# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 04:18:29 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2S)-2-azanyl-2-[2-chloranyl-3,5-bis(oxidanyl)phenyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C(O)=O)c1cc(O)cc(O)c1Cl
#
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
 HCL  HCL  '(2S)-2-azanyl-2-[2-chloranyl-3,5-bis(oxidanyl)phenyl]ethanoic acid'  L-peptide  21  14  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HCL
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
 HCL  C    C   C      0   0.424  -0.1204   5.7069  33.6536
 HCL  N    N   NH2    0  -0.802   1.7222   4.3255  34.5755
 HCL  O    O   O      0  -0.584  -0.4152   6.7380  33.0289
 HCL  C1   C   CR6    0   0.275   2.2850   6.4646  33.5359
 HCL  C2   C   CR6    0  -0.280   2.5942   7.7975  33.7807
 HCL  C3   C   CR6    0   0.446   3.5219   8.4834  32.9913
 HCL  O3   O   OH1    0  -0.616   3.7741   9.7686  33.2902
 HCL  C4   C   CR16   0  -0.498   4.1461   7.8307  31.9384
 HCL  C5   C   CR16   0  -0.468   2.9314   5.8219  32.4830
 HCL  C6   C   CR6    0   0.394   3.8455   6.4957  31.6862
 HCL  CA   C   CH1    0  -0.316   1.2800   5.6895  34.3529
 HCL  OXT  O   OC    -1  -0.593  -0.8229   4.6940  33.8292
 HCL  H2   H   HNH2   0   0.335   2.3344   4.2827  35.3794
 HCL  H    H   HNH2   0   0.341   0.9006   3.7751  34.7896
 HCL  HO3  H   HOH1   0   0.478   4.4375  10.1253  32.6881
 HCL  H4   H   HCR6   0   0.274   4.8665   8.3546  31.3195
 HCL  HO4  H   HOH1   0   0.472   4.1989   4.9884  30.5678
 HCL  H5   H   HCR6   0   0.257   2.7135   4.7754  32.3054
 HCL  HA   H   HCH1   0   0.228   1.1253   6.2250  35.3004
 HCL  O4   O   OH1    0  -0.632   4.4809   5.9064  30.6532
 HCL  CL   CL  CL     0  -0.136   1.8583   8.6821  35.0847

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
 HCL  C   O    deloc     1.231  0.020  1.231
 HCL  C   CA   single    1.525  0.021  1.525
 HCL  C   OXT  deloc     1.245  0.020  1.245
 HCL  N   CA   single    1.458  0.019  1.458
 HCL  N   H2   single    0.890  0.020  1.040
 HCL  N   H    single    0.860  0.020  0.860
 HCL  CL  C2   single    1.739  0.020  1.739
 HCL  C1  C2   aromatic  1.390  0.020  1.390
 HCL  C1  C5   aromatic  1.393  0.020  1.393
 HCL  C1  CA   single    1.509  0.020  1.509
 HCL  C2  C3   aromatic  1.398  0.020  1.398
 HCL  C3  O3   single    1.343  0.020  1.343
 HCL  C3  C4   aromatic  1.387  0.020  1.387
 HCL  O3  HO3  single    0.850  0.020  0.980
 HCL  C4  C6   aromatic  1.391  0.020  1.391
 HCL  C4  H4   single    0.930  0.020  1.080
 HCL  O4  C6   single    1.348  0.020  1.348
 HCL  O4  HO4  single    0.850  0.020  0.980
 HCL  C5  C6   aromatic  1.387  0.020  1.387
 HCL  C5  H5   single    0.930  0.020  1.080
 HCL  CA  HA   single    0.970  0.020  0.970

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
 HCL  OXT  C   CA  120.80  1.700
 HCL  OXT  C   O   127.80  3.000
 HCL  CA   C   O   120.80  1.700
 HCL  H    N   H2  107.48  3.000
 HCL  H    N   CA  114.00  3.000
 HCL  H2   N   CA  110.25  3.000
 HCL  CA   C1  C5  118.77  3.000
 HCL  CA   C1  C2  123.04  3.000
 HCL  C5   C1  C2  118.19  3.000
 HCL  C3   C2  C1  121.24  3.000
 HCL  C3   C2  CL  117.05  3.000
 HCL  C1   C2  CL  121.71  3.000
 HCL  C4   C3  O3  122.31  3.000
 HCL  C4   C3  C2  119.76  3.000
 HCL  O3   C3  C2  117.93  3.000
 HCL  HO3  O3  C3  110.13  3.000
 HCL  H4   C4  C6  120.24  3.000
 HCL  H4   C4  C3  120.31  3.000
 HCL  C6   C4  C3  119.46  3.000
 HCL  H5   C5  C6  120.49  3.000
 HCL  H5   C5  C1  118.44  3.000
 HCL  C6   C5  C1  121.06  3.000
 HCL  C5   C6  O4  122.56  3.000
 HCL  C5   C6  C4  120.28  3.000
 HCL  O4   C6  C4  117.15  3.000
 HCL  HA   CA  C1  108.06  3.000
 HCL  HA   CA  N   110.00  3.000
 HCL  C1   CA  N   111.27  3.000
 HCL  HA   CA  C   110.00  3.000
 HCL  C1   CA  C   110.37  3.000
 HCL  N    CA  C   111.00  2.800
 HCL  HO4  O4  C6  110.25  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
 HCL  CONST_01  C4  C3  C2  C1    0.00  0.0  0
 HCL  CONST_02  C4  C6  C5  C1    0.00  0.0  0
 HCL  CONST_03  C6  C5  C1  C2    0.00  0.0  0
 HCL  CONST_04  C6  C4  C3  C2    0.00  0.0  0
 HCL  CONST_05  C5  C1  C2  C3    0.00  0.0  0
 HCL  CONST_06  C5  C6  C4  C3    0.00  0.0  0
 HCL  CONST_07  C5  C1  C2  CL  180.00  0.0  0
 HCL  CONST_08  C4  C3  C2  CL  180.00  0.0  0
 HCL  CONST_09  O3  C3  C2  C1  180.00  0.0  0
 HCL  CONST_10  O4  C6  C5  C1  180.00  0.0  0
 HCL  CONST_11  CA  C1  C2  C3  180.00  0.0  0
 HCL  CONST_12  O4  C6  C4  C3  180.00  0.0  0
 HCL  CONST_13  C6  C4  C3  O3  180.00  0.0  0
 HCL  CONST_14  CA  C1  C5  C6  180.00  0.0  0
 HCL  CONST_15  H5  C5  C1  C2  180.00  0.0  0
 HCL  CONST_16  H4  C4  C3  C2  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
 HCL  chir_01  CA  C  N  C1  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
 HCL  plan-1  C1   0.020
 HCL  plan-1  C2   0.020
 HCL  plan-1  C3   0.020
 HCL  plan-1  O3   0.020
 HCL  plan-1  C4   0.020
 HCL  plan-1  C5   0.020
 HCL  plan-1  C6   0.020
 HCL  plan-1  CA   0.020
 HCL  plan-1  H4   0.020
 HCL  plan-1  H5   0.020
 HCL  plan-1  O4   0.020
 HCL  plan-1  CL   0.020
 HCL  plan-2  C    0.020
 HCL  plan-2  O    0.020
 HCL  plan-2  CA   0.020
 HCL  plan-2  OXT  0.020

