# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 06:03:48 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (4~{S})-4-azanyl-5-formamido-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(N)=O)CNC=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
 QQ8  QQ8  (4~{S})-4-azanyl-5-formamido-pentanamide  L-peptide  24  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QQ8
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
 QQ8  OCA  O  O     0  -0.486   1.7445  -13.3795  -2.9449
 QQ8  CAO  C  C1    0   0.247   1.8715  -13.6010  -4.1368
 QQ8  NM   N  NH1   0  -0.596   1.7736  -14.8036  -4.7168
 QQ8  CM   C  CH2   0  -0.273   1.4913  -16.0252  -3.9945
 QQ8  CAA  C  CH1   0  -0.091   0.0079  -16.2309  -3.6912
 QQ8  NA   N  NH2   0  -0.807  -0.7349  -16.2492  -4.9442
 QQ8  CB   C  CH2   0  -0.405  -0.1631  -17.5484  -2.9432
 QQ8  CG   C  CH2   0  -0.588  -1.5921  -17.7917  -2.4725
 QQ8  CD   C  C     0   0.527  -1.7385  -19.0668  -1.6670
 QQ8  OE1  O  O     0  -0.488  -1.0863  -20.0717  -1.9111
 QQ8  NE2  N  NH2   0  -0.805  -2.6554  -19.0172  -0.6874
 QQ8  H1   H  H     0   0.200   2.0925  -12.8071  -4.8672
 QQ8  H2   H  HNH1  0   0.406   1.8973  -14.8512  -5.7151
 QQ8  H3   H  HCH2  0   0.247   1.8547  -16.8565  -4.6006
 QQ8  H4   H  HCH2  0   0.244   2.0579  -16.0302  -3.0618
 QQ8  H5   H  HCH1  0   0.204  -0.3110  -15.4166  -3.0222
 QQ8  H6   H  HNH2  0   0.349  -1.7281  -16.3051  -4.7562
 QQ8  H7   H  HNH2  0   0.343  -0.6117  -15.3613  -5.4165
 QQ8  H9   H  HCH2  0   0.225   0.1644  -18.3684  -3.5865
 QQ8  H10  H  HCH2  0   0.230   0.5012  -17.5413  -2.0742
 QQ8  H11  H  HCH2  0   0.251  -1.9501  -16.9335  -1.8978
 QQ8  H12  H  HCH2  0   0.267  -2.2677  -17.8864  -3.3293
 QQ8  H13  H  HNH2  0   0.395  -2.8528  -19.8325  -0.1301
 QQ8  H14  H  HNH2  0   0.404  -3.1745  -18.1805  -0.4860

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
 QQ8  NA   CAA  single  1.457  0.020  1.457
 QQ8  NM   CAO  single  1.339  0.020  1.339
 QQ8  NM   CM   single  1.447  0.020  1.447
 QQ8  CAO  OCA  double  1.219  0.020  1.219
 QQ8  CM   CAA  single  1.528  0.020  1.528
 QQ8  CAA  CB   single  1.525  0.020  1.525
 QQ8  CB   CG   single  1.524  0.020  1.524
 QQ8  CG   CD   single  1.515  0.020  1.515
 QQ8  OE1  CD   double  1.223  0.020  1.223
 QQ8  CD   NE2  single  1.343  0.020  1.343
 QQ8  CAO  H1   single  0.930  0.020  1.080
 QQ8  NM   H2   single  0.860  0.020  1.020
 QQ8  CM   H3   single  0.970  0.020  1.090
 QQ8  CM   H4   single  0.970  0.020  1.090
 QQ8  CAA  H5   single  0.970  0.020  1.090
 QQ8  NA   H6   single  0.890  0.020  1.040
 QQ8  NA   H7   single  0.890  0.020  1.040
 QQ8  CB   H9   single  0.970  0.020  1.090
 QQ8  CB   H10  single  0.970  0.020  1.090
 QQ8  CG   H11  single  0.970  0.020  1.090
 QQ8  CG   H12  single  0.970  0.020  1.090
 QQ8  NE2  H13  single  0.860  0.020  1.020
 QQ8  NE2  H14  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
 QQ8  H1   CAO  NM   112.03  3.000
 QQ8  H1   CAO  OCA  122.58  3.000
 QQ8  NM   CAO  OCA  125.40  3.000
 QQ8  H2   NM   CM   118.61  3.000
 QQ8  H2   NM   CAO  117.58  3.000
 QQ8  CM   NM   CAO  123.81  3.000
 QQ8  H4   CM   H3   107.36  3.000
 QQ8  H4   CM   CAA  109.49  3.000
 QQ8  H3   CM   CAA  109.33  3.000
 QQ8  H4   CM   NM   109.22  3.000
 QQ8  H3   CM   NM   107.52  3.000
 QQ8  CAA  CM   NM   113.71  3.000
 QQ8  H5   CAA  CB   107.97  3.000
 QQ8  H5   CAA  NA   112.59  3.000
 QQ8  CB   CAA  NA   110.73  3.000
 QQ8  H5   CAA  CM   107.59  3.000
 QQ8  CB   CAA  CM   108.82  3.000
 QQ8  NA   CAA  CM   109.03  3.000
 QQ8  H7   NA   H6   104.73  3.000
 QQ8  H7   NA   CAA  109.15  3.000
 QQ8  H6   NA   CAA  109.95  3.000
 QQ8  H10  CB   H9   106.89  3.000
 QQ8  H10  CB   CG   108.97  3.000
 QQ8  H9   CB   CG   110.07  3.000
 QQ8  H10  CB   CAA  108.42  3.000
 QQ8  H9   CB   CAA  109.03  3.000
 QQ8  CG   CB   CAA  113.25  3.000
 QQ8  H12  CG   H11  106.09  3.000
 QQ8  H12  CG   CD   106.47  3.000
 QQ8  H11  CG   CD   110.46  3.000
 QQ8  H12  CG   CB   110.52  3.000
 QQ8  H11  CG   CB   110.13  3.000
 QQ8  CD   CG   CB   112.90  3.000
 QQ8  NE2  CD   OE1  122.71  3.000
 QQ8  NE2  CD   CG   115.00  3.000
 QQ8  OE1  CD   CG   122.27  3.000
 QQ8  H14  NE2  H13  117.51  3.000
 QQ8  H14  NE2  CD   121.99  3.000
 QQ8  H13  NE2  CD   120.50  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
 QQ8  CONST_01  CM   NM   CAO  OCA     0.00   0.0  0
 QQ8  CONST_02  H2   NM   CAO  OCA   180.00   0.0  0
 QQ8  CONST_03  H13  NE2  CD   CG    180.00   0.0  0
 QQ8  CONST_04  H14  NE2  CD   CG      0.00   0.0  0
 QQ8  Var_01    CAA  CM   NM   CAO    81.09  30.0  3
 QQ8  Var_02    CD   CG   CB   CAA  -176.95  30.0  3
 QQ8  Var_03    OE1  CD   CG   CB    -34.95  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
 QQ8  chir_01  CAA  NA  CM  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
 QQ8  plan-1  OCA  0.020
 QQ8  plan-1  CAO  0.020
 QQ8  plan-1  NM   0.020
 QQ8  plan-1  CM   0.020
 QQ8  plan-1  H1   0.020
 QQ8  plan-1  H2   0.020
 QQ8  plan-2  CG   0.020
 QQ8  plan-2  CD   0.020
 QQ8  plan-2  OE1  0.020
 QQ8  plan-2  NE2  0.020
 QQ8  plan-2  H13  0.020
 QQ8  plan-2  H14  0.020

