# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 20:20:02 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 4-phenoxy-N-(pyridin-2-ylmethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccccn1)c2ccc(Oc3ccccc3)cc2
#
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
 BI5  BI5  4-phenoxy-N-(pyridin-2-ylmethyl)benzamide  ligand  39  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BI5
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
 BI5  N1   N  N     0  -0.457   4.5466   0.8123   0.6292
 BI5  C1   C  CR6   0   0.228   4.9069  -0.3906   0.2080
 BI5  C2   C  CR16  0  -0.329   6.2399  -0.7868   0.1388
 BI5  C3   C  CR16  0  -0.145   7.2195   0.1099   0.5235
 BI5  C4   C  CR16  0  -0.336   6.8411   1.3723   0.9652
 BI5  C5   C  CR16  0  -0.058   5.4918   1.6726   0.9990
 BI5  C6   C  CH2   0  -0.284   3.8165  -1.3428  -0.2137
 BI5  N2   N  NH1   0  -0.674   2.5244  -0.7508  -0.0008
 BI5  C7   C  C     0   0.543   1.3852  -1.3848  -0.3094
 BI5  C8   C  CR6   0  -0.048   0.1201  -0.6541  -0.0098
 BI5  C9   C  CR16  0  -0.260  -1.0346  -1.0161  -0.6959
 BI5  C10  C  CR16  0  -0.331  -2.2433  -0.3795  -0.4639
 BI5  C11  C  CR6   0   0.369  -2.3088   0.6326   0.4885
 BI5  C12  C  CR16  0  -0.314  -1.1676   0.9948   1.2004
 BI5  C13  C  CR16  0  -0.284   0.0314   0.3562   0.9486
 BI5  O1   O  O2    0  -0.508  -3.4427   1.3091   0.7951
 BI5  C14  C  CR6   0   0.299  -4.5922   1.0629   0.0801
 BI5  C15  C  CR16  0  -0.302  -5.5292   0.1786   0.5908
 BI5  C16  C  CR16  0  -0.254  -6.7130  -0.0289  -0.1054
 BI5  C17  C  CR16  0  -0.254  -6.9492   0.6367  -1.3008
 BI5  C18  C  CR16  0  -0.253  -5.9982   1.5169  -1.8014
 BI5  C19  C  CR16  0  -0.298  -4.8123   1.7342  -1.1134
 BI5  O2   O  O     0  -0.500   1.3737  -2.5017  -0.8155
 BI5  H2   H  HCR6  0   0.272   6.4983  -1.7781  -0.2107
 BI5  H3   H  HCR6  0   0.277   8.2639  -0.1693   0.4802
 BI5  H4   H  HCR6  0   0.273   7.5736   2.1048   1.2747
 BI5  H5   H  HCR6  0   0.268   5.1513   2.6444   1.3369
 BI5  H61  H  HCH2  0   0.265   3.9146  -2.2745   0.3514
 BI5  H62  H  HCH2  0   0.265   3.9607  -1.6050  -1.2670
 BI5  HN2  H  HNH1  0   0.407   2.5331   0.2090   0.3138
 BI5  H9   H  HCR6  0   0.264  -0.9953  -1.8062  -1.4335
 BI5  H10  H  HCR6  0   0.283  -3.1170  -0.6819  -1.0253
 BI5  H12  H  HCR6  0   0.277  -1.2259   1.7705   1.9526
 BI5  H13  H  HCR6  0   0.256   0.8929   0.6462   1.5371
 BI5  H15  H  HCR6  0   0.274  -5.3391  -0.3356   1.5244
 BI5  H16  H  HCR6  0   0.265  -7.4508  -0.7139   0.2908
 BI5  H17  H  HCR6  0   0.262  -7.8736   0.4741  -1.8389
 BI5  H18  H  HCR6  0   0.265  -6.1782   2.0389  -2.7319
 BI5  H19  H  HCR6  0   0.276  -4.0694   2.4221  -1.4972

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
 BI5  N1   C1   aromatic  1.324  0.020  1.324
 BI5  N1   C5   aromatic  1.331  0.020  1.331
 BI5  C1   C2   aromatic  1.392  0.020  1.392
 BI5  C1   C6   single    1.508  0.020  1.508
 BI5  C2   C3   aromatic  1.383  0.020  1.383
 BI5  C2   H2   single    0.930  0.020  1.080
 BI5  C3   C4   aromatic  1.390  0.020  1.390
 BI5  C3   H3   single    0.930  0.020  1.080
 BI5  C4   C5   aromatic  1.383  0.020  1.383
 BI5  C4   H4   single    0.930  0.020  1.080
 BI5  C5   H5   single    0.930  0.020  1.080
 BI5  C6   N2   single    1.437  0.020  1.437
 BI5  C6   H61  single    0.970  0.020  1.090
 BI5  C6   H62  single    0.970  0.020  1.090
 BI5  N2   C7   single    1.340  0.020  1.340
 BI5  N2   HN2  single    0.860  0.020  1.020
 BI5  C7   C8   single    1.491  0.020  1.491
 BI5  C7   O2   double    1.226  0.020  1.226
 BI5  C8   C9   aromatic  1.391  0.020  1.391
 BI5  C8   C13  aromatic  1.395  0.020  1.395
 BI5  C9   C10  aromatic  1.386  0.020  1.386
 BI5  C9   H9   single    0.930  0.020  1.080
 BI5  C10  C11  aromatic  1.391  0.020  1.391
 BI5  C10  H10  single    0.930  0.020  1.080
 BI5  C11  C12  aromatic  1.393  0.020  1.393
 BI5  C11  O1   single    1.355  0.020  1.355
 BI5  C12  C13  aromatic  1.382  0.020  1.382
 BI5  C12  H12  single    0.930  0.020  1.080
 BI5  C13  H13  single    0.930  0.020  1.080
 BI5  O1   C14  single    1.376  0.020  1.376
 BI5  C14  C15  aromatic  1.386  0.020  1.386
 BI5  C14  C19  aromatic  1.387  0.020  1.387
 BI5  C15  C16  aromatic  1.389  0.020  1.389
 BI5  C15  H15  single    0.930  0.020  1.080
 BI5  C16  C17  aromatic  1.388  0.020  1.388
 BI5  C16  H16  single    0.930  0.020  1.080
 BI5  C17  C18  aromatic  1.389  0.020  1.389
 BI5  C17  H17  single    0.930  0.020  1.080
 BI5  C18  C19  aromatic  1.388  0.020  1.388
 BI5  C18  H18  single    0.930  0.020  1.080
 BI5  C19  H19  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
 BI5  C5   N1   C1   118.84  3.000
 BI5  C6   C1   C2   119.92  3.000
 BI5  C6   C1   N1   117.76  3.000
 BI5  C2   C1   N1   122.32  3.000
 BI5  H2   C2   C3   120.98  3.000
 BI5  H2   C2   C1   120.34  3.000
 BI5  C3   C2   C1   118.68  3.000
 BI5  H3   C3   C4   120.65  3.000
 BI5  H3   C3   C2   120.36  3.000
 BI5  C4   C3   C2   118.99  3.000
 BI5  H4   C4   C5   120.47  3.000
 BI5  H4   C4   C3   121.46  3.000
 BI5  C5   C4   C3   118.07  3.000
 BI5  H5   C5   C4   120.59  3.000
 BI5  H5   C5   N1   116.32  3.000
 BI5  C4   C5   N1   123.09  3.000
 BI5  H62  C6   H61  106.33  3.000
 BI5  H62  C6   N2   111.07  3.000
 BI5  H61  C6   N2   110.79  3.000
 BI5  H62  C6   C1   108.97  3.000
 BI5  H61  C6   C1   109.18  3.000
 BI5  N2   C6   C1   110.40  3.000
 BI5  HN2  N2   C7   121.92  3.000
 BI5  HN2  N2   C6   115.46  3.000
 BI5  C7   N2   C6   122.37  3.000
 BI5  O2   C7   C8   121.41  3.000
 BI5  O2   C7   N2   122.28  3.000
 BI5  C8   C7   N2   116.30  3.000
 BI5  C13  C8   C9   118.32  3.000
 BI5  C13  C8   C7   123.14  3.000
 BI5  C9   C8   C7   118.53  3.000
 BI5  H9   C9   C10  118.78  3.000
 BI5  H9   C9   C8   119.75  3.000
 BI5  C10  C9   C8   121.47  3.000
 BI5  H10  C10  C11  121.37  3.000
 BI5  H10  C10  C9   119.29  3.000
 BI5  C11  C10  C9   119.33  3.000
 BI5  O1   C11  C12  116.11  3.000
 BI5  O1   C11  C10  123.87  3.000
 BI5  C12  C11  C10  120.02  3.000
 BI5  H12  C12  C13  120.32  3.000
 BI5  H12  C12  C11  119.83  3.000
 BI5  C13  C12  C11  119.85  3.000
 BI5  H13  C13  C12  117.88  3.000
 BI5  H13  C13  C8   121.10  3.000
 BI5  C12  C13  C8   121.00  3.000
 BI5  C14  O1   C11  119.48  3.000
 BI5  C19  C14  C15  121.24  3.000
 BI5  C19  C14  O1   119.55  3.000
 BI5  C15  C14  O1   119.18  3.000
 BI5  H15  C15  C16  120.73  3.000
 BI5  H15  C15  C14  120.14  3.000
 BI5  C16  C15  C14  119.13  3.000
 BI5  H16  C16  C17  120.19  3.000
 BI5  H16  C16  C15  119.48  3.000
 BI5  C17  C16  C15  120.33  3.000
 BI5  H17  C17  C18  120.06  3.000
 BI5  H17  C17  C16  120.10  3.000
 BI5  C18  C17  C16  119.84  3.000
 BI5  H18  C18  C19  119.53  3.000
 BI5  H18  C18  C17  120.11  3.000
 BI5  C19  C18  C17  120.36  3.000
 BI5  H19  C19  C18  120.66  3.000
 BI5  H19  C19  C14  120.24  3.000
 BI5  C18  C19  C14  119.10  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
 BI5  CONST_01  C3   C2   C1   N1     0.00   0.0  0
 BI5  CONST_02  C3   C4   C5   N1     0.00   0.0  0
 BI5  CONST_03  C4   C5   N1   C1     0.00   0.0  0
 BI5  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 BI5  CONST_05  C5   N1   C1   C2     0.00   0.0  0
 BI5  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 BI5  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 BI5  CONST_08  C11  C12  C13  C8     0.00   0.0  0
 BI5  CONST_09  C12  C13  C8   C9     0.00   0.0  0
 BI5  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 BI5  CONST_11  C13  C8   C9   C10    0.00   0.0  0
 BI5  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 BI5  CONST_13  C17  C16  C15  C14    0.00   0.0  0
 BI5  CONST_14  C17  C18  C19  C14    0.00   0.0  0
 BI5  CONST_15  C18  C19  C14  C15    0.00   0.0  0
 BI5  CONST_16  C18  C17  C16  C15    0.00   0.0  0
 BI5  CONST_17  C19  C14  C15  C16    0.00   0.0  0
 BI5  CONST_18  C19  C18  C17  C16    0.00   0.0  0
 BI5  CONST_19  C6   C1   C2   C3   180.00   0.0  0
 BI5  CONST_20  C6   C1   N1   C5   180.00   0.0  0
 BI5  CONST_21  C10  C9   C8   C7   180.00   0.0  0
 BI5  CONST_22  C12  C13  C8   C7   180.00   0.0  0
 BI5  CONST_23  O1   C11  C10  C9   180.00   0.0  0
 BI5  CONST_24  O1   C11  C12  C13  180.00   0.0  0
 BI5  CONST_25  C16  C15  C14  O1   180.00   0.0  0
 BI5  CONST_26  C18  C19  C14  O1   180.00   0.0  0
 BI5  CONST_27  H2   C2   C1   N1   180.00   0.0  0
 BI5  CONST_28  H4   C4   C5   N1   180.00   0.0  0
 BI5  CONST_29  H5   C5   N1   C1   180.00   0.0  0
 BI5  CONST_30  H3   C3   C2   C1   180.00   0.0  0
 BI5  CONST_31  H10  C10  C9   C8   180.00   0.0  0
 BI5  CONST_32  H12  C12  C13  C8   180.00   0.0  0
 BI5  CONST_33  H13  C13  C8   C9   180.00   0.0  0
 BI5  CONST_34  H9   C9   C10  C11  180.00   0.0  0
 BI5  CONST_35  H16  C16  C15  C14  180.00   0.0  0
 BI5  CONST_36  H18  C18  C19  C14  180.00   0.0  0
 BI5  CONST_37  H19  C19  C14  C15  180.00   0.0  0
 BI5  CONST_38  H17  C17  C16  C15  180.00   0.0  0
 BI5  CONST_39  H15  C15  C16  C17  180.00   0.0  0
 BI5  CONST_40  C8   C7   N2   C6   180.00   0.0  0
 BI5  CONST_41  HN2  N2   C7   C8     0.00   0.0  0
 BI5  CONST_42  O2   C7   N2   C6     0.00   0.0  0
 BI5  Var_01    C15  C14  O1   C11   96.85  30.0  2
 BI5  Var_02    N2   C6   C1   N1    -3.08  30.0  2
 BI5  Var_03    C9   C8   C7   N2   158.13  30.0  2
 BI5  Var_04    C7   N2   C6   C1   179.18  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
 BI5  plan-1  N1   0.020
 BI5  plan-1  C1   0.020
 BI5  plan-1  C2   0.020
 BI5  plan-1  C3   0.020
 BI5  plan-1  C4   0.020
 BI5  plan-1  C5   0.020
 BI5  plan-1  C6   0.020
 BI5  plan-1  H2   0.020
 BI5  plan-1  H3   0.020
 BI5  plan-1  H4   0.020
 BI5  plan-1  H5   0.020
 BI5  plan-2  C7   0.020
 BI5  plan-2  C8   0.020
 BI5  plan-2  C9   0.020
 BI5  plan-2  C10  0.020
 BI5  plan-2  C11  0.020
 BI5  plan-2  C12  0.020
 BI5  plan-2  C13  0.020
 BI5  plan-2  O1   0.020
 BI5  plan-2  H9   0.020
 BI5  plan-2  H10  0.020
 BI5  plan-2  H12  0.020
 BI5  plan-2  H13  0.020
 BI5  plan-3  O1   0.020
 BI5  plan-3  C14  0.020
 BI5  plan-3  C15  0.020
 BI5  plan-3  C16  0.020
 BI5  plan-3  C17  0.020
 BI5  plan-3  C18  0.020
 BI5  plan-3  C19  0.020
 BI5  plan-3  H15  0.020
 BI5  plan-3  H16  0.020
 BI5  plan-3  H17  0.020
 BI5  plan-3  H18  0.020
 BI5  plan-3  H19  0.020
 BI5  plan-4  C6   0.020
 BI5  plan-4  N2   0.020
 BI5  plan-4  C7   0.020
 BI5  plan-4  C8   0.020
 BI5  plan-4  O2   0.020
 BI5  plan-4  HN2  0.020

