# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 10:09:21 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: N-[(3R)-1-propanoylpiperidine-3-carbonyl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCC[C@H](C1)C(=O)N[C@@H](C)C(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
 AQ7  AQ7  N-[(3R)-1-propanoylpiperidine-3-carbonyl]-L-alanine  ligand  37  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AQ7
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
 AQ7  C9   C  C      0   0.560   3.0943  -0.9163  -0.4741
 AQ7  C8   C  CH2    0  -0.293   1.1850   0.4679  -1.0790
 AQ7  C10  C  CH2    0  -0.595   4.4971  -0.9869   0.1019
 AQ7  C11  C  CH3    0  -0.650   5.0096  -2.4086   0.2497
 AQ7  N1   N  NT     0  -0.454   2.5717   0.3160  -0.6843
 AQ7  C3   C  C      0   0.574  -1.0945   1.1367  -0.3398
 AQ7  C4   C  CH1    0  -0.392   0.3423   0.9464   0.1124
 AQ7  C5   C  CH2    0  -0.428   0.9274   2.2414   0.6792
 AQ7  N    N  NH1    0  -0.633  -1.9531   0.2064   0.0827
 AQ7  CA   C  CH1    0  -0.204  -3.3683   0.1908  -0.2134
 AQ7  C    C  C      0   0.417  -4.0815  -0.7702   0.7693
 AQ7  O    O  O      0  -0.599  -3.3612  -1.4523   1.5259
 AQ7  CB   C  CH3    0  -0.657  -3.6504  -0.2255  -1.6562
 AQ7  C6   C  CH2    0  -0.436   2.4098   2.0791   0.9987
 AQ7  C7   C  CH2    0  -0.328   3.1664   1.5573  -0.2168
 AQ7  O1   O  O      0  -0.517  -1.4152   2.0747  -1.0647
 AQ7  O2   O  O      0  -0.503   2.4741  -1.9366  -0.7447
 AQ7  H3   H  HCH2   0   0.266   5.1798  -0.4095  -0.5272
 AQ7  H4   H  HCH2   0   0.263   4.5042  -0.4892   1.0761
 AQ7  H5   H  HCH3   0   0.226   5.0669  -2.9209  -0.7101
 AQ7  H6   H  HCH3   0   0.230   6.0122  -2.3930   0.6765
 AQ7  H7   H  HCH3   0   0.226   4.3770  -3.0005   0.9097
 AQ7  H8   H  HCH1   0   0.256   0.3870   0.1703   0.8844
 AQ7  H9   H  HCH2   0   0.227   0.8023   3.0414  -0.0562
 AQ7  H10  H  HCH2   0   0.247   0.3773   2.5412   1.5740
 AQ7  H11  H  HNH1   0   0.384  -1.6536  -0.5120   0.7273
 AQ7  H12  H  HCH1   0   0.236  -3.7724   1.1960  -0.0550
 AQ7  H14  H  HCH3   0   0.226  -4.7213  -0.2045  -1.8518
 AQ7  H15  H  HCH3   0   0.231  -3.1644   0.4468  -2.3621
 AQ7  H16  H  HCH3   0   0.217  -3.2885  -1.2378  -1.8451
 AQ7  H17  H  HCH2   0   0.243   2.8360   3.0352   1.3088
 AQ7  H18  H  HCH2   0   0.226   2.5427   1.3813   1.8316
 AQ7  H19  H  HCH2   0   0.274   4.2212   1.4231   0.0053
 AQ7  H20  H  HCH2   0   0.247   3.1078   2.2876  -1.0297
 AQ7  OXT  O  OC    -1  -0.604  -5.3221  -0.7845   0.6975
 AQ7  H1   H  HCH2   0   0.246   1.1301   1.2041  -1.8871
 AQ7  H2   H  HCH2   0   0.269   0.8120  -0.4774  -1.4654

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
 AQ7  C6   C5   single  1.525  0.020  1.525
 AQ7  C6   C7   single  1.524  0.020  1.524
 AQ7  C5   C4   single  1.530  0.020  1.530
 AQ7  C7   N1   single  1.454  0.020  1.454
 AQ7  C10  C11  single  1.518  0.020  1.518
 AQ7  C10  C9   single  1.518  0.020  1.518
 AQ7  C4   C3   single  1.518  0.020  1.518
 AQ7  C4   C8   single  1.536  0.020  1.536
 AQ7  N1   C9   single  1.355  0.020  1.355
 AQ7  N1   C8   single  1.450  0.020  1.450
 AQ7  O1   C3   double  1.228  0.020  1.228
 AQ7  C3   N    single  1.335  0.020  1.335
 AQ7  C9   O2   double  1.224  0.020  1.224
 AQ7  N    CA   single  1.446  0.020  1.446
 AQ7  CA   CB   single  1.528  0.020  1.528
 AQ7  CA   C    single  1.548  0.020  1.548
 AQ7  C    O    deloc   1.248  0.020  1.248
 AQ7  C8   H1   single  0.970  0.020  1.090
 AQ7  C8   H2   single  0.970  0.020  1.090
 AQ7  C10  H3   single  0.970  0.020  1.090
 AQ7  C10  H4   single  0.970  0.020  1.090
 AQ7  C11  H5   single  0.970  0.020  1.090
 AQ7  C11  H6   single  0.970  0.020  1.090
 AQ7  C11  H7   single  0.970  0.020  1.090
 AQ7  C4   H8   single  0.970  0.020  1.090
 AQ7  C5   H9   single  0.970  0.020  1.090
 AQ7  C5   H10  single  0.970  0.020  1.090
 AQ7  N    H11  single  0.860  0.020  1.020
 AQ7  CA   H12  single  0.970  0.020  1.090
 AQ7  CB   H14  single  0.970  0.020  1.090
 AQ7  CB   H15  single  0.970  0.020  1.090
 AQ7  CB   H16  single  0.970  0.020  1.090
 AQ7  C6   H17  single  0.970  0.020  1.090
 AQ7  C6   H18  single  0.970  0.020  1.090
 AQ7  C7   H19  single  0.970  0.020  1.090
 AQ7  C7   H20  single  0.970  0.020  1.090
 AQ7  C    OXT  deloc   1.243  0.020  1.243

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
 AQ7  O2   C9   N1   121.89  3.000
 AQ7  O2   C9   C10  120.87  3.000
 AQ7  N1   C9   C10  117.23  3.000
 AQ7  H2   C8   H1   107.77  3.000
 AQ7  H2   C8   C4   111.00  3.000
 AQ7  H1   C8   C4   109.61  3.000
 AQ7  H2   C8   N1   109.50  3.000
 AQ7  H1   C8   N1   108.63  3.000
 AQ7  C4   C8   N1   110.26  3.000
 AQ7  H4   C10  H3   105.55  3.000
 AQ7  H4   C10  C11  109.70  3.000
 AQ7  H3   C10  C11  109.86  3.000
 AQ7  H4   C10  C9   108.83  3.000
 AQ7  H3   C10  C9   109.52  3.000
 AQ7  C11  C10  C9   113.10  3.000
 AQ7  H7   C11  H6   107.75  3.000
 AQ7  H7   C11  H5   107.99  3.000
 AQ7  H6   C11  H5   107.66  3.000
 AQ7  H7   C11  C10  111.82  3.000
 AQ7  H6   C11  C10  109.59  3.000
 AQ7  H5   C11  C10  111.86  3.000
 AQ7  C7   N1   C8   112.92  3.000
 AQ7  C8   N1   C9   120.43  3.000
 AQ7  C7   N1   C9   124.68  3.000
 AQ7  O1   C3   N    123.46  3.000
 AQ7  N    C3   C4   115.29  3.000
 AQ7  O1   C3   C4   121.24  3.000
 AQ7  H8   C4   C5   108.84  3.000
 AQ7  H8   C4   C3   109.71  3.000
 AQ7  C5   C4   C3   111.48  3.000
 AQ7  H8   C4   C8   107.67  3.000
 AQ7  C3   C4   C8   109.11  3.000
 AQ7  C5   C4   C8   109.96  3.000
 AQ7  H10  C5   H9   107.00  3.000
 AQ7  H10  C5   C6   110.31  3.000
 AQ7  H9   C5   C6   109.26  3.000
 AQ7  H10  C5   C4   110.07  3.000
 AQ7  H9   C5   C4   109.04  3.000
 AQ7  C6   C5   C4   111.06  3.000
 AQ7  H11  N    CA   114.39  3.000
 AQ7  H11  N    C3   120.46  3.000
 AQ7  CA   N    C3   124.91  3.000
 AQ7  H12  CA   CB   108.58  3.000
 AQ7  H12  CA   C    107.94  3.000
 AQ7  CB   CA   C    110.19  3.000
 AQ7  H12  CA   N    108.77  3.000
 AQ7  C    CA   N    109.12  3.000
 AQ7  CB   CA   N    112.15  3.000
 AQ7  OXT  C    O    127.23  3.000
 AQ7  OXT  C    CA   115.49  3.000
 AQ7  O    C    CA   117.27  3.000
 AQ7  H16  CB   H15  108.20  3.000
 AQ7  H16  CB   H14  108.23  3.000
 AQ7  H15  CB   H14  108.08  3.000
 AQ7  H16  CB   CA   110.79  3.000
 AQ7  H15  CB   CA   111.19  3.000
 AQ7  H14  CB   CA   110.24  3.000
 AQ7  H18  C6   H17  107.15  3.000
 AQ7  H18  C6   C7   109.16  3.000
 AQ7  H17  C6   C7   109.43  3.000
 AQ7  H18  C6   C5   110.19  3.000
 AQ7  H17  C6   C5   110.23  3.000
 AQ7  C7   C6   C5   110.60  3.000
 AQ7  H20  C7   H19  106.64  3.000
 AQ7  H20  C7   C6   109.71  3.000
 AQ7  H19  C7   C6   111.18  3.000
 AQ7  H20  C7   N1   108.00  3.000
 AQ7  H19  C7   N1   110.95  3.000
 AQ7  C6   C7   N1   110.23  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
 AQ7  CONST_01  C10  C9   N1   C8    180.00   0.0  0
 AQ7  CONST_02  O2   C9   N1   C8      0.00   0.0  0
 AQ7  CONST_03  C7   N1   C9   C10     0.00   0.0  0
 AQ7  CONST_04  O2   C9   N1   C7    180.00   0.0  0
 AQ7  CONST_05  CA   N    C3   C4    180.00   0.0  0
 AQ7  CONST_06  H11  N    C3   C4      0.00   0.0  0
 AQ7  CONST_07  O1   C3   N    CA      0.00   0.0  0
 AQ7  Var_01    C6   C7   N1   C8     60.29  30.0  1
 AQ7  Var_02    C5   C6   C7   N1    -55.62  30.0  1
 AQ7  Var_03    C7   C6   C5   C4     53.31  30.0  1
 AQ7  Var_04    C7   N1   C8   C4    -60.46  30.0  1
 AQ7  Var_05    N1   C9   C10  C11  -177.81  30.0  3
 AQ7  Var_06    H5   C11  C10  C9     61.30  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
 AQ7  chir_01  C4  C5  C3  C8  negativ
 AQ7  chir_02  CA  N   CB  C   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
 AQ7  plan-1  C9   0.020
 AQ7  plan-1  C8   0.020
 AQ7  plan-1  C10  0.020
 AQ7  plan-1  N1   0.020
 AQ7  plan-1  C7   0.020
 AQ7  plan-1  O2   0.020
 AQ7  plan-2  C3   0.020
 AQ7  plan-2  C4   0.020
 AQ7  plan-2  N    0.020
 AQ7  plan-2  CA   0.020
 AQ7  plan-2  O1   0.020
 AQ7  plan-2  H11  0.020
 AQ7  plan-3  CA   0.020
 AQ7  plan-3  C    0.020
 AQ7  plan-3  O    0.020
 AQ7  plan-3  OXT  0.020

