# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 17:14:58 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 2-[3-(pyrimidin-4-ylamino)phenyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1cccc(Nc2ccncn2)c1
#
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
 HHB  HHB  '2-[3-(pyrimidin-4-ylamino)phenyl]ethanoic acid'  ligand  28  17  .  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_HHB
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
 HHB  C4   C  CR16  0  -0.319   2.1072   1.8249  -0.1962
 HHB  C5   C  CR16  0  -0.232   0.8697   2.3600   0.1211
 HHB  C6   C  CR16  0  -0.326  -0.2798   1.5813   0.1276
 HHB  C11  C  CR16  0   0.071  -4.3764   0.7887   0.5278
 HHB  C7   C  CR6   0   0.386  -0.1885   0.2263  -0.1963
 HHB  C8   C  CR6   0   0.566  -2.5851  -0.4923  -0.0063
 HHB  C9   C  CR16  0  -0.417  -3.4460  -1.6002  -0.1299
 HHB  C10  C  CR16  0  -0.032  -4.7767  -1.3775   0.1052
 HHB  C12  C  CR16  0  -0.413   1.0649  -0.3083  -0.5149
 HHB  N1   N  NH1   0  -0.777  -1.2591  -0.6651  -0.2319
 HHB  N2   N  N     0  -0.430  -5.2690  -0.1768   0.4398
 HHB  C3   C  CR6   0   0.161   2.2075   0.4743  -0.5171
 HHB  N3   N  N     0  -0.469  -3.0693   0.7011   0.3251
 HHB  O1   O  O     0  -0.434   3.8362  -0.6155   1.4932
 HHB  C1   C  C     0   0.558   4.2576  -0.6564   0.3663
 HHB  O2   O  OH1   0  -0.593   5.4368  -1.1754   0.0434
 HHB  C2   C  CH2   0  -0.691   3.5358  -0.1352  -0.8522
 HHB  H1   H  HCR6  0   0.251   2.9891   2.4531  -0.1983
 HHB  H2   H  HCR6  0   0.257   0.7870   3.4104   0.3687
 HHB  H3   H  HCR6  0   0.286  -1.2297   2.0227   0.3774
 HHB  H4   H  HCR6  0   0.257  -4.7457   1.7730   0.7965
 HHB  H5   H  HCR6  0   0.286  -3.0790  -2.5810  -0.4001
 HHB  H6   H  HCR6  0   0.277  -5.4881  -2.1910   0.0231
 HHB  H7   H  HCR6  0   0.266   1.1448  -1.3603  -0.7689
 HHB  H8   H  HNH1  0   0.419  -1.0010  -1.6088  -0.4770
 HHB  H9   H  HOH1  0   0.482   5.8845  -1.5015   0.8384
 HHB  H10  H  HCH2  0   0.305   3.4221  -0.9602  -1.5612
 HHB  H11  H  HCH2  0   0.306   4.1853   0.5931  -1.3457

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
 HHB  N2   C11  aromatic  1.318  0.020  1.318
 HHB  N2   C10  aromatic  1.340  0.020  1.340
 HHB  C11  N3   aromatic  1.326  0.020  1.326
 HHB  C10  C9   aromatic  1.370  0.020  1.370
 HHB  N3   C8   aromatic  1.330  0.020  1.330
 HHB  C9   C8   aromatic  1.409  0.020  1.409
 HHB  C8   N1   single    1.356  0.020  1.356
 HHB  C6   C5   aromatic  1.388  0.020  1.388
 HHB  C6   C7   aromatic  1.396  0.020  1.396
 HHB  C5   C4   aromatic  1.385  0.020  1.385
 HHB  N1   C7   single    1.394  0.020  1.394
 HHB  C7   C12  aromatic  1.399  0.020  1.399
 HHB  C4   C3   aromatic  1.392  0.020  1.392
 HHB  C12  C3   aromatic  1.385  0.020  1.385
 HHB  C3   C2   single    1.499  0.020  1.499
 HHB  O1   C1   double    1.204  0.020  1.204
 HHB  C2   C1   single    1.509  0.020  1.509
 HHB  C1   O2   single    1.328  0.020  1.328
 HHB  C4   H1   single    0.930  0.020  1.080
 HHB  C5   H2   single    0.930  0.020  1.080
 HHB  C6   H3   single    0.930  0.020  1.080
 HHB  C11  H4   single    0.930  0.020  1.080
 HHB  C9   H5   single    0.930  0.020  1.080
 HHB  C10  H6   single    0.930  0.020  1.080
 HHB  C12  H7   single    0.930  0.020  1.080
 HHB  N1   H8   single    0.860  0.020  1.020
 HHB  O2   H9   single    0.850  0.020  0.980
 HHB  C2   H10  single    0.970  0.020  1.090
 HHB  C2   H11  single    0.970  0.020  1.090

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
 HHB  H1   C4   C3   120.25  3.000
 HHB  H1   C4   C5   120.27  3.000
 HHB  C3   C4   C5   119.48  3.000
 HHB  H2   C5   C6   118.68  3.000
 HHB  H2   C5   C4   119.71  3.000
 HHB  C6   C5   C4   121.61  3.000
 HHB  H3   C6   C7   120.62  3.000
 HHB  H3   C6   C5   120.10  3.000
 HHB  C7   C6   C5   119.28  3.000
 HHB  H4   C11  N3   115.69  3.000
 HHB  H4   C11  N2   116.78  3.000
 HHB  N3   C11  N2   127.53  3.000
 HHB  N1   C7   C12  115.97  3.000
 HHB  C12  C7   C6   118.83  3.000
 HHB  N1   C7   C6   125.20  3.000
 HHB  N3   C8   N1   120.79  3.000
 HHB  N1   C8   C9   118.87  3.000
 HHB  N3   C8   C9   120.34  3.000
 HHB  H5   C9   C10  121.34  3.000
 HHB  H5   C9   C8   121.86  3.000
 HHB  C10  C9   C8   116.80  3.000
 HHB  H6   C10  N2   116.76  3.000
 HHB  H6   C10  C9   120.18  3.000
 HHB  N2   C10  C9   123.06  3.000
 HHB  H7   C12  C3   119.13  3.000
 HHB  H7   C12  C7   119.31  3.000
 HHB  C3   C12  C7   121.56  3.000
 HHB  H8   N1   C8   114.19  3.000
 HHB  H8   N1   C7   114.08  3.000
 HHB  C8   N1   C7   131.72  3.000
 HHB  C10  N2   C11  115.10  3.000
 HHB  C2   C3   C12  120.10  3.000
 HHB  C2   C3   C4   120.66  3.000
 HHB  C12  C3   C4   119.24  3.000
 HHB  C8   N3   C11  117.16  3.000
 HHB  C2   C1   O2   111.30  3.000
 HHB  O2   C1   O1   123.48  3.000
 HHB  C2   C1   O1   125.22  3.000
 HHB  H9   O2   C1   110.02  3.000
 HHB  H11  C2   H10  105.76  3.000
 HHB  H11  C2   C1   108.08  3.000
 HHB  H10  C2   C1   108.22  3.000
 HHB  H11  C2   C3   110.87  3.000
 HHB  H10  C2   C3   111.06  3.000
 HHB  C1   C2   C3   112.56  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
 HHB  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 HHB  CONST_02  C7   C12  C3   C4     0.00   0.0  0
 HHB  CONST_03  C12  C7   C6   C5     0.00   0.0  0
 HHB  CONST_04  C12  C3   C4   C5     0.00   0.0  0
 HHB  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 HHB  CONST_06  C3   C12  C7   C6     0.00   0.0  0
 HHB  CONST_07  C9   C10  N2   C11    0.00   0.0  0
 HHB  CONST_08  C9   C8   N3   C11    0.00   0.0  0
 HHB  CONST_09  N2   C11  N3   C8     0.00   0.0  0
 HHB  CONST_10  N2   C10  C9   C8     0.00   0.0  0
 HHB  CONST_11  N3   C11  N2   C10    0.00   0.0  0
 HHB  CONST_12  N3   C8   C9   C10    0.00   0.0  0
 HHB  CONST_13  N1   C7   C6   C5   180.00   0.0  0
 HHB  CONST_14  C2   C3   C4   C5   180.00   0.0  0
 HHB  CONST_15  N1   C8   N3   C11  180.00   0.0  0
 HHB  CONST_16  C2   C3   C12  C7   180.00   0.0  0
 HHB  CONST_17  N1   C8   C9   C10  180.00   0.0  0
 HHB  CONST_18  C3   C12  C7   N1   180.00   0.0  0
 HHB  CONST_19  H3   C6   C5   C4   180.00   0.0  0
 HHB  CONST_20  H7   C12  C3   C4   180.00   0.0  0
 HHB  CONST_21  H1   C4   C5   C6   180.00   0.0  0
 HHB  CONST_22  H6   C10  N2   C11  180.00   0.0  0
 HHB  CONST_23  H2   C5   C6   C7   180.00   0.0  0
 HHB  CONST_24  H4   C11  N3   C8   180.00   0.0  0
 HHB  CONST_25  H5   C9   C10  N2   180.00   0.0  0
 HHB  CONST_26  H9   O2   C1   O1     0.00   0.0  0
 HHB  Var_01    C8   N1   C7   C6     1.20  30.0  3
 HHB  Var_02    N3   C8   N1   C7    -0.50  30.0  2
 HHB  Var_03    C1   C2   C3   C4    89.12  30.0  2
 HHB  Var_04    O1   C1   C2   C3     0.73  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
 HHB  plan-1  C4   0.020
 HHB  plan-1  C5   0.020
 HHB  plan-1  C6   0.020
 HHB  plan-1  C7   0.020
 HHB  plan-1  C12  0.020
 HHB  plan-1  N1   0.020
 HHB  plan-1  C3   0.020
 HHB  plan-1  C2   0.020
 HHB  plan-1  H1   0.020
 HHB  plan-1  H2   0.020
 HHB  plan-1  H3   0.020
 HHB  plan-1  H7   0.020
 HHB  plan-2  C11  0.020
 HHB  plan-2  C8   0.020
 HHB  plan-2  C9   0.020
 HHB  plan-2  C10  0.020
 HHB  plan-2  N1   0.020
 HHB  plan-2  N2   0.020
 HHB  plan-2  N3   0.020
 HHB  plan-2  H4   0.020
 HHB  plan-2  H5   0.020
 HHB  plan-2  H6   0.020
 HHB  plan-3  O1   0.020
 HHB  plan-3  C1   0.020
 HHB  plan-3  O2   0.020
 HHB  plan-3  C2   0.020
 HHB  plan-3  H9   0.020

