# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 19:29:44 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-butyl-2,4,5-trideoxy-2-(methylamino)-L-xylonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@@H](C)[C@@H](O)[C@H](NC)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
 TMD  TMD  '4-butyl-2,4,5-trideoxy-2-(methylamino)-L-xylonic acid'  L-peptide  34  14  .  2012-08-28  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TMD
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
 TMD  N     N  NH1    0  -0.589  5.4396  34.7860  19.7918
 TMD  CN    C  CH3    0  -0.511  4.8778  36.1205  19.7194
 TMD  CA    C  CH1    0  -0.259  6.6478  34.5013  19.0372
 TMD  C     C  C      0   0.418  7.9356  35.1195  19.6542
 TMD  O     O  O      0  -0.592  7.8307  35.8146  20.6807
 TMD  OXT   O  OC    -1  -0.617  8.9972  34.8217  19.0667
 TMD  CB    C  CH1    0   0.074  6.6100  34.7736  17.5210
 TMD  CZ    C  CH2    0  -0.412  6.1742  34.5322  12.9843
 TMD  CH    C  CH3    0  -0.659  7.3257  34.1407  12.0692
 TMD  OG2   O  OH1    0  -0.680  6.7021  36.1754  17.3285
 TMD  CG1   C  CH1    0  -0.249  5.3806  34.1713  16.8237
 TMD  H     H  HNH1   0   0.335  4.7250  34.1143  19.5440
 TMD  HN1   H  HCH3   0   0.204  4.0687  36.2036  20.4487
 TMD  HN2   H  HCH3   0   0.219  5.6350  36.8532  19.9862
 TMD  HN3   H  HCH3   0   0.183  4.4662  36.4066  18.7444
 TMD  HA    H  HCH1   0   0.229  6.7916  33.4182  19.1335
 TMD  HB    H  HCH1   0   0.187  7.4983  34.2823  17.1011
 TMD  HE2   H  HCH2   0   0.209  7.3574  34.6479  14.7681
 TMD  HE3   H  HCH2   0   0.215  6.5993  33.0932  14.5182
 TMD  HZ2   H  HCH2   0   0.209  5.2548  34.0437  12.6471
 TMD  HZ3   H  HCH2   0   0.209  5.9914  35.6084  12.9042
 TMD  HH1   H  HCH3   0   0.224  7.1239  34.4101  11.0318
 TMD  HH2   H  HCH3   0   0.215  8.2510  34.6385  12.3653
 TMD  HH3   H  HCH3   0   0.215  7.5071  33.0648  12.1017
 TMD  HG2   H  HOH1   0   0.443  6.9373  36.3481  16.4126
 TMD  HG1   H  HCH1   0   0.216  4.4799  34.5581  17.3143
 TMD  CD1   C  CH2    0  -0.444  5.2685  34.5824  15.3491
 TMD  CD2   C  CH3    0  -0.680  5.3688  32.6485  16.9649
 TMD  HD13  H  HCH2   0   0.215  5.1246  35.6654  15.2774
 TMD  CE    C  CH2    0  -0.422  6.4258  34.1712  14.4436
 TMD  HD12  H  HCH2   0   0.219  4.3455  34.1455  14.9532
 TMD  HD21  H  HCH3   0   0.227  4.5870  32.2077  16.3437
 TMD  HD22  H  HCH3   0   0.218  6.3189  32.2041  16.6605
 TMD  HD23  H  HCH3   0   0.230  5.1795  32.3314  17.9910

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
 TMD  N    CN    single  1.450  0.020  1.450
 TMD  N    CA    single  1.458  0.019  1.458
 TMD  N    H     single  0.860  0.020  0.860
 TMD  CN   HN1   single  0.970  0.020  1.090
 TMD  CN   HN2   single  0.970  0.020  1.090
 TMD  CN   HN3   single  0.970  0.020  1.090
 TMD  CA   C     single  1.525  0.021  1.525
 TMD  CA   CB    single  1.540  0.027  1.540
 TMD  CA   HA    single  0.970  0.020  0.970
 TMD  C    O     deloc   1.231  0.020  1.231
 TMD  C    OXT   deloc   1.249  0.020  1.249
 TMD  CB   OG2   single  1.418  0.020  1.418
 TMD  CB   CG1   single  1.536  0.020  1.536
 TMD  CB   HB    single  0.970  0.020  1.090
 TMD  CD1  CE    single  1.526  0.020  1.526
 TMD  CD1  CG1   single  1.535  0.020  1.535
 TMD  CD1  HD13  single  0.970  0.020  1.090
 TMD  CD1  HD12  single  0.970  0.020  1.090
 TMD  CD2  CG1   single  1.529  0.020  1.529
 TMD  CD2  HD21  single  0.970  0.020  1.090
 TMD  CD2  HD22  single  0.970  0.020  1.090
 TMD  CD2  HD23  single  0.970  0.020  1.090
 TMD  CE   CZ    single  1.524  0.020  1.524
 TMD  CE   HE2   single  0.970  0.020  1.090
 TMD  CE   HE3   single  0.970  0.020  1.090
 TMD  CZ   CH    single  1.522  0.020  1.522
 TMD  CZ   HZ2   single  0.970  0.020  1.090
 TMD  CZ   HZ3   single  0.970  0.020  1.090
 TMD  CH   HH1   single  0.970  0.020  1.090
 TMD  CH   HH2   single  0.970  0.020  1.090
 TMD  CH   HH3   single  0.970  0.020  1.090
 TMD  OG2  HG2   single  0.850  0.020  0.980
 TMD  CG1  HG1   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
 TMD  H     N    CA    114.00  3.000
 TMD  H     N    CN    108.98  3.000
 TMD  CA    N    CN    118.48  3.000
 TMD  HN3   CN   HN2   107.70  3.000
 TMD  HN3   CN   HN1   107.21  3.000
 TMD  HN2   CN   HN1   107.51  3.000
 TMD  HN3   CN   N     115.48  3.000
 TMD  HN2   CN   N     109.77  3.000
 TMD  HN1   CN   N     108.88  3.000
 TMD  HA    CA   CB    109.00  3.000
 TMD  HA    CA   C     109.00  3.000
 TMD  CB    CA   C     109.10  2.200
 TMD  HA    CA   N     110.00  3.000
 TMD  CB    CA   N     111.50  1.700
 TMD  C     CA   N     111.00  2.800
 TMD  OXT   C    O     126.36  3.000
 TMD  OXT   C    CA    114.97  3.000
 TMD  O     C    CA    120.80  1.700
 TMD  HB    CB   CG1   107.35  3.000
 TMD  HB    CB   OG2   109.74  3.000
 TMD  CG1   CB   OG2   112.20  3.000
 TMD  HB    CB   CA    106.10  3.000
 TMD  CG1   CB   CA    113.39  3.000
 TMD  OG2   CB   CA    107.86  3.000
 TMD  HZ3   CZ   HZ2   106.02  3.000
 TMD  HZ3   CZ   CH    109.59  3.000
 TMD  HZ2   CZ   CH    109.60  3.000
 TMD  HZ3   CZ   CE    109.31  3.000
 TMD  HZ2   CZ   CE    109.15  3.000
 TMD  CH    CZ   CE    112.94  3.000
 TMD  HH3   CH   HH2   107.49  3.000
 TMD  HH3   CH   HH1   107.61  3.000
 TMD  HH2   CH   HH1   107.59  3.000
 TMD  HH3   CH   CZ    111.18  3.000
 TMD  HH2   CH   CZ    111.15  3.000
 TMD  HH1   CH   CZ    111.62  3.000
 TMD  HG2   OG2  CB    108.83  3.000
 TMD  HG1   CG1  CD2   107.67  3.000
 TMD  HG1   CG1  CD1   105.99  3.000
 TMD  CD2   CG1  CD1   110.78  3.000
 TMD  HG1   CG1  CB    108.42  3.000
 TMD  CD2   CG1  CB    110.77  3.000
 TMD  CD1   CG1  CB    112.92  3.000
 TMD  HD12  CD1  HD13  105.07  3.000
 TMD  HD12  CD1  CG1   107.58  3.000
 TMD  HD13  CD1  CG1   109.72  3.000
 TMD  HD12  CD1  CE    108.49  3.000
 TMD  HD13  CD1  CE    109.11  3.000
 TMD  CG1   CD1  CE    116.27  3.000
 TMD  HD23  CD2  HD22  107.15  3.000
 TMD  HD23  CD2  HD21  107.08  3.000
 TMD  HD22  CD2  HD21  107.47  3.000
 TMD  HD23  CD2  CG1   112.19  3.000
 TMD  HD22  CD2  CG1   111.88  3.000
 TMD  HD21  CD2  CG1   110.80  3.000
 TMD  HE3   CE   HE2   105.88  3.000
 TMD  HE3   CE   CZ    108.95  3.000
 TMD  HE2   CE   CZ    108.72  3.000
 TMD  HE3   CE   CD1   110.19  3.000
 TMD  HE2   CE   CD1   110.60  3.000
 TMD  CZ    CE   CD1   112.28  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
 TMD  Var_01  CH   CZ   CE  CD1   179.44  30.0  3
 TMD  Var_02  CG1  CD1  CE  CZ    175.73  30.0  1
 TMD  Var_03  HN1  CN   N   CA   -171.88  30.0  3
 TMD  Var_04  HH1  CH   CZ  CE   -179.90  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
 TMD  chir_01  CA   N    C    CB   positiv
 TMD  chir_02  CB   OG2  CA   CG1  negativ
 TMD  chir_03  CG1  CB   CD1  CD2  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
 TMD  plan-1  CA   0.020
 TMD  plan-1  C    0.020
 TMD  plan-1  O    0.020
 TMD  plan-1  OXT  0.020

