# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:30:57 2021
#   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  33  17  .  2022-03-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.440   3.6690   3.1424  -25.7555
 QNY  C    C  C     0   0.523   3.7032   3.9058  -24.8221
 QNY  CA   C  CH1   0  -0.184   4.8667   4.8344  -24.5256
 QNY  N    N  NH2   0  -0.808   4.3747   6.1939  -24.4146
 QNY  CB   C  CH1   0   0.044   5.5594   4.3985  -23.2224
 QNY  CG2  C  CH3   0  -0.687   5.9966   2.9432  -23.2645
 QNY  OG1  O  O2    0  -0.523   6.7061   5.2394  -23.0998
 QNY  CD   C  CT    0   0.714   7.0030   5.8095  -21.8828
 QNY  OE2  O  OH1   0  -0.655   5.9404   6.6559  -21.5494
 QNY  OE1  O  OH1   0  -0.666   7.1409   4.7903  -20.9426
 QNY  CE2  C  CH2   0  -0.549   8.3085   6.5875  -22.0476
 QNY  CZ   C  CH1   0  -0.178   8.2917   7.6596  -23.1359
 QNY  NH1  N  NH2   0  -0.802   9.6091   8.2840  -23.1804
 QNY  CH2  C  C     0   0.550   7.2668   8.7500  -22.8720
 QNY  OT1  O  OH1   0  -0.587   7.4629   9.3704  -21.7175
 QNY  OT2  O  O     0  -0.448   6.3964   9.0588  -23.6492
 QNY  H2   H  HCH1  0   0.241   5.5863   4.6869  -25.3433
 QNY  H    H  HNH2  0   0.358   5.1333   6.8026  -24.1353
 QNY  H4   H  HNH2  0   0.353   4.0808   6.5238  -25.3254
 QNY  H6   H  HCH1  0   0.239   4.8669   4.5594  -22.3917
 QNY  H7   H  HCH3  0   0.253   6.5315   2.6783  -22.3550
 QNY  H8   H  HCH3  0   0.233   5.1406   2.2715  -23.3379
 QNY  H9   H  HCH3  0   0.231   6.6519   2.7509  -24.1157
 QNY  H10  H  HOH1  0   0.456   6.0901   7.0459  -20.6802
 QNY  H11  H  HOH1  0   0.463   7.6188   5.1074  -20.1675
 QNY  H12  H  HCH2  0   0.266   9.1039   5.8767  -22.2884
 QNY  H13  H  HCH2  0   0.258   8.5818   7.0435  -21.0912
 QNY  H14  H  HCH1  0   0.253   8.0054   7.1989  -24.0876
 QNY  H15  H  HNH2  0   0.357  10.3024   7.5630  -23.3409
 QNY  H16  H  HNH2  0   0.355   9.6707   8.8962  -23.9853
 QNY  H18  H  HOH1  0   0.480   6.7968  10.0638  -21.5978
 QNY  OXT  O  OH1   0  -0.582   2.7241   4.0145  -23.9356
 QNY  HXT  H  HOH1  0   0.481   2.0121   3.3943  -24.1543

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    double  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  1.459  0.020  1.459
 QNY  CG2  CB   single  1.520  0.020  1.520
 QNY  OT2  CH2  double  1.207  0.020  1.207
 QNY  CB   OG1  single  1.427  0.020  1.427
 QNY  OG1  CD   single  1.376  0.020  1.376
 QNY  CZ   CH2  single  1.520  0.020  1.520
 QNY  CZ   CE2  single  1.528  0.020  1.528
 QNY  CH2  OT1  single  1.325  0.020  1.325
 QNY  OE2  CD   single  1.399  0.020  1.399
 QNY  CD   CE2  single  1.529  0.020  1.529
 QNY  CD   OE1  single  1.393  0.020  1.393
 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  OT1  H18  single  0.850  0.020  0.980
 QNY  C    OXT  single  1.325  0.020  1.325
 QNY  OXT  HXT  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
 QNY  OXT  C    CA   112.67  3.000
 QNY  OXT  C    O    123.27  3.000
 QNY  CA   C    O    120.80  1.700
 QNY  H2   CA   CB   107.29  3.000
 QNY  H2   CA   N    113.89  3.000
 QNY  CB   CA   N    111.50  1.700
 QNY  H2   CA   C    105.92  3.000
 QNY  CB   CA   C    109.10  2.200
 QNY  N    CA   C    111.00  2.800
 QNY  H4   N    H    105.66  3.000
 QNY  H4   N    CA   109.58  3.000
 QNY  H    N    CA   114.00  3.000
 QNY  H6   CB   OG1  110.92  3.000
 QNY  H6   CB   CG2  110.13  3.000
 QNY  OG1  CB   CG2  109.59  3.000
 QNY  H6   CB   CA   108.45  3.000
 QNY  OG1  CB   CA   105.51  3.000
 QNY  CG2  CB   CA   112.16  3.000
 QNY  H9   CG2  H8   108.08  3.000
 QNY  H9   CG2  H7   108.30  3.000
 QNY  H8   CG2  H7   106.99  3.000
 QNY  H9   CG2  CB   111.29  3.000
 QNY  H8   CG2  CB   111.46  3.000
 QNY  H7   CG2  CB   110.57  3.000
 QNY  CD   OG1  CB   119.55  3.000
 QNY  CE2  CD   OE1  111.13  3.000
 QNY  OE1  CD   OE2  110.91  3.000
 QNY  CE2  CD   OE2  111.50  3.000
 QNY  OE1  CD   OG1  108.36  3.000
 QNY  CE2  CD   OG1  107.44  3.000
 QNY  OE2  CD   OG1  107.31  3.000
 QNY  H10  OE2  CD   109.97  3.000
 QNY  H11  OE1  CD   110.54  3.000
 QNY  H13  CE2  H12  106.36  3.000
 QNY  H13  CE2  CZ   109.45  3.000
 QNY  H12  CE2  CZ   107.89  3.000
 QNY  H13  CE2  CD   109.34  3.000
 QNY  H12  CE2  CD   108.31  3.000
 QNY  CZ   CE2  CD   115.12  3.000
 QNY  H14  CZ   CH2  106.04  3.000
 QNY  H14  CZ   NH1  112.93  3.000
 QNY  CH2  CZ   NH1  107.89  3.000
 QNY  H14  CZ   CE2  109.07  3.000
 QNY  CH2  CZ   CE2  112.78  3.000
 QNY  NH1  CZ   CE2  108.19  3.000
 QNY  H16  NH1  H15  105.23  3.000
 QNY  H16  NH1  CZ   109.74  3.000
 QNY  H15  NH1  CZ   108.55  3.000
 QNY  OT2  CH2  OT1  123.22  3.000
 QNY  OT1  CH2  CZ   112.80  3.000
 QNY  OT2  CH2  CZ   123.92  3.000
 QNY  H18  OT1  CH2  109.93  3.000
 QNY  HXT  OXT  C    109.83  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  CONST_01  HXT  OXT  C    O      0.00   0.0  0
 QNY  CONST_02  H18  OT1  CH2  CZ   180.00   0.0  0
 QNY  Var_01    OE2  CD   OG1  CB   -62.76  30.0  3
 QNY  Var_02    CZ   CE2  CD   OG1   57.13  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-1  HXT  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
 QNY  plan-2  H18  0.020

