# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 05:38:31 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: 5-chloranylpyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ncncc1Cl
#
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
 6SM  6SM  '5-chloranylpyrimidine-4-carboxylic acid'  ligand  13  10  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6SM
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
 6SM  O2  O   OH1   0  -0.574  -1.7917  -2.1413   0.0176
 6SM  C5  C   C     0   0.528  -1.5427  -0.8479   0.0410
 6SM  O1  O   O     0  -0.404  -2.3833   0.0106   0.0749
 6SM  C2  C   CR6   0   0.196  -0.0669  -0.5663   0.0211
 6SM  N1  N   N     0  -0.389   0.7402  -1.6208   0.0465
 6SM  C3  C   CR6   0  -0.093   0.4634   0.7182  -0.0187
 6SM  CL  CL  CL    0  -0.062  -0.4433   2.1685  -0.0603
 6SM  C4  C   CR16  0   0.023   1.8536   0.8244  -0.0305
 6SM  N2  N   N     0  -0.368   2.6390  -0.2325  -0.0031
 6SM  C1  C   CR16  0   0.055   2.0403  -1.4168   0.0347
 6SM  H1  H   HOH1  0   0.494  -2.7501  -2.2882   0.0298
 6SM  H2  H   HCR6  0   0.311   2.3213   1.8018  -0.0636
 6SM  H3  H   HCR6  0   0.282   2.6784  -2.2915   0.0576

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
 6SM  N2  C1  aromatic  1.328  0.020  1.328
 6SM  N2  C4  aromatic  1.317  0.020  1.317
 6SM  C1  N1  aromatic  1.316  0.020  1.316
 6SM  C4  C3  aromatic  1.394  0.020  1.394
 6SM  N1  C2  aromatic  1.328  0.020  1.328
 6SM  C3  C2  aromatic  1.390  0.020  1.390
 6SM  C3  CL  single    1.711  0.020  1.711
 6SM  C2  C5  single    1.503  0.020  1.503
 6SM  C5  O1  double    1.202  0.020  1.202
 6SM  C5  O2  single    1.317  0.020  1.317
 6SM  O2  H1  single    0.850  0.020  0.980
 6SM  C4  H2  single    0.930  0.020  1.080
 6SM  C1  H3  single    0.930  0.020  1.080

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
 6SM  H1  O2  C5  109.59  3.000
 6SM  C2  C5  O1  123.60  3.000
 6SM  O1  C5  O2  124.72  3.000
 6SM  C2  C5  O2  111.68  3.000
 6SM  C3  C2  N1  120.15  3.000
 6SM  C3  C2  C5  123.24  3.000
 6SM  N1  C2  C5  116.60  3.000
 6SM  C1  N1  C2  118.49  3.000
 6SM  C4  C3  CL  117.63  3.000
 6SM  CL  C3  C2  125.57  3.000
 6SM  C4  C3  C2  116.80  3.000
 6SM  H2  C4  N2  117.83  3.000
 6SM  H2  C4  C3  119.94  3.000
 6SM  N2  C4  C3  122.23  3.000
 6SM  C1  N2  C4  116.58  3.000
 6SM  H3  C1  N2  117.09  3.000
 6SM  H3  C1  N1  117.17  3.000
 6SM  N2  C1  N1  125.74  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
 6SM  CONST_01  N2  C1  N1  C2    0.00   0.0  0
 6SM  CONST_02  N2  C4  C3  C2    0.00   0.0  0
 6SM  CONST_03  C4  N2  C1  N1    0.00   0.0  0
 6SM  CONST_04  C4  C3  C2  N1    0.00   0.0  0
 6SM  CONST_05  C1  N2  C4  C3    0.00   0.0  0
 6SM  CONST_06  C1  N1  C2  C3    0.00   0.0  0
 6SM  CONST_07  C1  N1  C2  C5  180.00   0.0  0
 6SM  CONST_08  C4  C3  C2  C5  180.00   0.0  0
 6SM  CONST_09  CL  C3  C2  N1  180.00   0.0  0
 6SM  CONST_10  N2  C4  C3  CL  180.00   0.0  0
 6SM  CONST_11  H3  C1  N1  C2  180.00   0.0  0
 6SM  CONST_12  H2  C4  C3  C2  180.00   0.0  0
 6SM  CONST_13  H1  O2  C5  C2  180.00   0.0  0
 6SM  Var_01    N1  C2  C5  O2   -3.00  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
 6SM  plan-1  C5  0.020
 6SM  plan-1  C2  0.020
 6SM  plan-1  N1  0.020
 6SM  plan-1  C3  0.020
 6SM  plan-1  CL  0.020
 6SM  plan-1  C4  0.020
 6SM  plan-1  N2  0.020
 6SM  plan-1  C1  0.020
 6SM  plan-1  H2  0.020
 6SM  plan-1  H3  0.020
 6SM  plan-2  O2  0.020
 6SM  plan-2  C5  0.020
 6SM  plan-2  O1  0.020
 6SM  plan-2  C2  0.020
 6SM  plan-2  H1  0.020

