# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 12:58:46 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-phenyl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](N)(C(O)=O)c1ccccc1
#
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
 GRN  GRN  '2-phenyl-L-alanine       '  ligand  22  12  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GRN
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
 GRN  O    O  O      0  -0.593   1.9924  -1.8045   0.3187
 GRN  C    C  C      0   0.433   1.7146  -0.6127   0.5396
 GRN  CA   C  CT     0  -0.085   1.0001   0.1868  -0.5965
 GRN  C1   C  CH3    0  -0.634   1.2317  -0.4310  -1.9738
 GRN  N    N  NH2    0  -0.798   1.5716   1.5240  -0.6154
 GRN  CB   C  C      0   0.147  -0.4925   0.1395  -0.2549
 GRN  CG2  C  C1     0  -0.297  -1.1686  -1.0840  -0.2282
 GRN  CD2  C  C1     0  -0.243  -2.5168  -1.1539   0.0874
 GRN  CE   C  C1     0  -0.278  -3.2286   0.0020   0.3881
 GRN  CD1  C  C1     0  -0.238  -2.5700   1.2217   0.3742
 GRN  CG1  C  C1     0  -0.348  -1.2165   1.2861   0.0591
 GRN  O1   O  OC    -1  -0.604   1.9094   0.0167   1.5976
 GRN  H1   H  HCH3   0   0.222   0.8541  -1.4482  -2.0466
 GRN  H2   H  HCH3   0   0.210   0.7344   0.1612  -2.7462
 GRN  H3   H  HCH3   0   0.221   2.2975  -0.4530  -2.2041
 GRN  H4   H  HNH2   0   0.333   1.0339   2.1349  -1.2190
 GRN  H5   H  HNH2   0   0.338   1.5393   1.9155   0.3170
 GRN  H7   H  H      0   0.244  -0.6302  -1.9985  -0.4429
 GRN  H8   H  H      0   0.248  -3.0143  -2.1158   0.1031
 GRN  H9   H  H      0   0.249  -4.2822  -0.0511   0.6311
 GRN  H10  H  H      0   0.248  -3.1070   2.1319   0.6111
 GRN  H11  H  H      0   0.228  -0.7284   2.2526   0.0622

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
 GRN  CD2  CE   aromatic  1.390  0.020  1.390
 GRN  CD2  CG2  aromatic  1.386  0.020  1.386
 GRN  CE   CD1  aromatic  1.386  0.020  1.386
 GRN  CG2  CB   aromatic  1.398  0.020  1.398
 GRN  CD1  CG1  aromatic  1.391  0.020  1.391
 GRN  CB   CG1  aromatic  1.392  0.020  1.392
 GRN  CB   CA   single    1.532  0.020  1.532
 GRN  N    CA   single    1.454  0.020  1.454
 GRN  CA   C1   single    1.527  0.020  1.527
 GRN  CA   C    single    1.562  0.020  1.562
 GRN  C    O    deloc     1.244  0.020  1.244
 GRN  C    O1   deloc     1.246  0.020  1.246
 GRN  C1   H1   single    0.970  0.020  1.090
 GRN  C1   H2   single    0.970  0.020  1.090
 GRN  C1   H3   single    0.970  0.020  1.090
 GRN  N    H4   single    0.890  0.020  1.040
 GRN  N    H5   single    0.890  0.020  1.040
 GRN  CG2  H7   single    0.930  0.020  1.080
 GRN  CD2  H8   single    0.930  0.020  1.080
 GRN  CE   H9   single    0.930  0.020  1.080
 GRN  CD1  H10  single    0.930  0.020  1.080
 GRN  CG1  H11  single    0.930  0.020  1.080

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
 GRN  O1   C    CA   115.49  3.000
 GRN  O1   C    O    126.85  3.000
 GRN  CA   C    O    117.62  3.000
 GRN  CB   CA   N    114.47  3.000
 GRN  N    CA   C1   107.50  3.000
 GRN  CB   CA   C1   109.65  3.000
 GRN  C1   CA   C    112.30  3.000
 GRN  N    CA   C    107.48  3.000
 GRN  CB   CA   C    105.52  3.000
 GRN  H3   C1   H2   107.83  3.000
 GRN  H3   C1   H1   107.84  3.000
 GRN  H2   C1   H1   107.55  3.000
 GRN  H3   C1   CA   110.29  3.000
 GRN  H2   C1   CA   110.44  3.000
 GRN  H1   C1   CA   112.72  3.000
 GRN  H5   N    H4   107.39  3.000
 GRN  H5   N    CA   109.34  3.000
 GRN  H4   N    CA   110.71  3.000
 GRN  CG1  CB   CG2  117.72  3.000
 GRN  CG1  CB   CA   122.11  3.000
 GRN  CG2  CB   CA   120.16  3.000
 GRN  H7   CG2  CD2  119.08  3.000
 GRN  H7   CG2  CB   119.67  3.000
 GRN  CD2  CG2  CB   121.24  3.000
 GRN  H8   CD2  CE   120.00  3.000
 GRN  H8   CD2  CG2  119.66  3.000
 GRN  CE   CD2  CG2  120.34  3.000
 GRN  H9   CE   CD1  120.51  3.000
 GRN  H9   CE   CD2  120.40  3.000
 GRN  CD1  CE   CD2  119.08  3.000
 GRN  H10  CD1  CG1  119.53  3.000
 GRN  H10  CD1  CE   120.12  3.000
 GRN  CG1  CD1  CE   120.35  3.000
 GRN  H11  CG1  CD1  118.64  3.000
 GRN  H11  CG1  CB   120.10  3.000
 GRN  CD1  CG1  CB   121.26  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
 GRN  CONST_01  CE   CD2  CG2  CB     0.00  0.0  0
 GRN  CONST_02  CE   CD1  CG1  CB     0.00  0.0  0
 GRN  CONST_03  CD1  CE   CD2  CG2    0.00  0.0  0
 GRN  CONST_04  CD1  CG1  CB   CG2    0.00  0.0  0
 GRN  CONST_05  CG1  CD1  CE   CD2    0.00  0.0  0
 GRN  CONST_06  CG1  CB   CG2  CD2    0.00  0.0  0
 GRN  CONST_07  CD2  CG2  CB   CA   180.00  0.0  0
 GRN  CONST_08  CD1  CG1  CB   CA   180.00  0.0  0
 GRN  CONST_09  H8   CD2  CG2  CB   180.00  0.0  0
 GRN  CONST_10  H10  CD1  CG1  CB   180.00  0.0  0
 GRN  CONST_11  H9   CE   CD2  CG2  180.00  0.0  0
 GRN  CONST_12  H11  CG1  CB   CG2  180.00  0.0  0
 GRN  CONST_13  H7   CG2  CD2  CE   180.00  0.0  0

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
 GRN  chir_01  CA  CB  C1  C  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
 GRN  plan-1  CA   0.020
 GRN  plan-1  CB   0.020
 GRN  plan-1  CG2  0.020
 GRN  plan-1  CD2  0.020
 GRN  plan-1  CE   0.020
 GRN  plan-1  CD1  0.020
 GRN  plan-1  CG1  0.020
 GRN  plan-1  H7   0.020
 GRN  plan-1  H8   0.020
 GRN  plan-1  H9   0.020
 GRN  plan-1  H10  0.020
 GRN  plan-1  H11  0.020
 GRN  plan-2  O    0.020
 GRN  plan-2  C    0.020
 GRN  plan-2  CA   0.020
 GRN  plan-2  O1   0.020

