# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:59:00 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2~{R})-2-(carboxycarbonylamino)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)C(O)=O)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
 I78  I78  "(2~{R})-2-(carboxycarbonylamino)propanoic acid"  ligand  16  11  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I78
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
 I78  N    N  NH1    0  -0.606  6.7262  -1.1076  49.4872
 I78  CA   C  CH1    0  -0.197  7.0663  -2.1876  50.3799
 I78  C    C  C      0   0.410  8.5977  -2.2122  50.6206
 I78  OXT  O  OC     0  -0.603  9.0195  -3.1895  51.2652
 I78  CB   C  CH3    0  -0.653  6.3219  -2.0741  51.7111
 I78  O    O  O     -1  -0.594  9.2606  -1.2567  50.1712
 I78  CAC  C  C      0   0.340  5.6050  -1.0221  48.7693
 I78  CAJ  C  C      0   0.328  5.5397   0.2449  47.8584
 I78  OAE  O  O      0  -0.514  4.7019  -1.8520  48.8058
 I78  OAI  O  OC    -1  -0.587  6.5286   1.0014  47.9040
 I78  OAK  O  O      0  -0.577  4.5065   0.3665  47.1881
 I78  H    H  HNH1   0   0.371  7.4340  -0.4040  49.3361
 I78  HA   H  HCH1   0   0.223  6.7839  -3.1360  49.9106
 I78  HB1  H  HCH3   0   0.221  6.5541  -2.9174  52.3597
 I78  HB3  H  HCH3   0   0.213  6.6011  -1.1566  52.2327
 I78  HB2  H  HCH3   0   0.224  5.2433  -2.0582  51.5559

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
 I78  OAK  CAJ  deloc   1.238  0.020  1.238
 I78  OAI  CAJ  deloc   1.246  0.020  1.246
 I78  CAJ  CAC  single  1.562  0.020  1.562
 I78  CAC  OAE  double  1.227  0.020  1.227
 I78  CAC  N    single  1.334  0.020  1.334
 I78  N    CA   single  1.442  0.020  1.442
 I78  O    C    deloc   1.247  0.020  1.247
 I78  CA   C    single  1.550  0.020  1.550
 I78  CA   CB   single  1.529  0.020  1.529
 I78  C    OXT  deloc   1.244  0.020  1.244
 I78  N    H    single  0.860  0.020  1.020
 I78  CA   HA   single  0.970  0.020  1.090
 I78  CB   HB1  single  0.970  0.020  1.090
 I78  CB   HB3  single  0.970  0.020  1.090
 I78  CB   HB2  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
 I78  H    N    CAC  117.66  3.000
 I78  H    N    CA   116.70  3.000
 I78  CAC  N    CA   125.40  3.000
 I78  HA   CA   CB   108.16  3.000
 I78  HA   CA   C    107.91  3.000
 I78  CB   CA   C    110.29  3.000
 I78  HA   CA   N    108.81  3.000
 I78  CB   CA   N    111.62  3.000
 I78  C    CA   N    109.94  3.000
 I78  O    C    OXT  127.47  3.000
 I78  OXT  C    CA   115.32  3.000
 I78  O    C    CA   117.19  3.000
 I78  HB2  CB   HB3  107.99  3.000
 I78  HB2  CB   HB1  107.89  3.000
 I78  HB3  CB   HB1  108.17  3.000
 I78  HB2  CB   CA   111.03  3.000
 I78  HB3  CB   CA   110.72  3.000
 I78  HB1  CB   CA   110.93  3.000
 I78  OAE  CAC  CAJ  122.36  3.000
 I78  OAE  CAC  N    124.01  3.000
 I78  CAJ  CAC  N    113.63  3.000
 I78  OAK  CAJ  OAI  128.52  3.000
 I78  OAI  CAJ  CAC  115.98  3.000
 I78  OAK  CAJ  CAC  115.50  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
 I78  CONST_01  CAJ  CAC  N    CA    180.00   0.0  0
 I78  CONST_02  OAE  CAC  N    CA      0.00   0.0  0
 I78  CONST_03  H    N    CAC  CAJ     0.00   0.0  0
 I78  CONST_04  H    N    CAC  OAE   180.00   0.0  0
 I78  Var_01    OAK  CAJ  CAC  N    -179.21  30.0  2
 I78  Var_02    OAI  CAJ  CAC  N       0.56  30.0  2
 I78  Var_03    OAK  CAJ  CAC  OAE     0.95  30.0  2
 I78  Var_04    OAI  CAJ  CAC  OAE  -179.27  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
 I78  chir_01  CA  N  C  CB  negativ

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
 I78  plan-1  N    0.020
 I78  plan-1  CA   0.020
 I78  plan-1  CAC  0.020
 I78  plan-1  CAJ  0.020
 I78  plan-1  OAE  0.020
 I78  plan-1  H    0.020
 I78  plan-2  CA   0.020
 I78  plan-2  C    0.020
 I78  plan-2  OXT  0.020
 I78  plan-2  O    0.020
 I78  plan-3  CAC  0.020
 I78  plan-3  CAJ  0.020
 I78  plan-3  OAI  0.020
 I78  plan-3  OAK  0.020

