# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 06:47:13 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: methyl (2~{S},4~{S})-2,4-bis(azanyl)-5-phenyl-pentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)C[C@@H](N)Cc1ccccc1
#
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
 O9N  O9N  'methyl (2~{S},4~{S})-2,4-bis(azanyl)-5-phenyl-pentanoate'  ligand  34  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O9N
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
 O9N  C26  C  CH1   0  -0.081  -4.4755  22.1785  12.9906
 O9N  C28  C  CR6   0   0.121  -6.8759  22.5920  13.6618
 O9N  N5   N  NH2   0  -0.805  -4.3603  23.5614  12.5442
 O9N  C27  C  CH2   0  -0.495  -5.9369  21.7259  12.8706
 O9N  C29  C  CR16  0  -0.309  -7.6060  23.6096  13.0518
 O9N  C30  C  CR16  0  -0.240  -8.4418  24.4331  13.7958
 O9N  C31  C  CR16  0  -0.272  -8.5568  24.2537  15.1675
 O9N  C32  C  CR16  0  -0.238  -7.8342  23.2422  15.7884
 O9N  C33  C  CR16  0  -0.304  -7.0026  22.4209  15.0400
 O9N  C34  C  CH2   0  -0.438  -3.5780  21.2853  12.1307
 O9N  C35  C  CH1   0  -0.186  -2.1283  21.1615  12.6366
 O9N  N6   N  NH2   0  -0.806  -1.5314  22.4617  12.8958
 O9N  C44  C  C     0   0.574  -1.3706  20.3720  11.5873
 O9N  O8   O  O     0  -0.452  -1.4952  19.1799  11.4505
 O9N  O9   O  O2    0  -0.440  -0.6030  21.1231  10.8156
 O9N  C45  C  CH3   0  -0.422   0.1079  20.4718   9.7625
 O9N  H1   H  HCH1  0   0.207  -4.1845  22.0457  14.0466
 O9N  H2   H  HNH2  0   0.344  -4.7670  24.1828  13.2322
 O9N  H3   H  HNH2  0   0.346  -3.3823  23.8129  12.4713
 O9N  H5   H  HCH2  0   0.237  -6.2195  21.7353  11.8142
 O9N  H6   H  HCH2  0   0.241  -6.0086  20.6912  13.2162
 O9N  H7   H  HCR6  0   0.243  -7.5229  23.7559  11.9814
 O9N  H8   H  HCR6  0   0.250  -9.0032  25.2165  13.3024
 O9N  H9   H  HCR6  0   0.251  -9.2079  24.8940  15.7487
 O9N  H10  H  HCR6  0   0.250  -7.9208  23.0909  16.8570
 O9N  H11  H  HCR6  0   0.243  -6.4447  21.6319  15.5318
 O9N  H12  H  HCH2  0   0.237  -3.5898  21.6786  11.1091
 O9N  H13  H  HCH2  0   0.246  -3.9945  20.2770  12.0896
 O9N  H14  H  HCH1  0   0.251  -2.1476  20.5226  13.5302
 O9N  H15  H  HNH2  0   0.360  -1.9173  22.8226  13.7598
 O9N  H16  H  HNH2  0   0.357  -0.5399  22.3630  13.0782
 O9N  H18  H  HCH3  0   0.250   0.6706  21.2506   9.2562
 O9N  H19  H  HCH3  0   0.238   0.7969  19.7219  10.1501
 O9N  H20  H  HCH3  0   0.238  -0.5740  20.0004   9.0548

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
 O9N  C45  O9   single    1.428  0.020  1.428
 O9N  O9   C44  single    1.322  0.020  1.322
 O9N  C44  O8   double    1.206  0.020  1.206
 O9N  C44  C35  single    1.516  0.020  1.516
 O9N  C34  C35  single    1.540  0.020  1.540
 O9N  C34  C26  single    1.531  0.020  1.531
 O9N  C35  N6   single    1.454  0.020  1.454
 O9N  C27  C26  single    1.535  0.020  1.535
 O9N  C27  C28  single    1.503  0.020  1.503
 O9N  C29  C28  aromatic  1.393  0.020  1.393
 O9N  C29  C30  aromatic  1.389  0.020  1.389
 O9N  N5   C26  single    1.458  0.020  1.458
 O9N  C28  C33  aromatic  1.395  0.020  1.395
 O9N  C30  C31  aromatic  1.388  0.020  1.388
 O9N  C31  C32  aromatic  1.390  0.020  1.390
 O9N  C33  C32  aromatic  1.388  0.020  1.388
 O9N  C26  H1   single    0.970  0.020  1.090
 O9N  N5   H2   single    0.890  0.020  1.040
 O9N  N5   H3   single    0.890  0.020  1.040
 O9N  C27  H5   single    0.970  0.020  1.090
 O9N  C27  H6   single    0.970  0.020  1.090
 O9N  C29  H7   single    0.930  0.020  1.080
 O9N  C30  H8   single    0.930  0.020  1.080
 O9N  C31  H9   single    0.930  0.020  1.080
 O9N  C32  H10  single    0.930  0.020  1.080
 O9N  C33  H11  single    0.930  0.020  1.080
 O9N  C34  H12  single    0.970  0.020  1.090
 O9N  C34  H13  single    0.970  0.020  1.090
 O9N  C35  H14  single    0.970  0.020  1.090
 O9N  N6   H15  single    0.890  0.020  1.040
 O9N  N6   H16  single    0.890  0.020  1.040
 O9N  C45  H18  single    0.970  0.020  1.090
 O9N  C45  H19  single    0.970  0.020  1.090
 O9N  C45  H20  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
 O9N  H1   C26  C34  108.23  3.000
 O9N  H1   C26  C27  106.88  3.000
 O9N  C34  C26  C27  110.02  3.000
 O9N  H1   C26  N5   112.73  3.000
 O9N  C27  C26  N5   109.33  3.000
 O9N  C34  C26  N5   109.59  3.000
 O9N  C33  C28  C29  118.34  3.000
 O9N  C33  C28  C27  120.43  3.000
 O9N  C29  C28  C27  121.20  3.000
 O9N  H3   N5   H2   106.53  3.000
 O9N  H3   N5   C26  109.52  3.000
 O9N  H2   N5   C26  110.03  3.000
 O9N  H6   C27  H5   107.25  3.000
 O9N  H6   C27  C28  109.77  3.000
 O9N  H5   C27  C28  110.01  3.000
 O9N  H6   C27  C26  108.47  3.000
 O9N  H5   C27  C26  108.61  3.000
 O9N  C28  C27  C26  112.58  3.000
 O9N  H7   C29  C30  119.68  3.000
 O9N  H7   C29  C28  119.40  3.000
 O9N  C30  C29  C28  120.92  3.000
 O9N  H8   C30  C31  120.05  3.000
 O9N  H8   C30  C29  119.79  3.000
 O9N  C31  C30  C29  120.16  3.000
 O9N  H9   C31  C32  120.23  3.000
 O9N  H9   C31  C30  120.26  3.000
 O9N  C32  C31  C30  119.50  3.000
 O9N  H10  C32  C33  119.83  3.000
 O9N  H10  C32  C31  120.07  3.000
 O9N  C33  C32  C31  120.09  3.000
 O9N  H11  C33  C32  119.62  3.000
 O9N  H11  C33  C28  119.39  3.000
 O9N  C32  C33  C28  120.98  3.000
 O9N  H13  C34  H12  107.01  3.000
 O9N  H13  C34  C35  107.29  3.000
 O9N  H12  C34  C35  110.21  3.000
 O9N  H13  C34  C26  109.66  3.000
 O9N  H12  C34  C26  107.96  3.000
 O9N  C35  C34  C26  114.47  3.000
 O9N  H14  C35  C44  105.59  3.000
 O9N  H14  C35  N6   112.47  3.000
 O9N  C44  C35  N6   112.57  3.000
 O9N  H14  C35  C34  107.30  3.000
 O9N  N6   C35  C34  111.91  3.000
 O9N  C44  C35  C34  106.55  3.000
 O9N  H16  N6   H15  104.72  3.000
 O9N  H16  N6   C35  110.30  3.000
 O9N  H15  N6   C35  108.32  3.000
 O9N  O9   C44  O8   123.71  3.000
 O9N  O8   C44  C35  122.79  3.000
 O9N  O9   C44  C35  113.46  3.000
 O9N  C45  O9   C44  117.41  3.000
 O9N  H20  C45  H19  109.20  3.000
 O9N  H20  C45  H18  109.37  3.000
 O9N  H19  C45  H18  109.37  3.000
 O9N  H20  C45  O9   111.39  3.000
 O9N  H19  C45  O9   111.49  3.000
 O9N  H18  C45  O9   105.94  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
 O9N  CONST_01  C31  C30  C29  C28     0.00   0.0  0
 O9N  CONST_02  C31  C32  C33  C28     0.00   0.0  0
 O9N  CONST_03  C32  C33  C28  C29     0.00   0.0  0
 O9N  CONST_04  C32  C31  C30  C29     0.00   0.0  0
 O9N  CONST_05  C33  C28  C29  C30     0.00   0.0  0
 O9N  CONST_06  C33  C32  C31  C30     0.00   0.0  0
 O9N  CONST_07  C30  C29  C28  C27   180.00   0.0  0
 O9N  CONST_08  C32  C33  C28  C27   180.00   0.0  0
 O9N  CONST_09  H8   C30  C29  C28   180.00   0.0  0
 O9N  CONST_10  H10  C32  C33  C28   180.00   0.0  0
 O9N  CONST_11  H11  C33  C28  C29   180.00   0.0  0
 O9N  CONST_12  H9   C31  C30  C29   180.00   0.0  0
 O9N  CONST_13  H7   C29  C30  C31   180.00   0.0  0
 O9N  Var_01    C29  C28  C27  C26    98.67  30.0  2
 O9N  Var_02    H18  C45  O9   C44  -179.92  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
 O9N  chir_01  C26  C34  C27  N5   positiv
 O9N  chir_02  C35  N6   C44  C34  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
 O9N  plan-1  C28  0.020
 O9N  plan-1  C27  0.020
 O9N  plan-1  C29  0.020
 O9N  plan-1  C30  0.020
 O9N  plan-1  C31  0.020
 O9N  plan-1  C32  0.020
 O9N  plan-1  C33  0.020
 O9N  plan-1  H7   0.020
 O9N  plan-1  H8   0.020
 O9N  plan-1  H9   0.020
 O9N  plan-1  H10  0.020
 O9N  plan-1  H11  0.020
 O9N  plan-2  C35  0.020
 O9N  plan-2  C44  0.020
 O9N  plan-2  O8   0.020
 O9N  plan-2  O9   0.020

