# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 17:22:23 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: 2,4,5-trideoxy-2-(methylamino)-4-[(2Z)-penta-2,4-dien-1-yl]-L-xylonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]([C@H](O)[C@H](C)C\C=C/C=C)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
 YYA  YYA  '2,4,5-trideoxy-2-(methylamino)-4-[(2Z)-penta-2,4-dien-1-yl]-L-xylonic acid'  L-peptide  33  15  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YYA
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
 YYA  C     C  C      0   0.419  59.0644  -3.6697  37.9829
 YYA  N     N  NH1    0  -0.589  57.2745  -3.5713  36.2057
 YYA  O     O  O      0  -0.591  59.6996  -4.4108  37.2114
 YYA  CA    C  CH1    0  -0.260  57.6665  -3.1495  37.5391
 YYA  CB    C  CH1    0   0.076  56.6464  -3.3655  38.6727
 YYA  CH    C  C1     0  -0.217  54.4771  -4.9003  42.0704
 YYA  CT    C  C2     0  -0.537  54.6041  -5.5464  43.2317
 YYA  CZ    C  C1     0  -0.261  54.7161  -3.4732  41.9187
 YYA  CD2   C  CH2    0  -0.510  54.2212  -3.2484  39.4317
 YYA  OG1   O  OH1    0  -0.679  56.6474  -4.7375  39.0316
 YYA  CG2   C  CH1    0  -0.259  55.2309  -2.8758  38.3286
 YYA  OXT   O  OC    -1  -0.616  59.4507  -3.2503  39.0941
 YYA  H1    H  HNH1   0   0.336  56.5483  -2.9565  35.8622
 YYA  HA    H  HCH1   0   0.229  57.7917  -2.0620  37.4666
 YYA  HB    H  HCH1   0   0.194  56.9996  -2.7645  39.5207
 YYA  HE    H  H      0   0.244  54.8110  -1.6938  40.8686
 YYA  HH    H  H      0   0.253  54.1737  -5.4641  41.1943
 YYA  HN    H  HCH3   0   0.206  56.7134  -5.1255  34.9455
 YYA  HNA   H  HCH3   0   0.219  57.6399  -5.6192  36.3544
 YYA  H8    H  HCH3   0   0.183  55.9270  -5.2328  36.5172
 YYA  HT    H  H      0   0.242  54.4173  -6.6086  43.3119
 YYA  HTA   H  H      0   0.240  54.8974  -5.0319  44.1394
 YYA  HZ    H  H      0   0.240  55.0085  -2.9500  42.8246
 YYA  HD1   H  HCH3   0   0.231  54.1928  -1.0160  37.9175
 YYA  HD1A  H  HCH3   0   0.221  55.6570  -0.8019  38.8717
 YYA  HD1B  H  HCH3   0   0.234  55.7645  -1.1176  37.1468
 YYA  HD2   H  HCH2   0   0.245  54.0611  -4.3270  39.4317
 YYA  HD2A  H  HCH2   0   0.248  53.2558  -2.8064  39.1614
 YYA  HOG1  H  HOH1   0   0.443  56.3916  -4.8073  39.9555
 YYA  HG2   H  HCH1   0   0.226  54.8872  -3.3879  37.4234
 YYA  CD1   C  CH3    0  -0.679  55.2147  -1.3737  38.0529
 YYA  CN    C  CH3    0  -0.514  56.8573  -4.9460  36.0132
 YYA  CE    C  C1     0  -0.219  54.6047  -2.7573  40.7913

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
 YYA  C    OXT   deloc   1.249  0.020  1.249
 YYA  N    CA    single  1.458  0.019  1.458
 YYA  O    C     deloc   1.231  0.020  1.231
 YYA  CA   C     single  1.525  0.021  1.525
 YYA  CA   CB    single  1.521  0.033  1.521
 YYA  CE   CZ    double  1.340  0.020  1.340
 YYA  CH   CT    double  1.335  0.020  1.335
 YYA  CN   N     single  1.450  0.020  1.450
 YYA  CZ   CH    single  1.455  0.020  1.455
 YYA  CD1  CG2   single  1.527  0.020  1.527
 YYA  CD2  CE    single  1.496  0.020  1.496
 YYA  OG1  CB    single  1.418  0.020  1.418
 YYA  CG2  CB    single  1.537  0.020  1.537
 YYA  CG2  CD2   single  1.541  0.020  1.541
 YYA  N    H1    single  0.890  0.020  1.040
 YYA  CA   HA    single  0.970  0.020  0.970
 YYA  CB   HB    single  0.970  0.020  1.090
 YYA  CE   HE    single  0.930  0.020  1.080
 YYA  CH   HH    single  0.930  0.020  1.080
 YYA  CN   HN    single  0.970  0.020  1.090
 YYA  CN   HNA   single  0.970  0.020  1.090
 YYA  CN   H8    single  0.970  0.020  1.090
 YYA  CT   HT    single  0.930  0.020  1.080
 YYA  CT   HTA   single  0.930  0.020  1.080
 YYA  CZ   HZ    single  0.930  0.020  1.080
 YYA  CD1  HD1   single  0.970  0.020  1.090
 YYA  CD1  HD1A  single  0.970  0.020  1.090
 YYA  CD1  HD1B  single  0.970  0.020  1.090
 YYA  CD2  HD2   single  0.970  0.020  1.090
 YYA  CD2  HD2A  single  0.970  0.020  1.090
 YYA  OG1  HOG1  single  0.850  0.020  0.980
 YYA  CG2  HG2   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
 YYA  OXT   C    CA    120.80  1.700
 YYA  CA    C    O     120.80  1.700
 YYA  OXT   C    O     126.43  3.000
 YYA  H1    N    CN    108.94  3.000
 YYA  H1    N    CA    109.21  3.000
 YYA  CN    N    CA    118.36  3.000
 YYA  HA    CA   CB    109.00  3.000
 YYA  HA    CA   N     110.00  3.000
 YYA  CB    CA   N     110.40  1.500
 YYA  HA    CA   C     110.00  3.000
 YYA  CB    CA   C     110.50  1.500
 YYA  N     CA   C     111.00  2.800
 YYA  HB    CB   CG2   107.14  3.000
 YYA  HB    CB   OG1   109.51  3.000
 YYA  CG2   CB   OG1   111.45  3.000
 YYA  HB    CB   CA    106.18  3.000
 YYA  CG2   CB   CA    113.61  3.000
 YYA  OG1   CB   CA    108.75  3.000
 YYA  HH    CH   CZ    118.12  3.000
 YYA  HH    CH   CT    118.52  3.000
 YYA  CZ    CH   CT    123.35  3.000
 YYA  HTA   CT   HT    116.80  3.000
 YYA  HTA   CT   CH    121.64  3.000
 YYA  HT    CT   CH    121.57  3.000
 YYA  HZ    CZ   CH    115.45  3.000
 YYA  HZ    CZ   CE    117.82  3.000
 YYA  CH    CZ   CE    126.73  3.000
 YYA  HD2A  CD2  HD2   105.65  3.000
 YYA  HD2A  CD2  CG2   107.65  3.000
 YYA  HD2   CD2  CG2   109.59  3.000
 YYA  HD2A  CD2  CE    108.53  3.000
 YYA  HD2   CD2  CE    111.26  3.000
 YYA  CG2   CD2  CE    113.78  3.000
 YYA  HOG1  OG1  CB    108.26  3.000
 YYA  HG2   CG2  CD2   105.83  3.000
 YYA  HG2   CG2  CD1   107.90  3.000
 YYA  CD2   CG2  CD1   111.11  3.000
 YYA  HG2   CG2  CB    108.97  3.000
 YYA  CD2   CG2  CB    111.48  3.000
 YYA  CD1   CG2  CB    111.32  3.000
 YYA  HD1B  CD1  HD1A  107.21  3.000
 YYA  HD1B  CD1  HD1   106.99  3.000
 YYA  HD1A  CD1  HD1   107.50  3.000
 YYA  HD1B  CD1  CG2   112.07  3.000
 YYA  HD1A  CD1  CG2   112.04  3.000
 YYA  HD1   CD1  CG2   110.77  3.000
 YYA  H8    CN   HNA   107.73  3.000
 YYA  H8    CN   HN    107.14  3.000
 YYA  HNA   CN   HN    107.45  3.000
 YYA  H8    CN   N     115.55  3.000
 YYA  HNA   CN   N     109.78  3.000
 YYA  HN    CN   N     108.88  3.000
 YYA  HE    CE   CD2   115.78  3.000
 YYA  HE    CE   CZ    116.58  3.000
 YYA  CD2   CE   CZ    127.63  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
 YYA  Var_01  CD2  CE   CZ  CH    -0.44   0.0  2
 YYA  Var_02  CT   CH   CZ  CE  -179.74  30.0  2
 YYA  Var_03  CG2  CD2  CE  CZ  -126.45  30.0  2
 YYA  Var_04  HT   CT   CH  CZ   179.89   0.0  2
 YYA  Var_05  HN   CN   N   CA  -173.35  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
 YYA  chir_01  CA   N    C   CB   positiv
 YYA  chir_02  CB   OG1  CA  CG2  negativ
 YYA  chir_03  CG2  CD2  CB  CD1  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
 YYA  plan-1  C    0.020
 YYA  plan-1  O    0.020
 YYA  plan-1  CA   0.020
 YYA  plan-1  OXT  0.020
 YYA  plan-2  CH   0.020
 YYA  plan-2  CZ   0.020
 YYA  plan-2  CD2  0.020
 YYA  plan-2  HE   0.020
 YYA  plan-2  HZ   0.020
 YYA  plan-2  CE   0.020
 YYA  plan-3  CH   0.020
 YYA  plan-3  CT   0.020
 YYA  plan-3  CZ   0.020
 YYA  plan-3  HH   0.020
 YYA  plan-3  HT   0.020
 YYA  plan-3  HTA  0.020

