# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 04:26:40 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: D-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
 PR9  PR9  'D-prolinamide            '  D-peptide  18  8  .  2019-03-22  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PR9
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
 PR9  O     O  O     0  -0.495  -15.8796  8.4166  13.3633
 PR9  C     C  C     0   0.489  -15.3387  7.4246  13.8337
 PR9  CA    C  CH1   0  -0.189  -14.3465  7.5666  14.9922
 PR9  NXT   N  NH2   0  -0.799  -15.5780  6.1839  13.3869
 PR9  N     N  NH1   0  -0.625  -13.5975  6.4017  15.3961
 PR9  CD    C  CH2   0  -0.272  -14.3425  5.6205  16.3840
 PR9  CG    C  CH2   0  -0.486  -15.4996  6.5361  16.8105
 PR9  CB    C  CH2   0  -0.453  -15.0996  7.9131  16.2820
 PR9  H     H  HNH1  0   0.354  -13.1736  5.8696  14.6510
 PR9  HA    H  HCH1  0   0.264  -13.6727  8.3803  14.7045
 PR9  HD1C  H  HCH2  0   0.217  -14.7207  4.6722  15.9886
 PR9  HD2C  H  HCH2  0   0.219  -13.6980  5.3704  17.2315
 PR9  HB1C  H  HCH2  0   0.245  -14.4131  8.4089  16.9707
 PR9  HB2C  H  HCH2  0   0.247  -15.9453  8.5796  16.1200
 PR9  HG1C  H  HCH2  0   0.247  -15.6580  6.5288  17.8883
 PR9  HG2C  H  HCH2  0   0.235  -16.4332  6.2145  16.3458
 PR9  HXT1  H  HNH2  0   0.405  -15.1246  5.3736  13.7704
 PR9  HXT2  H  HNH2  0   0.398  -16.2256  6.0347  12.6299

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
 PR9  N    CA    single  1.466  0.015  1.466
 PR9  N    CD    single  1.473  0.014  1.473
 PR9  CA   CB    single  1.530  0.020  1.530
 PR9  CA   C     single  1.525  0.021  1.525
 PR9  CB   CG    single  1.528  0.020  1.528
 PR9  CG   CD    single  1.536  0.020  1.536
 PR9  C    O     double  1.231  0.020  1.231
 PR9  C    NXT   single  1.340  0.020  1.340
 PR9  N    H     single  0.860  0.020  1.020
 PR9  CA   HA    single  0.970  0.020  0.970
 PR9  CD   HD1C  single  0.970  0.020  1.090
 PR9  CD   HD2C  single  0.970  0.020  1.090
 PR9  CB   HB1C  single  0.970  0.020  1.090
 PR9  CB   HB2C  single  0.970  0.020  1.090
 PR9  CG   HG1C  single  0.970  0.020  1.090
 PR9  CG   HG2C  single  0.970  0.020  1.090
 PR9  NXT  HXT1  single  0.860  0.020  1.020
 PR9  NXT  HXT2  single  0.860  0.020  1.020

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
 PR9  NXT   C    CA    116.97  3.000
 PR9  NXT   C    O     122.91  3.000
 PR9  CA    C    O     119.00  3.000
 PR9  HA    CA   CB    109.00  3.000
 PR9  HA    CA   N     110.00  3.000
 PR9  CB    CA   N     103.00  1.100
 PR9  HA    CA   C     109.00  3.000
 PR9  CB    CA   C     110.10  1.900
 PR9  N     CA   C     112.10  2.500
 PR9  HXT2  NXT  HXT1  117.23  3.000
 PR9  HXT2  NXT  C     120.16  3.000
 PR9  HXT1  NXT  C     122.60  3.000
 PR9  H     N    CD    115.53  3.000
 PR9  H     N    CA    115.93  3.000
 PR9  CD    N    CA    110.84  3.000
 PR9  HD2C  CD   HD1C  106.58  3.000
 PR9  HD2C  CD   CG    111.41  3.000
 PR9  HD1C  CD   CG    110.88  3.000
 PR9  HD2C  CD   N     110.20  3.000
 PR9  HD1C  CD   N     113.23  3.000
 PR9  CG    CD   N     103.20  1.500
 PR9  HG2C  CG   HG1C  107.15  3.000
 PR9  HG2C  CG   CB    110.01  3.000
 PR9  HG1C  CG   CB    112.72  3.000
 PR9  HG2C  CG   CD    110.52  3.000
 PR9  HG1C  CG   CD    112.36  3.000
 PR9  CB    CG   CD    104.11  3.000
 PR9  HB2C  CB   HB1C  107.71  3.000
 PR9  HB2C  CB   CG    113.56  3.000
 PR9  HB1C  CB   CG    110.83  3.000
 PR9  HB2C  CB   CA    113.25  3.000
 PR9  HB1C  CB   CA    108.94  3.000
 PR9  CG    CB   CA    102.47  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
 PR9  CONST_01  HXT1  NXT  C   CA    0.00   0.0  0
 PR9  CONST_02  HXT2  NXT  C   CA  180.00   0.0  0
 PR9  Var_01    CG    CD   N   CA  -11.93  30.0  1
 PR9  Var_02    CD    CG   CB  CA   33.35  30.0  1
 PR9  Var_03    CB    CG   CD  N   -14.25  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
 PR9  chir_01  CA  N  CB  C  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
 PR9  plan-1  O     0.020
 PR9  plan-1  C     0.020
 PR9  plan-1  CA    0.020
 PR9  plan-1  NXT   0.020
 PR9  plan-1  HXT1  0.020
 PR9  plan-1  HXT2  0.020

