# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 06:05:59 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: O-[(3S)-3-amino-3-carboxy-1,1-dihydroxypropyl]-L-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](OC(O)(O)C[C@H](N)C(O)=O)[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
 QNY  QNY  O-[(3S)-3-amino-3-carboxy-1,1-dihydroxypropyl]-L-threonine  L-peptide  31  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QNY
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
 QNY  O    O  O      0  -0.612  3.8580   2.9565  -25.6443
 QNY  C    C  C      0   0.378  3.7236   3.8150  -24.7479
 QNY  CA   C  CH1    0  -0.174  4.9449   4.7315  -24.4775
 QNY  N    N  NH2    0  -0.813  4.5234   6.1228  -24.3719
 QNY  CB   C  CH1    0   0.063  5.6403   4.3122  -23.1768
 QNY  CG2  C  CH3    0  -0.678  6.0709   2.8527  -23.1927
 QNY  OG1  O  O2     0  -0.539  6.7905   5.1437  -23.0291
 QNY  CD   C  CT     0   0.712  7.0419   5.7622  -21.8026
 QNY  OE2  O  OH1    0  -0.719  5.9641   6.4387  -21.3020
 QNY  OE1  O  OH1    0  -0.678  7.3702   4.7340  -20.9011
 QNY  CE2  C  CH2    0  -0.526  8.2672   6.6638  -22.0347
 QNY  CZ   C  CH1    0  -0.233  8.1617   7.7620  -23.1056
 QNY  NH1  N  NH2    0  -0.808  9.5120   8.1220  -23.5184
 QNY  CH2  C  C      0   0.469  7.3994   9.0209  -22.6452
 QNY  OT1  O  OC    -1  -0.616  6.3465   8.8284  -21.9710
 QNY  OT2  O  O      0  -0.560  7.8228  10.1276  -22.9930
 QNY  H2   H  HCH1   0   0.164  5.6675   4.5704  -25.2935
 QNY  H    H  HNH2   0   0.337  5.3409   6.7086  -24.2586
 QNY  H4   H  HNH2   0   0.331  4.1002   6.4123  -25.2448
 QNY  H6   H  HCH1   0   0.197  4.9380   4.4788  -22.3547
 QNY  H7   H  HCH3   0   0.230  6.6088   2.5999  -22.2807
 QNY  H8   H  HCH3   0   0.221  5.2110   2.1872  -23.2595
 QNY  H9   H  HCH3   0   0.211  6.7232   2.6411  -24.0423
 QNY  H10  H  HOH1   0   0.455  6.0520   7.4121  -21.5739
 QNY  H11  H  HOH1   0   0.439  7.4045   5.1115  -20.0153
 QNY  H12  H  HCH2   0   0.229  9.0906   6.0048  -22.3232
 QNY  H13  H  HCH2   0   0.228  8.5593   7.1100  -21.0782
 QNY  H14  H  HCH1   0   0.226  7.5732   7.3618  -23.9482
 QNY  H15  H  HNH2   0   0.333  9.8873   7.3880  -24.1056
 QNY  H16  H  HNH2   0   0.336  9.4682   8.9564  -24.0880
 QNY  OXT  O  OC    -1  -0.601  2.7146   4.0008  -24.0405

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
 QNY  O    C    deloc   1.231  0.020  1.231
 QNY  CA   C    single  1.525  0.021  1.525
 QNY  CA   N    single  1.458  0.019  1.458
 QNY  CA   CB   single  1.540  0.027  1.540
 QNY  NH1  CZ   single  1.457  0.020  1.457
 QNY  CG2  CB   single  1.522  0.020  1.522
 QNY  OT2  CH2  deloc   1.235  0.020  1.235
 QNY  CB   OG1  single  1.427  0.020  1.427
 QNY  OG1  CD   single  1.396  0.020  1.396
 QNY  CZ   CH2  single  1.542  0.020  1.542
 QNY  CZ   CE2  single  1.538  0.020  1.538
 QNY  CH2  OT1  deloc   1.265  0.020  1.265
 QNY  OE2  CD   single  1.367  0.020  1.367
 QNY  CD   CE2  single  1.539  0.020  1.539
 QNY  CD   OE1  single  1.406  0.020  1.406
 QNY  CA   H2   single  0.970  0.020  1.090
 QNY  N    H    single  0.860  0.020  0.860
 QNY  N    H4   single  0.890  0.020  1.040
 QNY  CB   H6   single  0.970  0.020  1.090
 QNY  CG2  H7   single  0.970  0.020  1.090
 QNY  CG2  H8   single  0.970  0.020  1.090
 QNY  CG2  H9   single  0.970  0.020  1.090
 QNY  OE2  H10  single  0.850  0.020  0.980
 QNY  OE1  H11  single  0.850  0.020  0.980
 QNY  CE2  H12  single  0.970  0.020  1.090
 QNY  CE2  H13  single  0.970  0.020  1.090
 QNY  CZ   H14  single  0.970  0.020  1.090
 QNY  NH1  H15  single  0.890  0.020  1.040
 QNY  NH1  H16  single  0.890  0.020  1.040
 QNY  C    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
 QNY  OXT  C    CA   116.78  3.000
 QNY  OXT  C    O    126.67  3.000
 QNY  CA   C    O    120.80  1.700
 QNY  H2   CA   CB   106.91  3.000
 QNY  H2   CA   N    112.51  3.000
 QNY  CB   CA   N    111.50  1.700
 QNY  H2   CA   C    107.51  3.000
 QNY  CB   CA   C    109.10  2.200
 QNY  N    CA   C    111.00  2.800
 QNY  H4   N    H    105.58  3.000
 QNY  H4   N    CA   109.35  3.000
 QNY  H    N    CA   114.00  3.000
 QNY  H6   CB   OG1  110.55  3.000
 QNY  H6   CB   CG2  109.61  3.000
 QNY  OG1  CB   CG2  109.38  3.000
 QNY  H6   CB   CA   107.74  3.000
 QNY  OG1  CB   CA   107.10  3.000
 QNY  CG2  CB   CA   112.44  3.000
 QNY  H9   CG2  H8   107.78  3.000
 QNY  H9   CG2  H7   108.17  3.000
 QNY  H8   CG2  H7   107.43  3.000
 QNY  H9   CG2  CB   111.29  3.000
 QNY  H8   CG2  CB   111.30  3.000
 QNY  H7   CG2  CB   110.72  3.000
 QNY  CD   OG1  CB   119.61  3.000
 QNY  CE2  CD   OE1  109.83  3.000
 QNY  OE1  CD   OE2  108.13  3.000
 QNY  CE2  CD   OE2  113.14  3.000
 QNY  OE1  CD   OG1  106.34  3.000
 QNY  CE2  CD   OG1  105.68  3.000
 QNY  OE2  CD   OG1  113.49  3.000
 QNY  H10  OE2  CD   107.95  3.000
 QNY  H11  OE1  CD   108.13  3.000
 QNY  H13  CE2  H12  105.97  3.000
 QNY  H13  CE2  CZ   109.61  3.000
 QNY  H12  CE2  CZ   107.36  3.000
 QNY  H13  CE2  CD   108.62  3.000
 QNY  H12  CE2  CD   106.64  3.000
 QNY  CZ   CE2  CD   117.96  3.000
 QNY  H14  CZ   CH2  105.10  3.000
 QNY  H14  CZ   NH1  111.57  3.000
 QNY  CH2  CZ   NH1  109.94  3.000
 QNY  H14  CZ   CE2  108.04  3.000
 QNY  CH2  CZ   CE2  114.15  3.000
 QNY  NH1  CZ   CE2  108.07  3.000
 QNY  H16  NH1  H15  106.72  3.000
 QNY  H16  NH1  CZ   108.86  3.000
 QNY  H15  NH1  CZ   109.19  3.000
 QNY  OT2  CH2  OT1  124.88  3.000
 QNY  OT1  CH2  CZ   116.50  3.000
 QNY  OT2  CH2  CZ   118.56  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
 QNY  Var_01  OE2  CD   OG1  CB   -50.59  30.0  3
 QNY  Var_02  CZ   CE2  CD   OG1   59.27  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
 QNY  chir_01  CA  C    N    CB   negativ
 QNY  chir_02  CB  OG1  CA   CG2  negativ
 QNY  chir_03  CZ  NH1  CH2  CE2  positiv

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
 QNY  plan-1  O    0.020
 QNY  plan-1  C    0.020
 QNY  plan-1  CA   0.020
 QNY  plan-1  OXT  0.020
 QNY  plan-2  CZ   0.020
 QNY  plan-2  CH2  0.020
 QNY  plan-2  OT1  0.020
 QNY  plan-2  OT2  0.020

