# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 15:22:06 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-[(2S)-2-amino-3-phenylpropyl]-D-methionine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@@H](NC[C@@H](N)Cc1ccccc1)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
 5DM  5DM  N-[(2S)-2-amino-3-phenylpropyl]-D-methionine  peptide  40  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5DM
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
 5DM  O     O  O      0  -0.597   1.9666  -3.0945  -0.3676
 5DM  C1    C  C      0   0.398   2.4639  -2.4516   0.5735
 5DM  N1    N  NH1    0  -0.595   1.0184  -0.5204  -0.0889
 5DM  SD    S  S2     0  -0.044   5.0067   1.9682  -0.3824
 5DM  CE    C  CH3    0  -0.764   4.6779   3.7321  -0.1767
 5DM  CA1   C  CH1    0  -0.162   2.2093  -0.9242   0.6308
 5DM  CB1   C  CH2    0  -0.440   3.4467  -0.2316   0.0502
 5DM  CG1   C  CH2    0  -0.559   3.4203   1.2857   0.1804
 5DM  C     C  CH2    0  -0.236  -0.2028  -1.0086   0.5166
 5DM  N     N  NH2    0  -0.778  -1.5285  -0.3325  -1.4295
 5DM  CA    C  CH1    0  -0.130  -1.4422  -0.2749   0.0189
 5DM  CB    C  CH2    0  -0.509  -2.6808  -0.8267   0.7529
 5DM  CG    C  CR6    0   0.130  -3.9322  -0.0677   0.4209
 5DM  CZ    C  CR16   0  -0.273  -6.2207   1.4086  -0.2477
 5DM  CD1   C  CR16   0  -0.323  -4.8418  -0.5456  -0.5201
 5DM  CD2   C  CR16   0  -0.303  -4.1880   1.1665   1.0188
 5DM  CE1   C  CR16   0  -0.242  -5.9781   0.1830  -0.8518
 5DM  CE2   C  CR16   0  -0.240  -5.3200   1.8986   0.6907
 5DM  HN1   H  HNH1   0   0.333   0.9702   0.4916  -0.1021
 5DM  HE    H  HCH3   0   0.260   3.8419   4.0510  -0.7980
 5DM  HEA   H  HCH3   0   0.260   4.4659   3.9734   0.8640
 5DM  HEB   H  HCH3   0   0.272   5.5688   4.2755  -0.4865
 5DM  HA1   H  HCH1   0   0.175   2.1442  -0.6500   1.6998
 5DM  HB1   H  HCH2   0   0.234   4.3250  -0.6164   0.5733
 5DM  HB1A  H  HCH2   0   0.228   3.5523  -0.5081  -1.0032
 5DM  HG1   H  HCH2   0   0.256   3.2543   1.5786   1.2204
 5DM  HG1A  H  HCH2   0   0.256   2.6275   1.7306  -0.4249
 5DM  H     H  HCH2   0   0.211  -0.3069  -2.0766   0.3035
 5DM  HA    H  HCH2   0   0.183  -0.1846  -0.9144   1.6162
 5DM  HN    H  HNH2   0   0.332  -1.5719  -1.3004  -1.7292
 5DM  HNA   H  HNH2   0   0.344  -2.3933   0.0938  -1.7415
 5DM  HAA   H  HCH1   0   0.220  -1.3397   0.7827   0.2967
 5DM  HB    H  HCH2   0   0.237  -2.8020  -1.8826   0.4916
 5DM  HBA   H  HCH2   0   0.238  -2.5024  -0.7846   1.8313
 5DM  HZ    H  HCR6   0   0.252  -7.1053   1.9775  -0.5039
 5DM  HD1   H  HCR6   0   0.247  -4.6643  -1.5054  -0.9913
 5DM  HD2   H  HCR6   0   0.245  -3.4936   1.5587   1.7534
 5DM  HE1   H  HCR6   0   0.253  -6.6737  -0.2101  -1.5824
 5DM  HE2   H  HCR6   0   0.252  -5.5015   2.8530   1.1685
 5DM  OXT   O  OC    -1  -0.621   3.1999  -2.9003   1.4773

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
 5DM  O    C1    deloc     1.244  0.020  1.244
 5DM  C1   CA1   single    1.550  0.020  1.550
 5DM  N1   CA1   single    1.449  0.020  1.449
 5DM  N1   C     single    1.448  0.020  1.448
 5DM  N1   HN1   single    0.890  0.020  1.040
 5DM  SD   CE    single    1.806  0.020  1.806
 5DM  SD   CG1   single    1.816  0.020  1.816
 5DM  CE   HE    single    0.970  0.020  1.090
 5DM  CE   HEA   single    0.970  0.020  1.090
 5DM  CE   HEB   single    0.970  0.020  1.090
 5DM  CA1  CB1   single    1.532  0.020  1.532
 5DM  CA1  HA1   single    0.970  0.020  1.090
 5DM  CB1  CG1   single    1.523  0.020  1.523
 5DM  CB1  HB1   single    0.970  0.020  1.090
 5DM  CB1  HB1A  single    0.970  0.020  1.090
 5DM  CG1  HG1   single    0.970  0.020  1.090
 5DM  CG1  HG1A  single    0.970  0.020  1.090
 5DM  C    CA    single    1.525  0.021  1.525
 5DM  C    H     single    0.970  0.020  1.090
 5DM  C    HA    single    0.970  0.020  1.090
 5DM  N    CA    single    1.458  0.019  1.458
 5DM  N    HN    single    0.890  0.020  1.040
 5DM  N    HNA   single    0.890  0.020  1.040
 5DM  CA   CB    single    1.521  0.033  1.521
 5DM  CA   HAA   single    0.970  0.020  1.090
 5DM  CB   CG    single    1.501  0.020  1.501
 5DM  CB   HB    single    0.970  0.020  1.090
 5DM  CB   HBA   single    0.970  0.020  1.090
 5DM  CG   CD1   aromatic  1.393  0.020  1.393
 5DM  CG   CD2   aromatic  1.395  0.020  1.395
 5DM  CZ   CE1   aromatic  1.388  0.020  1.388
 5DM  CZ   CE2   aromatic  1.390  0.020  1.390
 5DM  CZ   HZ    single    0.930  0.020  1.080
 5DM  CD1  CE1   aromatic  1.390  0.020  1.390
 5DM  CD1  HD1   single    0.930  0.020  1.080
 5DM  CD2  CE2   aromatic  1.387  0.020  1.387
 5DM  CD2  HD2   single    0.930  0.020  1.080
 5DM  CE1  HE1   single    0.930  0.020  1.080
 5DM  CE2  HE2   single    0.930  0.020  1.080
 5DM  C1   OXT   deloc     1.249  0.020  1.249

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
 5DM  OXT   C1   CA1  115.10  3.000
 5DM  OXT   C1   O    126.70  3.000
 5DM  CA1   C1   O    118.16  3.000
 5DM  HN1   N1   C    107.58  3.000
 5DM  HN1   N1   CA1  108.89  3.000
 5DM  C     N1   CA1  113.05  3.000
 5DM  CG1   SD   CE    99.95  3.000
 5DM  HEB   CE   HEA  108.70  3.000
 5DM  HEB   CE   HE   108.63  3.000
 5DM  HEA   CE   HE   109.31  3.000
 5DM  HEB   CE   SD   107.83  3.000
 5DM  HEA   CE   SD   111.14  3.000
 5DM  HE    CE   SD   111.14  3.000
 5DM  HA1   CA1  CB1  107.57  3.000
 5DM  HA1   CA1  N1   111.27  3.000
 5DM  CB1   CA1  N1   110.46  3.000
 5DM  HA1   CA1  C1   106.85  3.000
 5DM  CB1   CA1  C1   107.39  3.000
 5DM  N1    CA1  C1   113.04  3.000
 5DM  HB1A  CB1  HB1  107.12  3.000
 5DM  HB1A  CB1  CG1  109.61  3.000
 5DM  HB1   CB1  CG1  108.90  3.000
 5DM  HB1A  CB1  CA1  109.18  3.000
 5DM  HB1   CB1  CA1  107.97  3.000
 5DM  CG1   CB1  CA1  113.83  3.000
 5DM  HG1A  CG1  HG1  107.93  3.000
 5DM  HG1A  CG1  CB1  111.77  3.000
 5DM  HG1   CG1  CB1  110.54  3.000
 5DM  HG1A  CG1  SD   108.01  3.000
 5DM  HG1   CG1  SD   109.07  3.000
 5DM  CB1   CG1  SD   109.44  3.000
 5DM  HA    C    H    106.20  3.000
 5DM  HA    C    CA   110.00  3.000
 5DM  H     C    CA   109.21  3.000
 5DM  HA    C    N1   111.96  3.000
 5DM  H     C    N1   109.14  3.000
 5DM  CA    C    N1   112.77  3.000
 5DM  HNA   N    HN   105.89  3.000
 5DM  HNA   N    CA   109.95  3.000
 5DM  HN    N    CA   109.58  3.000
 5DM  HAA   CA   CB   107.41  3.000
 5DM  HAA   CA   N    107.22  3.000
 5DM  CB    CA   N    110.40  1.500
 5DM  HAA   CA   C    107.77  3.000
 5DM  CB    CA   C    110.50  1.500
 5DM  N     CA   C    111.00  2.800
 5DM  HBA   CB   HB   106.90  3.000
 5DM  HBA   CB   CG   109.55  3.000
 5DM  HB    CB   CG   110.05  3.000
 5DM  HBA   CB   CA   108.93  3.000
 5DM  HB    CB   CA   108.70  3.000
 5DM  CG    CB   CA   112.55  3.000
 5DM  CD2   CG   CD1  118.24  3.000
 5DM  CD2   CG   CB   120.37  3.000
 5DM  CD1   CG   CB   121.35  3.000
 5DM  HZ    CZ   CE2  120.27  3.000
 5DM  HZ    CZ   CE1  120.27  3.000
 5DM  CE2   CZ   CE1  119.47  3.000
 5DM  HD1   CD1  CE1  119.63  3.000
 5DM  HD1   CD1  CG   119.37  3.000
 5DM  CE1   CD1  CG   121.00  3.000
 5DM  HD2   CD2  CE2  119.46  3.000
 5DM  HD2   CD2  CG   119.54  3.000
 5DM  CE2   CD2  CG   121.01  3.000
 5DM  HE1   CE1  CD1  119.73  3.000
 5DM  HE1   CE1  CZ   120.14  3.000
 5DM  CD1   CE1  CZ   120.13  3.000
 5DM  HE2   CE2  CD2  119.84  3.000
 5DM  HE2   CE2  CZ   120.01  3.000
 5DM  CD2   CE2  CZ   120.15  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
 5DM  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 5DM  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 5DM  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 5DM  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 5DM  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 5DM  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 5DM  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 5DM  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 5DM  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 5DM  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 5DM  CONST_11  HD1  CD1  CE1  CZ   180.00   0.0  0
 5DM  CONST_12  HD2  CD2  CE2  CZ   180.00   0.0  0
 5DM  CONST_13  HZ   CZ   CE1  CD1  180.00   0.0  0
 5DM  Var_01    CD1  CG   CB   CA    99.21  30.0  2
 5DM  Var_02    CA1  CB1  CG1  SD   174.13  30.0  2
 5DM  Var_03    CB1  CG1  SD   CE   178.16  30.0  3
 5DM  Var_04    CA   C    N1   CA1  163.47  30.0  3
 5DM  Var_05    HE   CE   SD   CG1  -60.97  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
 5DM  chir_01  CA1  C1  N1  CB1  positiv
 5DM  chir_02  CA   N   C   CB   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
 5DM  plan-1  CB   0.020
 5DM  plan-1  CG   0.020
 5DM  plan-1  CZ   0.020
 5DM  plan-1  CD1  0.020
 5DM  plan-1  CD2  0.020
 5DM  plan-1  CE1  0.020
 5DM  plan-1  CE2  0.020
 5DM  plan-1  HZ   0.020
 5DM  plan-1  HD1  0.020
 5DM  plan-1  HD2  0.020
 5DM  plan-1  HE1  0.020
 5DM  plan-1  HE2  0.020
 5DM  plan-2  O    0.020
 5DM  plan-2  C1   0.020
 5DM  plan-2  CA1  0.020
 5DM  plan-2  OXT  0.020

