# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:45:34 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-2-amino-3-naphthalen-1-ylpropanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cccc2ccccc12)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
 ALN  ALN  '(2S)-2-amino-3-naphthalen-1-ylpropanoic 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_ALN
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
 ALN  N    N  NH2    0  -0.792  5.0058  19.9082  15.3436
 ALN  CA   C  CH1    0  -0.195  3.8602  20.1724  16.1909
 ALN  C    C  C      0   0.401  2.5369  20.0823  15.3954
 ALN  O    O  O      0  -0.598  2.6001  20.2708  14.1651
 ALN  CB   C  CH2    0  -0.554  3.8906  21.5557  16.8901
 ALN  CG1  C  CR6    0   0.118  5.0844  21.7317  17.7792
 ALN  CD1  C  CR16   0  -0.343  6.1896  22.4081  17.3225
 ALN  CE1  C  CR16   0  -0.241  7.3541  22.5466  18.1040
 ALN  CD2  C  CR66   0   0.084  5.1256  21.1540  19.0847
 ALN  CE2  C  CR66   0   0.114  6.2996  21.2950  19.8738
 ALN  CZ1  C  CR16   0  -0.336  7.4110  21.9999  19.3541
 ALN  CG2  C  CR16   0  -0.334  4.0320  20.4405  19.6357
 ALN  CD3  C  CR16   0  -0.251  4.0987  19.9018  20.8928
 ALN  CE3  C  CR16   0  -0.259  5.2642  20.0456  21.6709
 ALN  CZ2  C  CR16   0  -0.311  6.3385  20.7274  21.1694
 ALN  OXT  O  OC    -1  -0.611  1.5109  19.8723  16.0732
 ALN  H    H  HNH2   0   0.334  5.8641  20.1571  15.8208
 ALN  H2   H  HNH2   0   0.324  4.9455  20.4974  14.5224
 ALN  HA   H  HCH1   0   0.212  3.8333  19.4056  16.9725
 ALN  HB2  H  HCH2   0   0.245  3.9030  22.3294  16.1168
 ALN  HB3  H  HCH2   0   0.238  2.9652  21.6943  17.4525
 ALN  HD1  H  HCR6   0   0.248  6.1638  22.8553  16.3357
 ALN  HE1  H  HCR6   0   0.252  8.2020  23.0884  17.7051
 ALN  HZ1  H  HCR6   0   0.250  8.3017  22.0991  19.9630
 ALN  HG2  H  HCR6   0   0.247  3.1260  20.3140  19.0573
 ALN  HD3  H  HCR6   0   0.254  3.2506  19.3613  21.2931
 ALN  HE3  H  HCR6   0   0.254  5.3056  19.6152  22.6631
 ALN  HZ2  H  HCR6   0   0.252  7.2388  20.8421  21.7617

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
 ALN  N    CA   single    1.458  0.019  1.458
 ALN  N    H    single    0.860  0.020  0.860
 ALN  N    H2   single    0.890  0.020  1.040
 ALN  CA   C    single    1.525  0.021  1.525
 ALN  CA   CB   single    1.521  0.033  1.521
 ALN  CA   HA   single    0.970  0.020  0.970
 ALN  C    O    deloc     1.231  0.020  1.231
 ALN  C    OXT  deloc     1.247  0.020  1.247
 ALN  CB   CG1  single    1.499  0.020  1.499
 ALN  CB   HB2  single    0.970  0.020  1.090
 ALN  CB   HB3  single    0.970  0.020  1.090
 ALN  CG1  CD1  aromatic  1.374  0.020  1.374
 ALN  CG1  CD2  aromatic  1.428  0.020  1.428
 ALN  CD1  CE1  aromatic  1.409  0.020  1.409
 ALN  CD1  HD1  single    0.930  0.020  1.080
 ALN  CE1  CZ1  aromatic  1.366  0.020  1.366
 ALN  CE1  HE1  single    0.930  0.020  1.080
 ALN  CD2  CE2  aromatic  1.422  0.020  1.422
 ALN  CD2  CG2  aromatic  1.417  0.020  1.417
 ALN  CE2  CZ1  aromatic  1.415  0.020  1.415
 ALN  CE2  CZ2  aromatic  1.415  0.020  1.415
 ALN  CZ1  HZ1  single    0.930  0.020  1.080
 ALN  CG2  CD3  aromatic  1.369  0.020  1.369
 ALN  CG2  HG2  single    0.930  0.020  1.080
 ALN  CD3  CE3  aromatic  1.409  0.020  1.409
 ALN  CD3  HD3  single    0.930  0.020  1.080
 ALN  CE3  CZ2  aromatic  1.368  0.020  1.368
 ALN  CE3  HE3  single    0.930  0.020  1.080
 ALN  CZ2  HZ2  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
 ALN  H2   N    H    106.83  3.000
 ALN  H2   N    CA   108.73  3.000
 ALN  H    N    CA   114.00  3.000
 ALN  HA   CA   CB   109.00  3.000
 ALN  HA   CA   C    109.00  3.000
 ALN  CB   CA   C    110.50  1.500
 ALN  HA   CA   N    110.00  3.000
 ALN  CB   CA   N    110.40  1.500
 ALN  C    CA   N    111.00  2.800
 ALN  OXT  C    O    127.13  3.000
 ALN  OXT  C    CA   115.72  3.000
 ALN  O    C    CA   120.80  1.700
 ALN  HB3  CB   HB2  106.49  3.000
 ALN  HB3  CB   CG1  110.78  3.000
 ALN  HB2  CB   CG1  109.10  3.000
 ALN  HB3  CB   CA   109.21  3.000
 ALN  HB2  CB   CA   108.21  3.000
 ALN  CG1  CB   CA   112.83  3.000
 ALN  CD2  CG1  CD1  118.67  3.000
 ALN  CD2  CG1  CB   121.17  3.000
 ALN  CD1  CG1  CB   120.09  3.000
 ALN  HD1  CD1  CE1  118.95  3.000
 ALN  HD1  CD1  CG1  119.12  3.000
 ALN  CE1  CD1  CG1  121.92  3.000
 ALN  HE1  CE1  CZ1  120.34  3.000
 ALN  HE1  CE1  CD1  119.48  3.000
 ALN  CZ1  CE1  CD1  120.18  3.000
 ALN  CG2  CD2  CE2  118.13  3.000
 ALN  CG2  CD2  CG1  122.46  3.000
 ALN  CE2  CD2  CG1  119.41  3.000
 ALN  CZ2  CE2  CZ1  120.97  3.000
 ALN  CZ2  CE2  CD2  119.41  3.000
 ALN  CZ1  CE2  CD2  119.62  3.000
 ALN  HZ1  CZ1  CE2  119.00  3.000
 ALN  HZ1  CZ1  CE1  120.80  3.000
 ALN  CE2  CZ1  CE1  120.20  3.000
 ALN  HG2  CG2  CD3  119.04  3.000
 ALN  HG2  CG2  CD2  119.80  3.000
 ALN  CD3  CG2  CD2  121.16  3.000
 ALN  HD3  CD3  CE3  119.67  3.000
 ALN  HD3  CD3  CG2  119.85  3.000
 ALN  CE3  CD3  CG2  120.48  3.000
 ALN  HE3  CE3  CZ2  120.29  3.000
 ALN  HE3  CE3  CD3  119.83  3.000
 ALN  CZ2  CE3  CD3  119.88  3.000
 ALN  HZ2  CZ2  CE3  120.32  3.000
 ALN  HZ2  CZ2  CE2  118.73  3.000
 ALN  CE3  CZ2  CE2  120.95  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
 ALN  CONST_01  CZ1  CE1  CD1  CG1    0.00   0.0  0
 ALN  CONST_02  CZ1  CE2  CD2  CG1    0.00   0.0  0
 ALN  CONST_03  CZ2  CE2  CD2  CG1  180.00   0.0  0
 ALN  CONST_04  CD3  CG2  CD2  CG1  180.00   0.0  0
 ALN  CONST_05  CE2  CD2  CG1  CD1    0.00   0.0  0
 ALN  CONST_06  CG2  CD2  CG1  CD1  180.00   0.0  0
 ALN  CONST_07  CE2  CZ1  CE1  CD1    0.00   0.0  0
 ALN  CONST_08  CD2  CG1  CD1  CE1    0.00   0.0  0
 ALN  CONST_09  CD2  CE2  CZ1  CE1    0.00   0.0  0
 ALN  CONST_10  CZ2  CE2  CZ1  CE1  180.00   0.0  0
 ALN  CONST_11  CE3  CZ2  CE2  CD2    0.00   0.0  0
 ALN  CONST_12  CE3  CD3  CG2  CD2    0.00   0.0  0
 ALN  CONST_13  CD3  CG2  CD2  CE2    0.00   0.0  0
 ALN  CONST_14  CD3  CE3  CZ2  CE2    0.00   0.0  0
 ALN  CONST_15  CG2  CD2  CE2  CZ1  180.00   0.0  0
 ALN  CONST_16  CE3  CZ2  CE2  CZ1  180.00   0.0  0
 ALN  CONST_17  CZ2  CE2  CD2  CG2    0.00   0.0  0
 ALN  CONST_18  CZ2  CE3  CD3  CG2    0.00   0.0  0
 ALN  CONST_19  CE1  CD1  CG1  CB   180.00   0.0  0
 ALN  CONST_20  CE2  CD2  CG1  CB   180.00   0.0  0
 ALN  CONST_21  CG2  CD2  CG1  CB     0.00   0.0  0
 ALN  CONST_22  HE1  CE1  CD1  CG1  180.00   0.0  0
 ALN  CONST_23  HG2  CG2  CD2  CG1    0.00   0.0  0
 ALN  CONST_24  HZ1  CZ1  CE1  CD1  180.00   0.0  0
 ALN  CONST_25  HD1  CD1  CG1  CD2  180.00   0.0  0
 ALN  CONST_26  HZ2  CZ2  CE2  CD2  180.00   0.0  0
 ALN  CONST_27  HD3  CD3  CG2  CD2  180.00   0.0  0
 ALN  CONST_28  HE3  CE3  CZ2  CE2  180.00   0.0  0
 ALN  Var_01    CD1  CG1  CB   CA    97.98  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
 ALN  chir_01  CA  N  C  CB  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
 ALN  plan-1  CB   0.020
 ALN  plan-1  CG1  0.020
 ALN  plan-1  CD1  0.020
 ALN  plan-1  CE1  0.020
 ALN  plan-1  CD2  0.020
 ALN  plan-1  CE2  0.020
 ALN  plan-1  CZ1  0.020
 ALN  plan-1  CG2  0.020
 ALN  plan-1  CD3  0.020
 ALN  plan-1  CE3  0.020
 ALN  plan-1  CZ2  0.020
 ALN  plan-1  HD1  0.020
 ALN  plan-1  HE1  0.020
 ALN  plan-1  HZ1  0.020
 ALN  plan-1  HG2  0.020
 ALN  plan-1  HD3  0.020
 ALN  plan-1  HE3  0.020
 ALN  plan-1  HZ2  0.020
 ALN  plan-2  CA   0.020
 ALN  plan-2  C    0.020
 ALN  plan-2  O    0.020
 ALN  plan-2  OXT  0.020

