# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 06:18:03 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  27  20  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.252  -1.5712   0.3830   0.7952
 ON1  N1   N   N      0  -0.437   1.8684   0.5437   1.0522
 ON1  O1   O   OH1    0  -0.622   4.5356  -0.1043  -1.2696
 ON1  CL1  CL  CL     0  -0.101  -4.8083  -0.6840  -1.2945
 ON1  C2   C   CR6    0   0.023  -2.7162   0.4369   0.0173
 ON1  N2   N   N      0  -0.446   1.8638  -1.7488   0.5379
 ON1  O2   O   OH1    0  -0.614   3.3989  -2.6125  -0.9236
 ON1  CL2  CL  CL     0  -0.100  -3.3103   1.9685  -0.5051
 ON1  C3   C   CR6    0  -0.019  -3.3782  -0.7347  -0.3349
 ON1  O3   O   OC    -1  -0.588   2.7713   2.9157  -0.5899
 ON1  C4   C   CR16   0  -0.199  -2.8826  -1.9554   0.0949
 ON1  O4   O   O      0  -0.590   4.5052   2.3726   0.7204
 ON1  C5   C   CR16   0  -0.313  -1.7353  -2.0037   0.8705
 ON1  C6   C   CR6    0   0.129  -1.0710  -0.8382   1.2340
 ON1  C7   C   CH2    0  -0.590   0.1918  -0.8829   2.0552
 ON1  C8   C   CR6    0   0.343   1.3937  -0.6800   1.1737
 ON1  C9   C   CR6    0   0.042   2.9114   0.7305   0.2343
 ON1  C10  C   CR6    0   0.205   3.4794  -0.3205  -0.4591
 ON1  C11  C   CR6    0   0.405   2.8901  -1.5732  -0.2650
 ON1  C12  C   C      0   0.377   3.4523   2.1455   0.1045
 ON1  H1   H   HCR6   0   0.279  -1.0644   1.3027   1.0584
 ON1  H4   H   HCR6   0   0.287  -3.3961  -2.8678  -0.1760
 ON1  H5   H   HCR6   0   0.267  -1.3604  -2.9647   1.1977
 ON1  H7   H   HCH2   0   0.279   0.1706  -0.1008   2.8144
 ON1  H7A  H   HCH2   0   0.276   0.2663  -1.8441   2.5646
 ON1  H71  H   HOH1   0   0.476   4.7393  -0.8911  -1.7880
 ON1  H8   H   HOH1   0   0.483   2.8912  -3.4087  -0.7153

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  1.385  0.020  1.385
 ON1  C1   H1   single    0.930  0.020  1.080
 ON1  N1   C8   aromatic  1.318  0.020  1.318
 ON1  O1   C10  single    1.349  0.020  1.349
 ON1  C2   CL2  single    1.724  0.020  1.724
 ON1  C3   CL1  single    1.723  0.020  1.723
 ON1  C3   C2   aromatic  1.391  0.020  1.391
 ON1  C4   C3   aromatic  1.386  0.020  1.386
 ON1  C4   H4   single    0.930  0.020  1.080
 ON1  O4   C12  deloc     1.241  0.020  1.241
 ON1  C5   C4   aromatic  1.386  0.020  1.386
 ON1  C5   C6   aromatic  1.390  0.020  1.390
 ON1  C5   H5   single    0.930  0.020  1.080
 ON1  C6   C1   aromatic  1.391  0.020  1.391
 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  1.330  0.020  1.330
 ON1  C8   C7   single    1.504  0.020  1.504
 ON1  C9   N1   aromatic  1.339  0.020  1.339
 ON1  C9   C10  aromatic  1.381  0.020  1.381
 ON1  C10  C11  aromatic  1.398  0.020  1.398
 ON1  C11  N2   aromatic  1.315  0.020  1.315
 ON1  C11  O2   single    1.331  0.020  1.331
 ON1  C12  O3   deloc     1.241  0.020  1.241
 ON1  C12  C9   single    1.520  0.020  1.520
 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   120.06  3.000
 ON1  C6   C1   C2   120.58  3.000
 ON1  H1   C1   C2   119.36  3.000
 ON1  C9   N1   C8   117.81  3.000
 ON1  H71  O1   C10  110.96  3.000
 ON1  C3   C2   CL2  120.50  3.000
 ON1  C3   C2   C1   120.18  3.000
 ON1  CL2  C2   C1   119.32  3.000
 ON1  C11  N2   C8   117.43  3.000
 ON1  H8   O2   C11  109.60  3.000
 ON1  C4   C3   C2   119.55  3.000
 ON1  C4   C3   CL1  119.70  3.000
 ON1  C2   C3   CL1  120.75  3.000
 ON1  H4   C4   C5   120.26  3.000
 ON1  C5   C4   C3   120.03  3.000
 ON1  H4   C4   C3   119.71  3.000
 ON1  H5   C5   C6   120.00  3.000
 ON1  H5   C5   C4   119.15  3.000
 ON1  C6   C5   C4   120.85  3.000
 ON1  C7   C6   C5   121.21  3.000
 ON1  C7   C6   C1   119.96  3.000
 ON1  C5   C6   C1   118.81  3.000
 ON1  H7A  C7   H7   107.96  3.000
 ON1  H7A  C7   C8   109.76  3.000
 ON1  H7   C7   C8   109.08  3.000
 ON1  C8   C7   C6   110.25  3.000
 ON1  H7A  C7   C6   109.75  3.000
 ON1  H7   C7   C6   109.99  3.000
 ON1  C7   C8   N2   117.02  3.000
 ON1  C7   C8   N1   117.84  3.000
 ON1  N2   C8   N1   125.09  3.000
 ON1  C12  C9   C10  121.27  3.000
 ON1  C12  C9   N1   117.34  3.000
 ON1  C10  C9   N1   121.40  3.000
 ON1  C11  C10  C9   116.03  3.000
 ON1  C11  C10  O1   123.86  3.000
 ON1  C9   C10  O1   120.11  3.000
 ON1  C10  C11  O2   118.02  3.000
 ON1  O2   C11  N2   119.74  3.000
 ON1  C10  C11  N2   122.24  3.000
 ON1  C9   C12  O4   115.46  3.000
 ON1  C9   C12  O3   115.49  3.000
 ON1  O4   C12  O3   129.05  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  Var_01    C8   C7   C6   C1   -76.57  30.0  2
 ON1  Var_02    C6   C7   C8   N1    94.31  30.0  2
 ON1  Var_03    O4   C12  C9   N1   103.41  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

