# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:38:36 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: {2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C1=NC(=C)C(=O)N1CC(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
 MDO  MDO  '{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  24  14  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MDO
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
 MDO  N     N  NH2    0  -0.785   1.5849   3.0120   0.5394
 MDO  CA    C  CH1    0  -0.194   0.4225   2.1556   0.4019
 MDO  C1    C  CR5    0   0.531   0.8599   0.7320   0.2409
 MDO  CB    C  CH3    0  -0.668  -0.3846   2.5858  -0.8241
 MDO  N2    N  N      0  -0.467   2.0195   0.3736  -0.1883
 MDO  CA2   C  CR5    0   0.133   2.0045  -1.0198  -0.2150
 MDO  C2    C  CR5    0   0.519   0.6719  -1.4873   0.2581
 MDO  O2    O  O      0  -0.445   0.2351  -2.6109   0.3866
 MDO  CB2   C  C2     0  -0.587   2.9990  -1.8199  -0.5952
 MDO  N3    N  NR5    0  -0.536   0.0178  -0.3202   0.5539
 MDO  CA3   C  CH2    0  -0.476  -1.3733  -0.2994   0.9302
 MDO  C     C  C      0   0.420  -2.3326  -0.6037  -0.2456
 MDO  O     O  O      0  -0.589  -1.8408  -0.6430  -1.3841
 MDO  OXT   O  OC    -1  -0.609  -3.5203  -0.7620   0.0883
 MDO  H     H  HNH2   0   0.353   1.2621   3.9624   0.6729
 MDO  H2    H  HNH2   0   0.349   2.0923   2.7714   1.3816
 MDO  HCA   H  HCH1   0   0.245  -0.2416   2.2027   1.2765
 MDO  HB1   H  HCH3   0   0.243  -0.7650   3.5977  -0.6802
 MDO  HB2   H  HCH3   0   0.234   0.2507   2.5784  -1.7099
 MDO  HB3   H  HCH3   0   0.246  -1.2319   1.9288  -1.0070
 MDO  HB21  H  H      0   0.269   3.9464  -1.4208  -0.9294
 MDO  HB22  H  H      0   0.270   2.8796  -2.8943  -0.5784
 MDO  HA31  H  HCH2   0   0.268  -1.5284  -1.0248   1.7305
 MDO  HA32  H  HCH2   0   0.274  -1.6154   0.6764   1.3525

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
 MDO  N    CA    single  1.450  0.020  1.450
 MDO  CA   C1    single  1.498  0.020  1.498
 MDO  CA   CB    single  1.530  0.020  1.530
 MDO  C1   N2    double  1.287  0.020  1.287
 MDO  C1   N3    single  1.384  0.020  1.384
 MDO  N2   CA2   single  1.394  0.020  1.394
 MDO  CA2  C2    single  1.489  0.020  1.489
 MDO  CA2  CB2   double  1.332  0.020  1.332
 MDO  C2   O2    double  1.212  0.020  1.212
 MDO  C2   N3    single  1.370  0.020  1.370
 MDO  N3   CA3   single  1.441  0.020  1.441
 MDO  CA3  C     single  1.548  0.020  1.548
 MDO  C    O     deloc   1.241  0.020  1.241
 MDO  C    OXT   deloc   1.244  0.020  1.244
 MDO  N    H     single  0.860  0.020  1.020
 MDO  N    H2    single  0.890  0.020  1.040
 MDO  CA   HCA   single  0.970  0.020  1.090
 MDO  CB   HB1   single  0.970  0.020  1.090
 MDO  CB   HB2   single  0.970  0.020  1.090
 MDO  CB   HB3   single  0.970  0.020  1.090
 MDO  CB2  HB21  single  0.930  0.020  1.080
 MDO  CB2  HB22  single  0.930  0.020  1.080
 MDO  CA3  HA31  single  0.970  0.020  1.090
 MDO  CA3  HA32  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
 MDO  H2    N    H     105.85  3.000
 MDO  H2    N    CA    109.89  3.000
 MDO  H     N    CA    108.14  3.000
 MDO  HCA   CA   CB    107.87  3.000
 MDO  HCA   CA   C1    107.62  3.000
 MDO  CB    CA   C1    109.58  3.000
 MDO  HCA   CA   N     112.55  3.000
 MDO  CB    CA   N     109.44  3.000
 MDO  C1    CA   N     109.71  3.000
 MDO  N3    C1   N2    114.32  3.000
 MDO  N3    C1   CA    121.38  3.000
 MDO  N2    C1   CA    124.30  3.000
 MDO  HB3   CB   HB2   108.25  3.000
 MDO  HB3   CB   HB1   108.12  3.000
 MDO  HB2   CB   HB1   108.47  3.000
 MDO  HB3   CB   CA    112.09  3.000
 MDO  HB2   CB   CA    109.99  3.000
 MDO  HB1   CB   CA    109.83  3.000
 MDO  CA2   N2   C1    105.97  3.000
 MDO  CB2   CA2  C2    124.77  3.000
 MDO  CB2   CA2  N2    126.73  3.000
 MDO  C2    CA2  N2    108.50  3.000
 MDO  N3    C2   O2    126.48  3.000
 MDO  N3    C2   CA2   103.20  3.000
 MDO  O2    C2   CA2   130.31  3.000
 MDO  HB22  CB2  HB21  117.94  3.000
 MDO  HB22  CB2  CA2   120.67  3.000
 MDO  HB21  CB2  CA2   121.39  3.000
 MDO  CA3   N3   C2    121.97  3.000
 MDO  CA3   N3   C1    129.46  3.000
 MDO  C2    N3   C1    107.96  3.000
 MDO  HA32  CA3  HA31  106.22  3.000
 MDO  HA32  CA3  C     109.42  3.000
 MDO  HA31  CA3  C     109.78  3.000
 MDO  HA32  CA3  N3    109.17  3.000
 MDO  HA31  CA3  N3    108.61  3.000
 MDO  C     CA3  N3    113.39  3.000
 MDO  OXT   C    O     128.37  3.000
 MDO  OXT   C    CA3   114.38  3.000
 MDO  O     C    CA3   117.24  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
 MDO  CONST_01  C2    CA2  N2   C1     0.00   0.0  0
 MDO  CONST_02  CA2   C2   N3   C1     0.00   0.0  0
 MDO  CONST_03  C2    N3   C1   N2     0.00   0.0  0
 MDO  CONST_04  N3    C2   CA2  N2     0.00   0.0  0
 MDO  CONST_05  N3    C1   N2   CA2    0.00   0.0  0
 MDO  CONST_06  CA2   N2   C1   CA   180.00   0.0  0
 MDO  CONST_07  C2    N3   C1   CA   180.00   0.0  0
 MDO  CONST_08  O2    C2   N3   C1   180.00   0.0  0
 MDO  CONST_09  CA3   N3   C1   N2   180.00   0.0  0
 MDO  CONST_10  CA3   N3   C2   CA2  180.00   0.0  0
 MDO  CONST_11  CA3   N3   C1   CA     0.00   0.0  0
 MDO  CONST_12  CA3   N3   C2   O2     0.00   0.0  0
 MDO  Var_01    C     CA3  N3   C1    98.32  30.0  3
 MDO  Var_02    HB21  CB2  CA2  N2     0.07  30.0  2
 MDO  Var_03    O     C    CA3  N3    -9.73  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
 MDO  chir_01  CA  N  C1  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
 MDO  plan-1  CA   0.020
 MDO  plan-1  C1   0.020
 MDO  plan-1  N2   0.020
 MDO  plan-1  CA2  0.020
 MDO  plan-1  C2   0.020
 MDO  plan-1  O2   0.020
 MDO  plan-1  CB2  0.020
 MDO  plan-1  N3   0.020
 MDO  plan-1  CA3  0.020
 MDO  plan-2  CA3  0.020
 MDO  plan-2  C    0.020
 MDO  plan-2  O    0.020
 MDO  plan-2  OXT  0.020

