# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:17:41 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: 4-chloro-L-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H](O)CCl)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
 CTH  CTH  '4-chloro-L-threonine     '  L-peptide  16  9  .  2012-08-28  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CTH
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
 CTH  N     N   NH2    0  -0.790  1.4374  13.7052  3.1608
 CTH  CA    C   CH1    0  -0.233  2.8379  13.8791  3.4972
 CTH  C     C   C      0   0.408  3.6450  12.5713  3.2527
 CTH  O     O   O      0  -0.592  3.0046  11.5288  3.0301
 CTH  OXT   O   OC    -1  -0.613  4.8854  12.6910  3.3166
 CTH  CB    C   CH1    0   0.043  3.1623  14.3686  4.9175
 CTH  CG2   C   CH2    0  -0.492  2.7412  15.7943  5.2437
 CTH  CL2   CL  CL     0  -0.182  0.9675  16.0060  5.5048
 CTH  OG1   O   OH1    0  -0.658  2.6561  13.4354  5.8387
 CTH  H     H   HNH2   0   0.326  0.8999  14.5149  3.4379
 CTH  H2    H   HNH2   0   0.325  1.0643  12.9177  3.6732
 CTH  HA    H   HCH1   0   0.217  3.2533  14.6397  2.8248
 CTH  HB    H   HCH1   0   0.217  4.2605  14.4208  4.9649
 CTH  HG22  H   HCH2   0   0.291  3.2096  16.1267  6.1698
 CTH  HG23  H   HCH2   0   0.283  3.0368  16.4763  4.4480
 CTH  HG1   H   HOH1   0   0.449  2.9521  13.6760  6.7223

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
 CTH  N    CA    single  1.458  0.019  1.458
 CTH  N    H     single  0.860  0.020  0.860
 CTH  N    H2    single  0.890  0.020  1.040
 CTH  CA   C     single  1.525  0.021  1.525
 CTH  CA   CB    single  1.540  0.027  1.540
 CTH  CA   HA    single  0.970  0.020  0.970
 CTH  C    O     deloc   1.231  0.020  1.231
 CTH  C    OXT   deloc   1.248  0.020  1.248
 CTH  CB   CG2   single  1.522  0.020  1.522
 CTH  CB   OG1   single  1.406  0.020  1.406
 CTH  CB   HB    single  0.970  0.020  1.090
 CTH  CG2  CL2   single  1.805  0.020  1.805
 CTH  CG2  HG22  single  0.970  0.020  1.090
 CTH  CG2  HG23  single  0.970  0.020  1.090
 CTH  OG1  HG1   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
 CTH  H2    N    H     106.79  3.000
 CTH  H2    N    CA    109.40  3.000
 CTH  H     N    CA    114.00  3.000
 CTH  HA    CA   CB    109.00  3.000
 CTH  HA    CA   C     109.00  3.000
 CTH  CB    CA   C     109.10  2.200
 CTH  HA    CA   N     110.00  3.000
 CTH  CB    CA   N     111.50  1.700
 CTH  C     CA   N     111.00  2.800
 CTH  OXT   C    O     126.98  3.000
 CTH  OXT   C    CA    115.28  3.000
 CTH  O     C    CA    120.80  1.700
 CTH  HB    CB   OG1   111.26  3.000
 CTH  HB    CB   CG2   102.85  3.000
 CTH  OG1   CB   CG2   112.45  3.000
 CTH  HB    CB   CA    105.40  3.000
 CTH  OG1   CB   CA    108.55  3.000
 CTH  CG2   CB   CA    115.98  3.000
 CTH  HG23  CG2  HG22  108.26  3.000
 CTH  HG23  CG2  CL2   107.40  3.000
 CTH  HG22  CG2  CL2   105.28  3.000
 CTH  HG23  CG2  CB    110.79  3.000
 CTH  HG22  CG2  CB    110.42  3.000
 CTH  CL2   CG2  CB    114.37  3.000
 CTH  HG1   OG1  CB    108.96  3.000

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
 CTH  chir_01  CA  N    C   CB   positiv
 CTH  chir_02  CB  OG1  CA  CG2  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
 CTH  plan-1  CA   0.020
 CTH  plan-1  C    0.020
 CTH  plan-1  O    0.020
 CTH  plan-1  OXT  0.020

