# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:55:00 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: methyl (2S)-amino(3,5-dihydroxyphenyl)ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)c1cc(O)cc(O)c1
#
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
 MDF  MDF  'methyl (2S)-amino(3,5-dihydroxyphenyl)ethanoate'  L-peptide  25  14  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MDF
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
 MDF  N    N  NH2   0  -0.767  25.0296  19.8315  16.9202
 MDF  CA   C  CH1   0  -0.303  25.9618  20.2140  17.9541
 MDF  CG   C  CR6   0   0.181  27.1611  19.2873  17.9733
 MDF  CD1  C  CR16  0  -0.439  27.4044  18.4930  19.0806
 MDF  CD2  C  CR16  0  -0.454  28.0038  19.2360  16.8654
 MDF  CE1  C  CR6   0   0.391  28.5025  17.6317  19.0822
 MDF  CE2  C  CR6   0   0.390  29.0926  18.3707  16.8740
 MDF  CZ   C  CR16  0  -0.479  29.3469  17.5662  17.9821
 MDF  OH1  O  OH1   0  -0.629  28.6990  16.8829  20.1825
 MDF  OH2  O  OH1   0  -0.627  29.9449  18.2700  15.8372
 MDF  C    C  C     0   0.567  26.4668  21.6520  17.8475
 MDF  O    O  O     0  -0.436  26.3287  22.3544  16.8792
 MDF  OXT  O  O2    0  -0.445  27.0877  22.0253  18.9557
 MDF  CH3  C  CH3   0  -0.423  27.6438  23.3398  18.9929
 MDF  H    H  HNH2  0   0.352  25.4232  19.9978  16.0020
 MDF  H2   H  HNH2  0   0.358  24.1978  20.4061  16.9768
 MDF  HA   H  HCH1  0   0.290  25.4507  20.1255  18.9169
 MDF  HD1  H  HCR6  0   0.257  26.7502  18.5307  19.9427
 MDF  HD2  H  HCR6  0   0.265  27.8212  19.8640  15.9993
 MDF  HZ   H  HCR6  0   0.274  30.2020  16.8989  17.9752
 MDF  HH1  H  HOH1  0   0.474  29.4724  16.3174  20.0748
 MDF  HH2  H  HOH1  0   0.474  29.6771  18.8587  15.1222
 MDF  H31  H  HCH3  0   0.239  26.8753  24.1011  18.8603
 MDF  H32  H  HCH3  0   0.239  28.4116  23.4684  18.2303
 MDF  H33  H  HCH3  0   0.251  28.0913  23.4475  19.9765

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
 MDF  N    CA   single    1.458  0.019  1.458
 MDF  N    H    single    0.860  0.020  0.860
 MDF  N    H2   single    0.890  0.020  1.040
 MDF  CA   CG   single    1.516  0.020  1.516
 MDF  CA   C    single    1.525  0.021  1.525
 MDF  CA   HA   single    0.970  0.020  0.970
 MDF  CG   CD1  aromatic  1.384  0.020  1.384
 MDF  CG   CD2  aromatic  1.393  0.020  1.393
 MDF  CD1  CE1  aromatic  1.396  0.020  1.396
 MDF  CD1  HD1  single    0.930  0.020  1.080
 MDF  CD2  CE2  aromatic  1.391  0.020  1.391
 MDF  CD2  HD2  single    0.930  0.020  1.080
 MDF  CE1  CZ   aromatic  1.388  0.020  1.388
 MDF  CE1  OH1  single    1.345  0.020  1.345
 MDF  CE2  CZ   aromatic  1.393  0.020  1.393
 MDF  CE2  OH2  single    1.346  0.020  1.346
 MDF  CZ   HZ   single    0.930  0.020  1.080
 MDF  OH1  HH1  single    0.850  0.020  0.980
 MDF  OH2  HH2  single    0.850  0.020  0.980
 MDF  C    O    double    1.231  0.020  1.231
 MDF  C    OXT  single    1.324  0.020  1.324
 MDF  OXT  CH3  single    1.428  0.020  1.428
 MDF  CH3  H31  single    0.970  0.020  1.090
 MDF  CH3  H32  single    0.970  0.020  1.090
 MDF  CH3  H33  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
 MDF  H2   N    H    106.07  3.000
 MDF  H2   N    CA   109.88  3.000
 MDF  H    N    CA   114.00  3.000
 MDF  HA   CA   C    109.00  3.000
 MDF  HA   CA   CG   108.01  3.000
 MDF  C    CA   CG   108.35  3.000
 MDF  HA   CA   N    110.00  3.000
 MDF  C    CA   N    111.00  2.800
 MDF  CG   CA   N    110.98  3.000
 MDF  CD2  CG   CD1  120.58  3.000
 MDF  CD2  CG   CA   119.42  3.000
 MDF  CD1  CG   CA   120.00  3.000
 MDF  HD1  CD1  CE1  119.73  3.000
 MDF  HD1  CD1  CG   120.71  3.000
 MDF  CE1  CD1  CG   119.56  3.000
 MDF  HD2  CD2  CE2  119.78  3.000
 MDF  HD2  CD2  CG   120.77  3.000
 MDF  CE2  CD2  CG   119.45  3.000
 MDF  OH1  CE1  CZ   122.20  3.000
 MDF  OH1  CE1  CD1  117.35  3.000
 MDF  CZ   CE1  CD1  120.45  3.000
 MDF  OH2  CE2  CZ   117.01  3.000
 MDF  OH2  CE2  CD2  122.52  3.000
 MDF  CZ   CE2  CD2  120.48  3.000
 MDF  HZ   CZ   CE2  119.62  3.000
 MDF  HZ   CZ   CE1  120.90  3.000
 MDF  CE2  CZ   CE1  119.48  3.000
 MDF  HH1  OH1  CE1  110.63  3.000
 MDF  HH2  OH2  CE2  110.47  3.000
 MDF  OXT  C    O    124.23  3.000
 MDF  OXT  C    CA   111.22  3.000
 MDF  O    C    CA   120.80  1.700
 MDF  CH3  OXT  C    117.64  3.000
 MDF  H33  CH3  H32  109.37  3.000
 MDF  H33  CH3  H31  109.36  3.000
 MDF  H32  CH3  H31  109.22  3.000
 MDF  H33  CH3  OXT  105.98  3.000
 MDF  H32  CH3  OXT  111.40  3.000
 MDF  H31  CH3  OXT  111.43  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
 MDF  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 MDF  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 MDF  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 MDF  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 MDF  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 MDF  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 MDF  CONST_07  CE1  CD1  CG   CA   180.00   0.0  0
 MDF  CONST_08  CE2  CD2  CG   CA   180.00   0.0  0
 MDF  CONST_09  OH1  CE1  CD1  CG   180.00   0.0  0
 MDF  CONST_10  OH2  CE2  CD2  CG   180.00   0.0  0
 MDF  CONST_11  OH2  CE2  CZ   CE1  180.00   0.0  0
 MDF  CONST_12  OH1  CE1  CZ   CE2  180.00   0.0  0
 MDF  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 MDF  CONST_14  HZ   CZ   CE1  CD1  180.00   0.0  0
 MDF  CONST_15  HD1  CD1  CG   CD2  180.00   0.0  0
 MDF  Var_01    H31  CH3  OXT  C     60.57  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
 MDF  chir_01  CA  N  CG  C  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
 MDF  plan-1  CA   0.020
 MDF  plan-1  CG   0.020
 MDF  plan-1  CD1  0.020
 MDF  plan-1  CD2  0.020
 MDF  plan-1  CE1  0.020
 MDF  plan-1  CE2  0.020
 MDF  plan-1  CZ   0.020
 MDF  plan-1  OH1  0.020
 MDF  plan-1  OH2  0.020
 MDF  plan-1  HD1  0.020
 MDF  plan-1  HD2  0.020
 MDF  plan-1  HZ   0.020
 MDF  plan-2  CA   0.020
 MDF  plan-2  C    0.020
 MDF  plan-2  O    0.020
 MDF  plan-2  OXT  0.020

