# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 10:41:48 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 2-naphthalen-1-ylethanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CCc1cccc2ccccc12
#
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
 SGZ  SGZ  "2-naphthalen-1-ylethanal"
  ligand  23  13  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SGZ
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
 SGZ  C1   C  CR6   0   0.142   -7.9906   -8.4360  27.3691
 SGZ  C2   C  CR16  0  -0.327   -8.3515   -8.8412  26.1099
 SGZ  C3   C  CR16  0  -0.242   -9.3391   -9.8249  25.9054
 SGZ  C4   C  CR16  0  -0.328   -9.9629  -10.4022  26.9744
 SGZ  C5   C  CR66  0   0.113   -9.6259  -10.0149  28.2924
 SGZ  C6   C  CR66  0   0.094   -8.6315   -9.0206  28.4992
 SGZ  C13  C  CR16  0  -0.330   -8.3196   -8.6532  29.8310
 SGZ  C14  C  CR16  0  -0.248   -8.9536   -9.2398  30.8930
 SGZ  C15  C  CR16  0  -0.260   -9.9344  -10.2291  30.6831
 SGZ  C16  C  CR16  0  -0.308  -10.2622  -10.6045  29.4100
 SGZ  CA   C  C1    0   0.173   -5.5798   -7.9502  27.9565
 SGZ  C    C  CH2   0  -0.705   -6.9161   -7.4058  27.5360
 SGZ  OB   O  O     0  -0.363   -5.3264   -9.1145  28.1245
 SGZ  H1   H  HCR6  0   0.254   -7.8676   -8.3954  25.2490
 SGZ  H2   H  HCR6  0   0.256   -9.5969  -10.1182  24.8962
 SGZ  H3   H  HCR6  0   0.254  -10.7223  -11.1611  26.8281
 SGZ  H4   H  HCR6  0   0.248   -7.5745   -7.8924  30.0240
 SGZ  H5   H  HCR6  0   0.257   -8.7002   -8.9427  31.9024
 SGZ  H6   H  HCR6  0   0.257  -10.4264  -10.6870  31.5313
 SGZ  H7   H  HCR6  0   0.255  -11.0171  -11.3628  29.2390
 SGZ  H8   H  H     0   0.203   -4.8077   -7.1726  28.0970
 SGZ  H9   H  HCH2  0   0.312   -6.7439   -6.8705  26.5956
 SGZ  H10  H  HCH2  0   0.293   -7.1854   -6.6186  28.2492

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
 SGZ  C3   C2   aromatic  1.409  0.020  1.409
 SGZ  C3   C4   aromatic  1.366  0.020  1.366
 SGZ  C2   C1   aromatic  1.371  0.020  1.371
 SGZ  C4   C5   aromatic  1.414  0.020  1.414
 SGZ  C1   C    single    1.498  0.020  1.498
 SGZ  C1   C6   aromatic  1.425  0.020  1.425
 SGZ  C    CA   single    1.503  0.020  1.503
 SGZ  OB   CA   double    1.203  0.020  1.203
 SGZ  C5   C6   aromatic  1.421  0.020  1.421
 SGZ  C5   C16  aromatic  1.415  0.020  1.415
 SGZ  C6   C13  aromatic  1.416  0.020  1.416
 SGZ  C16  C15  aromatic  1.367  0.020  1.367
 SGZ  C13  C14  aromatic  1.369  0.020  1.369
 SGZ  C15  C14  aromatic  1.409  0.020  1.409
 SGZ  C2   H1   single    0.930  0.020  1.080
 SGZ  C3   H2   single    0.930  0.020  1.080
 SGZ  C4   H3   single    0.930  0.020  1.080
 SGZ  C13  H4   single    0.930  0.020  1.080
 SGZ  C14  H5   single    0.930  0.020  1.080
 SGZ  C15  H6   single    0.930  0.020  1.080
 SGZ  C16  H7   single    0.930  0.020  1.080
 SGZ  CA   H8   single    0.930  0.020  1.080
 SGZ  C    H9   single    0.970  0.020  1.090
 SGZ  C    H10  single    0.970  0.020  1.090

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
 SGZ  C    C1   C6   121.10  3.000
 SGZ  C6   C1   C2   119.26  3.000
 SGZ  C    C1   C2   119.63  3.000
 SGZ  H1   C2   C3   119.01  3.000
 SGZ  H1   C2   C1   119.38  3.000
 SGZ  C3   C2   C1   121.61  3.000
 SGZ  H2   C3   C4   120.44  3.000
 SGZ  H2   C3   C2   119.45  3.000
 SGZ  C4   C3   C2   120.12  3.000
 SGZ  H3   C4   C5   118.98  3.000
 SGZ  H3   C4   C3   120.70  3.000
 SGZ  C5   C4   C3   120.32  3.000
 SGZ  C16  C5   C6   119.42  3.000
 SGZ  C16  C5   C4   120.99  3.000
 SGZ  C6   C5   C4   119.59  3.000
 SGZ  C13  C6   C5   118.19  3.000
 SGZ  C13  C6   C1   122.71  3.000
 SGZ  C5   C6   C1   119.10  3.000
 SGZ  H4   C13  C14  118.80  3.000
 SGZ  H4   C13  C6   120.11  3.000
 SGZ  C14  C13  C6   121.09  3.000
 SGZ  H5   C14  C15  119.65  3.000
 SGZ  H5   C14  C13  119.84  3.000
 SGZ  C15  C14  C13  120.52  3.000
 SGZ  H6   C15  C16  120.31  3.000
 SGZ  H6   C15  C14  119.79  3.000
 SGZ  C16  C15  C14  119.90  3.000
 SGZ  H7   C16  C15  120.40  3.000
 SGZ  H7   C16  C5   118.71  3.000
 SGZ  C15  C16  C5   120.89  3.000
 SGZ  H8   CA   OB   121.07  3.000
 SGZ  H8   CA   C    113.70  3.000
 SGZ  OB   CA   C    125.23  3.000
 SGZ  H10  C    H9   104.26  3.000
 SGZ  H10  C    CA   107.26  3.000
 SGZ  H9   C    CA   106.10  3.000
 SGZ  H10  C    C1   112.97  3.000
 SGZ  H9   C    C1   110.67  3.000
 SGZ  CA   C    C1   114.82  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
 SGZ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 SGZ  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 SGZ  CONST_03  C16  C5   C6   C1    180.00   0.0  0
 SGZ  CONST_04  C14  C13  C6   C1    180.00   0.0  0
 SGZ  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 SGZ  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 SGZ  CONST_07  C13  C6   C1   C2    180.00   0.0  0
 SGZ  CONST_08  C6   C1   C2   C3      0.00   0.0  0
 SGZ  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 SGZ  CONST_10  C16  C5   C4   C3    180.00   0.0  0
 SGZ  CONST_11  C13  C6   C5   C4    180.00   0.0  0
 SGZ  CONST_12  C15  C16  C5   C4    180.00   0.0  0
 SGZ  CONST_13  C14  C13  C6   C5      0.00   0.0  0
 SGZ  CONST_14  C14  C15  C16  C5      0.00   0.0  0
 SGZ  CONST_15  C15  C16  C5   C6      0.00   0.0  0
 SGZ  CONST_16  C15  C14  C13  C6      0.00   0.0  0
 SGZ  CONST_17  C16  C5   C6   C13     0.00   0.0  0
 SGZ  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 SGZ  CONST_19  C    C1   C2   C3    180.00   0.0  0
 SGZ  CONST_20  C    C1   C6   C5    180.00   0.0  0
 SGZ  CONST_21  C    C1   C6   C13     0.00   0.0  0
 SGZ  CONST_22  H2   C3   C2   C1    180.00   0.0  0
 SGZ  CONST_23  H4   C13  C6   C1      0.00   0.0  0
 SGZ  CONST_24  H3   C4   C3   C2    180.00   0.0  0
 SGZ  CONST_25  H1   C2   C3   C4    180.00   0.0  0
 SGZ  CONST_26  H7   C16  C5   C4      0.00   0.0  0
 SGZ  CONST_27  H2   C3   C4   C5    180.00   0.0  0
 SGZ  CONST_28  H4   C13  C6   C5    180.00   0.0  0
 SGZ  CONST_29  H6   C15  C16  C5    180.00   0.0  0
 SGZ  CONST_30  H1   C2   C1   C6    180.00   0.0  0
 SGZ  CONST_31  H3   C4   C5   C6    180.00   0.0  0
 SGZ  CONST_32  H7   C16  C5   C6    180.00   0.0  0
 SGZ  CONST_33  H5   C14  C13  C6    180.00   0.0  0
 SGZ  CONST_34  H6   C15  C14  C13   180.00   0.0  0
 SGZ  CONST_35  H7   C16  C15  C14   180.00   0.0  0
 SGZ  CONST_36  H4   C13  C14  C15   180.00   0.0  0
 SGZ  CONST_37  H3   C4   C5   C16     0.00   0.0  0
 SGZ  CONST_38  H5   C14  C15  C16   180.00   0.0  0
 SGZ  Var_01    CA   C    C1   C2   -102.91  30.0  2
 SGZ  Var_02    CA   C    C1   C6     76.05  30.0  2
 SGZ  Var_03    H9   C    C1   C2     17.17  30.0  2
 SGZ  Var_04    H10  C    C1   C2    133.64  30.0  2
 SGZ  Var_05    H9   C    C1   C6   -163.88  30.0  2
 SGZ  Var_06    H10  C    C1   C6    -47.40  30.0  2
 SGZ  Var_07    OB   CA   C    C1      1.99  30.0  3
 SGZ  Var_08    H8   CA   C    C1   -178.64  30.0  3
 SGZ  Var_09    H9   C    CA   OB   -120.59  30.0  1
 SGZ  Var_10    H10  C    CA   OB    128.43  30.0  1

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
 SGZ  plan-1  C1   0.020
 SGZ  plan-1  C2   0.020
 SGZ  plan-1  C3   0.020
 SGZ  plan-1  C4   0.020
 SGZ  plan-1  C5   0.020
 SGZ  plan-1  C6   0.020
 SGZ  plan-1  C13  0.020
 SGZ  plan-1  C14  0.020
 SGZ  plan-1  C15  0.020
 SGZ  plan-1  C16  0.020
 SGZ  plan-1  C    0.020
 SGZ  plan-1  H1   0.020
 SGZ  plan-1  H2   0.020
 SGZ  plan-1  H3   0.020
 SGZ  plan-1  H4   0.020
 SGZ  plan-1  H5   0.020
 SGZ  plan-1  H6   0.020
 SGZ  plan-1  H7   0.020
 SGZ  plan-2  CA   0.020
 SGZ  plan-2  C    0.020
 SGZ  plan-2  OB   0.020
 SGZ  plan-2  H8   0.020

