# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:23:04 2020
#   Inital geometry file: a 35 line input string
#   Ligand name: 2-oxopropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)C(N)=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
 PYM  PYM  '2-oxopropanamide         '  ligand  11  6  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PYM
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
 PYM  C1    C  C     0   0.435   0.2235  -0.0111  -0.7287
 PYM  N1    N  NH2   0  -0.786  -0.8000  -0.0171  -1.5793
 PYM  O1    O  O     0  -0.459   1.4038   0.0137  -1.0331
 PYM  C2    C  C     0   0.296  -0.1936  -0.0401   0.7544
 PYM  O2    O  O     0  -0.365  -1.3633  -0.0681   1.0479
 PYM  C3    C  CH3   0  -0.766   0.9215  -0.0321   1.7462
 PYM  HN12  H  HNH2  0   0.413  -0.6416  -0.0006  -2.5737
 PYM  HN11  H  HNH2  0   0.414  -1.7514  -0.0365  -1.2523
 PYM  H33   H  HCH3  0   0.267   0.5309  -0.0509   2.7604
 PYM  H32   H  HCH3  0   0.276   1.5723  -0.8945   1.5938
 PYM  H31   H  HCH3  0   0.276   1.5437   0.8541   1.6141

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
 PYM  C1  N1    single  1.331  0.020  1.331
 PYM  C1  O1    double  1.219  0.020  1.219
 PYM  C1  C2    single  1.541  0.020  1.541
 PYM  N1  HN12  single  0.860  0.020  1.020
 PYM  N1  HN11  single  0.860  0.020  1.020
 PYM  C2  O2    double  1.206  0.020  1.206
 PYM  C2  C3    single  1.492  0.020  1.492
 PYM  C3  H33   single  0.970  0.020  1.090
 PYM  C3  H32   single  0.970  0.020  1.090
 PYM  C3  H31   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
 PYM  C2    C1  O1    120.18  3.000
 PYM  C2    C1  N1    114.01  3.000
 PYM  O1    C1  N1    125.81  3.000
 PYM  HN11  N1  HN12  118.03  3.000
 PYM  HN11  N1  C1    121.30  3.000
 PYM  HN12  N1  C1    120.67  3.000
 PYM  C3    C2  O2    124.26  3.000
 PYM  C3    C2  C1    115.93  3.000
 PYM  O2    C2  C1    119.81  3.000
 PYM  H31   C3  H32   106.56  3.000
 PYM  H31   C3  H33   109.38  3.000
 PYM  H32   C3  H33   109.33  3.000
 PYM  H31   C3  C2    110.49  3.000
 PYM  H32   C3  C2    110.40  3.000
 PYM  H33   C3  C2    110.58  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
 PYM  CONST_01  HN12  N1  C1  O1    0.00   0.0  0
 PYM  CONST_02  HN11  N1  C1  O1  180.00   0.0  0
 PYM  Var_01    O2    C2  C1  N1    0.16  30.0  2
 PYM  Var_02    H33   C3  C2  C1  179.82  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
 PYM  plan-1  C1    0.020
 PYM  plan-1  N1    0.020
 PYM  plan-1  O1    0.020
 PYM  plan-1  C2    0.020
 PYM  plan-1  HN12  0.020
 PYM  plan-1  HN11  0.020
 PYM  plan-2  C1    0.020
 PYM  plan-2  C2    0.020
 PYM  plan-2  O2    0.020
 PYM  plan-2  C3    0.020

