# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:52:10 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-[(2E)-but-2-en-1-yl]-2,4,5-trideoxy-2-(methylamino)-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(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
 BMT  BMT  '4-[(2E)-but-2-en-1-yl]-2,4,5-trideoxy-2-(methylamino)-L-xylonic acid'  L-peptide  32  14  .  2016-04-22  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BMT
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
 BMT  N     N  NH1    0  -0.594  47.0114   99.1518  34.0071
 BMT  CN    C  CH3    0  -0.509  48.3174   98.9372  33.4080
 BMT  CA    C  CH1    0  -0.248  45.9931   99.7770  33.1769
 BMT  C     C  C      0   0.409  45.4529   98.9197  31.9934
 BMT  O     O  O      0  -0.612  44.6163   99.4746  31.2509
 BMT  OXT   O  OC    -1  -0.599  45.8385   97.7364  31.9206
 BMT  CB    C  CH1    0   0.070  46.3544  101.1911  32.7179
 BMT  OG1   O  OH1    0  -0.680  47.2843  101.0998  31.6516
 BMT  CG2   C  CH1    0  -0.236  46.8702  102.0972  33.8445
 BMT  CD1   C  CH3    0  -0.679  45.8042  102.2917  34.9204
 BMT  CD2   C  CH2    0  -0.504  47.3634  103.4505  33.3005
 BMT  CE    C  C1     0  -0.201  46.3598  104.1844  32.4664
 BMT  CZ    C  C1     0  -0.241  46.5531  104.5574  31.2027
 BMT  CH    C  CH3    0  -0.705  45.5609  105.2902  30.3601
 BMT  H     H  HNH1   0   0.332  46.6486   98.2480  34.2783
 BMT  HN1   H  HCH3   0   0.208  48.8760   98.2472  34.0426
 BMT  HN2   H  HCH3   0   0.190  48.2973   98.5151  32.3985
 BMT  HN3   H  HCH3   0   0.206  48.8907   99.8637  33.3714
 BMT  HA    H  HCH1   0   0.229  45.1223   99.9023  33.8348
 BMT  HB    H  HCH1   0   0.194  45.4204  101.6339  32.3484
 BMT  HG1   H  HOH1   0   0.443  47.2098  101.8993  31.1219
 BMT  HG2   H  HCH1   0   0.227  47.7333  101.6194  34.3179
 BMT  HD11  H  HCH3   0   0.226  46.1294  103.0207  35.6647
 BMT  HD12  H  HCH3   0   0.215  44.8607  102.6490  34.5006
 BMT  HD13  H  HCH3   0   0.232  45.5962  101.3608  35.4474
 BMT  HD22  H  HCH2   0   0.235  47.6424  104.0710  34.1594
 BMT  HD23  H  HCH2   0   0.234  48.2822  103.3106  32.7254
 BMT  HE    H  H      0   0.229  45.4079  104.4218  32.9373
 BMT  HZ    H  H      0   0.228  47.5082  104.3298  30.7320
 BMT  HH1   H  HCH3   0   0.234  45.3107  104.7245  29.4601
 BMT  HH2   H  HCH3   0   0.233  44.6360  105.4850  30.9033
 BMT  HH3   H  HCH3   0   0.233  45.9617  106.2484  30.0221

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
 BMT  N    CN    single  1.453  0.020  1.453
 BMT  N    CA    single  1.458  0.019  1.458
 BMT  N    H     single  0.860  0.020  0.860
 BMT  CN   HN1   single  0.970  0.020  1.090
 BMT  CN   HN2   single  0.970  0.020  1.090
 BMT  CN   HN3   single  0.970  0.020  1.090
 BMT  CA   C     single  1.525  0.021  1.525
 BMT  CA   CB    single  1.540  0.027  1.540
 BMT  CA   HA    single  0.970  0.020  0.970
 BMT  C    O     deloc   1.231  0.020  1.231
 BMT  C    OXT   deloc   1.247  0.020  1.247
 BMT  CB   OG1   single  1.418  0.020  1.418
 BMT  CB   CG2   single  1.535  0.020  1.535
 BMT  CB   HB    single  0.970  0.020  1.090
 BMT  OG1  HG1   single  0.850  0.020  0.980
 BMT  CG2  CD1   single  1.527  0.020  1.527
 BMT  CG2  CD2   single  1.540  0.020  1.540
 BMT  CG2  HG2   single  0.970  0.020  1.090
 BMT  CD1  HD11  single  0.970  0.020  1.090
 BMT  CD1  HD12  single  0.970  0.020  1.090
 BMT  CD1  HD13  single  0.970  0.020  1.090
 BMT  CD2  CE    single  1.497  0.020  1.497
 BMT  CD2  HD22  single  0.970  0.020  1.090
 BMT  CD2  HD23  single  0.970  0.020  1.090
 BMT  CE   CZ    double  1.332  0.020  1.332
 BMT  CE   HE    single  0.930  0.020  1.080
 BMT  CZ   CH    single  1.494  0.020  1.494
 BMT  CZ   HZ    single  0.930  0.020  1.080
 BMT  CH   HH1   single  0.970  0.020  1.090
 BMT  CH   HH2   single  0.970  0.020  1.090
 BMT  CH   HH3   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
 BMT  H     N    CA    114.00  3.000
 BMT  H     N    CN    107.53  3.000
 BMT  CA    N    CN    117.22  3.000
 BMT  HN3   CN   HN2   107.85  3.000
 BMT  HN3   CN   HN1   106.72  3.000
 BMT  HN2   CN   HN1   107.57  3.000
 BMT  HN3   CN   N     111.17  3.000
 BMT  HN2   CN   N     114.89  3.000
 BMT  HN1   CN   N     108.28  3.000
 BMT  HA    CA   CB    109.00  3.000
 BMT  HA    CA   C     109.00  3.000
 BMT  CB    CA   C     109.10  2.200
 BMT  HA    CA   N     110.00  3.000
 BMT  CB    CA   N     111.50  1.700
 BMT  C     CA   N     111.00  2.800
 BMT  OXT   C    O     126.46  3.000
 BMT  OXT   C    CA    117.35  3.000
 BMT  O     C    CA    120.80  1.700
 BMT  HB    CB   CG2   107.15  3.000
 BMT  HB    CB   OG1   109.32  3.000
 BMT  CG2   CB   OG1   111.69  3.000
 BMT  HB    CB   CA    105.84  3.000
 BMT  CG2   CB   CA    113.88  3.000
 BMT  OG1   CB   CA    108.73  3.000
 BMT  HG1   OG1  CB    108.05  3.000
 BMT  HG2   CG2  CD2   106.50  3.000
 BMT  HG2   CG2  CD1   107.54  3.000
 BMT  CD2   CG2  CD1   111.14  3.000
 BMT  HG2   CG2  CB    108.95  3.000
 BMT  CD2   CG2  CB    111.54  3.000
 BMT  CD1   CG2  CB    110.96  3.000
 BMT  HD13  CD1  HD12  107.47  3.000
 BMT  HD13  CD1  HD11  107.32  3.000
 BMT  HD12  CD1  HD11  107.50  3.000
 BMT  HD13  CD1  CG2   111.42  3.000
 BMT  HD12  CD1  CG2   111.95  3.000
 BMT  HD11  CD1  CG2   110.96  3.000
 BMT  HD23  CD2  HD22  105.72  3.000
 BMT  HD23  CD2  CE    109.46  3.000
 BMT  HD22  CD2  CE    109.25  3.000
 BMT  HD23  CD2  CG2   110.04  3.000
 BMT  HD22  CD2  CG2   107.60  3.000
 BMT  CE    CD2  CG2   114.39  3.000
 BMT  HE    CE   CZ    118.46  3.000
 BMT  HE    CE   CD2   116.89  3.000
 BMT  CZ    CE   CD2   124.65  3.000
 BMT  HZ    CZ   CH    116.19  3.000
 BMT  HZ    CZ   CE    118.63  3.000
 BMT  CH    CZ   CE    125.18  3.000
 BMT  HH3   CH   HH2   107.99  3.000
 BMT  HH3   CH   HH1   106.47  3.000
 BMT  HH2   CH   HH1   107.98  3.000
 BMT  HH3   CH   CZ    111.18  3.000
 BMT  HH2   CH   CZ    111.73  3.000
 BMT  HH1   CH   CZ    111.28  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
 BMT  Var_01  CH   CZ  CE   CD2  -179.97   0.0  2
 BMT  Var_02  CZ   CE  CD2  CG2  -121.65  30.0  3
 BMT  Var_03  HN1  CN  N    CA   -165.71  30.0  3
 BMT  Var_04  HH1  CH  CZ   CE   -121.21  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
 BMT  chir_01  CA   N    C    CB   positiv
 BMT  chir_02  CB   OG1  CA   CG2  negativ
 BMT  chir_03  CG2  CB   CD1  CD2  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
 BMT  plan-1  CA   0.020
 BMT  plan-1  C    0.020
 BMT  plan-1  O    0.020
 BMT  plan-1  OXT  0.020
 BMT  plan-2  CD2  0.020
 BMT  plan-2  CE   0.020
 BMT  plan-2  CZ   0.020
 BMT  plan-2  CH   0.020
 BMT  plan-2  HE   0.020
 BMT  plan-2  HZ   0.020

