# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:16:31 2022
#   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  23  15  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

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  -0.810  -0.7880   3.5035  26.2542
 E9C  CA   C  CH1    0  -0.224  -1.8598   3.5700  27.2290
 E9C  C    C  C      0   0.423  -2.0361   5.0164  27.7780
 E9C  O    O  O      0  -0.590  -1.5132   5.9322  27.1141
 E9C  CB   C  CH2    0  -0.485  -1.5915   2.5935  28.3917
 E9C  CG   C  CR6    0   0.059  -1.4217   1.2003  27.9000
 E9C  CD1  C  CR16   0  -0.390  -0.2110   0.6252  27.7815
 E9C  CD2  C  CR6    0   0.385  -2.6491   0.4477  27.5096
 E9C  CAC  C  CR6    0   0.318   0.0073  -0.7382  27.3109
 E9C  CAD  C  CR6    0   0.330  -1.2311  -1.5566  26.9367
 E9C  CAE  C  C      0  -0.706  -2.4727  -0.7731  26.6401
 E9C  OAI  O  O      0  -0.355  -3.7459   0.8240  27.8443
 E9C  OAJ  O  O      0  -0.358   1.1020  -1.2435  27.2253
 E9C  OAK  O  O      0  -0.336  -1.1592  -2.7534  26.8729
 E9C  H    H  HNH2   0   0.335  -0.9991   2.8319  25.5290
 E9C  H2   H  HNH2   0   0.340  -0.7185   4.4127  25.8153
 E9C  HA   H  HCH1   0   0.218  -2.8348   3.3008  26.7928
 E9C  HB2  H  HCH2   0   0.247  -0.6843   2.9050  28.9121
 E9C  HB1  H  HCH2   0   0.253  -2.4206   2.6459  29.0959
 E9C  HD1  H  HCR6   0   0.292   0.6736   1.1719  28.0870
 E9C  HAE  H  H      0   0.338  -2.3706  -0.4019  25.6093
 E9C  HH2  H  H      0   0.315  -3.3591  -1.4062  26.6707
 E9C  OXT  O  OC    -1  -0.597  -2.7126   5.1330  28.8158

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  1.201  0.020  1.201
 E9C  CAE  CAD  single  1.498  0.020  1.498
 E9C  CAE  CD2  single  1.509  0.020  1.509
 E9C  CAD  CAC  single  1.531  0.020  1.531
 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  1.459  0.020  1.459
 E9C  CAC  OAJ  double  1.209  0.020  1.209
 E9C  CG   CD1  double  1.346  0.020  1.346
 E9C  CG   CB   single  1.487  0.020  1.487
 E9C  C    O    deloc   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  deloc   1.244  0.020  1.244

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    107.46  3.000
 E9C  H2   N    CA   107.53  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    127.13  3.000
 E9C  OXT  C    CA   116.27  3.000
 E9C  O    C    CA   120.80  1.700
 E9C  HB1  CB   HB2  108.11  3.000
 E9C  HB1  CB   CG   110.23  3.000
 E9C  HB2  CB   CG   109.28  3.000
 E9C  HB1  CB   CA   108.94  3.000
 E9C  HB2  CB   CA   108.88  3.000
 E9C  CG   CB   CA   111.34  3.000
 E9C  CD2  CG   CD1  120.11  3.000
 E9C  CD1  CG   CB   122.16  3.000
 E9C  CD2  CG   CB   117.72  3.000
 E9C  HD1  CD1  CAC  116.11  3.000
 E9C  HD1  CD1  CG   119.60  3.000
 E9C  CAC  CD1  CG   124.24  3.000
 E9C  OAI  CD2  CAE  121.21  3.000
 E9C  OAI  CD2  CG   121.19  3.000
 E9C  CAE  CD2  CG   117.57  3.000
 E9C  OAJ  CAC  CAD  119.47  3.000
 E9C  OAJ  CAC  CD1  123.30  3.000
 E9C  CAD  CAC  CD1  117.22  3.000
 E9C  OAK  CAD  CAE  124.10  3.000
 E9C  CAE  CAD  CAC  116.06  3.000
 E9C  OAK  CAD  CAC  119.83  3.000
 E9C  HH2  CAE  HAE  107.33  3.000
 E9C  HH2  CAE  CAD  111.39  3.000
 E9C  HAE  CAE  CAD  106.56  3.000
 E9C  HH2  CAE  CD2  111.03  3.000
 E9C  HAE  CAE  CD2  106.13  3.000
 E9C  CAD  CAE  CD2  113.95  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  Var_01  CAD  CAE  CD2  CG    35.72  30.0  1
 E9C  Var_02  CAD  CAC  CD1  CG    -0.25  30.0  1
 E9C  Var_03  CAE  CAD  CAC  CD1   20.12  30.0  1
 E9C  Var_04  CAE  CD2  CG   CD1  -16.90  30.0  1
 E9C  Var_05  CAC  CD1  CG   CD2   -1.43  30.0  1
 E9C  Var_06  CD2  CG   CB   CA   -76.66  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

