# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:47:51 2021
#   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  25  14  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.792   9.5129  -17.2787  10.5491
 MDO  CA    C  CH1   0  -0.219   8.9292  -17.8640  11.7548
 MDO  C1    C  CR5   0   0.569   9.7141  -19.1006  12.0847
 MDO  CB    C  CH3   0  -0.649   7.4684  -18.1968  11.5043
 MDO  N2    N  N     0  -0.464   9.4214  -20.2803  11.6747
 MDO  CA2   C  CR5   0   0.138  10.4253  -21.1259  12.1462
 MDO  C2    C  CR5   0   0.528  11.4052  -20.3146  12.9151
 MDO  O2    O  O     0  -0.428  12.4255  -20.6281  13.4842
 MDO  CB2   C  C2    0  -0.570  10.5097  -22.4405  11.9527
 MDO  N3    N  NR5   0  -0.559  10.8723  -19.0466  12.8496
 MDO  CA3   C  CH2   0  -0.466  11.5097  -17.9143  13.4515
 MDO  C     C  C     0   0.552  12.6611  -17.4094  12.6065
 MDO  O     O  O     0  -0.429  12.8924  -17.7861  11.4881
 MDO  OXT   O  OH1   0  -0.581  13.3573  -16.4951  13.2563
 MDO  H     H  HNH2  0   0.361   9.0051  -16.4310  10.3257
 MDO  H2    H  HNH2  0   0.349  10.4684  -16.9865  10.7126
 MDO  HCA   H  HCH1  0   0.247   8.9758  -17.1914  12.6225
 MDO  HB1   H  HCH3  0   0.237   7.0052  -18.6263  12.3913
 MDO  HB2   H  HCH3  0   0.240   6.9255  -17.2854  11.2521
 MDO  HB3   H  HCH3  0   0.234   7.3627  -18.9015  10.6816
 MDO  HB21  H  H     0   0.278   9.7590  -22.9731  11.3855
 MDO  HB22  H  H     0   0.278  11.3346  -23.0072  12.3614
 MDO  HA31  H  HCH2  0   0.330  10.7903  -17.1066  13.5975
 MDO  HA32  H  HCH2  0   0.325  11.8729  -18.1841  14.4448
 MDO  HXT   H  HOH1  0   0.491  14.0764  -16.1567  12.7007

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  1.462  0.020  1.462
 MDO  CA   C1    single  1.501  0.020  1.501
 MDO  CA   CB    single  1.519  0.020  1.519
 MDO  C1   N2    double  1.283  0.020  1.283
 MDO  C1   N3    single  1.389  0.020  1.389
 MDO  N2   CA2   single  1.395  0.020  1.395
 MDO  CA2  C2    single  1.486  0.020  1.486
 MDO  CA2  CB2   double  1.331  0.020  1.331
 MDO  C2   O2    double  1.210  0.020  1.210
 MDO  C2   N3    single  1.377  0.020  1.377
 MDO  N3   CA3   single  1.432  0.020  1.432
 MDO  CA3  C     single  1.515  0.020  1.515
 MDO  C    O     double  1.203  0.020  1.203
 MDO  C    OXT   single  1.320  0.020  1.320
 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
 MDO  OXT  HXT   single  0.850  0.020  0.980

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     105.50  3.000
 MDO  H2    N    CA    111.05  3.000
 MDO  H     N    CA    108.47  3.000
 MDO  HCA   CA   CB    107.76  3.000
 MDO  HCA   CA   C1    107.97  3.000
 MDO  CB    CA   C1    111.01  3.000
 MDO  HCA   CA   N     112.91  3.000
 MDO  CB    CA   N     109.61  3.000
 MDO  C1    CA   N     107.59  3.000
 MDO  N3    C1   N2    113.70  3.000
 MDO  N3    C1   CA    121.66  3.000
 MDO  N2    C1   CA    124.61  3.000
 MDO  HB3   CB   HB2   108.54  3.000
 MDO  HB3   CB   HB1   108.60  3.000
 MDO  HB2   CB   HB1   107.84  3.000
 MDO  HB3   CB   CA    111.09  3.000
 MDO  HB2   CB   CA    109.50  3.000
 MDO  HB1   CB   CA    111.17  3.000
 MDO  CA2   N2   C1    106.58  3.000
 MDO  CB2   CA2  C2    124.91  3.000
 MDO  CB2   CA2  N2    126.53  3.000
 MDO  C2    CA2  N2    108.56  3.000
 MDO  N3    C2   O2    125.98  3.000
 MDO  N3    C2   CA2   102.88  3.000
 MDO  O2    C2   CA2   131.14  3.000
 MDO  HB22  CB2  HB21  118.03  3.000
 MDO  HB22  CB2  CA2   120.73  3.000
 MDO  HB21  CB2  CA2   121.23  3.000
 MDO  CA3   N3   C2    122.40  3.000
 MDO  CA3   N3   C1    129.30  3.000
 MDO  C2    N3   C1    108.25  3.000
 MDO  HA32  CA3  HA31  106.29  3.000
 MDO  HA32  CA3  C     109.70  3.000
 MDO  HA31  CA3  C     109.21  3.000
 MDO  HA32  CA3  N3    109.58  3.000
 MDO  HA31  CA3  N3    110.36  3.000
 MDO  C     CA3  N3    111.56  3.000
 MDO  OXT   C    O     124.98  3.000
 MDO  OXT   C    CA3   110.92  3.000
 MDO  O     C    CA3   124.10  3.000
 MDO  HXT   OXT  C     110.52  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  CONST_13  HB21  CB2  CA2  N2     0.00   0.0  0
 MDO  CONST_14  HB22  CB2  CA2  N2   180.00   0.0  0
 MDO  CONST_15  HXT   OXT  C    CA3  180.00   0.0  0
 MDO  Var_01    C     CA3  N3   C1   -98.53  30.0  3
 MDO  Var_02    O     C    CA3  N3     9.82  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-1  HB21  0.020
 MDO  plan-1  HB22  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
 MDO  plan-2  HXT   0.020

