# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:17:35 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-chloro-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1Cl)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
 2L5  2L5  '2-chloro-L-phenylalanine '  L-peptide  22  13  .  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_2L5
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
 2L5  CL   CL  CL     0  -0.078   0.8935  -2.2586  -0.1763
 2L5  C15  C   CR6    0  -0.056   1.6070  -0.6784  -0.0286
 2L5  C19  C   CR16   0  -0.208   2.9360  -0.5314  -0.3997
 2L5  C18  C   CR16   0  -0.284   3.5409   0.7128  -0.2978
 2L5  C17  C   CR16   0  -0.282   2.8098   1.7915   0.1853
 2L5  C16  C   CR16   0  -0.320   1.4843   1.6195   0.5516
 2L5  C14  C   CR6    0   0.265   0.8438   0.3829   0.4569
 2L5  C13  C   CH2    0  -0.574  -0.6067   0.2575   0.8091
 2L5  C12  C   CH1    0  -0.186  -1.5368   0.3827  -0.4249
 2L5  N4   N   NH2    0  -0.796  -1.3587   1.5932  -1.1997
 2L5  C11  C   C      0   0.414  -2.9907   0.2610   0.0873
 2L5  O4   O   O      0  -0.586  -3.6515   1.3136   0.1808
 2L5  H1   H   HCR6   0   0.246   3.4939  -1.3833  -0.7652
 2L5  H2   H   HCR6   0   0.275   4.5763   0.8329  -0.5871
 2L5  H3   H   HCR6   0   0.247   3.2709   2.7664   0.2736
 2L5  H4   H   HCR6   0   0.245   0.9244   2.4644   0.9341
 2L5  H5   H   HCH2   0   0.225  -0.8037  -0.6946   1.3025
 2L5  H6   H   HCH2   0   0.257  -0.8614   1.0475   1.5216
 2L5  H7   H   HCH1   0   0.232  -1.3360  -0.4743  -1.0760
 2L5  H8   H   HNH2   0   0.334  -1.7477   2.3747  -0.6878
 2L5  H9   H   HNH2   0   0.330  -0.3764   1.7884  -1.3485
 2L5  OXT  O   OC    -1  -0.701  -3.3616  -0.8841   0.4116

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
 2L5  C17  C18  aromatic  1.390  0.020  1.390
 2L5  C17  C16  aromatic  1.386  0.020  1.386
 2L5  C18  C19  aromatic  1.387  0.020  1.387
 2L5  C16  C14  aromatic  1.396  0.020  1.396
 2L5  N4   C12  single    1.448  0.020  1.448
 2L5  C19  C15  aromatic  1.388  0.020  1.388
 2L5  C14  C15  aromatic  1.394  0.020  1.394
 2L5  C14  C13  single    1.498  0.020  1.498
 2L5  C15  CL   single    1.740  0.020  1.740
 2L5  C12  C13  single    1.550  0.020  1.550
 2L5  C12  C11  single    1.546  0.020  1.546
 2L5  O4   C11  deloc     1.246  0.020  1.246
 2L5  C19  H1   single    0.930  0.020  1.080
 2L5  C18  H2   single    0.930  0.020  1.080
 2L5  C17  H3   single    0.930  0.020  1.080
 2L5  C16  H4   single    0.930  0.020  1.080
 2L5  C13  H5   single    0.970  0.020  1.090
 2L5  C13  H6   single    0.970  0.020  1.090
 2L5  C12  H7   single    0.970  0.020  1.090
 2L5  N4   H8   single    0.890  0.020  1.040
 2L5  N4   H9   single    0.890  0.020  1.040
 2L5  C11  OXT  deloc     1.246  0.020  1.246

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
 2L5  C14  C15  C19  122.46  3.000
 2L5  C14  C15  CL   119.75  3.000
 2L5  C19  C15  CL   117.79  3.000
 2L5  H1   C19  C18  120.42  3.000
 2L5  H1   C19  C15  120.05  3.000
 2L5  C18  C19  C15  119.53  3.000
 2L5  H2   C18  C17  120.69  3.000
 2L5  H2   C18  C19  119.81  3.000
 2L5  C17  C18  C19  119.49  3.000
 2L5  H3   C17  C16  119.85  3.000
 2L5  H3   C17  C18  120.23  3.000
 2L5  C16  C17  C18  119.92  3.000
 2L5  H4   C16  C14  118.54  3.000
 2L5  H4   C16  C17  119.40  3.000
 2L5  C14  C16  C17  122.06  3.000
 2L5  C13  C14  C16  120.17  3.000
 2L5  C13  C14  C15  123.24  3.000
 2L5  C16  C14  C15  116.53  3.000
 2L5  H6   C13  H5   107.09  3.000
 2L5  H6   C13  C12  108.68  3.000
 2L5  H5   C13  C12  108.80  3.000
 2L5  H6   C13  C14  108.56  3.000
 2L5  H5   C13  C14  110.77  3.000
 2L5  C12  C13  C14  112.77  3.000
 2L5  H7   C12  C11  107.92  3.000
 2L5  H7   C12  N4   108.28  3.000
 2L5  C11  C12  N4   111.02  3.000
 2L5  H7   C12  C13  107.46  3.000
 2L5  C11  C12  C13  107.10  3.000
 2L5  N4   C12  C13  114.81  3.000
 2L5  H9   N4   H8   107.36  3.000
 2L5  H9   N4   C12  111.05  3.000
 2L5  H8   N4   C12  109.13  3.000
 2L5  OXT  C11  O4   126.76  3.000
 2L5  OXT  C11  C12  115.99  3.000
 2L5  O4   C11  C12  117.19  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
 2L5  CONST_01  C17  C18  C19  C15    0.00   0.0  0
 2L5  CONST_02  C17  C16  C14  C15    0.00   0.0  0
 2L5  CONST_03  C16  C17  C18  C19    0.00   0.0  0
 2L5  CONST_04  C16  C14  C15  C19    0.00   0.0  0
 2L5  CONST_05  C14  C16  C17  C18    0.00   0.0  0
 2L5  CONST_06  C14  C15  C19  C18    0.00   0.0  0
 2L5  CONST_07  C18  C19  C15  CL   180.00   0.0  0
 2L5  CONST_08  C16  C14  C15  CL   180.00   0.0  0
 2L5  CONST_09  C13  C14  C15  C19  180.00   0.0  0
 2L5  CONST_10  C13  C14  C16  C17  180.00   0.0  0
 2L5  CONST_11  H2   C18  C19  C15  180.00   0.0  0
 2L5  CONST_12  H4   C16  C14  C15  180.00   0.0  0
 2L5  CONST_13  H3   C17  C18  C19  180.00   0.0  0
 2L5  CONST_14  H1   C19  C18  C17  180.00   0.0  0
 2L5  Var_01    C12  C13  C14  C15  -82.59  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
 2L5  chir_01  C12  N4  C13  C11  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
 2L5  plan-1  CL   0.020
 2L5  plan-1  C15  0.020
 2L5  plan-1  C19  0.020
 2L5  plan-1  C18  0.020
 2L5  plan-1  C17  0.020
 2L5  plan-1  C16  0.020
 2L5  plan-1  C14  0.020
 2L5  plan-1  C13  0.020
 2L5  plan-1  H1   0.020
 2L5  plan-1  H2   0.020
 2L5  plan-1  H3   0.020
 2L5  plan-1  H4   0.020
 2L5  plan-2  C12  0.020
 2L5  plan-2  C11  0.020
 2L5  plan-2  O4   0.020
 2L5  plan-2  OXT  0.020

