# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 18:10:38 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-[(3Z)-4-hydroxy-6-oxo-3-(2-phenylhydrazinylidene)cyclohexa-1,4-dien-1-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=C/C(=N/Nc2ccccc2)C(=CC1=O)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
 YPZ  YPZ  3-[(3Z)-4-hydroxy-6-oxo-3-(2-phenylhydrazinylidene)cyclohexa-1,4-dien-1-yl]-L-alanine  L-peptide  36  22  .  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_YPZ
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
 YPZ  C5'  C  CR16   0  -0.242   5.1606  -2.1331  22.5921
 YPZ  C4'  C  CR16   0  -0.268   6.0220  -1.1224  22.9980
 YPZ  C3'  C  CR16   0  -0.243   5.5574  -0.1433  23.8679
 YPZ  C2'  C  CR16   0  -0.312   4.2519  -0.1622  24.3323
 YPZ  C1'  C  CR6    0   0.392   3.3940  -1.1796  23.9179
 YPZ  C6'  C  CR16   0  -0.331   3.8524  -2.1665  23.0466
 YPZ  NX1  N  NH1    0  -0.544   2.0715  -1.2570  24.3493
 YPZ  NX2  N  N      0  -0.201   1.5735  -0.3472  25.1183
 YPZ  N    N  NH2    0  -0.780  -1.5810   3.7306  25.9185
 YPZ  CA   C  CH1    0  -0.212  -2.3349   3.2299  27.0555
 YPZ  C    C  C      0   0.380  -2.8086   4.3056  28.0720
 YPZ  O    O  O      0  -0.599  -2.3086   5.4438  27.9775
 YPZ  CG   C  CR6    0   0.001  -1.1838   0.9669  26.9891
 YPZ  CD1  C  CR6    0   0.365  -2.2289  -0.0510  26.7926
 YPZ  CD2  C  CR16   0  -0.350   0.0186   0.7870  26.4119
 YPZ  CE1  C  CR16   0  -0.525  -1.9008  -1.1848  25.9471
 YPZ  CE2  C  CR6    0   0.167   0.3547  -0.3457  25.5827
 YPZ  CZ   C  CR6    0   0.404  -0.6895  -1.3333  25.3648
 YPZ  OH   O  OH1    0  -0.635  -0.3608  -2.3629  24.5743
 YPZ  OXT  O  OC    -1  -0.615  -3.6450   3.9208  28.9150
 YPZ  H5'  H  HCR6   0   0.261   5.5056  -2.9041  21.9157
 YPZ  H4'  H  HCR6   0   0.257   7.0431  -1.0979  22.6417
 YPZ  H3'  H  HCR6   0   0.260   6.2192   0.6490  24.1933
 YPZ  H2'  H  HCR6   0   0.273   3.9037   0.6045  25.0099
 YPZ  H6'  H  HCR6   0   0.272   3.1860  -2.9581  22.7240
 YPZ  H1   H  HNH1   0   0.428   1.5156  -2.0480  24.0408
 YPZ  HA   H  HCH1   0   0.218  -3.2288   2.7318  26.6680
 YPZ  HD2  H  HCR6   0   0.260   0.8078   1.5157  26.5575
 YPZ  HE1  H  HCR6   0   0.270  -2.6737  -1.9306  25.7913
 YPZ  HH   H  HOH1   0   0.493  -1.0942  -2.9849  24.4739
 YPZ  CB   C  CH2    0  -0.501  -1.5062   2.1733  27.8108
 YPZ  H    H  HNH2   0   0.332  -2.1971   4.2973  25.3480
 YPZ  HB2  H  HCH2   0   0.230  -0.5748   2.6391  28.1487
 YPZ  HB3  H  HCH2   0   0.236  -2.0543   1.8763  28.7054
 YPZ  OX1  O  O      0  -0.459  -3.3353   0.0462  27.3212
 YPZ  H2   H  HNH2   0   0.320  -0.8938   4.3872  26.2722

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
 YPZ  C5'  C4'  aromatic  1.389  0.020  1.389
 YPZ  C5'  C6'  aromatic  1.385  0.020  1.385
 YPZ  C4'  C3'  aromatic  1.390  0.020  1.390
 YPZ  C6'  C1'  aromatic  1.394  0.020  1.394
 YPZ  C3'  C2'  aromatic  1.386  0.020  1.386
 YPZ  C1'  C2'  aromatic  1.394  0.020  1.394
 YPZ  C1'  NX1  single    1.393  0.020  1.393
 YPZ  NX1  NX2  single    1.291  0.020  1.291
 YPZ  OH   CZ   single    1.339  0.020  1.339
 YPZ  N    CA   single    1.458  0.019  1.458
 YPZ  NX2  CE2  double    1.304  0.020  1.304
 YPZ  CZ   CE2  single    1.454  0.020  1.454
 YPZ  CZ   CE1  double    1.352  0.020  1.352
 YPZ  CE2  CD2  single    1.443  0.020  1.443
 YPZ  CE1  CD1  single    1.452  0.020  1.452
 YPZ  CD2  CG   double    1.346  0.020  1.346
 YPZ  CD1  CG   single    1.472  0.020  1.472
 YPZ  CD1  OX1  double    1.230  0.020  1.230
 YPZ  CA   CB   single    1.530  0.020  1.530
 YPZ  CA   C    single    1.525  0.021  1.525
 YPZ  CG   CB   single    1.495  0.020  1.495
 YPZ  C    O    deloc     1.231  0.020  1.231
 YPZ  C    OXT  deloc     1.248  0.020  1.248
 YPZ  C5'  H5'  single    0.930  0.020  1.080
 YPZ  C4'  H4'  single    0.930  0.020  1.080
 YPZ  C3'  H3'  single    0.930  0.020  1.080
 YPZ  C2'  H2'  single    0.930  0.020  1.080
 YPZ  C6'  H6'  single    0.930  0.020  1.080
 YPZ  NX1  H1   single    0.860  0.020  1.020
 YPZ  N    H    single    0.860  0.020  0.860
 YPZ  N    H2   single    0.890  0.020  1.040
 YPZ  CA   HA   single    0.970  0.020  0.970
 YPZ  CB   HB2  single    0.970  0.020  1.090
 YPZ  CB   HB3  single    0.970  0.020  1.090
 YPZ  CD2  HD2  single    0.930  0.020  1.080
 YPZ  CE1  HE1  single    0.930  0.020  1.080
 YPZ  OH   HH   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
 YPZ  H5'  C5'  C6'  119.27  3.000
 YPZ  H5'  C5'  C4'  120.23  3.000
 YPZ  C6'  C5'  C4'  120.50  3.000
 YPZ  H4'  C4'  C3'  120.38  3.000
 YPZ  H4'  C4'  C5'  120.39  3.000
 YPZ  C3'  C4'  C5'  119.23  3.000
 YPZ  H3'  C3'  C2'  119.03  3.000
 YPZ  H3'  C3'  C4'  119.97  3.000
 YPZ  C2'  C3'  C4'  121.01  3.000
 YPZ  H2'  C2'  C1'  120.39  3.000
 YPZ  H2'  C2'  C3'  120.26  3.000
 YPZ  C1'  C2'  C3'  119.35  3.000
 YPZ  NX1  C1'  C6'  117.80  3.000
 YPZ  NX1  C1'  C2'  122.19  3.000
 YPZ  C6'  C1'  C2'  120.01  3.000
 YPZ  H6'  C6'  C1'  120.06  3.000
 YPZ  H6'  C6'  C5'  120.04  3.000
 YPZ  C1'  C6'  C5'  119.90  3.000
 YPZ  H1   NX1  NX2  121.26  3.000
 YPZ  H1   NX1  C1'  117.98  3.000
 YPZ  NX2  NX1  C1'  120.75  3.000
 YPZ  CE2  NX2  NX1  124.98  3.000
 YPZ  H2   N    H    104.26  3.000
 YPZ  H2   N    CA   107.56  3.000
 YPZ  H    N    CA   114.00  3.000
 YPZ  HA   CA   CB   109.00  3.000
 YPZ  HA   CA   C    109.00  3.000
 YPZ  CB   CA   C    110.10  1.900
 YPZ  HA   CA   N    110.00  3.000
 YPZ  C    CA   N    111.00  2.800
 YPZ  CB   CA   N    110.50  1.700
 YPZ  OXT  C    O    126.96  3.000
 YPZ  OXT  C    CA   115.63  3.000
 YPZ  O    C    CA   120.80  1.700
 YPZ  CD2  CG   CD1  118.99  3.000
 YPZ  CD1  CG   CB   118.58  3.000
 YPZ  CD2  CG   CB   122.43  3.000
 YPZ  CE1  CD1  CG   117.21  3.000
 YPZ  CG   CD1  OX1  121.78  3.000
 YPZ  CE1  CD1  OX1  121.01  3.000
 YPZ  HD2  CD2  CE2  115.80  3.000
 YPZ  HD2  CD2  CG   120.20  3.000
 YPZ  CE2  CD2  CG   124.01  3.000
 YPZ  HE1  CE1  CZ   120.05  3.000
 YPZ  HE1  CE1  CD1  117.34  3.000
 YPZ  CZ   CE1  CD1  122.61  3.000
 YPZ  CZ   CE2  CD2  116.87  3.000
 YPZ  CD2  CE2  NX2  115.03  3.000
 YPZ  CZ   CE2  NX2  128.10  3.000
 YPZ  OH   CZ   CE2  115.76  3.000
 YPZ  CE2  CZ   CE1  120.29  3.000
 YPZ  OH   CZ   CE1  123.95  3.000
 YPZ  HH   OH   CZ   111.70  3.000
 YPZ  HB3  CB   HB2  106.88  3.000
 YPZ  HB3  CB   CG   109.85  3.000
 YPZ  HB2  CB   CG   109.24  3.000
 YPZ  HB3  CB   CA   108.58  3.000
 YPZ  HB2  CB   CA   108.49  3.000
 YPZ  CG   CB   CA   113.58  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
 YPZ  CONST_01  C2'  C3'  C4'  C5'    0.00   0.0  0
 YPZ  CONST_02  C2'  C1'  C6'  C5'    0.00   0.0  0
 YPZ  CONST_03  C1'  C6'  C5'  C4'    0.00   0.0  0
 YPZ  CONST_04  C1'  C2'  C3'  C4'    0.00   0.0  0
 YPZ  CONST_05  C6'  C5'  C4'  C3'    0.00   0.0  0
 YPZ  CONST_06  C6'  C1'  C2'  C3'    0.00   0.0  0
 YPZ  CONST_07  NX1  C1'  C6'  C5'  180.00   0.0  0
 YPZ  CONST_08  NX1  C1'  C2'  C3'  180.00   0.0  0
 YPZ  CONST_09  H3'  C3'  C4'  C5'  180.00   0.0  0
 YPZ  CONST_10  H6'  C6'  C5'  C4'  180.00   0.0  0
 YPZ  CONST_11  H2'  C2'  C3'  C4'  180.00   0.0  0
 YPZ  CONST_12  H5'  C5'  C4'  C3'  180.00   0.0  0
 YPZ  CONST_13  H4'  C4'  C3'  C2'  180.00   0.0  0
 YPZ  CONST_14  NX2  NX1  C1'  C2'    0.00   0.0  0
 YPZ  CONST_15  CE2  NX2  NX1  C1'  180.00   0.0  0
 YPZ  CONST_16  NX2  NX1  C1'  C6'  180.00   0.0  0
 YPZ  CONST_17  H1   NX1  C1'  C2'  180.00   0.0  0
 YPZ  Var_01    CZ   CE2  NX2  NX1    0.58   0.0  2
 YPZ  Var_02    CD2  CG   CB   CA   100.99  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
 YPZ  chir_01  CA  N  CB  C  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
 YPZ  plan-1  C5'  0.020
 YPZ  plan-1  C4'  0.020
 YPZ  plan-1  C3'  0.020
 YPZ  plan-1  C2'  0.020
 YPZ  plan-1  C1'  0.020
 YPZ  plan-1  C6'  0.020
 YPZ  plan-1  NX1  0.020
 YPZ  plan-1  H5'  0.020
 YPZ  plan-1  H4'  0.020
 YPZ  plan-1  H3'  0.020
 YPZ  plan-1  H2'  0.020
 YPZ  plan-1  H6'  0.020
 YPZ  plan-2  NX1  0.020
 YPZ  plan-2  NX2  0.020
 YPZ  plan-2  CG   0.020
 YPZ  plan-2  CD1  0.020
 YPZ  plan-2  CD2  0.020
 YPZ  plan-2  CE1  0.020
 YPZ  plan-2  CE2  0.020
 YPZ  plan-2  CZ   0.020
 YPZ  plan-2  OH   0.020
 YPZ  plan-2  HD2  0.020
 YPZ  plan-2  HE1  0.020
 YPZ  plan-2  CB   0.020
 YPZ  plan-2  OX1  0.020
 YPZ  plan-3  C1'  0.020
 YPZ  plan-3  NX1  0.020
 YPZ  plan-3  NX2  0.020
 YPZ  plan-3  H1   0.020
 YPZ  plan-4  CA   0.020
 YPZ  plan-4  C    0.020
 YPZ  plan-4  O    0.020
 YPZ  plan-4  OXT  0.020

