# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 18:52:05 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: O-benzyl-L-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](OCc1ccccc1)[C@H](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
 Z3E  Z3E  'O-benzyl-L-threonine     '  L-peptide  29  15  .  2012-08-28  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Z3E
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
 Z3E  C     C  C      0   0.405  -17.4718   2.0010  -22.9013
 Z3E  N     N  NH2    0  -0.813  -18.3991   4.1104  -22.1510
 Z3E  O     O  O      0  -0.599  -16.3042   1.8467  -22.4925
 Z3E  C1    C  C      0   0.085  -16.8931   7.8450  -24.5468
 Z3E  C2    C  C1     0  -0.304  -17.2566   8.7586  -23.5630
 Z3E  C3    C  C1     0  -0.240  -17.8809   9.9534  -23.9001
 Z3E  C4    C  C1     0  -0.264  -18.1541  10.2425  -25.2299
 Z3E  C5    C  C1     0  -0.242  -17.7988   9.3341  -26.2201
 Z3E  C6    C  C1     0  -0.288  -17.1744   8.1434  -25.8783
 Z3E  C7    C  CH2    0  -0.205  -16.2488   6.5374  -24.1884
 Z3E  CA    C  CH1    0  -0.207  -17.8950   3.4271  -23.3436
 Z3E  CB    C  CH1    0   0.087  -16.7471   4.2271  -23.9419
 Z3E  OG1   O  O2     0  -0.503  -17.2398   5.5378  -24.2058
 Z3E  CG2   C  CH3    0  -0.690  -16.2108   3.5980  -25.2197
 Z3E  OXT   O  OC    -1  -0.607  -18.3691   1.1361  -22.9445
 Z3E  H2    H  HNH2   0   0.335  -18.7756   5.0110  -22.4195
 Z3E  H     H  HNH2   0   0.335  -19.1829   3.5868  -21.7811
 Z3E  H8    H  H      0   0.249  -17.0453   8.5376  -22.5231
 Z3E  H3    H  H      0   0.253  -18.1535  10.6573  -23.1242
 Z3E  H4    H  H      0   0.254  -18.6389  11.1732  -25.4955
 Z3E  H5    H  H      0   0.253  -18.0063   9.5558  -27.2592
 Z3E  H6    H  H      0   0.248  -16.8933   7.4411  -26.6547
 Z3E  H7    H  HCH2   0   0.208  -15.4472   6.3165  -24.9051
 Z3E  H7A   H  HCH2   0   0.213  -15.7801   6.6041  -23.1972
 Z3E  HA    H  HCH1   0   0.173  -18.6697   3.3224  -24.1217
 Z3E  HB    H  HCH1   0   0.188  -15.9442   4.2833  -23.1956
 Z3E  HG2   H  HCH3   0   0.229  -15.4390   4.2175  -25.6790
 Z3E  HG2A  H  HCH3   0   0.230  -15.7639   2.6271  -25.0130
 Z3E  HG2B  H  HCH3   0   0.216  -17.0082   3.4583  -25.9527

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
 Z3E  C    O     deloc     1.231  0.020  1.231
 Z3E  C    CA    single    1.525  0.021  1.525
 Z3E  C    OXT   deloc     1.247  0.020  1.247
 Z3E  N    CA    single    1.458  0.019  1.458
 Z3E  N    H2    single    0.890  0.020  1.040
 Z3E  N    H     single    0.860  0.020  0.860
 Z3E  C1   C2    aromatic  1.391  0.020  1.391
 Z3E  C1   C6    aromatic  1.393  0.020  1.393
 Z3E  C1   C7    single    1.501  0.020  1.501
 Z3E  C2   C3    aromatic  1.390  0.020  1.390
 Z3E  C2   H8    single    0.930  0.020  1.080
 Z3E  C3   C4    aromatic  1.388  0.020  1.388
 Z3E  C3   H3    single    0.930  0.020  1.080
 Z3E  C4   C5    aromatic  1.390  0.020  1.390
 Z3E  C4   H4    single    0.930  0.020  1.080
 Z3E  C5   C6    aromatic  1.387  0.020  1.387
 Z3E  C5   H5    single    0.930  0.020  1.080
 Z3E  C6   H6    single    0.930  0.020  1.080
 Z3E  C7   OG1   single    1.408  0.020  1.408
 Z3E  C7   H7    single    0.970  0.020  1.090
 Z3E  C7   H7A   single    0.970  0.020  1.090
 Z3E  CA   CB    single    1.540  0.027  1.540
 Z3E  CA   HA    single    0.970  0.020  0.970
 Z3E  CB   OG1   single    1.425  0.020  1.425
 Z3E  CB   CG2   single    1.522  0.020  1.522
 Z3E  CB   HB    single    0.970  0.020  1.090
 Z3E  CG2  HG2   single    0.970  0.020  1.090
 Z3E  CG2  HG2A  single    0.970  0.020  1.090
 Z3E  CG2  HG2B  single    0.970  0.020  1.090

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
 Z3E  OXT   C    CA    115.55  3.000
 Z3E  OXT   C    O     126.83  3.000
 Z3E  CA    C    O     120.80  1.700
 Z3E  H     N    H2    105.61  3.000
 Z3E  H     N    CA    114.00  3.000
 Z3E  H2    N    CA    109.10  3.000
 Z3E  C7    C1   C6    120.10  3.000
 Z3E  C7    C1   C2    121.03  3.000
 Z3E  C6    C1   C2    118.85  3.000
 Z3E  H8    C2   C3    119.71  3.000
 Z3E  H8    C2   C1    119.59  3.000
 Z3E  C3    C2   C1    120.70  3.000
 Z3E  H3    C3   C4    120.11  3.000
 Z3E  H3    C3   C2    119.90  3.000
 Z3E  C4    C3   C2    120.00  3.000
 Z3E  H4    C4   C5    120.11  3.000
 Z3E  H4    C4   C3    120.15  3.000
 Z3E  C5    C4   C3    119.74  3.000
 Z3E  H5    C5   C6    119.91  3.000
 Z3E  H5    C5   C4    120.06  3.000
 Z3E  C6    C5   C4    120.03  3.000
 Z3E  H6    C6   C5    119.76  3.000
 Z3E  H6    C6   C1    119.56  3.000
 Z3E  C5    C6   C1    120.68  3.000
 Z3E  H7A   C7   H7    106.84  3.000
 Z3E  H7A   C7   OG1   110.77  3.000
 Z3E  H7    C7   OG1   111.29  3.000
 Z3E  H7A   C7   C1    110.23  3.000
 Z3E  H7    C7   C1    109.44  3.000
 Z3E  OG1   C7   C1    108.27  3.000
 Z3E  HA    CA   CB    109.00  3.000
 Z3E  HA    CA   N     110.00  3.000
 Z3E  CB    CA   N     111.50  1.700
 Z3E  HA    CA   C     109.00  3.000
 Z3E  CB    CA   C     109.10  2.200
 Z3E  N     CA   C     111.00  2.800
 Z3E  HB    CB   CG2   109.52  3.000
 Z3E  HB    CB   OG1   109.38  3.000
 Z3E  CG2   CB   OG1   110.28  3.000
 Z3E  HB    CB   CA    108.14  3.000
 Z3E  CG2   CB   CA    112.24  3.000
 Z3E  OG1   CB   CA    107.19  3.000
 Z3E  CB    OG1  C7    114.05  3.000
 Z3E  HG2B  CG2  HG2A  108.25  3.000
 Z3E  HG2B  CG2  HG2   107.86  3.000
 Z3E  HG2A  CG2  HG2   107.21  3.000
 Z3E  HG2B  CG2  CB    111.04  3.000
 Z3E  HG2A  CG2  CB    110.73  3.000
 Z3E  HG2   CG2  CB    111.59  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
 Z3E  CONST_01  C4   C3  C2  C1    0.00   0.0  0
 Z3E  CONST_02  C4   C5  C6  C1    0.00   0.0  0
 Z3E  CONST_03  C5   C6  C1  C2    0.00   0.0  0
 Z3E  CONST_04  C5   C4  C3  C2    0.00   0.0  0
 Z3E  CONST_05  C6   C1  C2  C3    0.00   0.0  0
 Z3E  CONST_06  C6   C5  C4  C3    0.00   0.0  0
 Z3E  CONST_07  C7   C1  C2  C3  180.00   0.0  0
 Z3E  CONST_08  C7   C1  C6  C5  180.00   0.0  0
 Z3E  CONST_09  H3   C3  C2  C1  180.00   0.0  0
 Z3E  CONST_10  H5   C5  C6  C1  180.00   0.0  0
 Z3E  CONST_11  H6   C6  C1  C2  180.00   0.0  0
 Z3E  CONST_12  H4   C4  C3  C2  180.00   0.0  0
 Z3E  CONST_13  H8   C2  C3  C4  180.00   0.0  0
 Z3E  Var_01    OG1  C7  C1  C2   99.17  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
 Z3E  chir_01  CA  C    N   CB   negativ
 Z3E  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
 Z3E  plan-1  C1   0.020
 Z3E  plan-1  C2   0.020
 Z3E  plan-1  C3   0.020
 Z3E  plan-1  C4   0.020
 Z3E  plan-1  C5   0.020
 Z3E  plan-1  C6   0.020
 Z3E  plan-1  C7   0.020
 Z3E  plan-1  H8   0.020
 Z3E  plan-1  H3   0.020
 Z3E  plan-1  H4   0.020
 Z3E  plan-1  H5   0.020
 Z3E  plan-1  H6   0.020
 Z3E  plan-2  C    0.020
 Z3E  plan-2  O    0.020
 Z3E  plan-2  CA   0.020
 Z3E  plan-2  OXT  0.020

