# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:07:25 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 4-[3-amino-6-(3-hydroxyphenyl)pyrazin-2-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(nc1c2ccc(cc2)C(O)=O)c3cccc(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
 3DV  3DV  '4-[3-amino-6-(3-hydroxyphenyl)pyrazin-2-yl]benzoic acid'  ligand  36  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3DV
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
 3DV  O2   O  OH1   0  -0.593   5.6317   2.3753   0.6775
 3DV  C11  C  C     0   0.533   5.5122   1.2797  -0.0584
 3DV  O1   O  O     0  -0.437   6.4213   0.8116  -0.7014
 3DV  C8   C  CR6   0  -0.090   4.1516   0.6913  -0.0077
 3DV  C7   C  CR16  0  -0.245   3.1235   1.2491   0.7517
 3DV  C6   C  CR16  0  -0.267   1.8714   0.6621   0.7655
 3DV  C9   C  CR16  0  -0.237   3.8997  -0.4592  -0.7497
 3DV  C10  C  CR16  0  -0.297   2.6491  -1.0509  -0.7265
 3DV  C5   C  CR6   0   0.057   1.6176  -0.4999   0.0354
 3DV  C1   C  CR6   0   0.121   0.2561  -1.0718   0.0378
 3DV  N2   N  N     0  -0.386  -0.7415  -0.2156  -0.0008
 3DV  C4   C  CR6   0   0.164  -2.0018  -0.6442  -0.0366
 3DV  C3   C  CR16  0  -0.108  -2.2375  -2.0146  -0.0659
 3DV  N1   N  N     0  -0.407  -1.2619  -2.9016   0.0190
 3DV  C2   C  CR6   0   0.414  -0.0091  -2.4671   0.1032
 3DV  N3   N  NH2   0  -0.831   0.9649  -3.4003   0.2264
 3DV  C12  C  CR6   0   0.083  -3.0749   0.3655  -0.0818
 3DV  C17  C  CR16  0  -0.479  -4.3848   0.0337   0.2670
 3DV  C16  C  CR6   0   0.393  -5.3964   0.9867   0.2121
 3DV  O3   O  OH1   0  -0.634  -6.6714   0.7020   0.5444
 3DV  C15  C  CR16  0  -0.350  -5.1057   2.2889  -0.1880
 3DV  C14  C  CR16  0  -0.227  -3.8022   2.6170  -0.5244
 3DV  C13  C  CR16  0  -0.324  -2.7876   1.6729  -0.4737
 3DV  H1   H  HOH1  0   0.489   6.5366   2.7160   0.6193
 3DV  H2   H  HCR6  0   0.271   3.2874   2.1422   1.3383
 3DV  H3   H  HCR6  0   0.263   1.0812   1.1059   1.3557
 3DV  H4   H  HCR6  0   0.270   4.6805  -0.8963  -1.3569
 3DV  H5   H  HCR6  0   0.275   2.4782  -1.9325  -1.3300
 3DV  H6   H  HCR6  0   0.269  -3.2394  -2.4152  -0.1673
 3DV  H7   H  HNH2  0   0.403   1.8516  -3.1361   0.6224
 3DV  H8   H  HNH2  0   0.396   0.6588  -4.3296   0.4671
 3DV  H9   H  HCR6  0   0.265  -4.6273  -0.9686   0.6024
 3DV  H10  H  HOH1  0   0.474  -6.7536  -0.2217   0.8063
 3DV  H11  H  HCR6  0   0.264  -5.8933   3.0305  -0.2290
 3DV  H12  H  HCR6  0   0.258  -3.5740   3.6288  -0.8337
 3DV  H13  H  HCR6  0   0.250  -1.7768   1.9454  -0.7424

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
 3DV  O1   C11  double    1.208  0.020  1.208
 3DV  O2   C11  single    1.325  0.020  1.325
 3DV  C11  C8   single    1.483  0.020  1.483
 3DV  C7   C8   aromatic  1.395  0.020  1.395
 3DV  C7   C6   aromatic  1.383  0.020  1.383
 3DV  C8   C9   aromatic  1.392  0.020  1.392
 3DV  C6   C5   aromatic  1.396  0.020  1.396
 3DV  C9   C10  aromatic  1.384  0.020  1.384
 3DV  C5   C10  aromatic  1.396  0.020  1.396
 3DV  C5   C1   single    1.477  0.020  1.477
 3DV  C14  C13  aromatic  1.387  0.020  1.387
 3DV  C14  C15  aromatic  1.386  0.020  1.386
 3DV  C13  C12  aromatic  1.395  0.020  1.395
 3DV  N2   C1   aromatic  1.315  0.020  1.315
 3DV  N2   C4   aromatic  1.332  0.020  1.332
 3DV  C1   C2   aromatic  1.422  0.020  1.422
 3DV  C15  C16  aromatic  1.393  0.020  1.393
 3DV  C12  C4   single    1.474  0.020  1.474
 3DV  C12  C17  aromatic  1.396  0.020  1.396
 3DV  C4   C3   aromatic  1.391  0.020  1.391
 3DV  N3   C2   single    1.354  0.020  1.354
 3DV  C2   N1   aromatic  1.329  0.020  1.329
 3DV  C3   N1   aromatic  1.321  0.020  1.321
 3DV  C16  C17  aromatic  1.391  0.020  1.391
 3DV  C16  O3   single    1.348  0.020  1.348
 3DV  O2   H1   single    0.850  0.020  0.980
 3DV  C7   H2   single    0.930  0.020  1.080
 3DV  C6   H3   single    0.930  0.020  1.080
 3DV  C9   H4   single    0.930  0.020  1.080
 3DV  C10  H5   single    0.930  0.020  1.080
 3DV  C3   H6   single    0.930  0.020  1.080
 3DV  N3   H7   single    0.890  0.020  1.040
 3DV  N3   H8   single    0.890  0.020  1.040
 3DV  C17  H9   single    0.930  0.020  1.080
 3DV  O3   H10  single    0.850  0.020  0.980
 3DV  C15  H11  single    0.930  0.020  1.080
 3DV  C14  H12  single    0.930  0.020  1.080
 3DV  C13  H13  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
 3DV  H1   O2   C11  109.98  3.000
 3DV  C8   C11  O1   123.70  3.000
 3DV  C8   C11  O2   113.06  3.000
 3DV  O1   C11  O2   123.25  3.000
 3DV  C9   C8   C7   119.17  3.000
 3DV  C9   C8   C11  118.40  3.000
 3DV  C7   C8   C11  122.43  3.000
 3DV  H2   C7   C6   118.85  3.000
 3DV  H2   C7   C8   120.94  3.000
 3DV  C6   C7   C8   120.21  3.000
 3DV  H3   C6   C5   119.62  3.000
 3DV  H3   C6   C7   119.52  3.000
 3DV  C5   C6   C7   120.85  3.000
 3DV  H4   C9   C10  119.29  3.000
 3DV  H4   C9   C8   120.18  3.000
 3DV  C10  C9   C8   120.54  3.000
 3DV  H5   C10  C5   120.62  3.000
 3DV  H5   C10  C9   118.81  3.000
 3DV  C5   C10  C9   120.55  3.000
 3DV  C1   C5   C10  121.96  3.000
 3DV  C1   C5   C6   119.29  3.000
 3DV  C10  C5   C6   118.68  3.000
 3DV  C2   C1   N2   119.92  3.000
 3DV  C2   C1   C5   123.51  3.000
 3DV  N2   C1   C5   116.56  3.000
 3DV  C4   N2   C1   120.60  3.000
 3DV  C12  C4   C3   123.42  3.000
 3DV  C3   C4   N2   118.56  3.000
 3DV  C12  C4   N2   117.99  3.000
 3DV  H6   C3   N1   116.14  3.000
 3DV  H6   C3   C4   121.52  3.000
 3DV  N1   C3   C4   122.34  3.000
 3DV  C2   N1   C3   118.74  3.000
 3DV  N3   C2   N1   117.29  3.000
 3DV  N1   C2   C1   119.59  3.000
 3DV  N3   C2   C1   123.11  3.000
 3DV  H8   N3   H7   114.57  3.000
 3DV  H8   N3   C2   116.03  3.000
 3DV  H7   N3   C2   119.24  3.000
 3DV  C13  C12  C17  119.10  3.000
 3DV  C17  C12  C4   120.85  3.000
 3DV  C13  C12  C4   120.05  3.000
 3DV  H9   C17  C16  118.87  3.000
 3DV  H9   C17  C12  120.46  3.000
 3DV  C16  C17  C12  120.66  3.000
 3DV  C15  C16  O3   117.75  3.000
 3DV  O3   C16  C17  122.24  3.000
 3DV  C15  C16  C17  120.00  3.000
 3DV  H10  O3   C16  110.50  3.000
 3DV  H11  C15  C14  120.87  3.000
 3DV  H11  C15  C16  119.96  3.000
 3DV  C14  C15  C16  119.17  3.000
 3DV  H12  C14  C13  119.51  3.000
 3DV  H12  C14  C15  119.27  3.000
 3DV  C13  C14  C15  121.21  3.000
 3DV  H13  C13  C14  120.23  3.000
 3DV  H13  C13  C12  119.92  3.000
 3DV  C14  C13  C12  119.85  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
 3DV  CONST_01  C5   C6   C7   C8     0.00   0.0  0
 3DV  CONST_02  C5   C10  C9   C8     0.00   0.0  0
 3DV  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 3DV  CONST_04  C10  C5   C6   C7     0.00   0.0  0
 3DV  CONST_05  C1   C5   C6   C7   180.00   0.0  0
 3DV  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 3DV  CONST_07  C9   C10  C5   C6     0.00   0.0  0
 3DV  CONST_10  C1   C5   C10  C9   180.00   0.0  0
 3DV  CONST_13  C4   N2   C1   C5   180.00   0.0  0
 3DV  CONST_14  N1   C2   C1   C5   180.00   0.0  0
 3DV  CONST_15  C12  C4   N2   C1   180.00   0.0  0
 3DV  CONST_16  C3   C4   N2   C1     0.00   0.0  0
 3DV  CONST_17  C3   N1   C2   C1     0.00   0.0  0
 3DV  CONST_18  N1   C2   C1   N2     0.00   0.0  0
 3DV  CONST_21  N1   C3   C4   N2     0.00   0.0  0
 3DV  CONST_22  C2   C1   N2   C4     0.00   0.0  0
 3DV  CONST_23  C14  C13  C12  C4   180.00   0.0  0
 3DV  CONST_24  C16  C17  C12  C4   180.00   0.0  0
 3DV  CONST_25  C2   N1   C3   C4     0.00   0.0  0
 3DV  CONST_28  C12  C4   C3   N1   180.00   0.0  0
 3DV  CONST_29  C15  C14  C13  C12    0.00   0.0  0
 3DV  CONST_30  C15  C16  C17  C12    0.00   0.0  0
 3DV  CONST_31  C14  C13  C12  C17    0.00   0.0  0
 3DV  CONST_32  C14  C15  C16  C17    0.00   0.0  0
 3DV  CONST_33  C13  C14  C15  C16    0.00   0.0  0
 3DV  CONST_34  C13  C12  C17  C16    0.00   0.0  0
 3DV  CONST_35  C6   C7   C8   C11  180.00   0.0  0
 3DV  CONST_36  C10  C9   C8   C11  180.00   0.0  0
 3DV  CONST_37  N3   C2   C1   C5     0.00   0.0  0
 3DV  CONST_38  N3   C2   C1   N2   180.00   0.0  0
 3DV  CONST_39  N3   C2   N1   C3   180.00   0.0  0
 3DV  CONST_40  O3   C16  C17  C12  180.00   0.0  0
 3DV  CONST_41  C14  C15  C16  O3   180.00   0.0  0
 3DV  CONST_42  H3   C6   C7   C8   180.00   0.0  0
 3DV  CONST_43  H5   C10  C9   C8   180.00   0.0  0
 3DV  CONST_44  H4   C9   C8   C7   180.00   0.0  0
 3DV  CONST_45  H2   C7   C8   C9   180.00   0.0  0
 3DV  CONST_46  H6   C3   C4   N2   180.00   0.0  0
 3DV  CONST_47  H13  C13  C12  C4     0.00   0.0  0
 3DV  CONST_48  H9   C17  C12  C4     0.00   0.0  0
 3DV  CONST_49  H12  C14  C13  C12  180.00   0.0  0
 3DV  CONST_50  H11  C15  C16  C17  180.00   0.0  0
 3DV  CONST_52  H8   N3   C2   C1   180.00   0.0  0
 3DV  CONST_53  H1   O2   C11  C8   180.00   0.0  0
 3DV  Var_01    C7   C8   C11  O2    -0.39  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
 3DV  plan-1  C11  0.020
 3DV  plan-1  C8   0.020
 3DV  plan-1  C7   0.020
 3DV  plan-1  C6   0.020
 3DV  plan-1  C9   0.020
 3DV  plan-1  C10  0.020
 3DV  plan-1  C5   0.020
 3DV  plan-1  C1   0.020
 3DV  plan-1  H2   0.020
 3DV  plan-1  H3   0.020
 3DV  plan-1  H4   0.020
 3DV  plan-1  H5   0.020
 3DV  plan-2  C5   0.020
 3DV  plan-2  C1   0.020
 3DV  plan-2  N2   0.020
 3DV  plan-2  C4   0.020
 3DV  plan-2  C3   0.020
 3DV  plan-2  N1   0.020
 3DV  plan-2  C2   0.020
 3DV  plan-2  N3   0.020
 3DV  plan-2  C12  0.020
 3DV  plan-2  H6   0.020
 3DV  plan-3  C4   0.020
 3DV  plan-3  C12  0.020
 3DV  plan-3  C17  0.020
 3DV  plan-3  C16  0.020
 3DV  plan-3  O3   0.020
 3DV  plan-3  C15  0.020
 3DV  plan-3  C14  0.020
 3DV  plan-3  C13  0.020
 3DV  plan-3  H9   0.020
 3DV  plan-3  H11  0.020
 3DV  plan-3  H12  0.020
 3DV  plan-3  H13  0.020
 3DV  plan-4  C2   0.020
 3DV  plan-4  N3   0.020
 3DV  plan-4  H7   0.020
 3DV  plan-4  H8   0.020
 3DV  plan-5  O2   0.020
 3DV  plan-5  C11  0.020
 3DV  plan-5  O1   0.020
 3DV  plan-5  C8   0.020
 3DV  plan-5  H1   0.020

