# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:09:52 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: (2Z)-2-(methylamino)but-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN\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
 MDH  MDH  '(2Z)-2-(methylamino)but-2-enoic acid'  peptide  16  8  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_MDH
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
 MDH  N    N  NH1    0  -0.638  4.6323   0.9710  3.6274
 MDH  CM   C  CH3    0  -0.529  5.0969  -0.1306  4.4514
 MDH  CA   C  C      0   0.118  3.6140   1.7823  4.1348
 MDH  C    C  C      0   0.368  2.2815   1.0994  4.4744
 MDH  O    O  O      0  -0.594  1.5266   1.6980  5.2645
 MDH  OXT  O  OC    -1  -0.598  2.0557   0.0153  3.9024
 MDH  CB   C  C1     0  -0.325  3.7110   3.1191  4.2157
 MDH  CG   C  CH3    0  -0.708  4.9022   3.9563  3.8675
 MDH  H    H  HNH1   0   0.351  5.4194   1.5156  3.3058
 MDH  HM1  H  HCH3   0   0.223  5.8609  -0.6856  3.9067
 MDH  HM2  H  HCH3   0   0.197  5.5328   0.1853  5.4072
 MDH  HM3  H  HCH3   0   0.233  4.2794  -0.8152  4.6634
 MDH  HB   H  H      0   0.219  2.8244   3.6571  4.5260
 MDH  HG1  H  HCH3   0   0.231  4.8205   4.3960  2.8691
 MDH  HG2  H  HCH3   0   0.233  5.0031   4.7911  4.5632
 MDH  HG3  H  HCH3   0   0.220  5.8425   3.4021  3.8952

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
 MDH  N   CM   single  1.452  0.020  1.452
 MDH  N   CA   single  1.458  0.019  1.458
 MDH  N   H    single  0.860  0.020  0.860
 MDH  CM  HM1  single  0.970  0.020  1.090
 MDH  CM  HM2  single  0.970  0.020  1.090
 MDH  CM  HM3  single  0.970  0.020  1.090
 MDH  CA  C    single  1.525  0.021  1.525
 MDH  CA  CB   double  1.521  0.033  1.521
 MDH  C   O    deloc   1.231  0.020  1.231
 MDH  C   OXT  deloc   1.246  0.020  1.246
 MDH  CB  CG   single  1.497  0.020  1.497
 MDH  CB  HB   single  0.930  0.020  1.080
 MDH  CG  HG1  single  0.970  0.020  1.090
 MDH  CG  HG2  single  0.970  0.020  1.090
 MDH  CG  HG3  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
 MDH  H    N   CA   114.00  3.000
 MDH  H    N   CM   109.91  3.000
 MDH  CA   N   CM   117.88  3.000
 MDH  HM3  CM  HM2  108.07  3.000
 MDH  HM3  CM  HM1  107.69  3.000
 MDH  HM2  CM  HM1  107.66  3.000
 MDH  HM3  CM  N    110.35  3.000
 MDH  HM2  CM  N    113.77  3.000
 MDH  HM1  CM  N    109.09  3.000
 MDH  CB   CA  C    110.50  1.500
 MDH  CB   CA  N    110.40  1.500
 MDH  C    CA  N    111.00  2.800
 MDH  OXT  C   O    126.81  3.000
 MDH  OXT  C   CA   120.80  1.700
 MDH  O    C   CA   120.80  1.700
 MDH  HB   CB  CG   116.13  3.000
 MDH  HB   CB  CA   116.93  3.000
 MDH  CG   CB  CA   126.89  3.000
 MDH  HG3  CG  HG2  107.01  3.000
 MDH  HG3  CG  HG1  106.95  3.000
 MDH  HG2  CG  HG1  106.33  3.000
 MDH  HG3  CG  CB   113.30  3.000
 MDH  HG2  CG  CB   110.68  3.000
 MDH  HG1  CG  CB   112.18  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
 MDH  Var_01  CG   CB  CA  N    -3.61   0.0  2
 MDH  Var_02  O    C   CA  N   159.71  30.0  2
 MDH  Var_03  C    CA  N   CM  -59.65  30.0  2
 MDH  Var_04  HM1  CM  N   CA  178.00  30.0  3
 MDH  Var_05  HG1  CG  CB  CA   98.79  30.0  3

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
 MDH  plan-1  CA   0.020
 MDH  plan-1  C    0.020
 MDH  plan-1  O    0.020
 MDH  plan-1  OXT  0.020
 MDH  plan-2  N    0.020
 MDH  plan-2  CA   0.020
 MDH  plan-2  C    0.020
 MDH  plan-2  CB   0.020
 MDH  plan-2  CG   0.020
 MDH  plan-2  HB   0.020

