# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:50:34 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: N-methyl-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=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
 9PR  9PR  'N-methyl-L-prolinamide   '  peptide  21  9  .  2019-03-22  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9PR
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
 9PR  C    C  C     0   0.556  17.0956  -0.9469  6.9922
 9PR  N    N  NH1   0  -0.581  15.5925  -2.5061  5.8361
 9PR  O    O  O     0  -0.488  17.0157  -0.1404  6.0767
 9PR  CA   C  CH1   0  -0.271  16.6034  -2.3847  6.8719
 9PR  CB   C  CH2   0  -0.445  17.7587  -3.3004  6.4268
 9PR  CD   C  CH2   0  -0.283  16.2748  -2.8276  4.5743
 9PR  CG   C  CH2   0  -0.487  17.7506  -3.1240  4.9101
 9PR  C1   C  CH3   0  -0.509  18.2752   0.6405  8.4284
 9PR  N1   N  NH1   0  -0.625  17.6702  -0.6439  8.1675
 9PR  HN   H  HNH1  0   0.353  14.9805  -3.2702  6.0854
 9PR  HA   H  HCH1  0   0.269  16.1888  -2.7019  7.8325
 9PR  HB   H  HCH2  0   0.241  18.7181  -3.0596  6.8868
 9PR  HBA  H  HCH2  0   0.242  17.5138  -4.3295  6.6980
 9PR  HD   H  HCH2  0   0.222  15.7932  -3.6859  4.1033
 9PR  HDA  H  HCH2  0   0.216  16.2013  -1.9968  3.8704
 9PR  HG   H  HCH2  0   0.234  18.3881  -2.2879  4.6196
 9PR  HGA  H  HCH2  0   0.241  18.1219  -4.0060  4.3886
 9PR  H1   H  HCH3  0   0.247  18.6812   0.6335  9.4359
 9PR  H1A  H  HCH3  0   0.234  19.0881   0.8531  7.7329
 9PR  H1B  H  HCH3  0   0.234  17.5483   1.4506  8.3586
 9PR  HN1  H  HNH1  0   0.401  17.7019  -1.3391  8.8944

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
 9PR  C   O    double  1.231  0.020  1.231
 9PR  C   CA   single  1.525  0.021  1.525
 9PR  C   N1   single  1.343  0.020  1.343
 9PR  N   CA   single  1.458  0.019  1.458
 9PR  N   CD   single  1.473  0.014  1.473
 9PR  CA  CB   single  1.521  0.033  1.521
 9PR  CB  CG   single  1.527  0.020  1.527
 9PR  CD  CG   single  1.542  0.020  1.542
 9PR  C1  N1   single  1.444  0.020  1.444
 9PR  N   HN   single  0.890  0.020  1.040
 9PR  CA  HA   single  0.970  0.020  0.970
 9PR  CB  HB   single  0.970  0.020  1.090
 9PR  CB  HBA  single  0.970  0.020  1.090
 9PR  CD  HD   single  0.970  0.020  1.090
 9PR  CD  HDA  single  0.970  0.020  1.090
 9PR  CG  HG   single  0.970  0.020  1.090
 9PR  CG  HGA  single  0.970  0.020  1.090
 9PR  C1  H1   single  0.970  0.020  1.090
 9PR  C1  H1A  single  0.970  0.020  1.090
 9PR  C1  H1B  single  0.970  0.020  1.090
 9PR  N1  HN1  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
 9PR  N1   C   CA   114.84  3.000
 9PR  N1   C   O    122.30  3.000
 9PR  CA   C   O    120.80  1.700
 9PR  HN   N   CD   109.12  3.000
 9PR  HN   N   CA   107.99  3.000
 9PR  CD   N   CA   107.90  3.000
 9PR  HA   CA  CB   109.00  3.000
 9PR  HA   CA  N    110.00  3.000
 9PR  CB   CA  N    110.40  1.500
 9PR  HA   CA  C    110.00  3.000
 9PR  CB   CA  C    110.50  1.500
 9PR  N    CA  C    111.00  2.800
 9PR  HBA  CB  HB   107.49  3.000
 9PR  HBA  CB  CG   110.76  3.000
 9PR  HB   CB  CG   113.45  3.000
 9PR  HBA  CB  CA   108.68  3.000
 9PR  HB   CB  CA   114.00  3.000
 9PR  CG   CB  CA   102.38  3.000
 9PR  HDA  CD  HD   106.89  3.000
 9PR  HDA  CD  CG   110.56  3.000
 9PR  HD   CD  CG   111.42  3.000
 9PR  HDA  CD  N    110.85  3.000
 9PR  HD   CD  N    109.74  3.000
 9PR  CG   CD  N    103.20  1.500
 9PR  HGA  CG  HG   107.09  3.000
 9PR  HGA  CG  CD   112.17  3.000
 9PR  HG   CG  CD   110.73  3.000
 9PR  HGA  CG  CB   112.33  3.000
 9PR  HG   CG  CB   110.49  3.000
 9PR  CD   CG  CB   104.09  3.000
 9PR  H1B  C1  H1A  108.13  3.000
 9PR  H1B  C1  H1   108.25  3.000
 9PR  H1A  C1  H1   108.31  3.000
 9PR  H1B  C1  N1   111.71  3.000
 9PR  H1A  C1  N1   111.75  3.000
 9PR  H1   C1  N1   108.58  3.000
 9PR  HN1  N1  C1   118.09  3.000
 9PR  HN1  N1  C    119.33  3.000
 9PR  C1   N1  C    122.57  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
 9PR  CONST_01  C1   N1  C   CA   180.00   0.0  0
 9PR  CONST_02  HN1  N1  C   CA     0.00   0.0  0
 9PR  CONST_03  C1   N1  C   O      0.00   0.0  0
 9PR  Var_01    CB   CG  CD  N     14.05  30.0  1
 9PR  Var_02    CG   CD  N   CA     8.83  30.0  1
 9PR  Var_03    H1   C1  N1  C   -179.12  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
 9PR  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
 9PR  plan-1  C    0.020
 9PR  plan-1  O    0.020
 9PR  plan-1  CA   0.020
 9PR  plan-1  C1   0.020
 9PR  plan-1  N1   0.020
 9PR  plan-1  HN1  0.020

