# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 06:14:18 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (3R)-3-(7-amino-1-methyl-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CC(O)=O)C1=NN(C)C2=C(C(=O)NC(=N2)N)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
 Z17  Z17  '(3R)-3-(7-amino-1-methyl-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoic acid'  ligand  33  20  .  2021-08-26  2021-08-26  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Z17
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
 Z17  C1   C  CH2   0  -0.582  -3.2386   0.6381   0.2548
 Z17  C2   C  C     0   0.550  -4.6544   0.2029   0.5232
 Z17  C3   C  CR6   0   0.368   0.1471  -1.1703   0.1078
 Z17  N2   N  NR16  0  -0.718   3.8494  -0.8415   0.3026
 Z17  C5   C  CR6   0   0.087  -0.8715  -0.1175  -0.0790
 Z17  C6   C  CH3   0  -0.648  -2.6541  -1.0433  -1.5345
 Z17  O1   O  O     0  -0.444  -0.1793  -2.3469   0.2347
 Z17  N3   N  N     0  -0.203  -0.5805   1.1257  -0.2189
 Z17  O2   O  O     0  -0.440  -5.0001  -0.9193   0.8003
 Z17  C7   C  CR6   0   0.750   3.9737   0.4971   0.1343
 Z17  N4   N  N     0  -0.529   2.9363   1.2841  -0.0331
 Z17  O4   O  OH1   0  -0.581  -5.5023   1.2245   0.4625
 Z17  C8   C  CR66  0   0.605   1.7299   0.7083  -0.0356
 Z17  C9   C  CR66  0  -0.349   1.4881  -0.6619   0.1264
 Z17  N5   N  NR6   0  -0.360   0.6816   1.5433  -0.2085
 Z17  C10  C  CR6   0   0.560   2.6346  -1.5206   0.3163
 Z17  C11  C  CH1   0  -0.292  -2.3213  -0.5151  -0.1350
 Z17  H1   H  HCH2  0   0.287  -3.2350   1.4246  -0.5021
 Z17  H2   H  HCH2  0   0.308  -2.8848   1.1123   1.1770
 Z17  H3   H  HNH2  0   0.391   6.0215   0.4580   0.2698
 Z17  H4   H  HNH2  0   0.405   5.3067   2.0081   0.0268
 Z17  H5   H  HNR6  0   0.401   4.6782  -1.4071   0.4362
 Z17  H6   H  HCH3  0   0.254  -0.0962   3.4116  -0.5750
 Z17  H7   H  HCH3  0   0.242   1.2868   3.4190   0.5357
 Z17  H8   H  HCH3  0   0.245   1.5480   3.1843  -1.1985
 Z17  H9   H  HCH3  0   0.217  -2.5418  -0.2535  -2.2792
 Z17  H10  H  HCH3  0   0.243  -2.0018  -1.8687  -1.8162
 Z17  H11  H  HCH3  0   0.235  -3.6796  -1.4095  -1.5806
 Z17  H13  H  HOH1  0   0.452  -6.3965   0.9267   0.6878
 Z17  H14  H  HCH1  0   0.258  -2.4611  -1.3294   0.5790
 Z17  N1   N  NH2   0  -0.825   5.1941   1.0152   0.1421
 Z17  C4   C  CH3   0  -0.491   0.8758   2.9765  -0.3698
 Z17  O3   O  O     0  -0.395   2.6314  -2.7249   0.4804

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
 Z17  O2   C2   double  1.206  0.020  1.206
 Z17  C2   O4   single  1.329  0.020  1.329
 Z17  C2   C1   single  1.505  0.020  1.505
 Z17  C1   C11  single  1.524  0.020  1.524
 Z17  C11  C6   single  1.532  0.020  1.532
 Z17  C11  C5   single  1.504  0.020  1.504
 Z17  N3   C5   double  1.284  0.020  1.284
 Z17  N3   N5   single  1.329  0.020  1.329
 Z17  C5   C3   single  1.477  0.020  1.477
 Z17  C4   N5   single  1.455  0.020  1.455
 Z17  N5   C8   single  1.351  0.020  1.351
 Z17  C3   O1   double  1.228  0.020  1.228
 Z17  C3   C9   single  1.434  0.020  1.434
 Z17  C8   C9   double  1.401  0.020  1.401
 Z17  C8   N4   single  1.337  0.020  1.337
 Z17  C9   C10  single  1.445  0.020  1.445
 Z17  N4   C7   double  1.313  0.020  1.313
 Z17  C10  O3   double  1.215  0.020  1.215
 Z17  C10  N2   single  1.392  0.020  1.392
 Z17  C7   N2   single  1.355  0.020  1.355
 Z17  C7   N1   single  1.326  0.020  1.326
 Z17  C1   H1   single  0.970  0.020  1.090
 Z17  C1   H2   single  0.970  0.020  1.090
 Z17  N1   H3   single  0.860  0.020  1.020
 Z17  N1   H4   single  0.860  0.020  1.020
 Z17  N2   H5   single  0.860  0.020  1.020
 Z17  C4   H6   single  0.970  0.020  1.090
 Z17  C4   H7   single  0.970  0.020  1.090
 Z17  C4   H8   single  0.970  0.020  1.090
 Z17  C6   H9   single  0.970  0.020  1.090
 Z17  C6   H10  single  0.970  0.020  1.090
 Z17  C6   H11  single  0.970  0.020  1.090
 Z17  O4   H13  single  0.850  0.020  0.980
 Z17  C11  H14  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
 Z17  H2   C1   H1   105.71  3.000
 Z17  H2   C1   C11  110.39  3.000
 Z17  H1   C1   C11  111.46  3.000
 Z17  H2   C1   C2   106.19  3.000
 Z17  H1   C1   C2   109.58  3.000
 Z17  C11  C1   C2   113.13  3.000
 Z17  O4   C2   O2   122.87  3.000
 Z17  O4   C2   C1   111.69  3.000
 Z17  O2   C2   C1   125.41  3.000
 Z17  C9   C3   O1   125.95  3.000
 Z17  C9   C3   C5   113.20  3.000
 Z17  O1   C3   C5   120.86  3.000
 Z17  H5   N2   C10  116.15  3.000
 Z17  H5   N2   C7   119.56  3.000
 Z17  C10  N2   C7   124.29  3.000
 Z17  C11  C5   N3   118.04  3.000
 Z17  N3   C5   C3   123.19  3.000
 Z17  C11  C5   C3   118.76  3.000
 Z17  H11  C6   H10  107.34  3.000
 Z17  H11  C6   H9   108.13  3.000
 Z17  H10  C6   H9   108.08  3.000
 Z17  H11  C6   C11  111.02  3.000
 Z17  H10  C6   C11  111.55  3.000
 Z17  H9   C6   C11  110.57  3.000
 Z17  N5   N3   C5   121.22  3.000
 Z17  N4   C7   N2   122.38  3.000
 Z17  N2   C7   N1   118.02  3.000
 Z17  N4   C7   N1   119.59  3.000
 Z17  C8   N4   C7   117.08  3.000
 Z17  H13  O4   C2   109.99  3.000
 Z17  N5   C8   C9   119.03  3.000
 Z17  C9   C8   N4   125.23  3.000
 Z17  N5   C8   N4   115.74  3.000
 Z17  C10  C9   C8   117.36  3.000
 Z17  C10  C9   C3   122.20  3.000
 Z17  C8   C9   C3   120.44  3.000
 Z17  C8   N5   N3   122.91  3.000
 Z17  C8   N5   C4   121.28  3.000
 Z17  N3   N5   C4   115.80  3.000
 Z17  C9   C10  O3   127.19  3.000
 Z17  O3   C10  N2   119.15  3.000
 Z17  C9   C10  N2   113.66  3.000
 Z17  H14  C11  C6   108.20  3.000
 Z17  H14  C11  C5   107.22  3.000
 Z17  C6   C11  C5   109.54  3.000
 Z17  H14  C11  C1   108.66  3.000
 Z17  C5   C11  C1   111.75  3.000
 Z17  C6   C11  C1   111.33  3.000
 Z17  H4   N1   H3   118.00  3.000
 Z17  H4   N1   C7   119.21  3.000
 Z17  H3   N1   C7   122.79  3.000
 Z17  H8   C4   H7   108.84  3.000
 Z17  H8   C4   H6   109.47  3.000
 Z17  H7   C4   H6   109.43  3.000
 Z17  H8   C4   N5   110.81  3.000
 Z17  H7   C4   N5   111.01  3.000
 Z17  H6   C4   N5   107.25  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
 Z17  CONST_01  C8   N4   C7  N2    0.00   0.0  0
 Z17  CONST_02  C9   C8   N5  N3    0.00   0.0  0
 Z17  CONST_03  N4   C8   N5  N3  180.00   0.0  0
 Z17  CONST_04  N5   C8   N4  C7  180.00   0.0  0
 Z17  CONST_05  C9   C8   N4  C7    0.00   0.0  0
 Z17  CONST_06  C9   C10  N2  C7    0.00   0.0  0
 Z17  CONST_07  C10  N2   C7  N4    0.00   0.0  0
 Z17  CONST_08  C8   N4   C7  N1  180.00   0.0  0
 Z17  CONST_09  C10  N2   C7  N1  180.00   0.0  0
 Z17  CONST_10  C9   C8   N5  C4  180.00   0.0  0
 Z17  CONST_11  N4   C8   N5  C4    0.00   0.0  0
 Z17  CONST_12  O3   C10  N2  C7  180.00   0.0  0
 Z17  CONST_13  H5   N2   C7  N4  180.00   0.0  0
 Z17  CONST_14  H3   N1   C7  N2    0.00   0.0  0
 Z17  CONST_15  H4   N1   C7  N2  180.00   0.0  0
 Z17  CONST_16  H13  O4   C2  C1  180.00   0.0  0
 Z17  Var_01    H6   C4   N5  N3   -5.89  30.0  3
 Z17  Var_02    C11  C1   C2  O2   20.91  30.0  3

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
 Z17  chir_01  C11  C1  C6  C5  negativ

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
 Z17  plan-1  C3   0.020
 Z17  plan-1  N2   0.020
 Z17  plan-1  C5   0.020
 Z17  plan-1  O1   0.020
 Z17  plan-1  N3   0.020
 Z17  plan-1  C7   0.020
 Z17  plan-1  N4   0.020
 Z17  plan-1  C8   0.020
 Z17  plan-1  C9   0.020
 Z17  plan-1  N5   0.020
 Z17  plan-1  C10  0.020
 Z17  plan-1  C11  0.020
 Z17  plan-1  H3   0.020
 Z17  plan-1  H4   0.020
 Z17  plan-1  H5   0.020
 Z17  plan-1  N1   0.020
 Z17  plan-1  C4   0.020
 Z17  plan-1  O3   0.020
 Z17  plan-2  C1   0.020
 Z17  plan-2  C2   0.020
 Z17  plan-2  O2   0.020
 Z17  plan-2  O4   0.020
 Z17  plan-2  H13  0.020

