2  180.00   0.0  0
 TOF  CONST_13  C11  N6   C7   C2  180.00   0.0  0
 TOF  CONST_14  C7   N8   C9   O2  180.00   0.0  0
 TOF  CONST_15  C11  N6   C7   N8    0.00   0.0  0
 TOF  CONST_16  C12  N10  C9   N8  180.00   0.0  0
 TOF  CONST_17  H4   C4   N3   C2  180.00   0.0  0
 TOF  CONST_18  C12  N10  C1   O1    0.00   0.0  0
 TOF  CONST_19  C12  N10  C9   O2    0.00   0.0  0
 TOF  Var_01    C4   N3   C2   C1  179.96   0.0  0
 TOF  Var_02    C7   C2   N3   C4   -0.20   0.0  0
 TOF  Var_03    H12  C12  N10  C1   87.58  30.0  3
 TOF  Var_04    H11  C11  N6   N5    0.43  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
 TOF  plan-1  C1   0.020
 TOF  plan-1  O1   0.020
 TOF  plan-1  C2   0.020
 TOF  plan-1  O2   0.020
 TOF  plan-1  N3   0.020
 TOF  plan-1  C4   0.020
 TOF  plan-1  N5   0.020
 TOF  plan-1  N6   0.020
 TOF  plan-1  C7   0.020
 TOF  plan-1  N8   0.020
 TOF  plan-1  C9   0.020
 TOF  plan-1  N10  0.020
 TOF  plan-1  C11  0.020
 TOF  plan-1  C12  0.020
 TOF  plan-1  H4   0.020

