# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:44:52 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  31  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  -0.342   0.3969   1.9501  -0.4577
 HJK  C5   C  CR16  0  -0.225   1.6679   2.4519  -0.6931
 HJK  C6   C  CR16  0  -0.296   2.7474   1.5937  -0.8358
 HJK  C11  C  CR56  0   0.029  -2.3272   0.7349  -0.0239
 HJK  C7   C  CR6   0   0.167   2.5660   0.2170  -0.7400
 HJK  C8   C  CH2   0  -0.692   3.7323  -0.7147  -0.8795
 HJK  C9   C  C     0   0.557   4.4194  -0.9796   0.4378
 HJK  C10  C  CR16  0  -0.328   1.2932  -0.2792  -0.5026
 HJK  C12  C  CR15  0   0.120  -3.9253   2.1256   0.0748
 HJK  C13  C  CR56  0   0.496  -3.4935  -0.0144   0.1970
 HJK  N2   N  N     0  -0.502  -1.2174  -1.3248   0.0018
 HJK  C3   C  CR6   0   0.060   0.1941   0.5717  -0.3619
 HJK  N3   N  N     0  -0.459  -2.6399   2.0753  -0.0952
 HJK  C1   C  CR6   0   0.524  -2.3961  -1.9261   0.2113
 HJK  C2   C  CR6   0   0.231  -1.1440  -0.0043  -0.1221
 HJK  O1   O  OH1   0  -0.592   5.5110  -1.7178   0.2732
 HJK  O2   O  O     0  -0.434   4.0387  -0.5851   1.5097
 HJK  N4   N  NR15  0  -0.657  -4.4954   0.8997   0.2555
 HJK  N5   N  N     0  -0.472  -3.5814  -1.3236   0.3206
 HJK  H1   H  HCR6  0   0.272  -0.4344   2.6322  -0.3550
 HJK  H2   H  HCR6  0   0.260   1.8148   3.5213  -0.7684
 HJK  H3   H  HCR6  0   0.258   3.7351   1.9959  -1.0279
 HJK  H4   H  HCH2  0   0.308   3.4169  -1.6769  -1.2936
 HJK  H5   H  HCH2  0   0.304   4.4712  -0.3161  -1.5796
 HJK  H6   H  HCR6  0   0.255   1.1424  -1.3486  -0.4307
 HJK  H7   H  HCR5  0   0.292  -4.5194   3.0267   0.0801
 HJK  H8   H  HNH2  0   0.392  -3.1863  -3.7399   0.6627
 HJK  H9   H  HNH2  0   0.392  -1.4936  -3.7245   0.4563
 HJK  H11  H  HOH1  0   0.482   5.9347  -1.8803   1.1292
 HJK  H12  H  HNR5  0   0.426  -5.4763   0.7126   0.3957
 HJK  N1   N  NH2   0  -0.827  -2.3778  -3.2785   0.2820

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    1.354  0.020  1.354
 HJK  C1   N5   aromatic  1.334  0.020  1.334
 HJK  C1   N2   aromatic  1.340  0.020  1.340
 HJK  N5   C13  aromatic  1.318  0.020  1.318
 HJK  N2   C2   aromatic  1.328  0.020  1.328
 HJK  C13  N4   aromatic  1.357  0.020  1.357
 HJK  C13  C11  aromatic  1.404  0.020  1.404
 HJK  N4   C12  aromatic  1.364  0.020  1.364
 HJK  C2   C11  aromatic  1.399  0.020  1.399
 HJK  C2   C3   single    1.477  0.020  1.477
 HJK  C4   C3   aromatic  1.396  0.020  1.396
 HJK  C4   C5   aromatic  1.387  0.020  1.387
 HJK  C11  N3   aromatic  1.378  0.020  1.378
 HJK  C3   C10  aromatic  1.397  0.020  1.397
 HJK  C12  N3   aromatic  1.298  0.020  1.298
 HJK  C5   C6   aromatic  1.386  0.020  1.386
 HJK  C10  C7   aromatic  1.387  0.020  1.387
 HJK  C6   C7   aromatic  1.392  0.020  1.392
 HJK  C7   C8   single    1.499  0.020  1.499
 HJK  C8   C9   single    1.509  0.020  1.509
 HJK  O2   C9   double    1.204  0.020  1.204
 HJK  C9   O1   single    1.328  0.020  1.328
 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  O1   H11  single    0.850  0.020  0.980
 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   120.33  3.000
 HJK  H1   C4   C5   119.54  3.000
 HJK  C3   C4   C5   120.13  3.000
 HJK  H2   C5   C6   119.92  3.000
 HJK  H2   C5   C4   119.60  3.000
 HJK  C6   C5   C4   120.48  3.000
 HJK  H3   C6   C7   119.87  3.000
 HJK  H3   C6   C5   119.88  3.000
 HJK  C7   C6   C5   120.24  3.000
 HJK  C2   C11  N3   134.61  3.000
 HJK  N3   C11  C13  109.80  3.000
 HJK  C2   C11  C13  115.59  3.000
 HJK  C10  C7   C8   120.50  3.000
 HJK  C8   C7   C6   120.46  3.000
 HJK  C10  C7   C6   119.04  3.000
 HJK  H5   C8   H4   105.85  3.000
 HJK  H5   C8   C9   108.37  3.000
 HJK  H4   C8   C9   107.89  3.000
 HJK  H5   C8   C7   111.03  3.000
 HJK  H4   C8   C7   110.95  3.000
 HJK  C9   C8   C7   112.46  3.000
 HJK  O2   C9   O1   123.54  3.000
 HJK  O1   C9   C8   111.32  3.000
 HJK  O2   C9   C8   125.14  3.000
 HJK  H6   C10  C3   119.05  3.000
 HJK  H6   C10  C7   119.53  3.000
 HJK  C3   C10  C7   121.42  3.000
 HJK  H7   C12  N4   121.31  3.000
 HJK  H7   C12  N3   125.32  3.000
 HJK  N4   C12  N3   113.36  3.000
 HJK  N5   C13  N4   128.00  3.000
 HJK  N4   C13  C11  105.10  3.000
 HJK  N5   C13  C11  126.89  3.000
 HJK  C2   N2   C1   120.62  3.000
 HJK  C2   C3   C10  119.45  3.000
 HJK  C10  C3   C4   118.69  3.000
 HJK  C2   C3   C4   121.86  3.000
 HJK  C12  N3   C11  104.81  3.000
 HJK  N5   C1   N2   126.29  3.000
 HJK  N2   C1   N1   116.39  3.000
 HJK  N5   C1   N1   117.30  3.000
 HJK  C3   C2   N2   116.94  3.000
 HJK  C3   C2   C11  124.88  3.000
 HJK  N2   C2   C11  118.18  3.000
 HJK  H11  O1   C9   110.07  3.000
 HJK  H12  N4   C13  126.80  3.000
 HJK  H12  N4   C12  126.28  3.000
 HJK  C13  N4   C12  106.92  3.000
 HJK  C1   N5   C13  112.44  3.000
 HJK  H9   N1   H8   115.97  3.000
 HJK  H9   N1   C1   117.64  3.000
 HJK  H8   N1   C1   117.84  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  CONST_45  H11  O1   C9   C8   180.00   0.0  0
 HJK  Var_01    C9   C8   C7   C6    88.61  30.0  2
 HJK  Var_02    O2   C9   C8   C7     5.37  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
 HJK  plan-4  H11  0.020

