# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 09:13:44 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (3S)-3,6-diamino-6-oxohexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(N)=O)CC(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
 B3Q  B3Q  '(3S)-3,6-diamino-6-oxohexanoic acid'  L-peptide  22  11  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B3Q
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
 B3Q  N    N  NH2    0  -0.791  -0.8613   1.2660   1.0480
 B3Q  CB   C  CH1    0  -0.090  -0.6050   0.2800   0.0046
 B3Q  CG   C  CH2    0  -0.411   0.7585  -0.4144   0.1081
 B3Q  CA   C  CH2    0  -0.544  -1.7265  -0.7513   0.0139
 B3Q  C    C  C      0   0.409  -3.1156  -0.1436  -0.2342
 B3Q  O    O  O      0  -0.625  -3.2317   0.5888  -1.2395
 B3Q  HN   H  HNH2   0   0.330  -0.7427   0.8342   1.9583
 B3Q  HB   H  HCH1   0   0.207  -0.6441   0.8119  -0.9517
 B3Q  HG   H  HCH2   0   0.216   0.7966  -0.9979   1.0333
 B3Q  HGA  H  HCH2   0   0.220   0.8525  -1.1302  -0.7146
 B3Q  HA   H  HCH2   0   0.219  -1.5272  -1.4930  -0.7680
 B3Q  HAA  H  HCH2   0   0.194  -1.7090  -1.2951   0.9646
 B3Q  HNA  H  HNH2   0   0.344  -0.1800   2.0136   1.0050
 B3Q  CD   C  CH2    0  -0.584   1.9299   0.5578   0.0624
 B3Q  OXT  O  OC    -1  -0.624  -4.0276  -0.4474   0.5621
 B3Q  CE   C  C      0   0.527   3.2771  -0.1288   0.1293
 B3Q  H8   H  HCH2   0   0.247   1.8648   1.1839  -0.8316
 B3Q  H9   H  HCH2   0   0.260   1.8847   1.2432   0.9157
 B3Q  NF2  N  NH2    0  -0.805   4.2502   0.4534  -0.5892
 B3Q  OF1  O  O      0  -0.500   3.4682  -1.1305   0.8063
 B3Q  H11  H  HNH2   0   0.404   4.0861   1.2850  -1.1287
 B3Q  H12  H  HNH2   0   0.396   5.1930   0.1014  -0.5543

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
 B3Q  N    HN   single  0.890  0.020  1.040
 B3Q  N    HNA  single  0.890  0.020  1.040
 B3Q  CB   N    single  1.458  0.020  1.458
 B3Q  CB   CG   single  1.534  0.020  1.534
 B3Q  CG   HG   single  0.970  0.020  1.090
 B3Q  CG   HGA  single  0.970  0.020  1.090
 B3Q  CG   CD   single  1.523  0.020  1.523
 B3Q  CA   CB   single  1.521  0.033  1.521
 B3Q  CA   HA   single  0.970  0.020  0.970
 B3Q  C    CA   single  1.525  0.021  1.525
 B3Q  C    OXT  deloc   1.248  0.020  1.248
 B3Q  O    C    deloc   1.231  0.020  1.231
 B3Q  HB   CB   single  0.970  0.020  1.090
 B3Q  HAA  CA   single  0.970  0.020  1.090
 B3Q  CD   CE   single  1.514  0.020  1.514
 B3Q  CD   H8   single  0.970  0.020  1.090
 B3Q  CD   H9   single  0.970  0.020  1.090
 B3Q  CE   NF2  single  1.342  0.020  1.342
 B3Q  CE   OF1  double  1.224  0.020  1.224
 B3Q  NF2  H11  single  0.860  0.020  1.020
 B3Q  NF2  H12  single  0.860  0.020  1.020

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
 B3Q  HNA  N    HN   105.88  3.000
 B3Q  HNA  N    CB   110.52  3.000
 B3Q  HN   N    CB   109.49  3.000
 B3Q  HB   CB   CA   107.93  3.000
 B3Q  HB   CB   CG   108.10  3.000
 B3Q  CA   CB   CG   110.33  3.000
 B3Q  HB   CB   N    106.87  3.000
 B3Q  CA   CB   N    110.40  1.500
 B3Q  CG   CB   N    114.47  3.000
 B3Q  CD   CG   HGA  109.20  3.000
 B3Q  CD   CG   HG   109.81  3.000
 B3Q  HGA  CG   HG   106.49  3.000
 B3Q  CD   CG   CB   113.12  3.000
 B3Q  HGA  CG   CB   108.77  3.000
 B3Q  HG   CG   CB   109.23  3.000
 B3Q  HAA  CA   HA   106.28  3.000
 B3Q  HAA  CA   C    110.55  3.000
 B3Q  HA   CA   C    110.00  3.000
 B3Q  HAA  CA   CB   109.24  3.000
 B3Q  C    CA   CB   110.50  1.500
 B3Q  HA   CA   CB   109.00  3.000
 B3Q  OXT  C    O    126.03  3.000
 B3Q  O    C    CA   120.80  1.700
 B3Q  OXT  C    CA   117.47  3.000
 B3Q  H9   CD   H8   106.03  3.000
 B3Q  H9   CD   CE   106.63  3.000
 B3Q  H8   CD   CE   110.42  3.000
 B3Q  H9   CD   CG   110.14  3.000
 B3Q  H8   CD   CG   110.14  3.000
 B3Q  CE   CD   CG   113.19  3.000
 B3Q  OF1  CE   NF2  122.54  3.000
 B3Q  OF1  CE   CD   122.32  3.000
 B3Q  NF2  CE   CD   115.14  3.000
 B3Q  H12  NF2  H11  117.43  3.000
 B3Q  H12  NF2  CE   120.57  3.000
 B3Q  H11  NF2  CE   121.87  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
 B3Q  CONST_01  H11  NF2  CE  CD     0.00   0.0  0
 B3Q  CONST_02  H12  NF2  CE  CD   180.00   0.0  0
 B3Q  Var_01    CE   CD   CG  CB  -178.55  30.0  3
 B3Q  Var_02    OXT  C    CA  CB  -129.99  30.0  2
 B3Q  Var_03    NF2  CE   CD  CG   145.18  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
 B3Q  chir_01  CB  N  CG  CA  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
 B3Q  plan-1  CD   0.020
 B3Q  plan-1  CE   0.020
 B3Q  plan-1  NF2  0.020
 B3Q  plan-1  OF1  0.020
 B3Q  plan-1  H11  0.020
 B3Q  plan-1  H12  0.020
 B3Q  plan-2  CA   0.020
 B3Q  plan-2  C    0.020
 B3Q  plan-2  O    0.020
 B3Q  plan-2  OXT  0.020

