# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 17:48:09 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2S)-2-[(3R)-3-benzyl-2-oxopiperazin-1-yl]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](N1CCN[C@H](Cc2ccccc2)C1=O)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
 PSS  PSS  '(2S)-2-[(3R)-3-benzyl-2-oxopiperazin-1-yl]hexanoic acid'  peptide  45  22  .  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_PSS
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
 PSS  C     C  C      0   0.430   3.2020   2.0380  -0.1776
 PSS  N     N  NT     0  -0.449   1.4069   0.5587   0.6935
 PSS  O     O  O      0  -0.604   2.5278   2.9847   0.2661
 PSS  C1    C  CH2    0  -0.350  -0.3159   0.9487   2.4015
 PSS  N1    N  NH1    0  -0.574  -1.2525   0.2684   1.5332
 PSS  C2    C  CH2    0  -0.281   1.1153   0.5438   2.1175
 PSS  C3    C  CH1    0  -0.190  -0.9994   0.6146   0.1511
 PSS  C4    C  C      0   0.565   0.4748   0.7121  -0.2543
 PSS  C5    C  CH2    0  -0.551  -1.7278  -0.3585  -0.7832
 PSS  C6    C  CR6    0   0.162  -3.2107  -0.3736  -0.5403
 PSS  C7    C  CR16   0  -0.320  -3.8122  -1.3927   0.1927
 PSS  C8    C  CR16   0  -0.242  -5.1813  -1.3919   0.4272
 PSS  C9    C  CR16   0  -0.275  -5.9724  -0.3640  -0.0676
 PSS  C10   C  CR16   0  -0.240  -5.3843   0.6583  -0.8024
 PSS  C11   C  CR16   0  -0.308  -4.0161   0.6502  -1.0360
 PSS  C12   C  CH1    0  -0.235   2.8138   0.6198   0.3206
 PSS  C13   C  CH2    0  -0.409   3.2661  -0.5244  -0.5837
 PSS  C14   C  CH2    0  -0.405   2.8254  -1.9001  -0.0988
 PSS  C15   C  CH2    0  -0.419   3.4718  -3.0344  -0.8855
 PSS  C16   C  CH3    0  -0.661   3.0104  -4.4106  -0.4267
 PSS  OXT   O  OC    -1  -0.604   4.1966   2.1099  -0.9241
 PSS  H1    H  HCH2   0   0.236  -0.4339   2.0266   2.2561
 PSS  H1A   H  HCH2   0   0.253  -0.5511   0.7390   3.4458
 PSS  HN1   H  HNH1   0   0.344  -1.1605  -0.7341   1.6598
 PSS  H2    H  HCH2   0   0.230   1.3149  -0.4539   2.5233
 PSS  H2A   H  HCH2   0   0.241   1.7988   1.2342   2.6168
 PSS  H3    H  HCH1   0   0.264  -1.4094   1.6184  -0.0266
 PSS  H5    H  HCH2   0   0.267  -1.5223  -0.0732  -1.8145
 PSS  H5A   H  HCH2   0   0.250  -1.3197  -1.3647  -0.6440
 PSS  H7    H  HCR6   0   0.242  -3.2051  -2.2023   0.5815
 PSS  H8    H  HCR6   0   0.252  -5.6302  -2.1960   0.9964
 PSS  H9    H  HCR6   0   0.252  -7.0395  -0.3610   0.1139
 PSS  H10   H  HCR6   0   0.252  -5.9927   1.4614  -1.1988
 PSS  H11   H  HCR6   0   0.245  -3.5674   1.4504  -1.6141
 PSS  H12   H  HCH1   0   0.247   3.3561   0.4876   1.2650
 PSS  H13   H  HCH2   0   0.216   2.9285  -0.3700  -1.6091
 PSS  H13A  H  HCH2   0   0.213   4.3576  -0.4926  -0.6134
 PSS  H14   H  HCH2   0   0.202   3.0708  -2.0172   0.9635
 PSS  H14A  H  HCH2   0   0.206   1.7368  -1.9945  -0.1693
 PSS  H15   H  HCH2   0   0.209   3.2504  -2.9099  -1.9503
 PSS  H15A  H  HCH2   0   0.209   4.5601  -2.9621  -0.7938
 PSS  H16   H  HCH3   0   0.215   3.2393  -4.5706   0.6286
 PSS  H16A  H  HCH3   0   0.215   1.9316  -4.5249  -0.5489
 PSS  H16B  H  HCH3   0   0.224   3.4930  -5.2075  -0.9939
 PSS  O1    O  O      0  -0.525   0.7587   0.9138  -1.4326

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
 PSS  C    C12   single    1.552  0.020  1.552
 PSS  C    OXT   deloc     1.246  0.020  1.246
 PSS  N    C4    single    1.338  0.020  1.338
 PSS  O    C     deloc     1.231  0.020  1.231
 PSS  C1   N1    single    1.447  0.020  1.447
 PSS  C1   H1    single    0.970  0.020  1.090
 PSS  C1   H1A   single    0.970  0.020  1.090
 PSS  N1   C3    single    1.447  0.020  1.447
 PSS  N1   HN1   single    0.890  0.020  1.040
 PSS  C2   N     single    1.454  0.020  1.454
 PSS  C2   C1    single    1.514  0.020  1.514
 PSS  C2   H2    single    0.970  0.020  1.090
 PSS  C2   H2A   single    0.970  0.020  1.090
 PSS  C3   C5    single    1.533  0.020  1.533
 PSS  C3   H3    single    0.970  0.020  1.090
 PSS  C4   O1    double    1.229  0.020  1.229
 PSS  C4   C3    single    1.532  0.020  1.532
 PSS  C5   H5    single    0.970  0.020  1.090
 PSS  C5   H5A   single    0.970  0.020  1.090
 PSS  C6   C5    single    1.503  0.020  1.503
 PSS  C6   C11   aromatic  1.394  0.020  1.394
 PSS  C7   C6    aromatic  1.392  0.020  1.392
 PSS  C7   H7    single    0.930  0.020  1.080
 PSS  C8   C7    aromatic  1.389  0.020  1.389
 PSS  C8   C9    aromatic  1.388  0.020  1.388
 PSS  C8   H8    single    0.930  0.020  1.080
 PSS  C9   C10   aromatic  1.390  0.020  1.390
 PSS  C9   H9    single    0.930  0.020  1.080
 PSS  C10  C11   aromatic  1.388  0.020  1.388
 PSS  C10  H10   single    0.930  0.020  1.080
 PSS  C11  H11   single    0.930  0.020  1.080
 PSS  C12  N     single    1.457  0.020  1.457
 PSS  C12  C13   single    1.527  0.020  1.527
 PSS  C12  H12   single    0.970  0.020  1.090
 PSS  C13  H13   single    0.970  0.020  1.090
 PSS  C13  H13A  single    0.970  0.020  1.090
 PSS  C14  C13   single    1.524  0.020  1.524
 PSS  C14  C15   single    1.524  0.020  1.524
 PSS  C14  H14   single    0.970  0.020  1.090
 PSS  C14  H14A  single    0.970  0.020  1.090
 PSS  C15  C16   single    1.522  0.020  1.522
 PSS  C15  H15   single    0.970  0.020  1.090
 PSS  C15  H15A  single    0.970  0.020  1.090
 PSS  C16  H16   single    0.970  0.020  1.090
 PSS  C16  H16A  single    0.970  0.020  1.090
 PSS  C16  H16B  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
 PSS  OXT   C    C12   116.41  3.000
 PSS  OXT   C    O     127.05  3.000
 PSS  C12   C    O     116.44  3.000
 PSS  C12   N    C4    119.12  3.000
 PSS  C12   N    C2    116.42  3.000
 PSS  C4    N    C2    123.73  3.000
 PSS  H1A   C1   H1    107.06  3.000
 PSS  H1A   C1   C2    109.39  3.000
 PSS  H1    C1   C2    109.90  3.000
 PSS  C2    C1   N1    111.94  3.000
 PSS  H1A   C1   N1    110.15  3.000
 PSS  H1    C1   N1    108.27  3.000
 PSS  HN1   N1   C3    109.86  3.000
 PSS  HN1   N1   C1    109.32  3.000
 PSS  C3    N1   C1    110.33  3.000
 PSS  H2A   C2   H2    107.00  3.000
 PSS  H2A   C2   C1    109.68  3.000
 PSS  H2    C2   C1    110.26  3.000
 PSS  H2A   C2   N     108.41  3.000
 PSS  H2    C2   N     109.61  3.000
 PSS  C1    C2   N     111.75  3.000
 PSS  H3    C3   C5    107.70  3.000
 PSS  H3    C3   C4    104.96  3.000
 PSS  C5    C3   C4    109.65  3.000
 PSS  C4    C3   N1    115.86  3.000
 PSS  H3    C3   N1    107.92  3.000
 PSS  C5    C3   N1    110.31  3.000
 PSS  C3    C4   O1    119.12  3.000
 PSS  C3    C4   N     118.40  3.000
 PSS  O1    C4   N     122.48  3.000
 PSS  H5A   C5   H5    106.90  3.000
 PSS  H5A   C5   C6    109.76  3.000
 PSS  H5    C5   C6    109.99  3.000
 PSS  C6    C5   C3    112.13  3.000
 PSS  H5A   C5   C3    109.20  3.000
 PSS  H5    C5   C3    108.72  3.000
 PSS  C11   C6   C7    118.39  3.000
 PSS  C7    C6   C5    121.26  3.000
 PSS  C11   C6   C5    120.35  3.000
 PSS  H7    C7   C8    119.46  3.000
 PSS  C8    C7   C6    120.95  3.000
 PSS  H7    C7   C6    119.58  3.000
 PSS  H8    C8   C9    120.07  3.000
 PSS  H8    C8   C7    119.80  3.000
 PSS  C9    C8   C7    120.13  3.000
 PSS  H9    C9   C10   120.26  3.000
 PSS  H9    C9   C8    120.27  3.000
 PSS  C10   C9   C8    119.47  3.000
 PSS  H10   C10  C11   119.78  3.000
 PSS  H10   C10  C9    120.09  3.000
 PSS  C11   C10  C9    120.12  3.000
 PSS  H11   C11  C10   119.55  3.000
 PSS  H11   C11  C6    119.51  3.000
 PSS  C10   C11  C6    120.93  3.000
 PSS  H12   C12  C13   105.85  3.000
 PSS  H12   C12  N     104.59  3.000
 PSS  C13   C12  N     113.97  3.000
 PSS  H12   C12  C     105.23  3.000
 PSS  C13   C12  C     114.86  3.000
 PSS  N     C12  C     111.22  3.000
 PSS  H13A  C13  H13   106.24  3.000
 PSS  H13A  C13  C14   108.90  3.000
 PSS  H13   C13  C14   109.72  3.000
 PSS  C14   C13  C12   113.73  3.000
 PSS  H13A  C13  C12   106.88  3.000
 PSS  H13   C13  C12   111.04  3.000
 PSS  H14A  C14  H14   106.00  3.000
 PSS  H14A  C14  C15   108.92  3.000
 PSS  H14   C14  C15   109.01  3.000
 PSS  H14A  C14  C13   110.17  3.000
 PSS  H14   C14  C13   109.87  3.000
 PSS  C15   C14  C13   112.64  3.000
 PSS  H15A  C15  H15   105.97  3.000
 PSS  H15A  C15  C16   109.62  3.000
 PSS  H15   C15  C16   109.55  3.000
 PSS  H15A  C15  C14   109.23  3.000
 PSS  H15   C15  C14   109.37  3.000
 PSS  C16   C15  C14   112.87  3.000
 PSS  H16B  C16  H16A  107.61  3.000
 PSS  H16B  C16  H16   107.63  3.000
 PSS  H16A  C16  H16   107.46  3.000
 PSS  H16B  C16  C15   111.70  3.000
 PSS  H16A  C16  C15   111.12  3.000
 PSS  H16   C16  C15   111.12  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
 PSS  CONST_01  C9   C10  C11  C6      0.00   0.0  0
 PSS  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 PSS  CONST_03  C10  C11  C6   C7      0.00   0.0  0
 PSS  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 PSS  CONST_05  C11  C6   C7   C8      0.00   0.0  0
 PSS  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 PSS  CONST_07  C3   C4   N    C2      0.00   0.0  0
 PSS  CONST_08  C10  C11  C6   C5    180.00   0.0  0
 PSS  CONST_09  C8   C7   C6   C5    180.00   0.0  0
 PSS  CONST_10  C2   N    C4   O1    180.00   0.0  0
 PSS  CONST_11  C12  N    C4   C3    180.00   0.0  0
 PSS  CONST_12  H10  C10  C11  C6    180.00   0.0  0
 PSS  CONST_13  H8   C8   C7   C6    180.00   0.0  0
 PSS  CONST_14  H11  C11  C6   C7    180.00   0.0  0
 PSS  CONST_15  H9   C9   C8   C7    180.00   0.0  0
 PSS  CONST_16  H7   C7   C8   C9    180.00   0.0  0
 PSS  CONST_17  C12  N    C4   O1      0.00   0.0  0
 PSS  Var_01    N1   C1   C2   N      46.63  30.0  1
 PSS  Var_02    C4   N    C2   C1     -9.45  30.0  1
 PSS  Var_03    C3   N1   C1   C2    -61.86  30.0  1
 PSS  Var_04    C11  C6   C5   C3     78.06  30.0  2
 PSS  Var_05    C15  C14  C13  C12  -170.79  30.0  2
 PSS  Var_06    C16  C15  C14  C13  -178.67  30.0  3
 PSS  Var_07    H16  C16  C15  C14   -59.13  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
 PSS  chir_01  C3   N1  C5   C4  positiv
 PSS  chir_02  C12  N   C13  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
 PSS  plan-1  C5   0.020
 PSS  plan-1  C6   0.020
 PSS  plan-1  C7   0.020
 PSS  plan-1  C8   0.020
 PSS  plan-1  C9   0.020
 PSS  plan-1  C10  0.020
 PSS  plan-1  C11  0.020
 PSS  plan-1  H7   0.020
 PSS  plan-1  H8   0.020
 PSS  plan-1  H9   0.020
 PSS  plan-1  H10  0.020
 PSS  plan-1  H11  0.020
 PSS  plan-2  C    0.020
 PSS  plan-2  O    0.020
 PSS  plan-2  C12  0.020
 PSS  plan-2  OXT  0.020
 PSS  plan-3  N    0.020
 PSS  plan-3  C2   0.020
 PSS  plan-3  C3   0.020
 PSS  plan-3  C4   0.020
 PSS  plan-3  C12  0.020
 PSS  plan-3  O1   0.020

