# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 13:15:18 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 4-[6-(3-hydroxyphenyl)pyrazin-2-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(c1)c2cncc(n2)c3ccc(cc3)C(O)=O
#
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
 3DL  3DL  '4-[6-(3-hydroxyphenyl)pyrazin-2-yl]benzoic acid'  ligand  33  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3DL
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
 3DL  O3   O  O      0  -0.590  -6.6087  -0.2491  -0.0496
 3DL  C17  C  C      0   0.398  -5.6612  -1.0333   0.1467
 3DL  O2   O  OC    -1  -0.590  -5.7346  -2.2570   0.3667
 3DL  C1   C  CR6    0  -0.105  -4.2612  -0.4318   0.1115
 3DL  C6   C  CR16   0  -0.268  -4.0722   0.9285  -0.1150
 3DL  C5   C  CR16   0  -0.318  -2.8017   1.4798  -0.1523
 3DL  C4   C  CR6    0   0.038  -1.6716   0.6818   0.0368
 3DL  C3   C  CR16   0  -0.273  -1.8601  -0.6836   0.2620
 3DL  C2   C  CR16   0  -0.271  -3.1328  -1.2266   0.2997
 3DL  C7   C  CR6    0   0.216  -0.3060   1.2406  -0.0030
 3DL  N2   N  N      0  -0.415   0.7080   0.3840  -0.0132
 3DL  C10  C  CR6    0   0.200   1.9512   0.8428  -0.0553
 3DL  C9   C  CR16   0  -0.114   2.1831   2.2186  -0.1152
 3DL  N1   N  N      0  -0.351   1.1867   3.0881  -0.0868
 3DL  C8   C  CR16   0  -0.116  -0.0459   2.6146  -0.0194
 3DL  C11  C  CR6    0   0.073   3.0464  -0.1478  -0.0586
 3DL  C16  C  CR16   0  -0.413   4.3308   0.2131   0.3402
 3DL  C15  C  CR6    0   0.383   5.3613  -0.7227   0.3311
 3DL  O1   O  OH1    0  -0.632   6.5784  -0.3091   0.7340
 3DL  C14  C  CR16   0  -0.385   5.1075  -2.0292  -0.0770
 3DL  C13  C  CR16   0  -0.228   3.8250  -2.3845  -0.4693
 3DL  C12  C  CR16   0  -0.315   2.7937  -1.4602  -0.4606
 3DL  H2   H  HCR6   0   0.248  -4.9325   1.5664  -0.2671
 3DL  H3   H  HCR6   0   0.248  -2.7069   2.5406  -0.3411
 3DL  H4   H  HCR6   0   0.254  -0.9998  -1.3224   0.4093
 3DL  H5   H  HCR6   0   0.246  -3.2531  -2.2873   0.4761
 3DL  H6   H  HCR6   0   0.273   3.1839   2.6234  -0.1999
 3DL  H7   H  HCR6   0   0.273  -0.8413   3.3471   0.0230
 3DL  H8   H  HCR6   0   0.262   4.5494   1.2172   0.6821
 3DL  H9   H  HOH1   0   0.476   7.2127  -1.0330   0.6881
 3DL  H10  H  HCR6   0   0.276   5.9034  -2.7649  -0.0855
 3DL  H11  H  HCR6   0   0.264   3.6312  -3.4007  -0.7868
 3DL  H12  H  HCR6   0   0.257   1.7993  -1.7498  -0.7696

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
 3DL  O3   C17  deloc     1.246  0.020  1.246
 3DL  O2   C17  deloc     1.245  0.020  1.245
 3DL  C17  C1   single    1.524  0.020  1.524
 3DL  C1   C6   aromatic  1.392  0.020  1.392
 3DL  C1   C2   aromatic  1.393  0.020  1.393
 3DL  C6   C5   aromatic  1.385  0.020  1.385
 3DL  C2   C3   aromatic  1.384  0.020  1.384
 3DL  C5   C4   aromatic  1.396  0.020  1.396
 3DL  C13  C12  aromatic  1.385  0.020  1.385
 3DL  C13  C14  aromatic  1.387  0.020  1.387
 3DL  C12  C11  aromatic  1.396  0.020  1.396
 3DL  C3   C4   aromatic  1.397  0.020  1.397
 3DL  C4   C7   single    1.476  0.020  1.476
 3DL  C14  C15  aromatic  1.392  0.020  1.392
 3DL  N2   C7   aromatic  1.327  0.020  1.327
 3DL  N2   C10  aromatic  1.326  0.020  1.326
 3DL  C7   C8   aromatic  1.398  0.020  1.398
 3DL  C11  C10  single    1.477  0.020  1.477
 3DL  C11  C16  aromatic  1.392  0.020  1.392
 3DL  C10  C9   aromatic  1.396  0.020  1.396
 3DL  C15  C16  aromatic  1.392  0.020  1.392
 3DL  C15  O1   single    1.347  0.020  1.347
 3DL  C8   N1   aromatic  1.322  0.020  1.322
 3DL  C9   N1   aromatic  1.323  0.020  1.323
 3DL  C6   H2   single    0.930  0.020  1.080
 3DL  C5   H3   single    0.930  0.020  1.080
 3DL  C3   H4   single    0.930  0.020  1.080
 3DL  C2   H5   single    0.930  0.020  1.080
 3DL  C9   H6   single    0.930  0.020  1.080
 3DL  C8   H7   single    0.930  0.020  1.080
 3DL  C16  H8   single    0.930  0.020  1.080
 3DL  O1   H9   single    0.850  0.020  0.980
 3DL  C14  H10  single    0.930  0.020  1.080
 3DL  C13  H11  single    0.930  0.020  1.080
 3DL  C12  H12  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
 3DL  C1   C17  O2   116.49  3.000
 3DL  C1   C17  O3   116.53  3.000
 3DL  O2   C17  O3   126.98  3.000
 3DL  C2   C1   C6   118.01  3.000
 3DL  C2   C1   C17  121.04  3.000
 3DL  C6   C1   C17  120.94  3.000
 3DL  H2   C6   C5   119.40  3.000
 3DL  H2   C6   C1   119.42  3.000
 3DL  C5   C6   C1   121.18  3.000
 3DL  H3   C5   C4   120.88  3.000
 3DL  H3   C5   C6   118.38  3.000
 3DL  C4   C5   C6   120.74  3.000
 3DL  C7   C4   C3   119.96  3.000
 3DL  C7   C4   C5   121.92  3.000
 3DL  C3   C4   C5   118.12  3.000
 3DL  H4   C3   C2   119.73  3.000
 3DL  H4   C3   C4   119.48  3.000
 3DL  C2   C3   C4   120.80  3.000
 3DL  H5   C2   C3   119.43  3.000
 3DL  H5   C2   C1   119.43  3.000
 3DL  C3   C2   C1   121.15  3.000
 3DL  C8   C7   N2   119.46  3.000
 3DL  C8   C7   C4   122.98  3.000
 3DL  N2   C7   C4   117.56  3.000
 3DL  C10  N2   C7   119.55  3.000
 3DL  C11  C10  C9   122.52  3.000
 3DL  C9   C10  N2   119.87  3.000
 3DL  C11  C10  N2   117.61  3.000
 3DL  H6   C9   N1   116.88  3.000
 3DL  H6   C9   C10  121.68  3.000
 3DL  N1   C9   C10  121.44  3.000
 3DL  C8   N1   C9   117.90  3.000
 3DL  H7   C8   N1   116.41  3.000
 3DL  H7   C8   C7   121.86  3.000
 3DL  N1   C8   C7   121.72  3.000
 3DL  C12  C11  C16  119.55  3.000
 3DL  C16  C11  C10  120.64  3.000
 3DL  C12  C11  C10  119.81  3.000
 3DL  H8   C16  C15  118.42  3.000
 3DL  H8   C16  C11  121.12  3.000
 3DL  C15  C16  C11  120.45  3.000
 3DL  C14  C15  O1   122.72  3.000
 3DL  O1   C15  C16  117.42  3.000
 3DL  C14  C15  C16  119.86  3.000
 3DL  H9   O1   C15  110.48  3.000
 3DL  H10  C14  C13  120.18  3.000
 3DL  H10  C14  C15  120.37  3.000
 3DL  C13  C14  C15  119.45  3.000
 3DL  H11  C13  C12  119.69  3.000
 3DL  H11  C13  C14  119.27  3.000
 3DL  C12  C13  C14  121.04  3.000
 3DL  H12  C12  C13  120.30  3.000
 3DL  H12  C12  C11  120.06  3.000
 3DL  C13  C12  C11  119.64  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
 3DL  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 3DL  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 3DL  CONST_03  C3   C2   C1   C6     0.00   0.0  0
 3DL  CONST_04  C3   C4   C5   C6     0.00   0.0  0
 3DL  CONST_05  C7   C4   C5   C6   180.00   0.0  0
 3DL  CONST_06  C2   C1   C6   C5     0.00   0.0  0
 3DL  CONST_07  C2   C3   C4   C5     0.00   0.0  0
 3DL  CONST_08  N2   C7   C4   C5   180.00   0.0  0
 3DL  CONST_09  C8   C7   C4   C5     0.00   0.0  0
 3DL  CONST_10  C10  N2   C7   C4   180.00   0.0  0
 3DL  CONST_11  N1   C8   C7   C4   180.00   0.0  0
 3DL  CONST_12  N2   C7   C4   C3     0.00   0.0  0
 3DL  CONST_13  C8   C7   C4   C3   180.00   0.0  0
 3DL  CONST_14  C7   C4   C3   C2   180.00   0.0  0
 3DL  CONST_15  C11  C10  N2   C7   180.00   0.0  0
 3DL  CONST_16  C9   C10  N2   C7     0.00   0.0  0
 3DL  CONST_17  C9   N1   C8   C7     0.00   0.0  0
 3DL  CONST_18  N1   C8   C7   N2     0.00   0.0  0
 3DL  CONST_21  N1   C9   C10  N2     0.00   0.0  0
 3DL  CONST_22  C8   C7   N2   C10    0.00   0.0  0
 3DL  CONST_23  C13  C12  C11  C10  180.00   0.0  0
 3DL  CONST_24  C15  C16  C11  C10  180.00   0.0  0
 3DL  CONST_25  C8   N1   C9   C10    0.00   0.0  0
 3DL  CONST_28  C11  C10  C9   N1   180.00   0.0  0
 3DL  CONST_29  C14  C13  C12  C11    0.00   0.0  0
 3DL  CONST_30  C14  C15  C16  C11    0.00   0.0  0
 3DL  CONST_31  C13  C12  C11  C16    0.00   0.0  0
 3DL  CONST_32  C13  C14  C15  C16    0.00   0.0  0
 3DL  CONST_33  C12  C13  C14  C15    0.00   0.0  0
 3DL  CONST_34  C12  C11  C16  C15    0.00   0.0  0
 3DL  CONST_35  C5   C6   C1   C17  180.00   0.0  0
 3DL  CONST_36  C3   C2   C1   C17  180.00   0.0  0
 3DL  CONST_37  O1   C15  C16  C11  180.00   0.0  0
 3DL  CONST_38  C13  C14  C15  O1   180.00   0.0  0
 3DL  CONST_39  H3   C5   C6   C1   180.00   0.0  0
 3DL  CONST_40  H4   C3   C2   C1   180.00   0.0  0
 3DL  CONST_41  H5   C2   C1   C6   180.00   0.0  0
 3DL  CONST_42  H2   C6   C5   C4   180.00   0.0  0
 3DL  CONST_43  H7   C8   C7   C4     0.00   0.0  0
 3DL  CONST_44  H6   C9   C10  N2   180.00   0.0  0
 3DL  CONST_45  H12  C12  C11  C10    0.00   0.0  0
 3DL  CONST_46  H8   C16  C11  C10    0.00   0.0  0
 3DL  CONST_47  H11  C13  C12  C11  180.00   0.0  0
 3DL  CONST_48  H10  C14  C15  C16  180.00   0.0  0
 3DL  Var_01    C6   C1   C17  O3     0.69  30.0  2

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
 3DL  plan-1  C17  0.020
 3DL  plan-1  C1   0.020
 3DL  plan-1  C6   0.020
 3DL  plan-1  C5   0.020
 3DL  plan-1  C4   0.020
 3DL  plan-1  C3   0.020
 3DL  plan-1  C2   0.020
 3DL  plan-1  C7   0.020
 3DL  plan-1  H2   0.020
 3DL  plan-1  H3   0.020
 3DL  plan-1  H4   0.020
 3DL  plan-1  H5   0.020
 3DL  plan-2  C4   0.020
 3DL  plan-2  C7   0.020
 3DL  plan-2  N2   0.020
 3DL  plan-2  C10  0.020
 3DL  plan-2  C9   0.020
 3DL  plan-2  N1   0.020
 3DL  plan-2  C8   0.020
 3DL  plan-2  C11  0.020
 3DL  plan-2  H6   0.020
 3DL  plan-2  H7   0.020
 3DL  plan-3  C10  0.020
 3DL  plan-3  C11  0.020
 3DL  plan-3  C16  0.020
 3DL  plan-3  C15  0.020
 3DL  plan-3  O1   0.020
 3DL  plan-3  C14  0.020
 3DL  plan-3  C13  0.020
 3DL  plan-3  C12  0.020
 3DL  plan-3  H8   0.020
 3DL  plan-3  H10  0.020
 3DL  plan-3  H11  0.020
 3DL  plan-3  H12  0.020
 3DL  plan-4  O3   0.020
 3DL  plan-4  C17  0.020
 3DL  plan-4  O2   0.020
 3DL  plan-4  C1   0.020

