# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:07:16 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  23  11  .  2022-03-15  2022-11-17
;
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  -0.793  -0.8619   1.2882   0.7914
 B3Q  CB   C  CH1   0  -0.100  -0.6101   0.2006  -0.1435
 B3Q  CG   C  CH2   0  -0.414   0.7518  -0.4840   0.0003
 B3Q  CA   C  CH2   0  -0.552  -1.7274  -0.8299   0.0096
 B3Q  C    C  C     0   0.545  -3.0756  -0.1998  -0.2075
 B3Q  O    O  O     0  -0.455  -3.3743   0.4430  -1.1845
 B3Q  HN   H  HNH2  0   0.340  -0.6645   0.9818   1.7380
 B3Q  HB   H  HCH1  0   0.235  -0.6740   0.6229  -1.1513
 B3Q  HG   H  HCH2  0   0.225   0.8286  -0.9207   1.0018
 B3Q  HGA  H  HCH2  0   0.230   0.8089  -1.3148  -0.7068
 B3Q  HA   H  HCH2  0   0.281  -1.6050  -1.6243  -0.7317
 B3Q  HAA  H  HCH2  0   0.255  -1.6752  -1.2983   0.9948
 B3Q  HNA  H  HNH2  0   0.354  -0.2386   2.0644   0.6089
 B3Q  CD   C  CH2   0  -0.591   1.9086   0.4707  -0.2433
 B3Q  OXT  O  OH1   0  -0.591  -3.9271  -0.4419   0.7831
 B3Q  CE   C  C     0   0.530   3.2716  -0.1891  -0.1756
 B3Q  H8   H  HCH2  0   0.273   1.8132   0.9231  -1.2372
 B3Q  H9   H  HCH2  0   0.251   1.8834   1.3033   0.4649
 B3Q  HXT  H  HOH1  0   0.476  -4.7842  -0.0344   0.5856
 B3Q  NF2  N  NH2   0  -0.806   4.2982   0.6650  -0.0327
 B3Q  OF1  O  O     0  -0.495   3.4270  -1.3991  -0.2588
 B3Q  H11  H  HNH2  0   0.405   4.1579   1.6594   0.0095
 B3Q  H12  H  HNH2  0   0.397   5.2481   0.3316  -0.0458

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  1.456  0.020  1.456
 B3Q  CB   CG   single  1.531  0.020  1.531
 B3Q  CG   HG   single  0.970  0.020  1.090
 B3Q  CG   HGA  single  0.970  0.020  1.090
 B3Q  CG   CD   single  1.519  0.020  1.519
 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  single  1.328  0.020  1.328
 B3Q  O    C    double  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  1.516  0.020  1.516
 B3Q  CD   H8   single  0.970  0.020  1.090
 B3Q  CD   H9   single  0.970  0.020  1.090
 B3Q  OXT  HXT  single  0.850  0.020  0.980
 B3Q  CE   NF2  single  1.343  0.020  1.343
 B3Q  CE   OF1  double  1.223  0.020  1.223
 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   106.26  3.000
 B3Q  HNA  N    CB   110.52  3.000
 B3Q  HN   N    CB   109.87  3.000
 B3Q  HB   CB   CA   108.05  3.000
 B3Q  HB   CB   CG   108.11  3.000
 B3Q  CA   CB   CG   109.85  3.000
 B3Q  HB   CB   N    107.03  3.000
 B3Q  CA   CB   N    110.40  1.500
 B3Q  CG   CB   N    115.31  3.000
 B3Q  CD   CG   HGA  109.53  3.000
 B3Q  CD   CG   HG   110.10  3.000
 B3Q  HGA  CG   HG   106.56  3.000
 B3Q  CD   CG   CB   112.41  3.000
 B3Q  HGA  CG   CB   109.01  3.000
 B3Q  HG   CG   CB   109.06  3.000
 B3Q  HAA  CA   HA   107.14  3.000
 B3Q  HAA  CA   C    110.66  3.000
 B3Q  HA   CA   C    110.00  3.000
 B3Q  HAA  CA   CB   110.17  3.000
 B3Q  C    CA   CB   110.50  1.500
 B3Q  HA   CA   CB   109.00  3.000
 B3Q  OXT  C    O    122.81  3.000
 B3Q  O    C    CA   120.80  1.700
 B3Q  OXT  C    CA   120.80  1.700
 B3Q  H9   CD   H8   105.72  3.000
 B3Q  H9   CD   CE   108.86  3.000
 B3Q  H8   CD   CE   107.36  3.000
 B3Q  H9   CD   CG   110.92  3.000
 B3Q  H8   CD   CG   109.79  3.000
 B3Q  CE   CD   CG   113.83  3.000
 B3Q  HXT  OXT  C    109.77  3.000
 B3Q  OF1  CE   NF2  122.64  3.000
 B3Q  OF1  CE   CD   122.81  3.000
 B3Q  NF2  CE   CD   114.54  3.000
 B3Q  H12  NF2  H11  117.37  3.000
 B3Q  H12  NF2  CE   120.61  3.000
 B3Q  H11  NF2  CE   121.80  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  CONST_03  HXT  OXT  C   CA   180.00   0.0  0
 B3Q  Var_01    CE   CD   CG  CB  -177.18  30.0  3
 B3Q  Var_02    OXT  C    CA  CB  -127.77  30.0  2
 B3Q  Var_03    NF2  CE   CD  CG  -163.20  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
 B3Q  plan-2  HXT  0.020

