# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:13:46 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: 3H-imidazo[2,1-b]purin-4(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Nc2nccn2c3nc[nH]c13
#
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
 28Y  28Y  3H-imidazo[2,1-b]purin-4(5H)-one  ligand  18  13  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_28Y
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
 28Y  C4   C  CR56  0   0.444  -0.4500   0.8686  -0.0112
 28Y  C5   C  CR56  0   0.097  -1.3057  -0.2042  -0.0052
 28Y  C6   C  CR6   0   0.528  -0.8903  -1.5812   0.0016
 28Y  C8   C  CR15  0   0.132  -2.3758   1.6907  -0.0113
 28Y  N1   N  NR16  0  -0.751   0.4866  -1.6828   0.0003
 28Y  N2   N  N     0  -0.483   2.6669  -0.6870  -0.0052
 28Y  N3   N  N     0  -0.569   0.9021   0.6489  -0.0114
 28Y  O6   O  O     0  -0.463  -1.6211  -2.5561   0.0072
 28Y  N7   N  NR15  0  -0.619  -2.5491   0.3636  -0.0048
 28Y  N9   N  N     0  -0.447  -1.1013   2.0403  -0.0151
 28Y  CAD  C  CR15  0  -0.122   2.0063   1.4762  -0.0164
 28Y  CAB  C  CR15  0  -0.193   3.0686   0.6273  -0.0124
 28Y  C2   C  CR56  0   0.705   1.3673  -0.6323  -0.0049
 28Y  H1   H  HCR5  0   0.304  -3.2064   2.3779  -0.0149
 28Y  H2   H  HNR6  0   0.432   0.8881  -2.6116   0.0020
 28Y  H3   H  HNR5  0   0.439  -3.4349  -0.1204  -0.0040
 28Y  H5   H  HCR5  0   0.302   1.9226   2.5484  -0.0211
 28Y  H6   H  HCR5  0   0.265   4.1138   0.8926  -0.0143

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
 28Y  C8   N9   aromatic  1.322  0.020  1.322
 28Y  C8   N7   aromatic  1.338  0.020  1.338
 28Y  N9   C4   aromatic  1.341  0.020  1.341
 28Y  N7   C5   aromatic  1.367  0.020  1.367
 28Y  C4   C5   aromatic  1.372  0.020  1.372
 28Y  C4   N3   aromatic  1.370  0.020  1.370
 28Y  CAD  N3   aromatic  1.380  0.020  1.380
 28Y  CAD  CAB  aromatic  1.360  0.020  1.360
 28Y  C5   C6   single    1.438  0.020  1.438
 28Y  N3   C2   aromatic  1.363  0.020  1.363
 28Y  CAB  N2   aromatic  1.374  0.020  1.374
 28Y  C6   O6   double    1.218  0.020  1.218
 28Y  C6   N1   single    1.381  0.020  1.381
 28Y  C2   N2   aromatic  1.301  0.020  1.301
 28Y  C2   N1   single    1.371  0.020  1.371
 28Y  C8   H1   single    0.930  0.020  1.080
 28Y  N1   H2   single    0.860  0.020  1.020
 28Y  N7   H3   single    0.860  0.020  1.020
 28Y  CAD  H5   single    0.930  0.020  1.080
 28Y  CAB  H6   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
 28Y  N9   C4   N3   128.30  3.000
 28Y  N3   C4   C5   119.35  3.000
 28Y  N9   C4   C5   112.35  3.000
 28Y  N7   C5   C6   131.33  3.000
 28Y  C6   C5   C4   124.63  3.000
 28Y  N7   C5   C4   104.03  3.000
 28Y  O6   C6   N1   122.64  3.000
 28Y  N1   C6   C5   111.01  3.000
 28Y  O6   C6   C5   126.35  3.000
 28Y  H1   C8   N9   125.06  3.000
 28Y  H1   C8   N7   122.16  3.000
 28Y  N9   C8   N7   112.78  3.000
 28Y  H2   N1   C2   116.65  3.000
 28Y  H2   N1   C6   117.59  3.000
 28Y  C2   N1   C6   125.76  3.000
 28Y  C2   N2   CAB  104.58  3.000
 28Y  C2   N3   CAD  106.88  3.000
 28Y  C2   N3   C4   119.19  3.000
 28Y  CAD  N3   C4   133.93  3.000
 28Y  H3   N7   C8   126.09  3.000
 28Y  H3   N7   C5   126.80  3.000
 28Y  C8   N7   C5   107.10  3.000
 28Y  C8   N9   C4   103.73  3.000
 28Y  H5   CAD  CAB  133.09  3.000
 28Y  H5   CAD  N3   122.38  3.000
 28Y  CAB  CAD  N3   104.53  3.000
 28Y  H6   CAB  CAD  127.13  3.000
 28Y  H6   CAB  N2   121.24  3.000
 28Y  CAD  CAB  N2   111.64  3.000
 28Y  N3   C2   N2   112.37  3.000
 28Y  N2   C2   N1   127.57  3.000
 28Y  N3   C2   N1   120.07  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
 28Y  CONST_01  N7   C8   N9   C4     0.00  0.0  0
 28Y  CONST_02  C8   N7   C5   C4     0.00  0.0  0
 28Y  CONST_03  CAB  CAD  N3   C4   180.00  0.0  0
 28Y  CONST_04  N2   C2   N3   C4   180.00  0.0  0
 28Y  CONST_05  N9   C8   N7   C5     0.00  0.0  0
 28Y  CONST_06  C8   N9   C4   C5     0.00  0.0  0
 28Y  CONST_07  CAD  N3   C4   C5   180.00  0.0  0
 28Y  CONST_08  C2   N3   C4   C5     0.00  0.0  0
 28Y  CONST_09  N3   C4   N9   C8   180.00  0.0  0
 28Y  CONST_10  N3   CAD  CAB  N2     0.00  0.0  0
 28Y  CONST_11  CAD  N3   C2   N2     0.00  0.0  0
 28Y  CONST_12  N7   C5   C4   N3   180.00  0.0  0
 28Y  CONST_13  CAB  N2   C2   N3     0.00  0.0  0
 28Y  CONST_14  N9   C4   C5   N7     0.00  0.0  0
 28Y  CONST_15  CAD  N3   C4   N9     0.00  0.0  0
 28Y  CONST_16  C2   N3   C4   N9   180.00  0.0  0
 28Y  CONST_17  C2   N2   CAB  CAD    0.00  0.0  0
 28Y  CONST_18  C2   N3   CAD  CAB    0.00  0.0  0
 28Y  CONST_19  C2   N1   C6   C5     0.00  0.0  0
 28Y  CONST_20  C2   N1   C6   O6   180.00  0.0  0
 28Y  CONST_21  H1   C8   N9   C4   180.00  0.0  0
 28Y  CONST_22  H3   N7   C5   C4   180.00  0.0  0
 28Y  CONST_23  H5   CAD  N3   C4     0.00  0.0  0
 28Y  CONST_24  H6   CAB  CAD  N3   180.00  0.0  0
 28Y  CONST_25  H2   N1   C6   C5   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
 28Y  plan-1  C4   0.020
 28Y  plan-1  C5   0.020
 28Y  plan-1  C6   0.020
 28Y  plan-1  C8   0.020
 28Y  plan-1  N1   0.020
 28Y  plan-1  N2   0.020
 28Y  plan-1  N3   0.020
 28Y  plan-1  O6   0.020
 28Y  plan-1  N7   0.020
 28Y  plan-1  N9   0.020
 28Y  plan-1  CAD  0.020
 28Y  plan-1  CAB  0.020
 28Y  plan-1  C2   0.020
 28Y  plan-1  H1   0.020
 28Y  plan-1  H2   0.020
 28Y  plan-1  H3   0.020
 28Y  plan-1  H5   0.020
 28Y  plan-1  H6   0.020

