# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:55:50 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 1-acetyl-D-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC[C@@H]1C(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
 N8P  N8P  '1-acetyl-D-proline       '  D-peptide  21  11  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N8P
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
 N8P  C7   C  C      0   0.500  -43.5345   2.4124  -44.2840
 N8P  O9   O  O      0  -0.519  -44.1593   2.7415  -43.2779
 N8P  C8   C  CH3    0  -0.794  -42.7105   3.4093  -45.0643
 N8P  N    N  NT     0  -0.428  -43.5695   1.1576  -44.7533
 N8P  CA   C  CH1    0  -0.216  -42.7948   0.6332  -45.8654
 N8P  CB   C  CH2    0  -0.450  -43.5580  -0.6504  -46.2009
 N8P  CG   C  CH2    0  -0.495  -43.9742  -1.1598  -44.8244
 N8P  CD   C  CH2    0  -0.248  -44.3124   0.1167  -44.0555
 N8P  C    C  C      0   0.414  -41.3115   0.3342  -45.5122
 N8P  O    O  O      0  -0.605  -40.6298  -0.0819  -46.4691
 N8P  OXT  O  OC    -1  -0.590  -40.9456   0.5216  -44.3389
 N8P  H81  H  HCH3   0   0.255  -42.7860   4.3899  -44.6008
 N8P  H82  H  HCH3   0   0.258  -41.6611   3.1163  -45.0903
 N8P  H83  H  HCH3   0   0.255  -43.0497   3.4906  -46.0984
 N8P  HA   H  HCH1   0   0.251  -42.8198   1.3245  -46.7120
 N8P  HB2  H  HCH2   0   0.241  -42.9519  -1.3575  -46.7640
 N8P  HB3  H  HCH2   0   0.233  -44.4402  -0.4151  -46.8014
 N8P  HG2  H  HCH2   0   0.235  -43.1420  -1.6826  -44.3497
 N8P  HG3  H  HCH2   0   0.244  -44.8168  -1.8499  -44.8576
 N8P  HD2  H  HCH2   0   0.232  -44.0249   0.0566  -43.0044
 N8P  HD3  H  HCH2   0   0.226  -45.3842   0.3299  -44.0879

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
 N8P  OXT  C    deloc   1.243  0.020  1.243
 N8P  C    O    deloc   1.231  0.020  1.231
 N8P  C    CA   single  1.525  0.021  1.525
 N8P  N    C7   single  1.340  0.020  1.340
 N8P  N    CD   single  1.473  0.014  1.473
 N8P  N    CA   single  1.458  0.019  1.458
 N8P  C7   O9   double  1.229  0.020  1.229
 N8P  C7   C8   single  1.510  0.020  1.510
 N8P  CD   CG   single  1.528  0.020  1.528
 N8P  CG   CB   single  1.526  0.020  1.526
 N8P  CB   CA   single  1.521  0.033  1.521
 N8P  CA   HA   single  0.970  0.020  0.970
 N8P  CD   HD2  single  0.970  0.020  1.090
 N8P  CD   HD3  single  0.970  0.020  1.090
 N8P  C8   H81  single  0.970  0.020  1.090
 N8P  C8   H82  single  0.970  0.020  1.090
 N8P  C8   H83  single  0.970  0.020  1.090
 N8P  CG   HG2  single  0.970  0.020  1.090
 N8P  CG   HG3  single  0.970  0.020  1.090
 N8P  CB   HB2  single  0.970  0.020  1.090
 N8P  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
 N8P  N    C7  C8   116.83  3.000
 N8P  C8   C7  O9   121.56  3.000
 N8P  N    C7  O9   121.60  3.000
 N8P  H83  C8  H82  107.26  3.000
 N8P  H83  C8  H81  108.37  3.000
 N8P  H82  C8  H81  108.63  3.000
 N8P  H83  C8  C7   111.66  3.000
 N8P  H82  C8  C7   111.11  3.000
 N8P  H81  C8  C7   109.70  3.000
 N8P  CD   N   CA   112.37  3.000
 N8P  CA   N   C7   126.29  3.000
 N8P  CD   N   C7   120.97  3.000
 N8P  HA   CA  C    110.00  3.000
 N8P  HA   CA  CB   109.00  3.000
 N8P  C    CA  CB   110.50  1.500
 N8P  HA   CA  N    110.00  3.000
 N8P  CB   CA  N    110.40  1.500
 N8P  C    CA  N    111.00  2.800
 N8P  HB3  CB  HB2  107.77  3.000
 N8P  HB3  CB  CG   110.33  3.000
 N8P  HB2  CB  CG   113.69  3.000
 N8P  HB3  CB  CA   110.02  3.000
 N8P  HB2  CB  CA   112.37  3.000
 N8P  CG   CB  CA   102.61  3.000
 N8P  HG3  CG  HG2  107.43  3.000
 N8P  HG3  CG  CD   111.91  3.000
 N8P  HG2  CG  CD   110.49  3.000
 N8P  HG3  CG  CB   113.26  3.000
 N8P  HG2  CG  CB   110.14  3.000
 N8P  CD   CG  CB   103.61  3.000
 N8P  HD3  CD  HD2  107.30  3.000
 N8P  HD3  CD  CG   111.40  3.000
 N8P  HD2  CD  CG   112.35  3.000
 N8P  HD3  CD  N    110.27  3.000
 N8P  HD2  CD  N    111.49  3.000
 N8P  CG   CD  N    103.20  1.500
 N8P  OXT  C   O    127.87  3.000
 N8P  O    C   CA   120.80  1.700
 N8P  OXT  C   CA   120.80  1.700

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
 N8P  CONST_01  CD   N   C7  O9    0.00   0.0  0
 N8P  CONST_02  CA   N   C7  O9  180.00   0.0  0
 N8P  CONST_03  CD   N   C7  C8  180.00   0.0  0
 N8P  CONST_04  CA   N   C7  C8    0.00   0.0  0
 N8P  Var_01    CB   CG  CD  N   -23.11  30.0  1
 N8P  Var_02    CG   CD  N   CA   -0.78  30.0  1
 N8P  Var_03    H81  C8  C7  N   178.39  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
 N8P  chir_01  CA  C  N  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
 N8P  plan-1  C7   0.020
 N8P  plan-1  O9   0.020
 N8P  plan-1  C8   0.020
 N8P  plan-1  N    0.020
 N8P  plan-1  CA   0.020
 N8P  plan-1  CD   0.020
 N8P  plan-2  CA   0.020
 N8P  plan-2  C    0.020
 N8P  plan-2  O    0.020
 N8P  plan-2  OXT  0.020

