# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 02:12:31 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 2,4-dimethoxypyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccnc(OC)n1
#
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
 LD8  LD8  '2,4-dimethoxypyrimidine  '  ligand  18  10  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LD8
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
 LD8  O01  O  O2    0  -0.448  -2.5188  -0.1033   0.0290
 LD8  O02  O  O2    0  -0.440   1.8606  -1.1249  -0.0324
 LD8  N03  N  N     0  -0.489  -0.2993  -0.6200  -0.0052
 LD8  N04  N  N     0  -0.476   1.3309   1.0947   0.0079
 LD8  C05  C  CR6   0   0.572  -1.2541   0.2816   0.0201
 LD8  C06  C  CR16  0  -0.400  -0.9857   1.6585   0.0394
 LD8  C07  C  CR6   0   0.596   0.9481  -0.1628  -0.0089
 LD8  C08  C  CR16  0   0.002   0.3421   1.9942   0.0314
 LD8  C09  C  CH3   0  -0.401  -2.7981  -1.4948   0.0137
 LD8  C10  C  CH3   0  -0.395   3.2268  -0.7489  -0.0316
 LD8  H1   H  HCR6  0   0.261  -1.7701   2.3986   0.0614
 LD8  H2   H  HCR6  0   0.249   0.6425   3.0354   0.0463
 LD8  H3   H  HCH3  0   0.227  -2.3802  -2.0008   0.8845
 LD8  H4   H  HCH3  0   0.234  -3.8814  -1.5785   0.0318
 LD8  H5   H  HCH3  0   0.227  -2.4120  -1.9747  -0.8862
 LD8  H6   H  HCH3  0   0.223   3.4937  -0.1887   0.8654
 LD8  H7   H  HCH3  0   0.232   3.7890  -1.6793  -0.0543
 LD8  H8   H  HCH3  0   0.224   3.4852  -0.1493  -0.9052

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
 LD8  C10  O02  single    1.417  0.020  1.417
 LD8  O02  C07  single    1.326  0.020  1.326
 LD8  C07  N03  aromatic  1.329  0.020  1.329
 LD8  C07  N04  aromatic  1.315  0.020  1.315
 LD8  N03  C05  aromatic  1.313  0.020  1.313
 LD8  N04  C08  aromatic  1.337  0.020  1.337
 LD8  C05  O01  single    1.322  0.020  1.322
 LD8  C05  C06  aromatic  1.403  0.020  1.403
 LD8  O01  C09  single    1.419  0.020  1.419
 LD8  C08  C06  aromatic  1.370  0.020  1.370
 LD8  C06  H1   single    0.930  0.020  1.080
 LD8  C08  H2   single    0.930  0.020  1.080
 LD8  C09  H3   single    0.970  0.020  1.090
 LD8  C09  H4   single    0.970  0.020  1.090
 LD8  C09  H5   single    0.970  0.020  1.090
 LD8  C10  H6   single    0.970  0.020  1.090
 LD8  C10  H7   single    0.970  0.020  1.090
 LD8  C10  H8   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
 LD8  C09  O01  C05  118.27  3.000
 LD8  C10  O02  C07  118.09  3.000
 LD8  C07  N03  C05  116.51  3.000
 LD8  C08  N04  C07  115.37  3.000
 LD8  C06  C05  N03  122.34  3.000
 LD8  C06  C05  O01  117.95  3.000
 LD8  N03  C05  O01  119.72  3.000
 LD8  H1   C06  C08  122.48  3.000
 LD8  H1   C06  C05  122.31  3.000
 LD8  C08  C06  C05  115.21  3.000
 LD8  N04  C07  N03  127.05  3.000
 LD8  N04  C07  O02  119.60  3.000
 LD8  N03  C07  O02  113.36  3.000
 LD8  H2   C08  C06  120.27  3.000
 LD8  H2   C08  N04  116.21  3.000
 LD8  C06  C08  N04  123.52  3.000
 LD8  H5   C09  H4   109.44  3.000
 LD8  H5   C09  H3   108.61  3.000
 LD8  H4   C09  H3   109.45  3.000
 LD8  H5   C09  O01  111.76  3.000
 LD8  H4   C09  O01  105.75  3.000
 LD8  H3   C09  O01  111.77  3.000
 LD8  H8   C10  H7   109.34  3.000
 LD8  H8   C10  H6   108.57  3.000
 LD8  H7   C10  H6   109.28  3.000
 LD8  H8   C10  O02  111.96  3.000
 LD8  H7   C10  O02  105.75  3.000
 LD8  H6   C10  O02  111.88  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
 LD8  CONST_01  C08  N04  C07  N03    0.00   0.0  0
 LD8  CONST_02  C08  C06  C05  N03    0.00   0.0  0
 LD8  CONST_03  C05  N03  C07  N04    0.00   0.0  0
 LD8  CONST_04  C05  C06  C08  N04    0.00   0.0  0
 LD8  CONST_05  C07  N03  C05  C06    0.00   0.0  0
 LD8  CONST_06  C07  N04  C08  C06    0.00   0.0  0
 LD8  CONST_07  C07  N03  C05  O01  180.00   0.0  0
 LD8  CONST_08  C08  C06  C05  O01  180.00   0.0  0
 LD8  CONST_09  C05  N03  C07  O02  180.00   0.0  0
 LD8  CONST_10  C08  N04  C07  O02  180.00   0.0  0
 LD8  CONST_11  H1   C06  C05  N03  180.00   0.0  0
 LD8  CONST_12  H2   C08  C06  C05  180.00   0.0  0
 LD8  Var_01    H3   C09  O01  C05   60.57  30.0  3
 LD8  Var_02    H6   C10  O02  C07   61.21  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
 LD8  plan-1  O01  0.020
 LD8  plan-1  O02  0.020
 LD8  plan-1  N03  0.020
 LD8  plan-1  N04  0.020
 LD8  plan-1  C05  0.020
 LD8  plan-1  C06  0.020
 LD8  plan-1  C07  0.020
 LD8  plan-1  C08  0.020
 LD8  plan-1  H1   0.020
 LD8  plan-1  H2   0.020

