# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 01:36:07 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: 4-[(2E)-but-2-en-1-yl]-2,4,5-trideoxy-4-methyl-2-(methylamino)-D-arabinonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]([C@H](O)C(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
 DMT  DMT  '4-[(2E)-but-2-en-1-yl]-2,4,5-trideoxy-4-methyl-2-(methylamino)-D-arabinonic acid'  L-peptide  35  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_DMT
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
 DMT  N     N  NH1    0  -0.590  5.3400  34.8711  19.3760
 DMT  CN    C  CH3    0  -0.515  4.6810  36.1596  19.3232
 DMT  CA    C  CH1    0  -0.259  6.4609  34.6112  18.4911
 DMT  C     C  C      0   0.419  7.7642  35.3548  18.9247
 DMT  CB    C  CH1    0   0.088  6.2783  34.7595  16.9684
 DMT  CG2   C  CT     0  -0.096  5.1867  33.9066  16.2745
 DMT  CD1   C  CH2    0  -0.491  5.3389  34.0714  14.7379
 DMT  CD2   C  CH3    0  -0.668  5.3796  32.4345  16.6455
 DMT  CD3   C  CH3    0  -0.648  3.7501  34.3199  16.5984
 DMT  CE    C  C1     0  -0.201  6.7172  33.8602  14.1952
 DMT  CZ    C  C1     0  -0.237  7.3996  34.7592  13.4891
 DMT  CH    C  CH3    0  -0.705  8.7750  34.5607  12.9413
 DMT  O     O  O      0  -0.590  7.7142  36.1156  19.9077
 DMT  OXT   O  OC    -1  -0.614  8.7833  35.0842  18.2538
 DMT  OG1   O  OH1    0  -0.678  6.1469  36.1363  16.6606
 DMT  H     H  HNH1   0   0.336  4.6536  34.1377  19.2688
 DMT  HCN1  H  HCH3   0   0.202  3.9677  36.2237  20.1486
 DMT  HCN2  H  HCH3   0   0.219  5.4104  36.9527  19.4654
 DMT  HCN3  H  HCH3   0   0.191  4.1292  36.3714  18.4019
 DMT  HA    H  HCH1   0   0.227  6.6973  33.5512  18.6452
 DMT  HB    H  HCH1   0   0.199  7.2265  34.3884  16.5602
 DMT  HD12  H  HCH2   0   0.237  4.6532  33.3565  14.2681
 DMT  HD13  H  HCH2   0   0.232  4.9777  35.0614  14.4398
 DMT  HD21  H  HCH3   0   0.227  4.7288  31.7979  16.0425
 DMT  HD22  H  HCH3   0   0.226  6.4072  32.0985  16.4902
 DMT  HD23  H  HCH3   0   0.229  5.1316  32.2524  17.6923
 DMT  HD31  H  HCH3   0   0.221  3.0536  33.7666  15.9636
 DMT  HD32  H  HCH3   0   0.218  3.4718  34.1100  17.6301
 DMT  HD33  H  HCH3   0   0.224  3.5877  35.3814  16.4120
 DMT  HE    H  H      0   0.231  7.1812  32.8969  14.3965
 DMT  HZ    H  H      0   0.227  6.9349  35.7211  13.2791
 DMT  HH1   H  HCH3   0   0.234  9.4674  35.3067  13.3376
 DMT  HH2   H  HCH3   0   0.233  9.1691  33.5736  13.1837
 DMT  HH3   H  HCH3   0   0.233  8.7886  34.6722  11.8549
 DMT  HG1   H  HOH1   0   0.441  6.4080  36.2652  15.7436

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
 DMT  N    CN    single  1.448  0.020  1.448
 DMT  N    CA    single  1.458  0.019  1.458
 DMT  N    H     single  0.860  0.020  0.860
 DMT  CN   HCN1  single  0.970  0.020  1.090
 DMT  CN   HCN2  single  0.970  0.020  1.090
 DMT  CN   HCN3  single  0.970  0.020  1.090
 DMT  CA   C     single  1.525  0.021  1.525
 DMT  CA   CB    single  1.521  0.033  1.521
 DMT  CA   HA    single  0.970  0.020  0.970
 DMT  C    O     deloc   1.231  0.020  1.231
 DMT  C    OXT   deloc   1.250  0.020  1.250
 DMT  CB   CG2   single  1.549  0.020  1.549
 DMT  CB   OG1   single  1.417  0.020  1.417
 DMT  CB   HB    single  0.970  0.020  1.090
 DMT  CG2  CD1   single  1.553  0.020  1.553
 DMT  CG2  CD2   single  1.530  0.020  1.530
 DMT  CG2  CD3   single  1.530  0.020  1.530
 DMT  CD1  CE    single  1.496  0.020  1.496
 DMT  CD1  HD12  single  0.970  0.020  1.090
 DMT  CD1  HD13  single  0.970  0.020  1.090
 DMT  CD2  HD21  single  0.970  0.020  1.090
 DMT  CD2  HD22  single  0.970  0.020  1.090
 DMT  CD2  HD23  single  0.970  0.020  1.090
 DMT  CD3  HD31  single  0.970  0.020  1.090
 DMT  CD3  HD32  single  0.970  0.020  1.090
 DMT  CD3  HD33  single  0.970  0.020  1.090
 DMT  CE   CZ    double  1.331  0.020  1.331
 DMT  CE   HE    single  0.930  0.020  1.080
 DMT  CZ   CH    single  1.494  0.020  1.494
 DMT  CZ   HZ    single  0.930  0.020  1.080
 DMT  CH   HH1   single  0.970  0.020  1.090
 DMT  CH   HH2   single  0.970  0.020  1.090
 DMT  CH   HH3   single  0.970  0.020  1.090
 DMT  OG1  HG1   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
 DMT  H     N    CA    114.00  3.000
 DMT  H     N    CN    109.44  3.000
 DMT  CA    N    CN    119.24  3.000
 DMT  HCN3  CN   HCN2  107.89  3.000
 DMT  HCN3  CN   HCN1  107.18  3.000
 DMT  HCN2  CN   HCN1  107.24  3.000
 DMT  HCN3  CN   N     115.61  3.000
 DMT  HCN2  CN   N     109.82  3.000
 DMT  HCN1  CN   N     108.77  3.000
 DMT  HA    CA   CB    109.00  3.000
 DMT  HA    CA   C     110.00  3.000
 DMT  CB    CA   C     110.50  1.500
 DMT  HA    CA   N     110.00  3.000
 DMT  CB    CA   N     110.40  1.500
 DMT  C     CA   N     111.00  2.800
 DMT  OXT   C    O     126.12  3.000
 DMT  OXT   C    CA    120.80  1.700
 DMT  O     C    CA    120.80  1.700
 DMT  HB    CB   OG1   109.15  3.000
 DMT  HB    CB   CG2   104.84  3.000
 DMT  OG1   CB   CG2   111.86  3.000
 DMT  HB    CB   CA    103.46  3.000
 DMT  OG1   CB   CA    108.62  3.000
 DMT  CG2   CB   CA    118.23  3.000
 DMT  CD3   CG2  CD2   109.09  3.000
 DMT  CD3   CG2  CD1   105.83  3.000
 DMT  CD2   CG2  CD1   109.24  3.000
 DMT  CD3   CG2  CB    114.72  3.000
 DMT  CD2   CG2  CB    109.40  3.000
 DMT  CD1   CG2  CB    108.40  3.000
 DMT  HD13  CD1  HD12  105.46  3.000
 DMT  HD13  CD1  CE    109.43  3.000
 DMT  HD12  CD1  CE    109.19  3.000
 DMT  HD13  CD1  CG2   109.45  3.000
 DMT  HD12  CD1  CG2   107.07  3.000
 DMT  CE    CD1  CG2   115.73  3.000
 DMT  HD23  CD2  HD22  107.39  3.000
 DMT  HD23  CD2  HD21  107.28  3.000
 DMT  HD22  CD2  HD21  107.62  3.000
 DMT  HD23  CD2  CG2   111.38  3.000
 DMT  HD22  CD2  CG2   112.34  3.000
 DMT  HD21  CD2  CG2   110.60  3.000
 DMT  HD33  CD3  HD32  108.16  3.000
 DMT  HD33  CD3  HD31  107.39  3.000
 DMT  HD32  CD3  HD31  106.85  3.000
 DMT  HD33  CD3  CG2   111.53  3.000
 DMT  HD32  CD3  CG2   112.86  3.000
 DMT  HD31  CD3  CG2   109.81  3.000
 DMT  HE    CE   CZ    118.51  3.000
 DMT  HE    CE   CD1   116.79  3.000
 DMT  CZ    CE   CD1   124.69  3.000
 DMT  HZ    CZ   CH    116.09  3.000
 DMT  HZ    CZ   CE    118.69  3.000
 DMT  CH    CZ   CE    125.22  3.000
 DMT  HH3   CH   HH2   108.00  3.000
 DMT  HH3   CH   HH1   106.46  3.000
 DMT  HH2   CH   HH1   107.97  3.000
 DMT  HH3   CH   CZ    111.27  3.000
 DMT  HH2   CH   CZ    111.82  3.000
 DMT  HH1   CH   CZ    111.10  3.000
 DMT  HG1   OG1  CB    108.18  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
 DMT  Var_01  CH    CZ   CE   CD1  -179.97   0.0  2
 DMT  Var_02  CE    CD1  CG2  CB     50.31  30.0  3
 DMT  Var_03  CZ    CE   CD1  CG2  -122.65  30.0  3
 DMT  Var_04  HCN1  CN   N    CA   -171.86  30.0  3
 DMT  Var_05  HD21  CD2  CG2  CB   -170.68  30.0  3
 DMT  Var_06  HD31  CD3  CG2  CB    171.96  30.0  3
 DMT  Var_07  HH1   CH   CZ   CE   -120.44  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
 DMT  chir_01  CA  N    C    CB  positiv
 DMT  chir_02  CB  OG1  CG2  CA  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
 DMT  plan-1  CA   0.020
 DMT  plan-1  C    0.020
 DMT  plan-1  O    0.020
 DMT  plan-1  OXT  0.020
 DMT  plan-2  CD1  0.020
 DMT  plan-2  CE   0.020
 DMT  plan-2  CZ   0.020
 DMT  plan-2  CH   0.020
 DMT  plan-2  HE   0.020
 DMT  plan-2  HZ   0.020

