# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:54:48 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: N-methyl-L-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]([C@@H](C)O)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
 NZC  NZC  'N-methyl-L-threonine     '  L-peptide  19  9  .  2016-04-26  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_NZC
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
 NZC  N     N  NH1    0  -0.592  -25.0329  62.2169  -27.0211
 NZC  O     O  O      0  -0.600  -26.6494  61.6859  -24.8320
 NZC  OG1   O  OH1    0  -0.672  -27.0715  64.5002  -27.3048
 NZC  C     C  C      0   0.403  -26.3794  62.8961  -24.9605
 NZC  CA    C  CH1    0  -0.241  -25.3831  63.2833  -26.0959
 NZC  CB    C  CH1    0   0.053  -25.7557  64.5968  -26.7835
 NZC  CG2   C  CH3    0  -0.679  -24.7562  65.0046  -27.8574
 NZC  C40   C  CH3    0  -0.507  -26.0800  61.7412  -27.9083
 NZC  OXT   O  OC    -1  -0.609  -26.7676  63.8248  -24.2228
 NZC  HG1   H  HOH1   0   0.439  -27.2919  65.3442  -27.7101
 NZC  HA    H  HCH1   0   0.223  -24.4480  63.5211  -25.5677
 NZC  HB    H  HCH1   0   0.189  -25.7307  65.3643  -26.0000
 NZC  HG2   H  HCH3   0   0.215  -23.7498  65.0714  -27.4413
 NZC  HG2A  H  HCH3   0   0.225  -24.7298  64.2956  -28.6847
 NZC  HG2B  H  HCH3   0   0.218  -25.0057  65.9884  -28.2626
 NZC  H40   H  HCH3   0   0.207  -25.7639  60.7872  -28.3334
 NZC  H40A  H  HCH3   0   0.188  -27.0520  61.5821  -27.4301
 NZC  H40B  H  HCH3   0   0.205  -26.2272  62.4255  -28.7433
 NZC  H     H  HNH1   0   0.332  -24.7324  61.4335  -26.4578

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
 NZC  C40  N     single  1.453  0.020  1.453
 NZC  N    CA    single  1.458  0.019  1.458
 NZC  O    C     deloc   1.231  0.020  1.231
 NZC  OG1  CB    single  1.419  0.020  1.419
 NZC  OG1  HG1   single  0.850  0.020  0.980
 NZC  CA   C     single  1.525  0.021  1.525
 NZC  C    OXT   deloc   1.248  0.020  1.248
 NZC  CB   CA    single  1.540  0.027  1.540
 NZC  CA   HA    single  0.970  0.020  0.970
 NZC  CG2  CB    single  1.523  0.020  1.523
 NZC  CB   HB    single  0.970  0.020  1.090
 NZC  CG2  HG2   single  0.970  0.020  1.090
 NZC  CG2  HG2A  single  0.970  0.020  1.090
 NZC  CG2  HG2B  single  0.970  0.020  1.090
 NZC  C40  H40   single  0.970  0.020  1.090
 NZC  C40  H40A  single  0.970  0.020  1.090
 NZC  C40  H40B  single  0.970  0.020  1.090
 NZC  N    H     single  0.860  0.020  0.860

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
 NZC  H     N    C40   107.51  3.000
 NZC  H     N    CA    114.00  3.000
 NZC  C40   N    CA    117.07  3.000
 NZC  HG1   OG1  CB    107.92  3.000
 NZC  OXT   C    CA    116.38  3.000
 NZC  OXT   C    O     126.45  3.000
 NZC  CA    C    O     120.80  1.700
 NZC  HA    CA   CB    109.00  3.000
 NZC  HA    CA   C     109.00  3.000
 NZC  CB    CA   C     109.10  2.200
 NZC  HA    CA   N     110.00  3.000
 NZC  CB    CA   N     111.50  1.700
 NZC  C     CA   N     111.00  2.800
 NZC  HB    CB   CG2   107.54  3.000
 NZC  HB    CB   CA    105.92  3.000
 NZC  CG2   CB   CA    112.79  3.000
 NZC  HB    CB   OG1   109.35  3.000
 NZC  CG2   CB   OG1   111.59  3.000
 NZC  CA    CB   OG1   109.44  3.000
 NZC  HG2B  CG2  HG2A  108.04  3.000
 NZC  HG2B  CG2  HG2   107.27  3.000
 NZC  HG2A  CG2  HG2   107.88  3.000
 NZC  HG2B  CG2  CB    110.65  3.000
 NZC  HG2A  CG2  CB    112.15  3.000
 NZC  HG2   CG2  CB    110.66  3.000
 NZC  H40B  C40  H40A  107.82  3.000
 NZC  H40B  C40  H40   106.84  3.000
 NZC  H40A  C40  H40   107.48  3.000
 NZC  H40B  C40  N     111.09  3.000
 NZC  H40A  C40  N     114.88  3.000
 NZC  H40   C40  N     108.39  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
 NZC  Var_01  H40  C40  N  CA  -164.67  30.0  3

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
 NZC  chir_01  CA  N    C   CB   positiv
 NZC  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
 NZC  plan-1  O    0.020
 NZC  plan-1  C    0.020
 NZC  plan-1  CA   0.020
 NZC  plan-1  OXT  0.020

