# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:18:45 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-naphthalen-2-yl-~{N}-pyridin-2-yl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cc1ccc2ccccc2c1)Nc3ccccn3
#
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
 G8H  G8H  2-naphthalen-2-yl-~{N}-pyridin-2-yl-ethanamide  ligand  34  20  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G8H
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
 G8H  C4   C  CR16  0  -0.344   6.1485   1.0765   0.5819
 G8H  C14  C  CR16  0  -0.310  -5.0921   0.0589   1.0554
 G8H  C5   C  CR16  0  -0.064   4.9353   1.6294   0.9451
 G8H  C6   C  C     0   0.551   1.2509  -0.1998  -0.1376
 G8H  C11  C  CR66  0   0.098  -3.7799  -0.2371   0.6185
 G8H  C7   C  CH2   0  -0.713   0.2108  -1.1109  -0.7747
 G8H  C8   C  CR6   0   0.161  -1.1794  -0.8007  -0.3139
 G8H  C9   C  CR16  0  -0.286  -1.5986  -1.2182   0.9723
 G8H  C10  C  CR16  0  -0.302  -2.8581  -0.9462   1.4254
 G8H  C12  C  CR66  0   0.137  -3.3699   0.1833  -0.6723
 G8H  C13  C  CR16  0  -0.386  -2.0569  -0.1142  -1.1089
 G8H  N1   N  N     0  -0.426   3.7541   1.0964   0.6420
 G8H  C3   C  CR16  0  -0.144   6.1243  -0.1110  -0.1426
 G8H  C1   C  CR6   0   0.525   3.7411  -0.0285  -0.0497
 G8H  C2   C  CR16  0  -0.404   4.9101  -0.6775  -0.4678
 G8H  O1   O  O     0  -0.428   0.9569   0.7835   0.5027
 G8H  C15  C  CR16  0  -0.260  -5.9586   0.7427   0.2460
 G8H  C16  C  CR16  0  -0.258  -5.5510   1.1618  -1.0382
 G8H  C17  C  CR16  0  -0.315  -4.2868   0.8890  -1.4862
 G8H  H1   H  HCR6  0   0.269   7.0780   1.5562   0.8532
 G8H  H3   H  HCR6  0   0.263   4.9049   2.5533   1.5120
 G8H  H4   H  HCH2  0   0.308   0.2903  -0.9989  -1.8601
 G8H  H5   H  HCH2  0   0.295   0.4611  -2.1543  -0.5602
 G8H  H6   H  HCR6  0   0.253  -0.9093  -1.7702   1.6003
 G8H  H7   H  HCR6  0   0.255  -3.1647  -1.2758   2.4108
 G8H  H8   H  HCR6  0   0.250  -1.7526   0.2140  -2.0970
 G8H  H10  H  HCR6  0   0.277   7.0443  -0.5899  -0.4504
 G8H  H11  H  HCR6  0   0.280   4.8600  -1.5996  -1.0330
 G8H  H12  H  HCR6  0   0.258  -6.9614   0.9645   0.5868
 G8H  H13  H  HCR6  0   0.258  -6.2450   1.7023  -1.6687
 G8H  H14  H  HCR6  0   0.254  -3.9751   1.2120  -2.4724
 G8H  N2   N  NH1   0  -0.731   2.5275  -0.6161  -0.3923
 G8H  H2   H  HCR6  0   0.255  -5.4022  -0.2669   2.0411
 G8H  H9   H  HNH1  0   0.424   2.6096  -1.4645  -0.9322

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
 G8H  N1   C5   aromatic  1.331  0.020  1.331
 G8H  N1   C1   aromatic  1.321  0.020  1.321
 G8H  C7   C6   single    1.522  0.020  1.522
 G8H  C7   C8   single    1.497  0.020  1.497
 G8H  N2   C1   single    1.391  0.020  1.391
 G8H  N2   C6   single    1.367  0.020  1.367
 G8H  C5   C4   aromatic  1.382  0.020  1.382
 G8H  C1   C2   aromatic  1.401  0.020  1.401
 G8H  C6   O1   double    1.210  0.020  1.210
 G8H  C4   C3   aromatic  1.391  0.020  1.391
 G8H  C2   C3   aromatic  1.379  0.020  1.379
 G8H  C9   C8   aromatic  1.416  0.020  1.416
 G8H  C9   C10  aromatic  1.366  0.020  1.366
 G8H  C8   C13  aromatic  1.369  0.020  1.369
 G8H  C10  C11  aromatic  1.415  0.020  1.415
 G8H  C13  C12  aromatic  1.415  0.020  1.415
 G8H  C11  C12  aromatic  1.418  0.020  1.418
 G8H  C11  C14  aromatic  1.414  0.020  1.414
 G8H  C12  C17  aromatic  1.415  0.020  1.415
 G8H  C14  C15  aromatic  1.369  0.020  1.369
 G8H  C17  C16  aromatic  1.369  0.020  1.369
 G8H  C15  C16  aromatic  1.411  0.020  1.411
 G8H  C4   H1   single    0.930  0.020  1.080
 G8H  C14  H2   single    0.930  0.020  1.080
 G8H  C5   H3   single    0.930  0.020  1.080
 G8H  C7   H4   single    0.970  0.020  1.090
 G8H  C7   H5   single    0.970  0.020  1.090
 G8H  C9   H6   single    0.930  0.020  1.080
 G8H  C10  H7   single    0.930  0.020  1.080
 G8H  C13  H8   single    0.930  0.020  1.080
 G8H  N2   H9   single    0.860  0.020  1.020
 G8H  C3   H10  single    0.930  0.020  1.080
 G8H  C2   H11  single    0.930  0.020  1.080
 G8H  C15  H12  single    0.930  0.020  1.080
 G8H  C16  H13  single    0.930  0.020  1.080
 G8H  C17  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
 G8H  H1   C4   C3   121.64  3.000
 G8H  H1   C4   C5   120.78  3.000
 G8H  C3   C4   C5   117.59  3.000
 G8H  H2   C14  C15  120.47  3.000
 G8H  H2   C14  C11  118.92  3.000
 G8H  C15  C14  C11  120.61  3.000
 G8H  H3   C5   N1   115.81  3.000
 G8H  H3   C5   C4   120.19  3.000
 G8H  N1   C5   C4   124.00  3.000
 G8H  O1   C6   N2   124.98  3.000
 G8H  O1   C6   C7   122.82  3.000
 G8H  N2   C6   C7   112.20  3.000
 G8H  C12  C11  C10  118.62  3.000
 G8H  C12  C11  C14  119.17  3.000
 G8H  C10  C11  C14  122.21  3.000
 G8H  H5   C7   H4   105.99  3.000
 G8H  H5   C7   C8   110.46  3.000
 G8H  H4   C7   C8   110.59  3.000
 G8H  H5   C7   C6   109.41  3.000
 G8H  H4   C7   C6   107.72  3.000
 G8H  C8   C7   C6   112.43  3.000
 G8H  C13  C8   C9   119.06  3.000
 G8H  C13  C8   C7   121.37  3.000
 G8H  C9   C8   C7   119.57  3.000
 G8H  H6   C9   C10  119.73  3.000
 G8H  H6   C9   C8   119.23  3.000
 G8H  C10  C9   C8   121.04  3.000
 G8H  H7   C10  C9   120.14  3.000
 G8H  H7   C10  C11  119.12  3.000
 G8H  C9   C10  C11  120.75  3.000
 G8H  C17  C12  C13  121.92  3.000
 G8H  C17  C12  C11  118.96  3.000
 G8H  C13  C12  C11  119.13  3.000
 G8H  H8   C13  C12  118.54  3.000
 G8H  H8   C13  C8   120.06  3.000
 G8H  C12  C13  C8   121.40  3.000
 G8H  C1   N1   C5   117.98  3.000
 G8H  H10  C3   C2   119.99  3.000
 G8H  H10  C3   C4   120.74  3.000
 G8H  C2   C3   C4   119.26  3.000
 G8H  C2   C1   N2   117.31  3.000
 G8H  C2   C1   N1   122.86  3.000
 G8H  N2   C1   N1   119.83  3.000
 G8H  H11  C2   C1   120.78  3.000
 G8H  H11  C2   C3   120.92  3.000
 G8H  C1   C2   C3   118.30  3.000
 G8H  H12  C15  C16  119.56  3.000
 G8H  H12  C15  C14  120.19  3.000
 G8H  C16  C15  C14  120.25  3.000
 G8H  H13  C16  C17  120.07  3.000
 G8H  H13  C16  C15  119.56  3.000
 G8H  C17  C16  C15  120.37  3.000
 G8H  H14  C17  C16  120.28  3.000
 G8H  H14  C17  C12  119.07  3.000
 G8H  C16  C17  C12  120.65  3.000
 G8H  H9   N2   C1   114.57  3.000
 G8H  H9   N2   C6   115.59  3.000
 G8H  C1   N2   C6   129.81  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
 G8H  CONST_01  C1   N1   C5   C4     0.00   0.0  0
 G8H  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 G8H  CONST_03  C9   C10  C11  C14  180.00   0.0  0
 G8H  CONST_04  C13  C12  C11  C14  180.00   0.0  0
 G8H  CONST_05  C17  C12  C11  C14    0.00   0.0  0
 G8H  CONST_06  C17  C16  C15  C14    0.00   0.0  0
 G8H  CONST_07  C2   C1   N1   C5     0.00   0.0  0
 G8H  CONST_08  C2   C3   C4   C5     0.00   0.0  0
 G8H  CONST_09  C8   C9   C10  C11    0.00   0.0  0
 G8H  CONST_10  C8   C13  C12  C11    0.00   0.0  0
 G8H  CONST_11  C16  C17  C12  C11    0.00   0.0  0
 G8H  CONST_12  C16  C15  C14  C11    0.00   0.0  0
 G8H  CONST_13  C17  C12  C13  C8   180.00   0.0  0
 G8H  CONST_14  C12  C13  C8   C9     0.00   0.0  0
 G8H  CONST_15  C12  C11  C10  C9     0.00   0.0  0
 G8H  CONST_16  C13  C8   C9   C10    0.00   0.0  0
 G8H  CONST_17  C13  C12  C11  C10    0.00   0.0  0
 G8H  CONST_18  C17  C12  C11  C10  180.00   0.0  0
 G8H  CONST_19  C15  C14  C11  C10  180.00   0.0  0
 G8H  CONST_20  C15  C14  C11  C12    0.00   0.0  0
 G8H  CONST_21  C15  C16  C17  C12    0.00   0.0  0
 G8H  CONST_22  C16  C17  C12  C13  180.00   0.0  0
 G8H  CONST_23  C3   C4   C5   N1     0.00   0.0  0
 G8H  CONST_24  C3   C2   C1   N1     0.00   0.0  0
 G8H  CONST_25  N2   C1   N1   C5   180.00   0.0  0
 G8H  CONST_26  C10  C9   C8   C7   180.00   0.0  0
 G8H  CONST_27  C12  C13  C8   C7   180.00   0.0  0
 G8H  CONST_28  C3   C2   C1   N2   180.00   0.0  0
 G8H  CONST_29  H11  C2   C3   C4   180.00   0.0  0
 G8H  CONST_30  H7   C10  C11  C14    0.00   0.0  0
 G8H  CONST_31  H13  C16  C15  C14  180.00   0.0  0
 G8H  CONST_32  H10  C3   C4   C5   180.00   0.0  0
 G8H  CONST_33  H6   C9   C10  C11  180.00   0.0  0
 G8H  CONST_34  H8   C13  C12  C11  180.00   0.0  0
 G8H  CONST_35  H14  C17  C12  C11  180.00   0.0  0
 G8H  CONST_36  H12  C15  C14  C11  180.00   0.0  0
 G8H  CONST_37  H2   C14  C11  C10    0.00   0.0  0
 G8H  CONST_38  H1   C4   C5   N1   180.00   0.0  0
 G8H  CONST_39  H3   C5   C4   C3   180.00   0.0  0
 G8H  CONST_40  N1   C1   N2   C6     0.00   0.0  0
 G8H  CONST_41  C2   C1   N2   C6   180.00   0.0  0
 G8H  CONST_42  H9   N2   C1   N1   180.00   0.0  0
 G8H  CONST_43  C1   N2   C6   C7   180.00   0.0  0
 G8H  CONST_44  O1   C6   N2   C1     0.00   0.0  0
 G8H  Var_01    C9   C8   C7   C6   -76.35  30.0  2
 G8H  Var_02    N2   C6   C7   C8   170.34  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
 G8H  plan-1  C4   0.020
 G8H  plan-1  C5   0.020
 G8H  plan-1  N1   0.020
 G8H  plan-1  C3   0.020
 G8H  plan-1  C1   0.020
 G8H  plan-1  C2   0.020
 G8H  plan-1  H1   0.020
 G8H  plan-1  H3   0.020
 G8H  plan-1  H10  0.020
 G8H  plan-1  H11  0.020
 G8H  plan-1  N2   0.020
 G8H  plan-2  C14  0.020
 G8H  plan-2  C11  0.020
 G8H  plan-2  C7   0.020
 G8H  plan-2  C8   0.020
 G8H  plan-2  C9   0.020
 G8H  plan-2  C10  0.020
 G8H  plan-2  C12  0.020
 G8H  plan-2  C13  0.020
 G8H  plan-2  C15  0.020
 G8H  plan-2  C16  0.020
 G8H  plan-2  C17  0.020
 G8H  plan-2  H6   0.020
 G8H  plan-2  H7   0.020
 G8H  plan-2  H8   0.020
 G8H  plan-2  H12  0.020
 G8H  plan-2  H13  0.020
 G8H  plan-2  H14  0.020
 G8H  plan-2  H2   0.020
 G8H  plan-3  C6   0.020
 G8H  plan-3  C7   0.020
 G8H  plan-3  C1   0.020
 G8H  plan-3  O1   0.020
 G8H  plan-3  N2   0.020
 G8H  plan-3  H9   0.020

