# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 11:19:38 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1nc(Cc2ccc(Cl)c(Cl)c2)nc(O)c1O
#
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
 ON1  ON1  '2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid'  ligand  28  20  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ON1
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
 ON1  C1   C   CR16  0  -0.256  -1.7558   0.4342   0.7739
 ON1  N1   N   N     0  -0.413   1.8925   0.5342   1.0712
 ON1  O1   O   OH1   0  -0.614   4.4314  -0.6049  -1.2693
 ON1  CL1  CL  CL    0  -0.099  -4.8660  -0.8922  -1.3588
 ON1  C2   C   CR6   0   0.022  -2.8853   0.3955  -0.0283
 ON1  N2   N   N     0  -0.405   1.6366  -1.7530   0.5977
 ON1  O2   O   OH1   0  -0.580   2.9942  -2.8671  -0.7921
 ON1  CL2  CL  CL    0  -0.099  -3.5709   1.8724  -0.5925
 ON1  C3   C   CR6   0  -0.018  -3.4565  -0.8251  -0.3706
 ON1  O3   O   OH1   0  -0.563   3.1594   2.8529   0.7559
 ON1  C4   C   CR16  0  -0.200  -2.8870  -2.0010   0.0930
 ON1  O4   O   O     0  -0.463   4.6374   1.9587  -0.6582
 ON1  C5   C   CR16  0  -0.304  -1.7568  -1.9568   0.8926
 ON1  C6   C   CR6   0   0.129  -1.1829  -0.7406   1.2463
 ON1  C7   C   CH2   0  -0.599   0.0648  -0.6797   2.0889
 ON1  C8   C   CR6   0   0.342   1.2829  -0.6147   1.2102
 ON1  C9   C   CR6   0  -0.019   2.9521   0.5747   0.2496
 ON1  C10  C   CR6   0   0.209   3.4000  -0.5380  -0.4333
 ON1  C11  C   CR6   0   0.461   2.6641  -1.7303  -0.2023
 ON1  C12  C   C     0   0.579   3.6671   1.8601   0.0694
 ON1  H1   H   HCR6  0   0.281  -1.3219   1.3920   1.0315
 ON1  HO3  H   HOH1  0   0.497   3.6689   3.6634   0.6007
 ON1  H4   H   HCR6  0   0.288  -3.3309  -2.9513  -0.1704
 ON1  H5   H   HCR6  0   0.268  -1.3246  -2.8836   1.2459
 ON1  H7   H   HCH2  0   0.283   0.0433   0.2001   2.7309
 ON1  H7A  H   HCH2  0   0.286   0.1254  -1.5617   2.7279
 ON1  H71  H   HOH1  0   0.492   4.8453   0.2796  -1.3271
 ON1  H8   H   HOH1  0   0.493   3.7736  -2.7665  -1.3555

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
 ON1  C1   C2   aromatic  1.386  0.020  1.386
 ON1  C1   H1   single    0.930  0.020  1.080
 ON1  N1   C8   aromatic  1.308  0.020  1.308
 ON1  O1   C10  single    1.329  0.020  1.329
 ON1  C2   CL2  single    1.723  0.020  1.723
 ON1  C3   CL1  single    1.723  0.020  1.723
 ON1  C3   C2   aromatic  1.390  0.020  1.390
 ON1  O3   HO3  single    0.850  0.020  0.980
 ON1  C4   C3   aromatic  1.386  0.020  1.386
 ON1  C4   H4   single    0.930  0.020  1.080
 ON1  O4   C12  double    1.217  0.020  1.217
 ON1  C5   C4   aromatic  1.385  0.020  1.385
 ON1  C5   C6   aromatic  1.391  0.020  1.391
 ON1  C5   H5   single    0.930  0.020  1.080
 ON1  C6   C1   aromatic  1.390  0.020  1.390
 ON1  C7   C6   single    1.507  0.020  1.507
 ON1  C7   H7   single    0.970  0.020  1.090
 ON1  C7   H7A  single    0.970  0.020  1.090
 ON1  C8   N2   aromatic  1.340  0.020  1.340
 ON1  C8   C7   single    1.503  0.020  1.503
 ON1  C9   N1   aromatic  1.341  0.020  1.341
 ON1  C9   C10  aromatic  1.380  0.020  1.380
 ON1  C10  C11  aromatic  1.420  0.020  1.420
 ON1  C11  N2   aromatic  1.302  0.020  1.302
 ON1  C11  O2   single    1.322  0.020  1.322
 ON1  C12  O3   single    1.309  0.020  1.309
 ON1  C12  C9   single    1.482  0.020  1.482
 ON1  O1   H71  single    0.850  0.020  0.980
 ON1  O2   H8   single    0.850  0.020  0.980

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
 ON1  H1   C1   C6   120.12  3.000
 ON1  C6   C1   C2   120.60  3.000
 ON1  H1   C1   C2   119.28  3.000
 ON1  C9   N1   C8   117.37  3.000
 ON1  H71  O1   C10  108.66  3.000
 ON1  C3   C2   CL2  120.55  3.000
 ON1  C3   C2   C1   120.12  3.000
 ON1  CL2  C2   C1   119.32  3.000
 ON1  C11  N2   C8   118.31  3.000
 ON1  H8   O2   C11  111.81  3.000
 ON1  C4   C3   C2   119.57  3.000
 ON1  C4   C3   CL1  119.66  3.000
 ON1  C2   C3   CL1  120.77  3.000
 ON1  HO3  O3   C12  110.24  3.000
 ON1  H4   C4   C5   120.24  3.000
 ON1  C5   C4   C3   120.07  3.000
 ON1  H4   C4   C3   119.69  3.000
 ON1  H5   C5   C6   120.09  3.000
 ON1  H5   C5   C4   119.15  3.000
 ON1  C6   C5   C4   120.77  3.000
 ON1  C7   C6   C5   121.29  3.000
 ON1  C7   C6   C1   119.82  3.000
 ON1  C5   C6   C1   118.86  3.000
 ON1  H7A  C7   H7   108.00  3.000
 ON1  H7A  C7   C8   109.41  3.000
 ON1  H7   C7   C8   109.00  3.000
 ON1  C8   C7   C6   110.23  3.000
 ON1  H7A  C7   C6   109.93  3.000
 ON1  H7   C7   C6   110.23  3.000
 ON1  C7   C8   N2   116.38  3.000
 ON1  C7   C8   N1   118.53  3.000
 ON1  N2   C8   N1   125.06  3.000
 ON1  C12  C9   C10  118.85  3.000
 ON1  C12  C9   N1   118.80  3.000
 ON1  C10  C9   N1   122.35  3.000
 ON1  C11  C10  C9   115.36  3.000
 ON1  C11  C10  O1   117.52  3.000
 ON1  C9   C10  O1   127.12  3.000
 ON1  C10  C11  O2   121.32  3.000
 ON1  O2   C11  N2   117.12  3.000
 ON1  C10  C11  N2   121.56  3.000
 ON1  C9   C12  O4   121.86  3.000
 ON1  C9   C12  O3   114.00  3.000
 ON1  O4   C12  O3   124.14  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
 ON1  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 ON1  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 ON1  CONST_03  C11  N2   C8   N1     0.00   0.0  0
 ON1  CONST_04  C11  C10  C9   N1     0.00   0.0  0
 ON1  CONST_05  C5   C6   C1   C2     0.00   0.0  0
 ON1  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 ON1  CONST_07  C9   N1   C8   N2     0.00   0.0  0
 ON1  CONST_08  C9   C10  C11  N2     0.00   0.0  0
 ON1  CONST_09  C6   C1   C2   C3     0.00   0.0  0
 ON1  CONST_10  C6   C5   C4   C3     0.00   0.0  0
 ON1  CONST_11  C10  C9   N1   C8     0.00   0.0  0
 ON1  CONST_12  C10  C11  N2   C8     0.00   0.0  0
 ON1  CONST_13  CL1  C3   C2   C1   180.00   0.0  0
 ON1  CONST_14  O1   C10  C9   N1   180.00   0.0  0
 ON1  CONST_15  N2   C11  C10  O1   180.00   0.0  0
 ON1  CONST_16  C5   C4   C3   CL1  180.00   0.0  0
 ON1  CONST_17  C7   C6   C1   C2   180.00   0.0  0
 ON1  CONST_18  C9   C10  C11  O2   180.00   0.0  0
 ON1  CONST_19  C8   N2   C11  O2   180.00   0.0  0
 ON1  CONST_20  C6   C1   C2   CL2  180.00   0.0  0
 ON1  CONST_21  C4   C3   C2   CL2  180.00   0.0  0
 ON1  CONST_22  C7   C6   C5   C4   180.00   0.0  0
 ON1  CONST_23  C9   N1   C8   C7   180.00   0.0  0
 ON1  CONST_24  C11  N2   C8   C7   180.00   0.0  0
 ON1  CONST_25  C12  C9   N1   C8   180.00   0.0  0
 ON1  CONST_26  C12  C9   C10  C11  180.00   0.0  0
 ON1  CONST_27  H5   C5   C6   C1   180.00   0.0  0
 ON1  CONST_28  H4   C4   C3   C2   180.00   0.0  0
 ON1  CONST_29  H1   C1   C2   C3   180.00   0.0  0
 ON1  CONST_30  HO3  O3   C12  C9   180.00   0.0  0
 ON1  Var_01    C8   C7   C6   C1   -84.85  30.0  2
 ON1  Var_02    C6   C7   C8   N1   103.81  30.0  2
 ON1  Var_03    O4   C12  C9   N1   179.73  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
 ON1  plan-1  C1   0.020
 ON1  plan-1  CL1  0.020
 ON1  plan-1  C2   0.020
 ON1  plan-1  CL2  0.020
 ON1  plan-1  C3   0.020
 ON1  plan-1  C4   0.020
 ON1  plan-1  C5   0.020
 ON1  plan-1  C6   0.020
 ON1  plan-1  C7   0.020
 ON1  plan-1  H1   0.020
 ON1  plan-1  H4   0.020
 ON1  plan-1  H5   0.020
 ON1  plan-2  N1   0.020
 ON1  plan-2  O1   0.020
 ON1  plan-2  N2   0.020
 ON1  plan-2  O2   0.020
 ON1  plan-2  C7   0.020
 ON1  plan-2  C8   0.020
 ON1  plan-2  C9   0.020
 ON1  plan-2  C10  0.020
 ON1  plan-2  C11  0.020
 ON1  plan-2  C12  0.020
 ON1  plan-3  O3   0.020
 ON1  plan-3  O4   0.020
 ON1  plan-3  C9   0.020
 ON1  plan-3  C12  0.020
 ON1  plan-3  HO3  0.020

