# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 21:49:38 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[3,4,6-tris(oxidanylidene)cyclohexen-1-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=CC(=O)C(=O)C(C1=O)([2H])[2H])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
 E9C  E9C  '(2~{S})-2-azanyl-3-[3,4,6-tris(oxidanylidene)cyclohexen-1-yl]propanoic acid'  L-peptide  24  15  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E9C
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
 E9C  N    N  NH2   0  -0.792  -0.7911   3.5894  26.2336
 E9C  CA   C  CH1   0  -0.204  -1.8480   3.6055  27.2189
 E9C  C    C  C     0   0.544  -1.9614   4.9976  27.8117
 E9C  O    O  O     0  -0.428  -1.2586   5.9282  27.5149
 E9C  CB   C  CH2   0  -0.501  -1.5260   2.6013  28.3468
 E9C  CG   C  CR6   0   0.023  -1.3816   1.2110  27.8235
 E9C  CD1  C  CR16  0  -0.372  -0.1827   0.6159  27.7105
 E9C  CD2  C  CR6   0   0.396  -2.6282   0.4871  27.4396
 E9C  CAC  C  CR6   0   0.325   0.0021  -0.7613  27.2503
 E9C  CAD  C  CR6   0   0.337  -1.2584  -1.5640  26.9232
 E9C  CAE  C  C     0  -0.709  -2.4840  -0.7632  26.6100
 E9C  OAI  O  O     0  -0.355  -3.7126   0.9156  27.7517
 E9C  OAJ  O  O     0  -0.350   1.0862  -1.2811  27.1470
 E9C  OAK  O  O     0  -0.337  -1.2122  -2.7631  26.9053
 E9C  H    H  HNH2  0   0.357  -0.8127   2.7154  25.7243
 E9C  H2   H  HNH2  0   0.359  -0.9464   4.3124  25.5430
 E9C  HA   H  HCH1  0   0.271  -2.8416   3.3626  26.8146
 E9C  HB2  H  HCH2  0   0.280  -0.5946   2.9034  28.8272
 E9C  HB1  H  HCH2  0   0.287  -2.3150   2.6216  29.0990
 E9C  HD1  H  HCR6  0   0.305   0.7160   1.1435  28.0076
 E9C  HAE  H  H     0   0.345  -2.3794  -0.4281  25.5674
 E9C  HH2  H  H     0   0.323  -3.3834  -1.3755  26.6648
 E9C  OXT  O  OH1   0  -0.592  -2.9473   5.0724  28.6953
 E9C  HXT  H  HOH1  0   0.486  -2.9951   5.9651  29.0694

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
 E9C  N    CA   single  1.458  0.019  1.458
 E9C  OAK  CAD  double  1.200  0.020  1.200
 E9C  CAE  CAD  single  1.497  0.020  1.497
 E9C  CAE  CD2  single  1.507  0.020  1.507
 E9C  CAD  CAC  single  1.530  0.020  1.530
 E9C  CA   C    single  1.525  0.021  1.525
 E9C  CA   CB   single  1.530  0.020  1.530
 E9C  CD2  OAI  double  1.207  0.020  1.207
 E9C  CD2  CG   single  1.492  0.020  1.492
 E9C  CAC  CD1  single  1.464  0.020  1.464
 E9C  CAC  OAJ  double  1.207  0.020  1.207
 E9C  CG   CD1  double  1.343  0.020  1.343
 E9C  CG   CB   single  1.493  0.020  1.493
 E9C  C    O    double  1.231  0.020  1.231
 E9C  N    H    single  0.860  0.020  0.860
 E9C  N    H2   single  0.890  0.020  1.040
 E9C  CA   HA   single  0.970  0.020  0.970
 E9C  CB   HB2  single  0.970  0.020  1.090
 E9C  CB   HB1  single  0.970  0.020  1.090
 E9C  CD1  HD1  single  0.930  0.020  1.080
 E9C  CAE  HAE  single  0.970  0.020  1.090
 E9C  CAE  HH2  single  0.970  0.020  1.090
 E9C  C    OXT  single  1.326  0.020  1.326
 E9C  OXT  HXT  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
 E9C  H2   N    H    105.69  3.000
 E9C  H2   N    CA   110.20  3.000
 E9C  H    N    CA   114.00  3.000
 E9C  HA   CA   CB   109.00  3.000
 E9C  HA   CA   C    109.00  3.000
 E9C  CB   CA   C    110.10  1.900
 E9C  HA   CA   N    110.00  3.000
 E9C  CB   CA   N    110.50  1.700
 E9C  C    CA   N    111.00  2.800
 E9C  OXT  C    O    123.71  3.000
 E9C  OXT  C    CA   111.57  3.000
 E9C  O    C    CA   120.80  1.700
 E9C  HB1  CB   HB2  107.99  3.000
 E9C  HB1  CB   CG   109.22  3.000
 E9C  HB2  CB   CG   109.26  3.000
 E9C  HB1  CB   CA   109.94  3.000
 E9C  HB2  CB   CA   108.64  3.000
 E9C  CG   CB   CA   111.71  3.000
 E9C  CD2  CG   CD1  120.62  3.000
 E9C  CD1  CG   CB   121.91  3.000
 E9C  CD2  CG   CB   117.47  3.000
 E9C  HD1  CD1  CAC  116.08  3.000
 E9C  HD1  CD1  CG   120.10  3.000
 E9C  CAC  CD1  CG   123.77  3.000
 E9C  OAI  CD2  CAE  121.52  3.000
 E9C  OAI  CD2  CG   120.79  3.000
 E9C  CAE  CD2  CG   117.65  3.000
 E9C  OAJ  CAC  CAD  119.73  3.000
 E9C  OAJ  CAC  CD1  123.06  3.000
 E9C  CAD  CAC  CD1  117.19  3.000
 E9C  OAK  CAD  CAE  124.25  3.000
 E9C  CAE  CAD  CAC  116.01  3.000
 E9C  OAK  CAD  CAC  119.72  3.000
 E9C  HH2  CAE  HAE  107.30  3.000
 E9C  HH2  CAE  CAD  111.39  3.000
 E9C  HAE  CAE  CAD  106.46  3.000
 E9C  HH2  CAE  CD2  111.07  3.000
 E9C  HAE  CAE  CD2  106.14  3.000
 E9C  CAD  CAE  CD2  114.00  3.000
 E9C  HXT  OXT  C    110.23  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
 E9C  CONST_01  HXT  OXT  C    CA   180.00   0.0  0
 E9C  Var_01    CAD  CAE  CD2  CG    34.45  30.0  1
 E9C  Var_02    CAD  CAC  CD1  CG    -1.84  30.0  1
 E9C  Var_03    CAE  CAD  CAC  CD1   22.00  30.0  1
 E9C  Var_04    CAE  CD2  CG   CD1  -15.24  30.0  1
 E9C  Var_05    CAC  CD1  CG   CD2   -1.63  30.0  1
 E9C  Var_06    CD2  CG   CB   CA   -74.71  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
 E9C  chir_01  CA  N  C  CB  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
 E9C  plan-1  CG   0.020
 E9C  plan-1  CD2  0.020
 E9C  plan-1  CAE  0.020
 E9C  plan-1  OAI  0.020
 E9C  plan-2  CD1  0.020
 E9C  plan-2  CAC  0.020
 E9C  plan-2  CAD  0.020
 E9C  plan-2  OAJ  0.020
 E9C  plan-3  CAC  0.020
 E9C  plan-3  CAD  0.020
 E9C  plan-3  CAE  0.020
 E9C  plan-3  OAK  0.020
 E9C  plan-4  CA   0.020
 E9C  plan-4  C    0.020
 E9C  plan-4  O    0.020
 E9C  plan-4  OXT  0.020
 E9C  plan-4  HXT  0.020

