# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:14:26 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@@H]1CCCN1
#
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
 LPD  LPD  'L-prolinamide            '  L-peptide  18  8  .  2019-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LPD
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
 LPD  O     O  O     0  -0.477  46.3619  -9.3310  64.7779
 LPD  C     C  C     0   0.524  46.4548  -8.5409  63.8516
 LPD  N2    N  NH2   0  -0.803  47.3446  -8.6866  62.8545
 LPD  CA    C  CH1   0  -0.265  45.5999  -7.2829  63.7528
 LPD  N     N  NH1   0  -0.580  44.4014  -7.4003  64.5634
 LPD  CD    C  CH2   0  -0.285  44.7128  -6.8817  65.9029
 LPD  CG    C  CH2   0  -0.488  46.0950  -6.1997  65.8255
 LPD  CB    C  CH2   0  -0.446  46.3660  -6.0763  64.3278
 LPD  HN21  H  HNH2  0   0.403  47.4148  -8.0252  62.1002
 LPD  HN22  H  HNH2  0   0.395  48.0090  -9.4432  62.8680
 LPD  HA    H  HCH1  0   0.272  45.3278  -7.1206  62.7067
 LPD  H     H  HNH1  0   0.353  43.6869  -6.8218  64.1443
 LPD  HD3   H  HCH2  0   0.223  43.9377  -6.1803  66.2149
 LPD  HD2   H  HCH2  0   0.216  44.7249  -7.6882  66.6380
 LPD  HG3   H  HCH2  0   0.241  46.1063  -5.2327  66.3281
 LPD  HG2   H  HCH2  0   0.234  46.8581  -6.8171  66.3016
 LPD  HB2   H  HCH2  0   0.241  47.4278  -6.0622  64.0780
 LPD  HB3   H  HCH2  0   0.242  45.9231  -5.1616  63.9283

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
 LPD  O   C     double  1.231  0.020  1.231
 LPD  C   N2    single  1.344  0.020  1.344
 LPD  C   CA    single  1.525  0.021  1.525
 LPD  N2  HN21  single  0.860  0.020  1.020
 LPD  N2  HN22  single  0.860  0.020  1.020
 LPD  CA  N     single  1.466  0.015  1.466
 LPD  CA  CB    single  1.530  0.020  1.530
 LPD  CA  HA    single  0.970  0.020  0.970
 LPD  N   CD    single  1.473  0.014  1.473
 LPD  N   H     single  0.860  0.020  1.020
 LPD  CD  CG    single  1.543  0.020  1.543
 LPD  CD  HD3   single  0.970  0.020  1.090
 LPD  CD  HD2   single  0.970  0.020  1.090
 LPD  CG  CB    single  1.527  0.020  1.527
 LPD  CG  HG3   single  0.970  0.020  1.090
 LPD  CG  HG2   single  0.970  0.020  1.090
 LPD  CB  HB2   single  0.970  0.020  1.090
 LPD  CB  HB3   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
 LPD  CA    C   N2    114.37  3.000
 LPD  CA    C   O     119.00  3.000
 LPD  N2    C   O     122.88  3.000
 LPD  HN22  N2  HN21  117.27  3.000
 LPD  HN22  N2  C     120.55  3.000
 LPD  HN21  N2  C     122.09  3.000
 LPD  HA    CA  CB    109.00  3.000
 LPD  HA    CA  N     110.00  3.000
 LPD  CB    CA  N     103.00  1.100
 LPD  HA    CA  C     109.00  3.000
 LPD  CB    CA  C     110.10  1.900
 LPD  N     CA  C     112.10  2.500
 LPD  H     N   CD    109.02  3.000
 LPD  H     N   CA    107.82  3.000
 LPD  CD    N   CA    107.79  3.000
 LPD  HD2   CD  HD3   106.89  3.000
 LPD  HD2   CD  CG    110.51  3.000
 LPD  HD3   CD  CG    111.50  3.000
 LPD  HD2   CD  N     110.82  3.000
 LPD  HD3   CD  N     109.70  3.000
 LPD  CG    CD  N     103.20  1.500
 LPD  HG2   CG  HG3   107.08  3.000
 LPD  HG2   CG  CB    110.46  3.000
 LPD  HG3   CG  CB    112.25  3.000
 LPD  HG2   CG  CD    110.76  3.000
 LPD  HG3   CG  CD    112.23  3.000
 LPD  CB    CG  CD    104.12  3.000
 LPD  HB3   CB  HB2   107.47  3.000
 LPD  HB3   CB  CG    110.77  3.000
 LPD  HB2   CB  CG    113.48  3.000
 LPD  HB3   CB  CA    108.53  3.000
 LPD  HB2   CB  CA    114.12  3.000
 LPD  CG    CB  CA    102.39  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
 LPD  CONST_01  HN21  N2  C   CA    0.00   0.0  0
 LPD  CONST_02  HN22  N2  C   CA  180.00   0.0  0
 LPD  Var_01    CG    CD  N   CA    9.89  30.0  1
 LPD  Var_02    CD    CG  CB  CA  -29.42  30.0  1
 LPD  Var_03    CB    CG  CD  N    13.14  30.0  1

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
 LPD  chir_01  CA  C  N  CB  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
 LPD  plan-1  O     0.020
 LPD  plan-1  C     0.020
 LPD  plan-1  N2    0.020
 LPD  plan-1  CA    0.020
 LPD  plan-1  HN21  0.020
 LPD  plan-1  HN22  0.020

