# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 05:09:02 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: 2,4,5-trideoxy-2-(methylamino)-4-[(2E)-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
 XXA  XXA  '2,4,5-trideoxy-2-(methylamino)-4-[(2E)-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_XXA
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
 XXA  C     C  C      0   0.417  5.7089  -31.7878  27.7148
 XXA  N     N  NH1    0  -0.588  7.8872  -31.6010  26.4525
 XXA  O     O  O      0  -0.591  5.5018  -32.8348  27.0758
 XXA  CA    C  CH1    0  -0.255  7.0006  -30.9750  27.4185
 XXA  CB    C  CH1    0   0.074  6.6348  -29.4985  27.1808
 XXA  CH    C  C1     0  -0.190  4.3502  -25.4446  28.0666
 XXA  CT    C  C2     0  -0.547  3.1327  -24.9999  27.7493
 XXA  CZ    C  C1     0  -0.270  5.2596  -26.0720  27.1222
 XXA  CD2   C  CH2    0  -0.506  7.4181  -27.1781  26.4863
 XXA  OG1   O  OH1    0  -0.679  5.6802  -29.4377  26.1355
 XXA  CG2   C  CH1    0  -0.261  7.8494  -28.5987  26.9018
 XXA  OXT   O  OC    -1  -0.618  4.9889  -31.3186  28.6217
 XXA  H1    H  HNH1   0   0.335  8.8184  -31.2224  26.5674
 XXA  HA    H  HCH1   0   0.228  7.5605  -30.9878  28.3613
 XXA  HB    H  HCH1   0   0.192  6.1791  -29.1454  28.1154
 XXA  HE    H  H      0   0.245  6.8161  -26.4087  28.4718
 XXA  HH    H  H      0   0.245  4.7040  -25.3459  29.0891
 XXA  HN    H  HCH3   0   0.205  8.2500  -32.1433  24.4809
 XXA  HNA   H  HCH3   0   0.218  6.5494  -31.9938  24.8981
 XXA  H8    H  HCH3   0   0.184  7.5145  -30.5478  24.6031
 XXA  HT    H  H      0   0.240  2.4868  -24.5424  28.4861
 XXA  HTA   H  H      0   0.238  2.7434  -25.0823  26.7413
 XXA  HZ    H  H      0   0.243  4.9094  -26.1675  26.0958
 XXA  HD1   H  HCH3   0   0.234  9.2349  -29.5308  28.3090
 XXA  HD1A  H  HCH3   0   0.230  9.6079  -27.8573  27.9336
 XXA  HD1B  H  HCH3   0   0.220  8.2701  -28.2406  29.0132
 XXA  HD2   H  HCH2   0   0.242  6.9700  -27.2000  25.4903
 XXA  HD2A  H  HCH2   0   0.244  8.3241  -26.5689  26.3983
 XXA  HOG1  H  HOH1   0   0.443  5.1743  -28.6259  26.2364
 XXA  HG2   H  HCH1   0   0.226  8.4092  -29.0045  26.0521
 XXA  CD1   C  CH3    0  -0.677  8.7888  -28.5569  28.1054
 XXA  CN    C  CH3    0  -0.511  7.5303  -31.5490  25.0482
 XXA  CE    C  C1     0  -0.212  6.4782  -26.5207  27.4439

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
 XXA  C    OXT   deloc   1.249  0.020  1.249
 XXA  N    CA    single  1.458  0.019  1.458
 XXA  O    C     deloc   1.231  0.020  1.231
 XXA  CA   C     single  1.525  0.021  1.525
 XXA  CB   CA    single  1.521  0.033  1.521
 XXA  CN   N     single  1.450  0.020  1.450
 XXA  CT   CH    double  1.334  0.020  1.334
 XXA  CZ   CE    double  1.338  0.020  1.338
 XXA  CZ   CH    single  1.453  0.020  1.453
 XXA  CD2  CE    single  1.494  0.020  1.494
 XXA  CD2  CG2   single  1.542  0.020  1.542
 XXA  OG1  CB    single  1.417  0.020  1.417
 XXA  CG2  CB    single  1.537  0.020  1.537
 XXA  CG2  CD1   single  1.527  0.020  1.527
 XXA  N    H1    single  0.890  0.020  1.040
 XXA  CA   HA    single  0.970  0.020  0.970
 XXA  CB   HB    single  0.970  0.020  1.090
 XXA  CE   HE    single  0.930  0.020  1.080
 XXA  CH   HH    single  0.930  0.020  1.080
 XXA  CN   HN    single  0.970  0.020  1.090
 XXA  CN   HNA   single  0.970  0.020  1.090
 XXA  CN   H8    single  0.970  0.020  1.090
 XXA  CT   HT    single  0.930  0.020  1.080
 XXA  CT   HTA   single  0.930  0.020  1.080
 XXA  CZ   HZ    single  0.930  0.020  1.080
 XXA  CD1  HD1   single  0.970  0.020  1.090
 XXA  CD1  HD1A  single  0.970  0.020  1.090
 XXA  CD1  HD1B  single  0.970  0.020  1.090
 XXA  CD2  HD2   single  0.970  0.020  1.090
 XXA  CD2  HD2A  single  0.970  0.020  1.090
 XXA  OG1  HOG1  single  0.850  0.020  0.980
 XXA  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
 XXA  OXT   C    CA    120.80  1.700
 XXA  CA    C    O     120.80  1.700
 XXA  OXT   C    O     126.38  3.000
 XXA  H1    N    CN    108.85  3.000
 XXA  H1    N    CA    108.96  3.000
 XXA  CN    N    CA    118.57  3.000
 XXA  HA    CA   CB    109.00  3.000
 XXA  HA    CA   N     110.00  3.000
 XXA  CB    CA   N     110.40  1.500
 XXA  HA    CA   C     110.00  3.000
 XXA  CB    CA   C     110.50  1.500
 XXA  N     CA   C     111.00  2.800
 XXA  HB    CB   CG2   107.11  3.000
 XXA  HB    CB   OG1   109.55  3.000
 XXA  CG2   CB   OG1   111.92  3.000
 XXA  HB    CB   CA    106.00  3.000
 XXA  CG2   CB   CA    113.68  3.000
 XXA  OG1   CB   CA    108.37  3.000
 XXA  HH    CH   CZ    116.55  3.000
 XXA  HH    CH   CT    119.38  3.000
 XXA  CZ    CH   CT    124.07  3.000
 XXA  HTA   CT   HT    116.83  3.000
 XXA  HTA   CT   CH    121.57  3.000
 XXA  HT    CT   CH    121.60  3.000
 XXA  HZ    CZ   CH    116.69  3.000
 XXA  HZ    CZ   CE    119.36  3.000
 XXA  CH    CZ   CE    123.95  3.000
 XXA  HD2A  CD2  HD2   106.09  3.000
 XXA  HD2A  CD2  CG2   107.63  3.000
 XXA  HD2   CD2  CG2   110.00  3.000
 XXA  HD2A  CD2  CE    109.09  3.000
 XXA  HD2   CD2  CE    109.58  3.000
 XXA  CG2   CD2  CE    114.12  3.000
 XXA  HOG1  OG1  CB    108.25  3.000
 XXA  HG2   CG2  CD2   105.98  3.000
 XXA  HG2   CG2  CD1   107.88  3.000
 XXA  CD2   CG2  CD1   111.05  3.000
 XXA  HG2   CG2  CB    109.13  3.000
 XXA  CD1   CG2  CB    111.03  3.000
 XXA  CD2   CG2  CB    111.55  3.000
 XXA  HD1B  CD1  HD1A  107.56  3.000
 XXA  HD1B  CD1  HD1   107.32  3.000
 XXA  HD1A  CD1  HD1   107.16  3.000
 XXA  HD1B  CD1  CG2   111.76  3.000
 XXA  HD1A  CD1  CG2   110.81  3.000
 XXA  HD1   CD1  CG2   111.98  3.000
 XXA  H8    CN   HNA   107.74  3.000
 XXA  H8    CN   HN    107.20  3.000
 XXA  HNA   CN   HN    107.46  3.000
 XXA  H8    CN   N     115.45  3.000
 XXA  HNA   CN   N     109.94  3.000
 XXA  HN    CN   N     108.74  3.000
 XXA  HE    CE   CD2   117.10  3.000
 XXA  HE    CE   CZ    118.40  3.000
 XXA  CD2   CE   CZ    124.50  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
 XXA  Var_01  CD2  CE   CZ  CH   179.44   0.0  2
 XXA  Var_02  CT   CH   CZ  CE  -179.78  30.0  2
 XXA  Var_03  CG2  CD2  CE  CZ  -121.88  30.0  1
 XXA  Var_04  HT   CT   CH  CZ   179.74   0.0  2
 XXA  Var_05  HN   CN   N   CA  -174.74  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
 XXA  chir_01  CA   N    C   CB   positiv
 XXA  chir_02  CB   OG1  CA  CG2  negativ
 XXA  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
 XXA  plan-1  C    0.020
 XXA  plan-1  O    0.020
 XXA  plan-1  CA   0.020
 XXA  plan-1  OXT  0.020
 XXA  plan-2  CH   0.020
 XXA  plan-2  CT   0.020
 XXA  plan-2  CZ   0.020
 XXA  plan-2  HH   0.020
 XXA  plan-2  HT   0.020
 XXA  plan-2  HTA  0.020
 XXA  plan-3  CH   0.020
 XXA  plan-3  CZ   0.020
 XXA  plan-3  CD2  0.020
 XXA  plan-3  HE   0.020
 XXA  plan-3  HZ   0.020
 XXA  plan-3  CE   0.020

