# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:07:21 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-(4-methylphenyl)-3-(pyridin-2-ylmethoxy)pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2ncccc2OCc3ccccn3
#
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
 GDK  GDK  2-(4-methylphenyl)-3-(pyridin-2-ylmethoxy)pyridine  ligand  37  21  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GDK
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
 GDK  N1   N  N     0  -0.402  -2.8106  -2.0197   0.0865
 GDK  C4   C  CR16  0  -0.274  -2.9625   0.7471  -0.7212
 GDK  C5   C  CR6   0   0.063  -1.9635   0.2130   0.0918
 GDK  C6   C  CR16  0  -0.274  -1.2572   1.0812   0.9239
 GDK  C7   C  CR16  0  -0.289  -1.5338   2.4398   0.9260
 GDK  C8   C  CR6   0   0.088  -1.7310  -1.2494   0.0853
 GDK  C10  C  CR16  0  -0.304  -1.4534  -3.9689   0.0525
 GDK  C13  C  CH2   0  -0.208   1.9070  -1.4562  -0.0572
 GDK  C15  C  CR16  0  -0.336   2.4882   1.0222  -0.1472
 GDK  C17  C  CR16  0  -0.327   4.8065   1.6114  -0.1865
 GDK  C2   C  CR6   0   0.089  -2.5156   2.9801   0.0983
 GDK  C3   C  CR16  0  -0.288  -3.2287   2.1071  -0.7210
 GDK  C12  C  CR6   0   0.346  -0.4378  -1.8056   0.0376
 GDK  C11  C  CR16  0  -0.288  -0.3069  -3.1880   0.0305
 GDK  C9   C  CR16  0  -0.104  -2.6844  -3.3407   0.0706
 GDK  O    O  O2    0  -0.471   0.5942  -0.9487  -0.0232
 GDK  C14  C  CR6   0   0.187   2.8789  -0.3104  -0.1043
 GDK  N2   N  N     0  -0.428   4.1551  -0.6842  -0.1035
 GDK  C18  C  CR16  0  -0.075   5.0904   0.2540  -0.1441
 GDK  C16  C  CR16  0  -0.146   3.4759   1.9961  -0.1880
 GDK  H1   H  HCR6  0   0.248  -3.5326   0.0903  -1.3658
 GDK  H2   H  HCR6  0   0.254  -0.5010   0.6996   1.5965
 GDK  H3   H  HCR6  0   0.248  -0.9775   3.0907   1.5902
 GDK  H4   H  HCR6  0   0.274  -1.3833  -5.0477   0.0474
 GDK  H5   H  HCH2  0   0.256   2.1140  -2.0677   0.8286
 GDK  H6   H  HCH2  0   0.256   2.0575  -2.0949  -0.9356
 GDK  H8   H  HCR6  0   0.271   5.6060   2.3381  -0.2171
 GDK  H12  H  HCR6  0   0.247  -4.0063   2.4954  -1.3686
 GDK  H13  H  HCR6  0   0.298   0.6632  -3.6650  -0.0036
 GDK  H14  H  HCR6  0   0.259  -3.6017  -3.9179   0.0760
 GDK  H15  H  HCR6  0   0.265   6.1190  -0.0897  -0.1420
 GDK  H16  H  HCR6  0   0.275   3.2053   3.0434  -0.2209
 GDK  C1   C  CH3   0  -0.722  -2.7802   4.4567   0.0727
 GDK  H7   H  HCR6  0   0.274   1.4442   1.3012  -0.1502
 GDK  H9   H  HCH3  0   0.250  -2.1621   4.9480  -0.6819
 GDK  H10  H  HCH3  0   0.244  -3.8196   4.6734  -0.1715
 GDK  H11  H  HCH3  0   0.244  -2.5504   4.9221   1.0307

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
 GDK  C17  C18  aromatic  1.387  0.020  1.387
 GDK  C17  C16  aromatic  1.385  0.020  1.385
 GDK  C18  N2   aromatic  1.325  0.020  1.325
 GDK  C16  C15  aromatic  1.388  0.020  1.388
 GDK  N2   C14  aromatic  1.330  0.020  1.330
 GDK  C15  C14  aromatic  1.389  0.020  1.389
 GDK  C14  C13  single    1.503  0.020  1.503
 GDK  C13  O    single    1.408  0.020  1.408
 GDK  C1   C2   single    1.500  0.020  1.500
 GDK  O    C12  single    1.343  0.020  1.343
 GDK  C7   C2   aromatic  1.393  0.020  1.393
 GDK  C7   C6   aromatic  1.386  0.020  1.386
 GDK  C2   C3   aromatic  1.394  0.020  1.394
 GDK  C6   C5   aromatic  1.395  0.020  1.395
 GDK  C3   C4   aromatic  1.386  0.020  1.386
 GDK  C12  C11  aromatic  1.389  0.020  1.389
 GDK  C12  C8   aromatic  1.409  0.020  1.409
 GDK  C5   C4   aromatic  1.394  0.020  1.394
 GDK  C5   C8   single    1.481  0.020  1.481
 GDK  C11  C10  aromatic  1.387  0.020  1.387
 GDK  C8   N1   aromatic  1.326  0.020  1.326
 GDK  C10  C9   aromatic  1.382  0.020  1.382
 GDK  N1   C9   aromatic  1.327  0.020  1.327
 GDK  C4   H1   single    0.930  0.020  1.080
 GDK  C6   H2   single    0.930  0.020  1.080
 GDK  C7   H3   single    0.930  0.020  1.080
 GDK  C10  H4   single    0.930  0.020  1.080
 GDK  C13  H5   single    0.970  0.020  1.090
 GDK  C13  H6   single    0.970  0.020  1.090
 GDK  C15  H7   single    0.930  0.020  1.080
 GDK  C17  H8   single    0.930  0.020  1.080
 GDK  C1   H9   single    0.970  0.020  1.090
 GDK  C1   H10  single    0.970  0.020  1.090
 GDK  C1   H11  single    0.970  0.020  1.090
 GDK  C3   H12  single    0.930  0.020  1.080
 GDK  C11  H13  single    0.930  0.020  1.080
 GDK  C9   H14  single    0.930  0.020  1.080
 GDK  C18  H15  single    0.930  0.020  1.080
 GDK  C16  H16  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
 GDK  C9   N1   C8   120.04  3.000
 GDK  H1   C4   C3   119.63  3.000
 GDK  H1   C4   C5   119.48  3.000
 GDK  C3   C4   C5   120.89  3.000
 GDK  C8   C5   C6   122.55  3.000
 GDK  C8   C5   C4   119.22  3.000
 GDK  C6   C5   C4   118.18  3.000
 GDK  H2   C6   C7   118.97  3.000
 GDK  H2   C6   C5   120.35  3.000
 GDK  C7   C6   C5   120.66  3.000
 GDK  H3   C7   C2   119.54  3.000
 GDK  H3   C7   C6   119.15  3.000
 GDK  C2   C7   C6   121.31  3.000
 GDK  C12  C8   C5   122.29  3.000
 GDK  C5   C8   N1   116.48  3.000
 GDK  C12  C8   N1   121.20  3.000
 GDK  H4   C10  C9   120.75  3.000
 GDK  H4   C10  C11  120.53  3.000
 GDK  C9   C10  C11  118.71  3.000
 GDK  H6   C13  H5   107.25  3.000
 GDK  H6   C13  C14  109.28  3.000
 GDK  H5   C13  C14  109.17  3.000
 GDK  H6   C13  O    110.94  3.000
 GDK  H5   C13  O    110.96  3.000
 GDK  C14  C13  O    109.20  3.000
 GDK  H7   C15  C16  120.42  3.000
 GDK  H7   C15  C14  121.29  3.000
 GDK  C16  C15  C14  118.29  3.000
 GDK  H8   C17  C16  121.59  3.000
 GDK  H8   C17  C18  120.48  3.000
 GDK  C16  C17  C18  117.93  3.000
 GDK  C3   C2   C1   121.08  3.000
 GDK  C3   C2   C7   117.84  3.000
 GDK  C1   C2   C7   121.07  3.000
 GDK  H12  C3   C2   119.61  3.000
 GDK  H12  C3   C4   119.29  3.000
 GDK  C2   C3   C4   121.10  3.000
 GDK  O    C12  C11  124.24  3.000
 GDK  C11  C12  C8   118.67  3.000
 GDK  O    C12  C8   117.07  3.000
 GDK  H13  C11  C12  121.59  3.000
 GDK  H13  C11  C10  119.57  3.000
 GDK  C12  C11  C10  118.84  3.000
 GDK  H14  C9   C10  120.79  3.000
 GDK  H14  C9   N1   116.71  3.000
 GDK  C10  C9   N1   122.50  3.000
 GDK  C12  O    C13  119.19  3.000
 GDK  N2   C14  C15  122.65  3.000
 GDK  C15  C14  C13  123.38  3.000
 GDK  N2   C14  C13  113.97  3.000
 GDK  C18  N2   C14  118.57  3.000
 GDK  H15  C18  N2   116.42  3.000
 GDK  H15  C18  C17  120.28  3.000
 GDK  N2   C18  C17  123.30  3.000
 GDK  H16  C16  C17  120.60  3.000
 GDK  H16  C16  C15  120.14  3.000
 GDK  C17  C16  C15  119.26  3.000
 GDK  H11  C1   H10  108.26  3.000
 GDK  H11  C1   H9   107.22  3.000
 GDK  H10  C1   H9   107.20  3.000
 GDK  H11  C1   C2   111.60  3.000
 GDK  H10  C1   C2   111.58  3.000
 GDK  H9   C1   C2   110.78  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
 GDK  CONST_01  C11  C12  C8   N1      0.00   0.0  0
 GDK  CONST_04  C11  C10  C9   N1      0.00   0.0  0
 GDK  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 GDK  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 GDK  CONST_08  C2   C7   C6   C5      0.00   0.0  0
 GDK  CONST_09  C2   C3   C4   C5      0.00   0.0  0
 GDK  CONST_10  C11  C12  C8   C5    180.00   0.0  0
 GDK  CONST_11  C9   N1   C8   C5    180.00   0.0  0
 GDK  CONST_12  C3   C2   C7   C6      0.00   0.0  0
 GDK  CONST_13  C3   C4   C5   C6      0.00   0.0  0
 GDK  CONST_15  C8   C5   C6   C7    180.00   0.0  0
 GDK  CONST_16  C10  C11  C12  C8      0.00   0.0  0
 GDK  CONST_17  C3   C4   C5   C8    180.00   0.0  0
 GDK  CONST_18  C10  C9   N1   C8      0.00   0.0  0
 GDK  CONST_19  C18  C17  C16  C15     0.00   0.0  0
 GDK  CONST_20  C18  N2   C14  C15     0.00   0.0  0
 GDK  CONST_21  C14  N2   C18  C17     0.00   0.0  0
 GDK  CONST_22  C14  C15  C16  C17     0.00   0.0  0
 GDK  CONST_23  C9   C10  C11  C12     0.00   0.0  0
 GDK  CONST_24  C9   N1   C8   C12     0.00   0.0  0
 GDK  CONST_25  C16  C17  C18  N2      0.00   0.0  0
 GDK  CONST_26  C16  C15  C14  N2      0.00   0.0  0
 GDK  CONST_27  O    C12  C8   N1    180.00   0.0  0
 GDK  CONST_28  C1   C2   C3   C4    180.00   0.0  0
 GDK  CONST_29  O    C12  C8   C5      0.00   0.0  0
 GDK  CONST_30  C1   C2   C7   C6    180.00   0.0  0
 GDK  CONST_31  O    C12  C11  C10   180.00   0.0  0
 GDK  CONST_32  C18  N2   C14  C13   180.00   0.0  0
 GDK  CONST_33  C16  C15  C14  C13   180.00   0.0  0
 GDK  CONST_34  H4   C10  C9   N1    180.00   0.0  0
 GDK  CONST_35  H2   C6   C5   C4    180.00   0.0  0
 GDK  CONST_36  H3   C7   C6   C5    180.00   0.0  0
 GDK  CONST_37  H12  C3   C4   C5    180.00   0.0  0
 GDK  CONST_38  H1   C4   C5   C6    180.00   0.0  0
 GDK  CONST_39  H13  C11  C12  C8    180.00   0.0  0
 GDK  CONST_40  H14  C9   N1   C8    180.00   0.0  0
 GDK  CONST_41  H8   C17  C16  C15   180.00   0.0  0
 GDK  CONST_42  H7   C15  C16  C17   180.00   0.0  0
 GDK  CONST_43  H15  C18  N2   C14   180.00   0.0  0
 GDK  CONST_44  H16  C16  C15  C14   180.00   0.0  0
 GDK  Var_01    C11  C12  O    C13    -1.99  30.0  2
 GDK  Var_02    O    C13  C14  C15    -1.78  30.0  2
 GDK  Var_03    C14  C13  O    C12  -179.22  30.0  2
 GDK  Var_04    H9   C1   C2   C7     90.22  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
 GDK  plan-1  C4   0.020
 GDK  plan-1  C5   0.020
 GDK  plan-1  C6   0.020
 GDK  plan-1  C7   0.020
 GDK  plan-1  C8   0.020
 GDK  plan-1  C2   0.020
 GDK  plan-1  C3   0.020
 GDK  plan-1  H1   0.020
 GDK  plan-1  H2   0.020
 GDK  plan-1  H3   0.020
 GDK  plan-1  H12  0.020
 GDK  plan-1  C1   0.020
 GDK  plan-2  C13  0.020
 GDK  plan-2  C15  0.020
 GDK  plan-2  C17  0.020
 GDK  plan-2  C14  0.020
 GDK  plan-2  N2   0.020
 GDK  plan-2  C18  0.020
 GDK  plan-2  C16  0.020
 GDK  plan-2  H8   0.020
 GDK  plan-2  H15  0.020
 GDK  plan-2  H16  0.020
 GDK  plan-2  H7   0.020
 GDK  plan-3  N1   0.020
 GDK  plan-3  C5   0.020
 GDK  plan-3  C8   0.020
 GDK  plan-3  C10  0.020
 GDK  plan-3  C12  0.020
 GDK  plan-3  C11  0.020
 GDK  plan-3  C9   0.020
 GDK  plan-3  O    0.020
 GDK  plan-3  H4   0.020
 GDK  plan-3  H13  0.020
 GDK  plan-3  H14  0.020

