# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Sep 20 11:09:57 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-cyano-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1C#N)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
 9IJ  9IJ  "2-cyano-L-phenylalanine"  ligand  24  14  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9IJ
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
 9IJ  N    N  NH2   0  -0.793   9.2340   0.0383   -7.2852
 9IJ  CA   C  CH1   0  -0.191   9.5912   0.5626   -8.5850
 9IJ  C    C  C     0   0.537   8.5850   0.0885   -9.6168
 9IJ  CB   C  CH2   0  -0.532  11.0072   0.0975   -8.9792
 9IJ  CG   C  CR6   0   0.154  12.0285   0.5227   -7.9650
 9IJ  CD1  C  CR16  0  -0.296  12.5204   1.8241   -7.9796
 9IJ  CD2  C  CR6   0  -0.032  12.5018  -0.3387   -6.9674
 9IJ  CE1  C  CR16  0  -0.218  13.4470   2.2558   -7.0434
 9IJ  CE2  C  CR16  0  -0.232  13.4378   0.0892   -6.0223
 9IJ  CZ   C  CR16  0  -0.260  13.9089   1.3877   -6.0615
 9IJ  C01  C  CSP   0   0.022  12.0435  -1.6901   -6.8977
 9IJ  N01  N  NS    0  -0.247  11.7031  -2.7886   -6.8224
 9IJ  O    O  O     0  -0.423   7.6148  -0.5808   -9.3739
 9IJ  H    H  HNH2  0   0.360   9.7710   0.5175   -6.5736
 9IJ  H2   H  HNH2  0   0.357   8.2642   0.2425   -7.0802
 9IJ  HA   H  HCH1  0   0.266   9.5798   1.6633   -8.6340
 9IJ  HB2  H  HCH2  0   0.268  11.0062  -0.9879   -9.0989
 9IJ  HB3  H  HCH2  0   0.282  11.2738   0.5284   -9.9441
 9IJ  HD1  H  HCR6  0   0.267  12.1717   2.5077   -8.7443
 9IJ  HE1  H  HCR6  0   0.271  13.8151   3.2726   -7.0822
 9IJ  HE2  H  HCR6  0   0.280  13.7902  -0.5986   -5.2653
 9IJ  HZ   H  HCR6  0   0.272  14.6347   1.7207   -5.3325
 9IJ  OXT  O  OH1   0  -0.592   8.8909   0.5212  -10.8337
 9IJ  H1   H  HOH1  0   0.483   8.2347   0.2061  -11.4739

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
 9IJ  C    O    double    1.203  0.020  1.203
 9IJ  C    CA   single    1.517  0.020  1.517
 9IJ  CA   CB   single    1.542  0.020  1.542
 9IJ  CA   N    single    1.446  0.020  1.446
 9IJ  CB   CG   single    1.501  0.020  1.501
 9IJ  CG   CD1  aromatic  1.391  0.020  1.391
 9IJ  CG   CD2  aromatic  1.400  0.020  1.400
 9IJ  CD1  CE1  aromatic  1.386  0.020  1.386
 9IJ  N01  C01  triple    1.152  0.020  1.152
 9IJ  C01  CD2  single    1.429  0.020  1.429
 9IJ  CD2  CE2  aromatic  1.397  0.020  1.397
 9IJ  CE1  CZ   aromatic  1.390  0.020  1.390
 9IJ  CE2  CZ   aromatic  1.382  0.020  1.382
 9IJ  N    H    single    0.860  0.020  1.020
 9IJ  N    H2   single    0.890  0.020  1.040
 9IJ  CA   HA   single    0.970  0.020  1.090
 9IJ  CB   HB2  single    0.970  0.020  1.090
 9IJ  CB   HB3  single    0.970  0.020  1.090
 9IJ  CD1  HD1  single    0.930  0.020  1.080
 9IJ  CE1  HE1  single    0.930  0.020  1.080
 9IJ  CE2  HE2  single    0.930  0.020  1.080
 9IJ  CZ   HZ   single    0.930  0.020  1.080
 9IJ  C    OXT  single    1.327  0.020  1.327
 9IJ  OXT  H1   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
 9IJ  H2   N    H    105.69  3.000
 9IJ  H2   N    CA   110.22  3.000
 9IJ  H    N    CA   109.22  3.000
 9IJ  HA   CA   CB   107.43  3.000
 9IJ  HA   CA   C    105.96  3.000
 9IJ  CB   CA   C    109.93  3.000
 9IJ  HA   CA   N    113.55  3.000
 9IJ  CB   CA   N    110.32  3.000
 9IJ  C    CA   N    109.52  3.000
 9IJ  OXT  C    O    123.52  3.000
 9IJ  OXT  C    CA   111.64  3.000
 9IJ  O    C    CA   124.83  3.000
 9IJ  HB3  CB   HB2  107.23  3.000
 9IJ  HB3  CB   CG   108.65  3.000
 9IJ  HB2  CB   CG   110.88  3.000
 9IJ  HB3  CB   CA   109.37  3.000
 9IJ  HB2  CB   CA   109.09  3.000
 9IJ  CG   CB   CA   111.51  3.000
 9IJ  CD2  CG   CD1  117.60  3.000
 9IJ  CD2  CG   CB   122.49  3.000
 9IJ  CD1  CG   CB   119.90  3.000
 9IJ  HD1  CD1  CE1  119.69  3.000
 9IJ  HD1  CD1  CG   118.94  3.000
 9IJ  CE1  CD1  CG   121.37  3.000
 9IJ  C01  CD2  CE2  118.14  3.000
 9IJ  CE2  CD2  CG   121.32  3.000
 9IJ  C01  CD2  CG   120.54  3.000
 9IJ  HE1  CE1  CZ   119.96  3.000
 9IJ  HE1  CE1  CD1  119.72  3.000
 9IJ  CZ   CE1  CD1  120.32  3.000
 9IJ  HE2  CE2  CZ   120.41  3.000
 9IJ  HE2  CE2  CD2  119.79  3.000
 9IJ  CZ   CE2  CD2  119.80  3.000
 9IJ  HZ   CZ   CE2  119.94  3.000
 9IJ  HZ   CZ   CE1  120.47  3.000
 9IJ  CE2  CZ   CE1  119.59  3.000
 9IJ  N01  C01  CD2  180.00  3.000
 9IJ  H1   OXT  C    110.09  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
 9IJ  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 9IJ  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 9IJ  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 9IJ  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 9IJ  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 9IJ  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 9IJ  CONST_07  CE1  CD1  CG   CB    180.00   0.0  0
 9IJ  CONST_08  CE2  CD2  CG   CB    180.00   0.0  0
 9IJ  CONST_09  C01  CD2  CG   CD1   180.00   0.0  0
 9IJ  CONST_10  C01  CD2  CE2  CZ    180.00   0.0  0
 9IJ  CONST_11  HE1  CE1  CD1  CG    180.00   0.0  0
 9IJ  CONST_12  HE2  CE2  CD2  CG    180.00   0.0  0
 9IJ  CONST_13  HZ   CZ   CE1  CD1   180.00   0.0  0
 9IJ  CONST_14  HD1  CD1  CG   CD2   180.00   0.0  0
 9IJ  CONST_15  HZ   CZ   CE2  CD2   180.00   0.0  0
 9IJ  CONST_16  HE2  CE2  CZ   CE1   180.00   0.0  0
 9IJ  CONST_17  HE1  CE1  CZ   CE2   180.00   0.0  0
 9IJ  CONST_18  HD1  CD1  CE1  CZ    180.00   0.0  0
 9IJ  CONST_19  H1   OXT  C    CA    180.00   0.0  0
 9IJ  CONST_20  H1   OXT  C    O       0.00   0.0  0
 9IJ  Var_01    CD1  CG   CB   CA    -80.18  30.0  2
 9IJ  Var_02    CD2  CG   CB   CA     98.57  30.0  2
 9IJ  Var_03    HB2  CB   CG   CD1   158.04  30.0  3
 9IJ  Var_04    HB3  CB   CG   CD1    40.44  30.0  3
 9IJ  Var_05    HB2  CB   CG   CD2   -23.21  30.0  3
 9IJ  Var_06    HB3  CB   CG   CD2  -140.81  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
 9IJ  chir_01  CA  C  CB  N  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
 9IJ  plan-1  CB   0.020
 9IJ  plan-1  CG   0.020
 9IJ  plan-1  CD1  0.020
 9IJ  plan-1  CD2  0.020
 9IJ  plan-1  CE1  0.020
 9IJ  plan-1  CE2  0.020
 9IJ  plan-1  CZ   0.020
 9IJ  plan-1  C01  0.020
 9IJ  plan-1  N01  0.020
 9IJ  plan-1  HD1  0.020
 9IJ  plan-1  HE1  0.020
 9IJ  plan-1  HE2  0.020
 9IJ  plan-1  HZ   0.020
 9IJ  plan-2  CA   0.020
 9IJ  plan-2  C    0.020
 9IJ  plan-2  O    0.020
 9IJ  plan-2  OXT  0.020
 9IJ  plan-2  H1   0.020

