# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 15:15:23 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: phenanthrene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1ccc2c(c1)ccc3ccccc23
#
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
 PEY  PEY  'phenanthrene             '  ligand  24  14  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PEY
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
 PEY  C1   C  CR16  0  -0.349  -1.4948  -1.5581  -0.0046
 PEY  C2   C  CR16  0  -0.243  -2.8696  -1.5239   0.0008
 PEY  C3   C  CR16  0  -0.264  -3.5482  -0.2983   0.0120
 PEY  C4   C  CR16  0  -0.307  -2.8325   0.8734   0.0174
 PEY  C5   C  CR66  0   0.079  -1.4251   0.8605   0.0118
 PEY  C6   C  CR66  0   0.120  -0.7352  -0.3730   0.0009
 PEY  C7   C  CR66  0   0.120   0.7144  -0.3708  -0.0039
 PEY  C8   C  CR66  0   0.078   1.4005   0.8648   0.0029
 PEY  C9   C  CR16  0  -0.322   0.6614   2.0896   0.0137
 PEY  C10  C  CR16  0  -0.322  -0.6897   2.0875   0.0179
 PEY  C11  C  CR16  0  -0.349   1.4776  -1.5535  -0.0146
 PEY  C12  C  CR16  0  -0.243   2.8523  -1.5151  -0.0187
 PEY  C13  C  CR16  0  -0.264   3.5272  -0.2873  -0.0119
 PEY  C14  C  CR16  0  -0.307   2.8078   0.8822  -0.0010
 PEY  H1   H  HCR6  0   0.254  -1.0041  -2.5216  -0.0131
 PEY  H2   H  HCR6  0   0.261  -3.4295  -2.4499  -0.0038
 PEY  H3   H  HCR6  0   0.259  -4.6299  -0.2771   0.0164
 PEY  H4   H  HCR6  0   0.257  -3.3469   1.8268   0.0268
 PEY  H9   H  HCR6  0   0.256   1.2098   3.0239   0.0187
 PEY  H10  H  HCR6  0   0.256  -1.2409   3.0202   0.0265
 PEY  H11  H  HCR6  0   0.254   0.9899  -2.5186  -0.0203
 PEY  H12  H  HCR6  0   0.261   3.4150  -2.4394  -0.0277
 PEY  H13  H  HCR6  0   0.259   4.6088  -0.2630  -0.0157
 PEY  H14  H  HCR6  0   0.257   3.3192   1.8372   0.0046

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
 PEY  C1   C2   aromatic  1.375  0.020  1.375
 PEY  C1   C6   aromatic  1.408  0.020  1.408
 PEY  C1   H1   single    0.930  0.020  1.080
 PEY  C2   C3   aromatic  1.401  0.020  1.401
 PEY  C2   H2   single    0.930  0.020  1.080
 PEY  C3   C4   aromatic  1.373  0.020  1.373
 PEY  C3   H3   single    0.930  0.020  1.080
 PEY  C4   C5   aromatic  1.407  0.020  1.407
 PEY  C4   H4   single    0.930  0.020  1.080
 PEY  C5   C6   aromatic  1.413  0.020  1.413
 PEY  C5   C10  aromatic  1.431  0.020  1.431
 PEY  C6   C7   aromatic  1.450  0.020  1.450
 PEY  C7   C8   aromatic  1.413  0.020  1.413
 PEY  C7   C11  aromatic  1.408  0.020  1.408
 PEY  C8   C9   aromatic  1.431  0.020  1.431
 PEY  C8   C14  aromatic  1.407  0.020  1.407
 PEY  C9   C10  aromatic  1.351  0.020  1.351
 PEY  C9   H9   single    0.930  0.020  1.080
 PEY  C10  H10  single    0.930  0.020  1.080
 PEY  C11  C12  aromatic  1.375  0.020  1.375
 PEY  C11  H11  single    0.930  0.020  1.080
 PEY  C12  C13  aromatic  1.401  0.020  1.401
 PEY  C12  H12  single    0.930  0.020  1.080
 PEY  C13  C14  aromatic  1.373  0.020  1.373
 PEY  C13  H13  single    0.930  0.020  1.080
 PEY  C14  H14  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
 PEY  H1   C1   C6   120.35  3.000
 PEY  H1   C1   C2   118.41  3.000
 PEY  C6   C1   C2   121.24  3.000
 PEY  H2   C2   C3   119.86  3.000
 PEY  H2   C2   C1   119.74  3.000
 PEY  C3   C2   C1   120.40  3.000
 PEY  H3   C3   C4   120.29  3.000
 PEY  H3   C3   C2   120.10  3.000
 PEY  C4   C3   C2   119.61  3.000
 PEY  H4   C4   C5   118.88  3.000
 PEY  H4   C4   C3   120.23  3.000
 PEY  C5   C4   C3   120.89  3.000
 PEY  C10  C5   C6   119.85  3.000
 PEY  C10  C5   C4   120.41  3.000
 PEY  C6   C5   C4   119.74  3.000
 PEY  C7   C6   C5   119.13  3.000
 PEY  C7   C6   C1   122.75  3.000
 PEY  C5   C6   C1   118.12  3.000
 PEY  C11  C7   C8   118.12  3.000
 PEY  C11  C7   C6   122.75  3.000
 PEY  C8   C7   C6   119.13  3.000
 PEY  C14  C8   C9   120.41  3.000
 PEY  C14  C8   C7   119.75  3.000
 PEY  C9   C8   C7   119.85  3.000
 PEY  H9   C9   C10  120.50  3.000
 PEY  H9   C9   C8   118.48  3.000
 PEY  C10  C9   C8   121.02  3.000
 PEY  H10  C10  C9   120.50  3.000
 PEY  H10  C10  C5   118.48  3.000
 PEY  C9   C10  C5   121.02  3.000
 PEY  H11  C11  C12  118.41  3.000
 PEY  H11  C11  C7   120.36  3.000
 PEY  C12  C11  C7   121.23  3.000
 PEY  H12  C12  C13  119.87  3.000
 PEY  H12  C12  C11  119.73  3.000
 PEY  C13  C12  C11  120.40  3.000
 PEY  H13  C13  C14  120.31  3.000
 PEY  H13  C13  C12  120.08  3.000
 PEY  C14  C13  C12  119.61  3.000
 PEY  H14  C14  C13  120.23  3.000
 PEY  H14  C14  C8   118.87  3.000
 PEY  C13  C14  C8   120.89  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
 PEY  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 PEY  CONST_02  C4   C5   C6   C1     0.00  0.0  0
 PEY  CONST_03  C10  C5   C6   C1   180.00  0.0  0
 PEY  CONST_04  C8   C7   C6   C1   180.00  0.0  0
 PEY  CONST_05  C11  C7   C6   C1     0.00  0.0  0
 PEY  CONST_06  C5   C6   C1   C2     0.00  0.0  0
 PEY  CONST_07  C7   C6   C1   C2   180.00  0.0  0
 PEY  CONST_08  C5   C4   C3   C2     0.00  0.0  0
 PEY  CONST_09  C6   C1   C2   C3     0.00  0.0  0
 PEY  CONST_10  C6   C5   C4   C3     0.00  0.0  0
 PEY  CONST_11  C10  C5   C4   C3   180.00  0.0  0
 PEY  CONST_12  C7   C6   C5   C4   180.00  0.0  0
 PEY  CONST_13  C9   C10  C5   C4   180.00  0.0  0
 PEY  CONST_14  C8   C7   C6   C5     0.00  0.0  0
 PEY  CONST_15  C11  C7   C6   C5   180.00  0.0  0
 PEY  CONST_16  C8   C9   C10  C5     0.00  0.0  0
 PEY  CONST_17  C9   C10  C5   C6     0.00  0.0  0
 PEY  CONST_18  C9   C8   C7   C6     0.00  0.0  0
 PEY  CONST_19  C14  C8   C7   C6   180.00  0.0  0
 PEY  CONST_20  C12  C11  C7   C6   180.00  0.0  0
 PEY  CONST_21  C10  C5   C6   C7     0.00  0.0  0
 PEY  CONST_22  C10  C9   C8   C7     0.00  0.0  0
 PEY  CONST_23  C13  C14  C8   C7     0.00  0.0  0
 PEY  CONST_24  C13  C12  C11  C7     0.00  0.0  0
 PEY  CONST_25  C12  C11  C7   C8     0.00  0.0  0
 PEY  CONST_26  C12  C13  C14  C8     0.00  0.0  0
 PEY  CONST_27  C11  C7   C8   C9   180.00  0.0  0
 PEY  CONST_28  C13  C14  C8   C9   180.00  0.0  0
 PEY  CONST_29  C14  C8   C9   C10  180.00  0.0  0
 PEY  CONST_30  C14  C8   C7   C11    0.00  0.0  0
 PEY  CONST_31  C14  C13  C12  C11    0.00  0.0  0
 PEY  CONST_32  H3   C3   C2   C1   180.00  0.0  0
 PEY  CONST_33  H4   C4   C3   C2   180.00  0.0  0
 PEY  CONST_34  H1   C1   C2   C3   180.00  0.0  0
 PEY  CONST_35  H2   C2   C3   C4   180.00  0.0  0
 PEY  CONST_36  H10  C10  C5   C4     0.00  0.0  0
 PEY  CONST_37  H9   C9   C10  C5   180.00  0.0  0
 PEY  CONST_38  H11  C11  C7   C6     0.00  0.0  0
 PEY  CONST_39  H14  C14  C8   C7   180.00  0.0  0
 PEY  CONST_40  H12  C12  C11  C7   180.00  0.0  0
 PEY  CONST_41  H13  C13  C14  C8   180.00  0.0  0

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
 PEY  plan-1  C1   0.020
 PEY  plan-1  C2   0.020
 PEY  plan-1  C3   0.020
 PEY  plan-1  C4   0.020
 PEY  plan-1  C5   0.020
 PEY  plan-1  C6   0.020
 PEY  plan-1  C7   0.020
 PEY  plan-1  C8   0.020
 PEY  plan-1  C9   0.020
 PEY  plan-1  C10  0.020
 PEY  plan-1  C11  0.020
 PEY  plan-1  C12  0.020
 PEY  plan-1  C13  0.020
 PEY  plan-1  C14  0.020
 PEY  plan-1  H1   0.020
 PEY  plan-1  H2   0.020
 PEY  plan-1  H3   0.020
 PEY  plan-1  H4   0.020
 PEY  plan-1  H9   0.020
 PEY  plan-1  H10  0.020
 PEY  plan-1  H11  0.020
 PEY  plan-1  H12  0.020
 PEY  plan-1  H13  0.020
 PEY  plan-1  H14  0.020

