# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 09:24:17 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  20  10  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.783  -0.9084   1.8781   0.0156
 LV8  CA   C  CH1   0  -0.240  -1.0022   0.4964  -0.3841
 LV8  CB   C  CH2   0  -0.256   0.1180  -0.3120   0.2825
 LV8  NG   N  NH1   0  -0.624   1.3845   0.3094  -0.0085
 LV8  CD   C  C     0   0.517   2.5382  -0.3617  -0.1444
 LV8  OD2  O  O     0  -0.512   2.6182  -1.5807  -0.0505
 LV8  CE   C  CH3   0  -0.775   3.7499   0.4906  -0.4296
 LV8  C    C  C     0   0.527  -2.3525  -0.1456  -0.0908
 LV8  O    O  O     0  -0.433  -3.2474   0.3923   0.5094
 LV8  OXT  O  OH1   0  -0.592  -2.4321  -1.3760  -0.5808
 LV8  H1   H  HNH2  0   0.366  -1.5212   2.4566  -0.5428
 LV8  H2   H  HNH2  0   0.352  -1.1975   1.9926   0.9795
 LV8  H4   H  HCH1  0   0.288  -0.8498   0.4431  -1.4672
 LV8  H5   H  HCH2  0   0.245  -0.0544  -0.3547   1.3645
 LV8  H6   H  HCH2  0   0.263   0.1274  -1.3357  -0.0852
 LV8  H7   H  HNH1  0   0.397   1.3784   1.3176  -0.0471
 LV8  H8   H  HCH3  0   0.264   4.1950   0.1816  -1.3755
 LV8  H9   H  HCH3  0   0.247   3.5346   1.5562  -0.4816
 LV8  H10  H  HCH3  0   0.264   4.4963   0.3276   0.3476
 LV8  H11  H  HOH1  0   0.484  -3.2964  -1.7631  -0.3742

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  1.509  0.020  1.509
 LV8  O    C    double  1.231  0.020  1.231
 LV8  CD   OD2  double  1.225  0.020  1.225
 LV8  CD   NG   single  1.342  0.020  1.342
 LV8  C    CA   single  1.525  0.021  1.525
 LV8  NG   CB   single  1.440  0.020  1.440
 LV8  CA   CB   single  1.521  0.033  1.521
 LV8  CA   N    single  1.458  0.019  1.458
 LV8  C    OXT  single  1.327  0.020  1.327
 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
 LV8  OXT  H11  single  0.850  0.020  0.980

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   106.73  3.000
 LV8  H2   N    CA   110.71  3.000
 LV8  H1   N    CA   110.85  3.000
 LV8  H4   CA   C    107.05  3.000
 LV8  H4   CA   CB   107.61  3.000
 LV8  C    CA   CB   110.50  1.500
 LV8  H4   CA   N    108.17  3.000
 LV8  CB   CA   N    110.40  1.500
 LV8  C    CA   N    111.00  2.800
 LV8  H6   CB   H5   107.36  3.000
 LV8  H6   CB   NG   109.28  3.000
 LV8  H5   CB   NG   110.76  3.000
 LV8  H6   CB   CA   110.82  3.000
 LV8  H5   CB   CA   109.54  3.000
 LV8  NG   CB   CA   109.09  3.000
 LV8  H7   NG   CD   120.07  3.000
 LV8  H7   NG   CB   115.69  3.000
 LV8  CD   NG   CB   124.11  3.000
 LV8  CE   CD   OD2  121.61  3.000
 LV8  OD2  CD   NG   123.09  3.000
 LV8  CE   CD   NG   115.29  3.000
 LV8  H10  CE   H9   108.42  3.000
 LV8  H10  CE   H8   107.25  3.000
 LV8  H9   CE   H8   108.47  3.000
 LV8  H10  CE   CD   109.32  3.000
 LV8  H9   CE   CD   113.79  3.000
 LV8  H8   CE   CD   109.38  3.000
 LV8  OXT  C    O    123.62  3.000
 LV8  OXT  C    CA   120.80  1.700
 LV8  O    C    CA   120.80  1.700
 LV8  H11  OXT  C    110.19  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
 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  CONST_04  H11  OXT  C   CA    180.00   0.0  0
 LV8  Var_01    CD   NG   CB  CA   -148.10  30.0  1
 LV8  Var_02    H8   CE   CD  NG   -120.99  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
 LV8  plan-2  H11  0.020

