# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:17:27 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-2-amino-3-(naphthalen-2-yl)propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc2ccccc2c1)C(O)=O
#
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
 NAL  NAL  '(2S)-2-amino-3-(naphthalen-2-yl)propanoic acid (non-preferred name)'  L-peptide  28  16  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_NAL
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
 NAL  C1   C  CR16   0  -0.387  40.7444  28.4174  22.5522
 NAL  C2   C  CR6    0   0.168  39.4546  28.6977  22.9275
 NAL  C3   C  CR16   0  -0.309  38.3964  28.1320  22.1763
 NAL  C4   C  CR16   0  -0.300  38.6397  27.3217  21.1019
 NAL  C4A  C  CR66   0   0.092  39.9638  27.0149  20.7119
 NAL  C5   C  CR16   0  -0.309  40.2539  26.1727  19.6129
 NAL  C6   C  CR16   0  -0.262  41.5487  25.8992  19.2649
 NAL  C7   C  CR16   0  -0.258  42.6153  26.4607  19.9997
 NAL  C8   C  CR16   0  -0.316  42.3638  27.2805  21.0660
 NAL  C8A  C  CR66   0   0.141  41.0350  27.5788  21.4523
 NAL  C9   C  CH2    0  -0.521  39.1749  29.5546  24.1271
 NAL  CA   C  CH1    0  -0.197  39.2417  28.7773  25.4531
 NAL  C    C  C      0   0.380  39.1324  29.7961  26.6197
 NAL  N    N  NH2    0  -0.782  38.2520  27.7137  25.4529
 NAL  O    O  O      0  -0.600  38.0334  29.8760  27.2034
 NAL  OXT  O  OC    -1  -0.614  40.1559  30.4732  26.8472
 NAL  H1   H  HCR6   0   0.238  41.5725  28.8440  23.1096
 NAL  H3   H  HCR6   0   0.241  37.3751  28.3547  22.4606
 NAL  H4   H  HCR6   0   0.247  37.8154  26.8989  20.5394
 NAL  H5   H  HCR6   0   0.250  39.4325  25.7442  19.0505
 NAL  H6   H  HCR6   0   0.252  41.7608  25.2515  18.4241
 NAL  H7   H  HCR6   0   0.253  43.6358  26.2386  19.7155
 NAL  H8   H  HCR6   0   0.249  43.1827  27.7111  21.6303
 NAL  H91  H  HCH2   0   0.242  39.8956  30.3735  24.1691
 NAL  H92  H  HCH2   0   0.233  38.1835  30.0103  24.0343
 NAL  HA   H  HCH1   0   0.214  40.2319  28.3120  25.5055
 NAL  H    H  HNH2   0   0.334  38.4094  27.1228  26.2607
 NAL  H2   H  HNH2   0   0.322  37.3457  28.1367  25.6211

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
 NAL  C6   C5   aromatic  1.368  0.020  1.368
 NAL  C6   C7   aromatic  1.412  0.020  1.412
 NAL  C5   C4A  aromatic  1.415  0.020  1.415
 NAL  C7   C8   aromatic  1.368  0.020  1.368
 NAL  C4A  C4   aromatic  1.414  0.020  1.414
 NAL  C4A  C8A  aromatic  1.419  0.020  1.419
 NAL  C8   C8A  aromatic  1.416  0.020  1.416
 NAL  C4   C3   aromatic  1.367  0.020  1.367
 NAL  C8A  C1   aromatic  1.413  0.020  1.413
 NAL  C3   C2   aromatic  1.416  0.020  1.416
 NAL  C1   C2   aromatic  1.372  0.020  1.372
 NAL  C2   C9   single    1.501  0.020  1.501
 NAL  C9   CA   single    1.538  0.020  1.538
 NAL  CA   N    single    1.458  0.019  1.458
 NAL  CA   C    single    1.525  0.021  1.525
 NAL  C    O    deloc     1.231  0.020  1.231
 NAL  C    OXT  deloc     1.248  0.020  1.248
 NAL  C1   H1   single    0.930  0.020  1.080
 NAL  C3   H3   single    0.930  0.020  1.080
 NAL  C4   H4   single    0.930  0.020  1.080
 NAL  C5   H5   single    0.930  0.020  1.080
 NAL  C6   H6   single    0.930  0.020  1.080
 NAL  C7   H7   single    0.930  0.020  1.080
 NAL  C8   H8   single    0.930  0.020  1.080
 NAL  C9   H91  single    0.970  0.020  1.090
 NAL  C9   H92  single    0.970  0.020  1.090
 NAL  CA   HA   single    0.970  0.020  0.970
 NAL  N    H    single    0.860  0.020  0.860
 NAL  N    H2   single    0.890  0.020  1.040

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
 NAL  H1   C1   C8A  118.42  3.000
 NAL  H1   C1   C2   119.76  3.000
 NAL  C8A  C1   C2   121.82  3.000
 NAL  C9   C2   C3   120.87  3.000
 NAL  C9   C2   C1   120.70  3.000
 NAL  C3   C2   C1   118.42  3.000
 NAL  H3   C3   C4   119.72  3.000
 NAL  H3   C3   C2   118.90  3.000
 NAL  C4   C3   C2   121.37  3.000
 NAL  H4   C4   C4A  118.97  3.000
 NAL  H4   C4   C3   120.24  3.000
 NAL  C4A  C4   C3   120.79  3.000
 NAL  C8A  C4A  C5   119.15  3.000
 NAL  C8A  C4A  C4   118.47  3.000
 NAL  C5   C4A  C4   122.38  3.000
 NAL  H5   C5   C6   120.41  3.000
 NAL  H5   C5   C4A  118.89  3.000
 NAL  C6   C5   C4A  120.70  3.000
 NAL  H6   C6   C7   119.63  3.000
 NAL  H6   C6   C5   120.17  3.000
 NAL  C7   C6   C5   120.20  3.000
 NAL  H7   C7   C8   120.06  3.000
 NAL  H7   C7   C6   119.60  3.000
 NAL  C8   C7   C6   120.34  3.000
 NAL  H8   C8   C8A  118.91  3.000
 NAL  H8   C8   C7   120.32  3.000
 NAL  C8A  C8   C7   120.76  3.000
 NAL  C8   C8A  C4A  118.85  3.000
 NAL  C8   C8A  C1   122.03  3.000
 NAL  C4A  C8A  C1   119.12  3.000
 NAL  H92  C9   H91  106.78  3.000
 NAL  H92  C9   CA   108.82  3.000
 NAL  H91  C9   CA   108.49  3.000
 NAL  H92  C9   C2   109.80  3.000
 NAL  H91  C9   C2   109.64  3.000
 NAL  CA   C9   C2   113.11  3.000
 NAL  HA   CA   N    110.00  3.000
 NAL  HA   CA   C    109.00  3.000
 NAL  N    CA   C    111.00  2.800
 NAL  HA   CA   C9   107.17  3.000
 NAL  C    CA   C9   108.24  3.000
 NAL  N    CA   C9   109.89  3.000
 NAL  OXT  C    O    127.06  3.000
 NAL  OXT  C    CA   115.80  3.000
 NAL  O    C    CA   120.80  1.700
 NAL  H2   N    H    104.47  3.000
 NAL  H2   N    CA   107.66  3.000
 NAL  H    N    CA   114.00  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
 NAL  CONST_01  C5   C4A  C8A  C1   180.00   0.0  0
 NAL  CONST_02  C4   C4A  C8A  C1     0.00   0.0  0
 NAL  CONST_03  C7   C8   C8A  C1   180.00   0.0  0
 NAL  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 NAL  CONST_05  C4A  C4   C3   C2     0.00   0.0  0
 NAL  CONST_06  C4A  C8A  C1   C2     0.00   0.0  0
 NAL  CONST_07  C8   C8A  C1   C2   180.00   0.0  0
 NAL  CONST_08  C5   C4A  C4   C3   180.00   0.0  0
 NAL  CONST_09  C8A  C4A  C4   C3     0.00   0.0  0
 NAL  CONST_10  C8A  C1   C2   C3     0.00   0.0  0
 NAL  CONST_11  C6   C5   C4A  C4   180.00   0.0  0
 NAL  CONST_12  C8   C8A  C4A  C4   180.00   0.0  0
 NAL  CONST_13  C7   C6   C5   C4A    0.00   0.0  0
 NAL  CONST_14  C7   C8   C8A  C4A    0.00   0.0  0
 NAL  CONST_15  C8   C7   C6   C5     0.00   0.0  0
 NAL  CONST_16  C8   C8A  C4A  C5     0.00   0.0  0
 NAL  CONST_17  C8A  C4A  C5   C6     0.00   0.0  0
 NAL  CONST_18  C8A  C8   C7   C6     0.00   0.0  0
 NAL  CONST_19  C9   C2   C3   C4   180.00   0.0  0
 NAL  CONST_20  C9   C2   C1   C8A  180.00   0.0  0
 NAL  CONST_21  H8   C8   C8A  C1     0.00   0.0  0
 NAL  CONST_22  H3   C3   C2   C1   180.00   0.0  0
 NAL  CONST_23  H4   C4   C3   C2   180.00   0.0  0
 NAL  CONST_24  H1   C1   C2   C3   180.00   0.0  0
 NAL  CONST_25  H5   C5   C4A  C4     0.00   0.0  0
 NAL  CONST_26  H6   C6   C5   C4A  180.00   0.0  0
 NAL  CONST_27  H7   C7   C6   C5   180.00   0.0  0
 NAL  Var_01    CA   C9   C2   C1   -82.10  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NAL  chir_01  CA  C9  N  C  positiv

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
 NAL  plan-1  C1   0.020
 NAL  plan-1  C2   0.020
 NAL  plan-1  C3   0.020
 NAL  plan-1  C4   0.020
 NAL  plan-1  C4A  0.020
 NAL  plan-1  C5   0.020
 NAL  plan-1  C6   0.020
 NAL  plan-1  C7   0.020
 NAL  plan-1  C8   0.020
 NAL  plan-1  C8A  0.020
 NAL  plan-1  C9   0.020
 NAL  plan-1  H1   0.020
 NAL  plan-1  H3   0.020
 NAL  plan-1  H4   0.020
 NAL  plan-1  H5   0.020
 NAL  plan-1  H6   0.020
 NAL  plan-1  H7   0.020
 NAL  plan-1  H8   0.020
 NAL  plan-2  CA   0.020
 NAL  plan-2  C    0.020
 NAL  plan-2  O    0.020
 NAL  plan-2  OXT  0.020

