# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 07:09:25 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 5-ethynylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=C(C#C)C(=O)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
 Y3G  Y3G  5-ethynylpyrimidine-2,4(1H,3H)-dione  ligand  14  10  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y3G
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
 Y3G  C10  C  CSP1  0  -0.534  20.7105  39.2033  47.6175
 Y3G  C01  C  CR6   0   0.558  23.0398  41.8152  48.2733
 Y3G  C03  C  CR6   0   0.690  24.4557  42.1387  50.2795
 Y3G  C05  C  CR16  0   0.087  22.9728  40.2547  50.1240
 Y3G  C06  C  CR6   0  -0.353  22.5125  40.6088  48.8998
 Y3G  C09  C  CSP   0   0.324  21.5379  39.8458  48.2098
 Y3G  N02  N  NR16  0  -0.719  23.9806  42.4832  49.0392
 Y3G  N04  N  NR16  0  -0.667  23.9001  40.9839  50.7800
 Y3G  O07  O  O     0  -0.452  25.2831  42.7844  50.8799
 Y3G  O08  O  O     0  -0.424  22.7107  42.2311  47.1832
 Y3G  H1   H  H     0   0.282  19.9796  38.6280  47.0963
 Y3G  H2   H  HCR6  0   0.332  22.6210  39.3708  50.6367
 Y3G  H4   H  HNR6  0   0.431  24.3695  43.3297  48.6404
 Y3G  H3   H  HNR6  0   0.445  24.2163  40.6818  51.6910

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
 Y3G  O08  C01  double  1.212  0.020  1.212
 Y3G  C10  C09  triple  1.203  0.020  1.203
 Y3G  C09  C06  single  1.417  0.020  1.417
 Y3G  C01  C06  single  1.458  0.020  1.458
 Y3G  C01  N02  single  1.385  0.020  1.385
 Y3G  C06  C05  double  1.355  0.020  1.355
 Y3G  N02  C03  single  1.372  0.020  1.372
 Y3G  C05  N04  single  1.350  0.020  1.350
 Y3G  C03  N04  single  1.376  0.020  1.376
 Y3G  C03  O07  double  1.209  0.020  1.209
 Y3G  C10  H1   single  0.913  0.020  1.066
 Y3G  C05  H2   single  0.930  0.020  1.086
 Y3G  N02  H4   single  0.868  0.020  1.013
 Y3G  N04  H3   single  0.868  0.020  1.013

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
 Y3G  H1   C10  C09  180.00  3.000
 Y3G  O08  C01  N02  121.08  3.000
 Y3G  N02  C01  C06  114.02  3.000
 Y3G  O08  C01  C06  124.89  3.000
 Y3G  O07  C03  N04  122.96  3.000
 Y3G  O07  C03  N02  123.48  3.000
 Y3G  N04  C03  N02  113.56  3.000
 Y3G  H2   C05  N04  115.78  3.000
 Y3G  H2   C05  C06  122.13  3.000
 Y3G  N04  C05  C06  122.09  3.000
 Y3G  C09  C06  C05  122.20  3.000
 Y3G  C05  C06  C01  118.79  3.000
 Y3G  C09  C06  C01  119.01  3.000
 Y3G  C06  C09  C10  180.00  3.000
 Y3G  H4   N02  C03  115.63  3.000
 Y3G  H4   N02  C01  116.49  3.000
 Y3G  C03  N02  C01  127.88  3.000
 Y3G  H3   N04  C05  119.44  3.000
 Y3G  H3   N04  C03  116.91  3.000
 Y3G  C05  N04  C03  123.65  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
 Y3G  CONST_01  N04  C03  N02  C01    0.00  0.0  0
 Y3G  CONST_02  C06  C01  N02  C03    0.00  0.0  0
 Y3G  CONST_03  N02  C03  N04  C05    0.00  0.0  0
 Y3G  CONST_04  O07  C03  N02  C01  180.00  0.0  0
 Y3G  CONST_05  O08  C01  N02  C03  180.00  0.0  0
 Y3G  CONST_06  O07  C03  N04  C05  180.00  0.0  0
 Y3G  CONST_07  H4   N02  C01  C06  180.00  0.0  0
 Y3G  CONST_08  H3   N04  C03  N02  180.00  0.0  0

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
 Y3G  plan-1  C10  0.020
 Y3G  plan-1  C01  0.020
 Y3G  plan-1  C03  0.020
 Y3G  plan-1  C05  0.020
 Y3G  plan-1  C06  0.020
 Y3G  plan-1  C09  0.020
 Y3G  plan-1  N02  0.020
 Y3G  plan-1  N04  0.020
 Y3G  plan-1  O07  0.020
 Y3G  plan-1  O08  0.020
 Y3G  plan-1  H2   0.020
 Y3G  plan-1  H4   0.020
 Y3G  plan-1  H3   0.020

