# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 21:43:43 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-[3-(2-azanyl-9~{H}-purin-6-yl)phenyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2[nH]cnc2c(n1)c3cccc(CC(O)=O)c3
#
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
 HJK  HJK  '2-[3-(2-azanyl-9~{H}-purin-6-yl)phenyl]ethanoic acid'  ligand  30  20  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HJK
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
 HJK  C4   C  CR16   0  -0.347   0.4314   1.9090  -0.2036
 HJK  C5   C  CR16   0  -0.230   1.7193   2.3876  -0.4001
 HJK  C6   C  CR16   0  -0.302   2.7585   1.5168  -0.6848
 HJK  C11  C  CR56   0   0.025  -2.3469   0.7424  -0.0217
 HJK  C7   C  CR6    0   0.201   2.5314   0.1441  -0.7825
 HJK  C8   C  CH2    0  -0.697   3.6538  -0.7934  -1.0950
 HJK  C9   C  C      0   0.423   4.5971  -1.0965   0.0976
 HJK  C10  C  CR16   0  -0.352   1.2415  -0.3243  -0.5764
 HJK  C12  C  CR15   0   0.115  -3.9228   2.1608   0.0228
 HJK  C13  C  CR56   0   0.494  -3.5320   0.0137   0.1594
 HJK  N2   N  N      0  -0.500  -1.2740  -1.3362   0.0248
 HJK  C3   C  CR6    0   0.064   0.1788   0.5391  -0.2898
 HJK  N3   N  N      0  -0.457  -2.6336   2.0880  -0.1050
 HJK  C1   C  CR6    0   0.522  -2.4693  -1.9168   0.1967
 HJK  C2   C  CR6    0   0.226  -1.1730  -0.0162  -0.0885
 HJK  O1   O  OC    -1  -0.623   5.4350  -1.9966  -0.1071
 HJK  O2   O  O      0  -0.596   4.4565  -0.4229   1.1326
 HJK  N4   N  NR15   0  -0.656  -4.5196   0.9449   0.1859
 HJK  N5   N  N      0  -0.473  -3.6466  -1.2949   0.2752
 HJK  H1   H  HCR6   0   0.263  -0.3701   2.6019   0.0079
 HJK  H2   H  HCR6   0   0.252   1.9083   3.4514  -0.3313
 HJK  H3   H  HCR6   0   0.245   3.7566   1.9064  -0.8471
 HJK  H4   H  HCH2   0   0.243   3.2631  -1.7374  -1.4841
 HJK  H5   H  HCH2   0   0.248   4.2697  -0.3736  -1.8974
 HJK  H6   H  HCR6   0   0.244   1.0480  -1.3873  -0.6465
 HJK  H7   H  HCR5   0   0.290  -4.5014   3.0718   0.0068
 HJK  H8   H  HNH2   0   0.391  -3.3015  -3.7180   0.6223
 HJK  H9   H  HNH2   0   0.391  -1.6047  -3.7304   0.4611
 HJK  H12  H  HNR5   0   0.425  -5.5080   0.7738   0.2885
 HJK  N1   N  NH2    0  -0.827  -2.4762  -3.2704   0.2616

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
 HJK  N1   C1   single    1.355  0.020  1.355
 HJK  C1   N5   aromatic  1.334  0.020  1.334
 HJK  C1   N2   aromatic  1.340  0.020  1.340
 HJK  N5   C13  aromatic  1.319  0.020  1.319
 HJK  N2   C2   aromatic  1.329  0.020  1.329
 HJK  C13  N4   aromatic  1.358  0.020  1.358
 HJK  C13  C11  aromatic  1.403  0.020  1.403
 HJK  N4   C12  aromatic  1.364  0.020  1.364
 HJK  C2   C11  aromatic  1.399  0.020  1.399
 HJK  C2   C3   single    1.475  0.020  1.475
 HJK  C4   C3   aromatic  1.396  0.020  1.396
 HJK  C4   C5   aromatic  1.388  0.020  1.388
 HJK  C11  N3   aromatic  1.378  0.020  1.378
 HJK  C3   C10  aromatic  1.399  0.020  1.399
 HJK  C12  N3   aromatic  1.298  0.020  1.298
 HJK  C5   C6   aromatic  1.385  0.020  1.385
 HJK  C10  C7   aromatic  1.388  0.020  1.388
 HJK  C6   C7   aromatic  1.395  0.020  1.395
 HJK  C7   C8   single    1.495  0.020  1.495
 HJK  C8   C9   single    1.550  0.020  1.550
 HJK  O2   C9   deloc     1.243  0.020  1.243
 HJK  C9   O1   deloc     1.247  0.020  1.247
 HJK  C4   H1   single    0.930  0.020  1.080
 HJK  C5   H2   single    0.930  0.020  1.080
 HJK  C6   H3   single    0.930  0.020  1.080
 HJK  C8   H4   single    0.970  0.020  1.090
 HJK  C8   H5   single    0.970  0.020  1.090
 HJK  C10  H6   single    0.930  0.020  1.080
 HJK  C12  H7   single    0.930  0.020  1.080
 HJK  N1   H8   single    0.890  0.020  1.040
 HJK  N1   H9   single    0.890  0.020  1.040
 HJK  N4   H12  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
 HJK  H1   C4   C3   120.49  3.000
 HJK  H1   C4   C5   119.66  3.000
 HJK  C3   C4   C5   119.84  3.000
 HJK  H2   C5   C6   119.98  3.000
 HJK  H2   C5   C4   119.46  3.000
 HJK  C6   C5   C4   120.56  3.000
 HJK  H3   C6   C7   119.55  3.000
 HJK  H3   C6   C5   119.72  3.000
 HJK  C7   C6   C5   120.72  3.000
 HJK  C2   C11  N3   134.50  3.000
 HJK  N3   C11  C13  109.83  3.000
 HJK  C2   C11  C13  115.67  3.000
 HJK  C10  C7   C8   121.13  3.000
 HJK  C8   C7   C6   120.63  3.000
 HJK  C10  C7   C6   118.24  3.000
 HJK  H5   C8   H4   105.74  3.000
 HJK  H5   C8   C9   107.24  3.000
 HJK  H4   C8   C9   108.81  3.000
 HJK  H5   C8   C7   109.56  3.000
 HJK  H4   C8   C7   110.33  3.000
 HJK  C9   C8   C7   114.74  3.000
 HJK  O2   C9   O1   127.16  3.000
 HJK  O1   C9   C8   115.07  3.000
 HJK  O2   C9   C8   117.76  3.000
 HJK  H6   C10  C3   118.91  3.000
 HJK  H6   C10  C7   119.20  3.000
 HJK  C3   C10  C7   121.88  3.000
 HJK  H7   C12  N4   121.30  3.000
 HJK  H7   C12  N3   125.34  3.000
 HJK  N4   C12  N3   113.35  3.000
 HJK  N5   C13  N4   128.00  3.000
 HJK  N4   C13  C11  105.11  3.000
 HJK  N5   C13  C11  126.88  3.000
 HJK  C2   N2   C1   120.61  3.000
 HJK  C2   C3   C10  119.45  3.000
 HJK  C10  C3   C4   118.75  3.000
 HJK  C2   C3   C4   121.79  3.000
 HJK  C12  N3   C11  104.80  3.000
 HJK  N5   C1   N2   126.37  3.000
 HJK  N2   C1   N1   116.33  3.000
 HJK  N5   C1   N1   117.28  3.000
 HJK  C3   C2   N2   117.08  3.000
 HJK  C3   C2   C11  124.83  3.000
 HJK  N2   C2   C11  118.09  3.000
 HJK  H12  N4   C13  126.78  3.000
 HJK  H12  N4   C12  126.31  3.000
 HJK  C13  N4   C12  106.90  3.000
 HJK  C1   N5   C13  112.38  3.000
 HJK  H9   N1   H8   115.88  3.000
 HJK  H9   N1   C1   117.52  3.000
 HJK  H8   N1   C1   117.77  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
 HJK  CONST_01  N2   C2   C3   C4   180.00   0.0  0
 HJK  CONST_02  C11  C2   C3   C4     0.00   0.0  0
 HJK  CONST_03  C7   C10  C3   C4     0.00   0.0  0
 HJK  CONST_04  C7   C6   C5   C4     0.00   0.0  0
 HJK  CONST_05  C2   C3   C4   C5   180.00   0.0  0
 HJK  CONST_06  C10  C3   C4   C5     0.00   0.0  0
 HJK  CONST_07  C10  C7   C6   C5     0.00   0.0  0
 HJK  CONST_08  C3   C4   C5   C6     0.00   0.0  0
 HJK  CONST_09  C3   C10  C7   C6     0.00   0.0  0
 HJK  CONST_10  C1   N5   C13  C11    0.00   0.0  0
 HJK  CONST_11  C12  N4   C13  C11    0.00   0.0  0
 HJK  CONST_12  C1   N2   C2   C11    0.00   0.0  0
 HJK  CONST_13  C10  C3   C2   C11  180.00   0.0  0
 HJK  CONST_14  N4   C12  N3   C11    0.00   0.0  0
 HJK  CONST_15  C2   C3   C10  C7   180.00   0.0  0
 HJK  CONST_16  N2   C2   C3   C10    0.00   0.0  0
 HJK  CONST_17  N5   C13  N4   C12  180.00   0.0  0
 HJK  CONST_18  C13  C11  N3   C12    0.00   0.0  0
 HJK  CONST_19  C2   C11  N3   C12  180.00   0.0  0
 HJK  CONST_20  N2   C1   N5   C13    0.00   0.0  0
 HJK  CONST_21  N3   C12  N4   C13    0.00   0.0  0
 HJK  CONST_22  N2   C2   C11  C13    0.00   0.0  0
 HJK  CONST_23  C3   C2   C11  C13  180.00   0.0  0
 HJK  CONST_24  N3   C11  C2   N2   180.00   0.0  0
 HJK  CONST_25  C1   N2   C2   C3   180.00   0.0  0
 HJK  CONST_26  N3   C11  C2   C3     0.00   0.0  0
 HJK  CONST_27  N5   C13  C11  N3   180.00   0.0  0
 HJK  CONST_28  N4   C13  C11  N3     0.00   0.0  0
 HJK  CONST_29  N4   C13  N5   C1   180.00   0.0  0
 HJK  CONST_30  N5   C1   N2   C2     0.00   0.0  0
 HJK  CONST_31  N5   C13  C11  C2     0.00   0.0  0
 HJK  CONST_32  N4   C13  C11  C2   180.00   0.0  0
 HJK  CONST_33  C8   C7   C6   C5   180.00   0.0  0
 HJK  CONST_34  C3   C10  C7   C8   180.00   0.0  0
 HJK  CONST_35  N1   C1   N5   C13  180.00   0.0  0
 HJK  CONST_36  C2   N2   C1   N1   180.00   0.0  0
 HJK  CONST_37  H6   C10  C3   C4   180.00   0.0  0
 HJK  CONST_38  H3   C6   C5   C4   180.00   0.0  0
 HJK  CONST_39  H1   C4   C5   C6   180.00   0.0  0
 HJK  CONST_40  H12  N4   C13  C11  180.00   0.0  0
 HJK  CONST_41  H7   C12  N3   C11  180.00   0.0  0
 HJK  CONST_42  H2   C5   C6   C7   180.00   0.0  0
 HJK  Var_01    C9   C8   C7   C6    77.15  30.0  2
 HJK  Var_02    O2   C9   C8   C7    -9.10  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
 HJK  plan-1  C4   0.020
 HJK  plan-1  C5   0.020
 HJK  plan-1  C6   0.020
 HJK  plan-1  C7   0.020
 HJK  plan-1  C8   0.020
 HJK  plan-1  C10  0.020
 HJK  plan-1  C3   0.020
 HJK  plan-1  C2   0.020
 HJK  plan-1  H1   0.020
 HJK  plan-1  H2   0.020
 HJK  plan-1  H3   0.020
 HJK  plan-1  H6   0.020
 HJK  plan-2  C11  0.020
 HJK  plan-2  C12  0.020
 HJK  plan-2  C13  0.020
 HJK  plan-2  N2   0.020
 HJK  plan-2  C3   0.020
 HJK  plan-2  N3   0.020
 HJK  plan-2  C1   0.020
 HJK  plan-2  C2   0.020
 HJK  plan-2  N4   0.020
 HJK  plan-2  N5   0.020
 HJK  plan-2  H7   0.020
 HJK  plan-2  H12  0.020
 HJK  plan-2  N1   0.020
 HJK  plan-3  C1   0.020
 HJK  plan-3  H8   0.020
 HJK  plan-3  H9   0.020
 HJK  plan-3  N1   0.020
 HJK  plan-4  C8   0.020
 HJK  plan-4  C9   0.020
 HJK  plan-4  O1   0.020
 HJK  plan-4  O2   0.020

