# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 03:06:15 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2~{S})-3-acetamido-2-azanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC[C@H](N)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
 LV8  LV8  '(2~{S})-3-acetamido-2-azanyl-propanoic acid'  L-peptide  19  10  .  2022-07-25  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_LV8
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
 LV8  N    N  NH2    0  -0.753  -0.8775   1.8519   0.0313
 LV8  CA   C  CH1    0  -0.240  -1.0073   0.4753  -0.4183
 LV8  CB   C  CH2    0  -0.220   0.1201  -0.3626   0.1880
 LV8  NG   N  NH1    0  -0.566   1.3886   0.2852  -0.0492
 LV8  CD   C  C      0   0.430   2.5685  -0.3441  -0.0706
 LV8  OD2  O  O      0  -0.364   2.6857  -1.5558   0.0874
 LV8  CE   C  CH3    0  -0.797   3.7699   0.5369  -0.3161
 LV8  C    C  C      0   0.376  -2.3626  -0.2137  -0.1174
 LV8  O    O  O      0  -0.452  -3.1837   0.4109   0.5796
 LV8  OXT  O  OC    -1  -0.796  -2.5028  -1.3572  -0.5972
 LV8  H1   H  HNH2   0   0.312  -1.4486   2.4498  -0.5520
 LV8  H2   H  HNH2   0   0.341  -1.2839   1.9253   0.9572
 LV8  H4   H  HCH1   0   0.205  -0.8640   0.4704  -1.5041
 LV8  H5   H  HCH2   0   0.147  -0.0485  -0.4886   1.2654
 LV8  H6   H  HCH2   0   0.267   0.1228  -1.3555  -0.2563
 LV8  H7   H  HNH1   0   0.404   1.3447   1.2924  -0.1100
 LV8  H8   H  HCH3   0   0.248   4.2783   0.2106  -1.2237
 LV8  H9   H  HCH3   0   0.199   3.5242   1.5921  -0.4200
 LV8  H10  H  HCH3   0   0.258   4.4757   0.4258   0.5068

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
 LV8  CE  CD   single  1.510  0.020  1.510
 LV8  O   C    deloc   1.231  0.020  1.231
 LV8  CD  OD2  double  1.228  0.020  1.228
 LV8  CD  NG   single  1.337  0.020  1.337
 LV8  C   CA   single  1.525  0.021  1.525
 LV8  NG  CB   single  1.444  0.020  1.444
 LV8  CA  CB   single  1.521  0.033  1.521
 LV8  CA  N    single  1.458  0.019  1.458
 LV8  C   OXT  deloc   1.248  0.020  1.248
 LV8  N   H1   single  0.890  0.020  1.040
 LV8  N   H2   single  0.890  0.020  1.040
 LV8  CA  H4   single  0.970  0.020  1.090
 LV8  CB  H5   single  0.970  0.020  1.090
 LV8  CB  H6   single  0.970  0.020  1.090
 LV8  NG  H7   single  0.860  0.020  1.020
 LV8  CE  H8   single  0.970  0.020  1.090
 LV8  CE  H9   single  0.970  0.020  1.090
 LV8  CE  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
 LV8  H2   N   H1   104.91  3.000
 LV8  H2   N   CA   108.37  3.000
 LV8  H1   N   CA   109.32  3.000
 LV8  H4   CA  C    107.75  3.000
 LV8  H4   CA  CB   107.10  3.000
 LV8  C    CA  CB   110.50  1.500
 LV8  H4   CA  N    107.40  3.000
 LV8  CB   CA  N    110.40  1.500
 LV8  C    CA  N    111.00  2.800
 LV8  H6   CB  H5   107.25  3.000
 LV8  H6   CB  NG   109.89  3.000
 LV8  H5   CB  NG   110.34  3.000
 LV8  H6   CB  CA   109.87  3.000
 LV8  H5   CB  CA   109.79  3.000
 LV8  NG   CB  CA   109.67  3.000
 LV8  H7   NG  CD   120.44  3.000
 LV8  H7   NG  CB   114.77  3.000
 LV8  CD   NG  CB   124.51  3.000
 LV8  CE   CD  OD2  121.40  3.000
 LV8  OD2  CD  NG   123.13  3.000
 LV8  CE   CD  NG   115.47  3.000
 LV8  H10  CE  H9   108.49  3.000
 LV8  H10  CE  H8   107.22  3.000
 LV8  H9   CE  H8   108.42  3.000
 LV8  H10  CE  CD   109.46  3.000
 LV8  H9   CE  CD   113.68  3.000
 LV8  H8   CE  CD   109.37  3.000
 LV8  OXT  C   O    126.93  3.000
 LV8  OXT  C   CA   120.80  1.700
 LV8  O    C   CA   120.80  1.700

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
 LV8  CONST_01  CE   CD  NG  CB    180.00   0.0  0
 LV8  CONST_02  OD2  CD  NG  CB      0.00   0.0  0
 LV8  CONST_03  H7   NG  CD  OD2   180.00   0.0  0
 LV8  Var_01    CD   NG  CB  CA   -156.35  30.0  1
 LV8  Var_02    H8   CE  CD  NG   -119.77  30.0  3

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
 LV8  chir_01  CA  C  CB  N  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
 LV8  plan-1  CB   0.020
 LV8  plan-1  NG   0.020
 LV8  plan-1  CD   0.020
 LV8  plan-1  OD2  0.020
 LV8  plan-1  CE   0.020
 LV8  plan-1  H7   0.020
 LV8  plan-2  CA   0.020
 LV8  plan-2  C    0.020
 LV8  plan-2  O    0.020
 LV8  plan-2  OXT  0.020

