# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:21:57 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 6-amino-4-phenyl-1,3,5-triazin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=NC(=O)N1)c2ccccc2
#
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
 2YL  2YL  6-amino-4-phenyl-1,3,5-triazin-2(1H)-one  ligand  22  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2YL
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
 2YL  N1   N  NR16  0  -0.692  -2.7874   0.0318  -0.0002
 2YL  C2   C  CR6   0   0.571  -2.1209   1.2564   0.0076
 2YL  N3   N  N     0  -0.509  -0.7679   1.1981   0.0085
 2YL  C4   C  CR6   0   0.392  -0.1915   0.0181   0.0005
 2YL  N5   N  N     0  -0.503  -0.8031  -1.1712  -0.0077
 2YL  C6   C  CR6   0   0.734  -2.1223  -1.1419  -0.0080
 2YL  N7   N  NH2   0  -0.816  -2.8119  -2.2705  -0.0175
 2YL  O8   O  O     0  -0.482  -2.7643   2.2891   0.0127
 2YL  C9   C  CR16  0  -0.249   4.0766  -0.0631   0.0040
 2YL  C10  C  CR16  0  -0.241   3.4018   1.1517   0.0078
 2YL  C11  C  CR16  0  -0.268   2.0164   1.1773   0.0063
 2YL  C12  C  CR6   0  -0.007   1.2883  -0.0130   0.0009
 2YL  C13  C  CR16  0  -0.273   1.9730  -1.2286  -0.0030
 2YL  C14  C  CR16  0  -0.240   3.3591  -1.2524  -0.0014
 2YL  H2   H  HNH2  0   0.424  -2.3197  -3.1481  -0.0196
 2YL  H3   H  HNH2  0   0.427  -3.8178  -2.2901  -0.0091
 2YL  H5   H  HCR6  0   0.261   3.9572   2.0803   0.0124
 2YL  H6   H  HCR6  0   0.258   1.4910   2.1225   0.0103
 2YL  H7   H  HCR6  0   0.259   1.4161  -2.1554  -0.0070
 2YL  H8   H  HCR6  0   0.261   3.8804  -2.2006  -0.0045
 2YL  H9   H  HNR6  0   0.431  -3.7991   0.0462  -0.0006
 2YL  H4   H  HCR6  0   0.263   5.1586  -0.0826   0.0048

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
 2YL  C9   C10  aromatic  1.390  0.020  1.390
 2YL  C9   C14  aromatic  1.389  0.020  1.389
 2YL  C10  C11  aromatic  1.386  0.020  1.386
 2YL  C14  C13  aromatic  1.386  0.020  1.386
 2YL  C11  C12  aromatic  1.395  0.020  1.395
 2YL  C13  C12  aromatic  1.395  0.020  1.395
 2YL  C12  C4   single    1.480  0.020  1.480
 2YL  C4   N3   double    1.313  0.020  1.313
 2YL  C4   N5   single    1.337  0.020  1.337
 2YL  N3   C2   single    1.354  0.020  1.354
 2YL  N5   C6   double    1.320  0.020  1.320
 2YL  C2   O8   double    1.217  0.020  1.217
 2YL  C2   N1   single    1.394  0.020  1.394
 2YL  C6   N1   single    1.349  0.020  1.349
 2YL  C6   N7   single    1.323  0.020  1.323
 2YL  N7   H2   single    0.860  0.020  1.020
 2YL  N7   H3   single    0.860  0.020  1.020
 2YL  C9   H4   single    0.930  0.020  1.080
 2YL  C10  H5   single    0.930  0.020  1.080
 2YL  C11  H6   single    0.930  0.020  1.080
 2YL  C13  H7   single    0.930  0.020  1.080
 2YL  C14  H8   single    0.930  0.020  1.080
 2YL  N1   H9   single    0.860  0.020  1.020

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
 2YL  H9   N1   C6   120.36  3.000
 2YL  H9   N1   C2   117.74  3.000
 2YL  C6   N1   C2   121.90  3.000
 2YL  O8   C2   N3   124.39  3.000
 2YL  O8   C2   N1   119.52  3.000
 2YL  N3   C2   N1   116.09  3.000
 2YL  C4   N3   C2   118.50  3.000
 2YL  C12  C4   N5   116.01  3.000
 2YL  N5   C4   N3   126.75  3.000
 2YL  C12  C4   N3   117.23  3.000
 2YL  C6   N5   C4   115.94  3.000
 2YL  N7   C6   N5   120.15  3.000
 2YL  N7   C6   N1   119.04  3.000
 2YL  N5   C6   N1   120.81  3.000
 2YL  H3   N7   H2   118.17  3.000
 2YL  H3   N7   C6   122.53  3.000
 2YL  H2   N7   C6   119.29  3.000
 2YL  H4   C9   C14  120.07  3.000
 2YL  H4   C9   C10  120.08  3.000
 2YL  C14  C9   C10  119.85  3.000
 2YL  H5   C10  C11  119.82  3.000
 2YL  H5   C10  C9   120.06  3.000
 2YL  C11  C10  C9   120.11  3.000
 2YL  H6   C11  C12  119.48  3.000
 2YL  H6   C11  C10  120.13  3.000
 2YL  C12  C11  C10  120.39  3.000
 2YL  C13  C12  C11  119.16  3.000
 2YL  C13  C12  C4   120.59  3.000
 2YL  C11  C12  C4   120.25  3.000
 2YL  H7   C13  C14  120.01  3.000
 2YL  H7   C13  C12  119.61  3.000
 2YL  C14  C13  C12  120.37  3.000
 2YL  H8   C14  C13  119.78  3.000
 2YL  H8   C14  C9   120.10  3.000
 2YL  C13  C14  C9   120.12  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
 2YL  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 2YL  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 2YL  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 2YL  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 2YL  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 2YL  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 2YL  CONST_07  C10  C11  C12  C4   180.00   0.0  0
 2YL  CONST_08  C14  C13  C12  C4   180.00   0.0  0
 2YL  CONST_09  C4   N3   C2   N1     0.00   0.0  0
 2YL  CONST_10  C4   N5   C6   N1     0.00   0.0  0
 2YL  CONST_11  C12  C4   N3   C2   180.00   0.0  0
 2YL  CONST_12  N5   C4   N3   C2     0.00   0.0  0
 2YL  CONST_13  N5   C6   N1   C2     0.00   0.0  0
 2YL  CONST_14  C6   N5   C4   N3     0.00   0.0  0
 2YL  CONST_15  C6   N1   C2   N3     0.00   0.0  0
 2YL  CONST_16  C12  C4   N5   C6   180.00   0.0  0
 2YL  CONST_17  N7   C6   N1   C2   180.00   0.0  0
 2YL  CONST_18  O8   C2   N3   C4   180.00   0.0  0
 2YL  CONST_19  N7   C6   N5   C4   180.00   0.0  0
 2YL  CONST_20  O8   C2   N1   C6   180.00   0.0  0
 2YL  CONST_21  H6   C11  C12  C4     0.00   0.0  0
 2YL  CONST_22  H7   C13  C12  C4     0.00   0.0  0
 2YL  CONST_23  H8   C14  C9   C10  180.00   0.0  0
 2YL  CONST_24  H4   C9   C10  C11  180.00   0.0  0
 2YL  CONST_25  H5   C10  C11  C12  180.00   0.0  0
 2YL  CONST_26  H9   N1   C2   N3   180.00   0.0  0
 2YL  CONST_27  H2   N7   C6   N1   180.00   0.0  0
 2YL  CONST_28  H3   N7   C6   N1     0.00   0.0  0
 2YL  Var_01    C11  C12  C4   N3    -0.15  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
 2YL  plan-1  N1   0.020
 2YL  plan-1  C2   0.020
 2YL  plan-1  N3   0.020
 2YL  plan-1  C4   0.020
 2YL  plan-1  N5   0.020
 2YL  plan-1  C6   0.020
 2YL  plan-1  N7   0.020
 2YL  plan-1  O8   0.020
 2YL  plan-1  C12  0.020
 2YL  plan-1  H2   0.020
 2YL  plan-1  H3   0.020
 2YL  plan-1  H9   0.020
 2YL  plan-2  C4   0.020
 2YL  plan-2  C9   0.020
 2YL  plan-2  C10  0.020
 2YL  plan-2  C11  0.020
 2YL  plan-2  C12  0.020
 2YL  plan-2  C13  0.020
 2YL  plan-2  C14  0.020
 2YL  plan-2  H5   0.020
 2YL  plan-2  H6   0.020
 2YL  plan-2  H7   0.020
 2YL  plan-2  H8   0.020
 2YL  plan-2  H4   0.020

