# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 00:16:25 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 5-hydroxy-2-(1-methyl-1H-imidazol-4-yl)-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc(c1)C2=NC(=C(O)C(=O)N2)C(O)=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
 0N9  0N9  '5-hydroxy-2-(1-methyl-1H-imidazol-4-yl)-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid'  ligand  24  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0N9
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
 0N9  O16  O  OC    -1  -0.589   2.0261  -2.8229   0.5048
 0N9  C14  C  C      0   0.382   2.5444  -1.8437  -0.0559
 0N9  O15  O  O      0  -0.587   3.6454  -1.7872  -0.6295
 0N9  C3   C  CR6    0  -0.043   1.7184  -0.5603  -0.0325
 0N9  C2   C  CR6    0   0.198   2.2777   0.6863  -0.0087
 0N9  O13  O  OH1    0  -0.612   3.5972   0.9265  -0.0001
 0N9  N4   N  N      0  -0.448   0.3622  -0.7251  -0.0245
 0N9  C5   C  CR6    0   0.413  -0.3983   0.3156   0.0069
 0N9  N6   N  NR16   0  -0.688   0.0969   1.5816   0.0506
 0N9  C1   C  CR6    0   0.456   1.4315   1.8608   0.0537
 0N9  O12  O  O      0  -0.501   1.8773   3.0047   0.1028
 0N9  C7   C  CR5    0   0.075  -1.8465   0.2036   0.0025
 0N9  N11  N  N      0  -0.471  -2.6447   1.3098   0.0491
 0N9  C10  C  CR15   0   0.105  -3.8672   0.8521   0.0343
 0N9  N9   N  NR5    0  -0.401  -3.8984  -0.4985  -0.0206
 0N9  C17  C  CH3    0  -0.518  -5.0831  -1.3298  -0.0489
 0N9  C8   C  CR15   0  -0.052  -2.6117  -0.9327  -0.0411
 0N9  H3   H  HOH1   0   0.462   3.7159   1.8859   0.0687
 0N9  H4   H  HCR5   0   0.291  -4.7678   1.4465   0.0614
 0N9  H5   H  HCH3   0   0.268  -5.1003  -1.9318  -0.9545
 0N9  H6   H  HCH3   0   0.268  -5.1066  -1.9847   0.8190
 0N9  H7   H  HCH3   0   0.268  -5.9630  -0.6932  -0.0334
 0N9  H8   H  HCR5   0   0.299  -2.3508  -1.9767  -0.0848
 0N9  H2   H  HNR6   0   0.425  -0.5610   2.3531   0.0873

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
 0N9  C17  N9   single    1.448  0.020  1.448
 0N9  C10  N9   aromatic  1.352  0.020  1.352
 0N9  C10  N11  aromatic  1.305  0.020  1.305
 0N9  N9   C8   aromatic  1.358  0.020  1.358
 0N9  N11  C7   aromatic  1.365  0.020  1.365
 0N9  C8   C7   aromatic  1.371  0.020  1.371
 0N9  C7   C5   single    1.452  0.020  1.452
 0N9  C5   N6   single    1.360  0.020  1.360
 0N9  C5   N4   double    1.289  0.020  1.289
 0N9  N6   C1   single    1.363  0.020  1.363
 0N9  N4   C3   single    1.366  0.020  1.366
 0N9  C1   O12  double    1.229  0.020  1.229
 0N9  C1   C2   single    1.449  0.020  1.449
 0N9  C3   C2   double    1.367  0.020  1.367
 0N9  C3   C14  single    1.526  0.020  1.526
 0N9  C2   O13  single    1.341  0.020  1.341
 0N9  O15  C14  deloc     1.243  0.020  1.243
 0N9  C14  O16  deloc     1.242  0.020  1.242
 0N9  O13  H3   single    0.850  0.020  0.980
 0N9  C10  H4   single    0.930  0.020  1.080
 0N9  C17  H5   single    0.970  0.020  1.090
 0N9  C17  H6   single    0.970  0.020  1.090
 0N9  C17  H7   single    0.970  0.020  1.090
 0N9  C8   H8   single    0.930  0.020  1.080
 0N9  N6   H2   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
 0N9  C3   C14  O15  116.64  3.000
 0N9  O15  C14  O16  127.88  3.000
 0N9  C3   C14  O16  115.48  3.000
 0N9  N4   C3   C2   121.08  3.000
 0N9  C2   C3   C14  123.08  3.000
 0N9  N4   C3   C14  115.84  3.000
 0N9  C1   C2   O13  115.41  3.000
 0N9  O13  C2   C3   124.48  3.000
 0N9  C1   C2   C3   120.08  3.000
 0N9  H3   O13  C2   107.35  3.000
 0N9  C5   N4   C3   119.23  3.000
 0N9  C7   C5   N6   115.78  3.000
 0N9  N6   C5   N4   122.50  3.000
 0N9  C7   C5   N4   121.72  3.000
 0N9  H2   N6   C1   118.62  3.000
 0N9  H2   N6   C5   118.21  3.000
 0N9  C1   N6   C5   123.17  3.000
 0N9  O12  C1   N6   123.09  3.000
 0N9  O12  C1   C2   122.98  3.000
 0N9  N6   C1   C2   113.93  3.000
 0N9  C8   C7   N11  110.27  3.000
 0N9  C8   C7   C5   128.37  3.000
 0N9  N11  C7   C5   121.36  3.000
 0N9  C10  N11  C7   105.25  3.000
 0N9  H4   C10  N9   122.13  3.000
 0N9  H4   C10  N11  126.01  3.000
 0N9  N9   C10  N11  111.86  3.000
 0N9  C8   N9   C17  126.26  3.000
 0N9  C8   N9   C10  107.34  3.000
 0N9  C17  N9   C10  126.40  3.000
 0N9  H7   C17  H6   108.90  3.000
 0N9  H7   C17  H5   108.88  3.000
 0N9  H6   C17  H5   109.32  3.000
 0N9  H7   C17  N9   109.03  3.000
 0N9  H6   C17  N9   110.36  3.000
 0N9  H5   C17  N9   110.31  3.000
 0N9  H8   C8   N9   122.69  3.000
 0N9  H8   C8   C7   132.04  3.000
 0N9  N9   C8   C7   105.27  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
 0N9  CONST_01  N9   C10  N11  C7     0.00   0.0  0
 0N9  CONST_02  C10  N9   C8   C7     0.00   0.0  0
 0N9  CONST_03  C8   N9   C10  N11    0.00   0.0  0
 0N9  CONST_04  N9   C8   C7   N11    0.00   0.0  0
 0N9  CONST_05  C8   C7   N11  C10    0.00   0.0  0
 0N9  CONST_06  C10  N11  C7   C5   180.00   0.0  0
 0N9  CONST_07  N9   C8   C7   C5   180.00   0.0  0
 0N9  CONST_08  C7   C5   N4   C3   180.00   0.0  0
 0N9  CONST_09  N6   C5   N4   C3     0.00   0.0  0
 0N9  CONST_10  C5   N6   C1   C2     0.00   0.0  0
 0N9  CONST_11  C1   N6   C5   N4     0.00   0.0  0
 0N9  CONST_12  C7   C5   N6   C1   180.00   0.0  0
 0N9  CONST_13  C17  N9   C8   C7   180.00   0.0  0
 0N9  CONST_14  C17  N9   C10  N11  180.00   0.0  0
 0N9  CONST_15  O12  C1   N6   C5   180.00   0.0  0
 0N9  CONST_16  H8   C8   C7   C5     0.00   0.0  0
 0N9  CONST_17  H4   C10  N11  C7   180.00   0.0  0
 0N9  CONST_18  H2   N6   C1   C2   180.00   0.0  0
 0N9  Var_01    N11  C7   C5   N4   179.35  30.0  2
 0N9  Var_02    N4   C3   C14  O16  -30.56  30.0  2
 0N9  Var_03    H5   C17  N9   C10  120.32  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
 0N9  plan-1  C5   0.020
 0N9  plan-1  C7   0.020
 0N9  plan-1  N11  0.020
 0N9  plan-1  C10  0.020
 0N9  plan-1  N9   0.020
 0N9  plan-1  C17  0.020
 0N9  plan-1  C8   0.020
 0N9  plan-1  H4   0.020
 0N9  plan-1  H8   0.020
 0N9  plan-2  C14  0.020
 0N9  plan-2  C3   0.020
 0N9  plan-2  C2   0.020
 0N9  plan-2  O13  0.020
 0N9  plan-2  N4   0.020
 0N9  plan-2  C5   0.020
 0N9  plan-2  N6   0.020
 0N9  plan-2  C1   0.020
 0N9  plan-2  O12  0.020
 0N9  plan-2  C7   0.020
 0N9  plan-2  H2   0.020
 0N9  plan-3  O16  0.020
 0N9  plan-3  C14  0.020
 0N9  plan-3  O15  0.020
 0N9  plan-3  C3   0.020

