# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 11:56:57 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (2S,4R)-1-[(2R,3S)-3-amino-2-hydroxy-4-phenylbutyl]-4-(pyridin-4-ylsulfonyl)piperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@H](O)CN2CC[C@H](C[C@H]2C(O)=O)[S](=O)(=O)c3ccncc3
#
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
 SZ0  SZ0  '(2S,4R)-1-[(2R,3S)-3-amino-2-hydroxy-4-phenylbutyl]-4-(pyridin-4-ylsulfonyl)piperidine-2-carboxylic acid'  peptide  57  30  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SZ0
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
 SZ0  N    N  NH2   0  -0.780   4.3064   1.1593  -0.5982
 SZ0  C1   C  CH1   0  -0.133   3.8821  -0.1450  -0.1245
 SZ0  C2   C  CH1   0   0.051   2.4391  -0.1812   0.4215
 SZ0  O1   O  OH1   0  -0.662   2.1119  -1.4509   0.9515
 SZ0  C3   C  CH2   0  -0.517   4.8776  -0.6314   0.9372
 SZ0  C4   C  CR6   0   0.171   6.2673  -0.7913   0.3931
 SZ0  C5   C  CR16  0  -0.312   7.2278   0.2051   0.5469
 SZ0  C6   C  CR16  0  -0.313   6.6213  -1.9482  -0.2990
 SZ0  C7   C  CR16  0  -0.245   8.5081   0.0493   0.0321
 SZ0  C8   C  CR16  0  -0.241   7.8975  -2.1080  -0.8225
 SZ0  C9   C  CR16  0  -0.277   8.8475  -1.1082  -0.6571
 SZ0  C10  C  CH2   0  -0.322   1.4195   0.2546  -0.6278
 SZ0  N2   N  NT    0  -0.423   0.0658   0.3526  -0.0863
 SZ0  C11  C  CH1   0  -0.157  -0.6102   1.5843  -0.4293
 SZ0  C12  C  CH2   0  -0.438  -1.9930   1.6690   0.2402
 SZ0  C13  C  CH1   0  -0.471  -2.8178   0.4484  -0.1398
 SZ0  C14  C  CH2   0  -0.437  -2.0839  -0.8251   0.2370
 SZ0  C15  C  CH2   0  -0.290  -0.7233  -0.8165  -0.4382
 SZ0  C    C  C     0   0.520   0.1649   2.7893   0.0783
 SZ0  O    O  O     0  -0.422   0.8834   2.7916   1.0434
 SZ0  N3   N  N     0  -0.388  -6.7317  -2.9204  -1.1124
 SZ0  C17  C  CR16  0  -0.045  -6.1685  -3.0187   0.0839
 SZ0  C18  C  CR16  0  -0.312  -5.4531  -1.9879   0.6796
 SZ0  C19  C  CR6   0  -0.068  -5.3346  -0.8066  -0.0298
 SZ0  C20  C  CR16  0  -0.305  -5.9201  -0.6783  -1.2779
 SZ0  C21  C  CR16  0  -0.045  -6.6088  -1.7763  -1.7734
 SZ0  S1   S  S     0   1.234  -4.4297   0.5663   0.6587
 SZ0  O3   O  OS    0  -0.657  -4.2710   0.3346   2.0926
 SZ0  O4   O  OS    0  -0.658  -5.0780   1.7959   0.2092
 SZ0  H    H  HNH2  0   0.352   3.7713   1.4569  -1.4022
 SZ0  H1   H  HCH1  0   0.229   3.9359  -0.8318  -0.9808
 SZ0  H3   H  HCH1  0   0.222   2.3727   0.5150   1.2644
 SZ0  H4   H  HOH1  0   0.442   2.2185  -2.1072   0.2536
 SZ0  H5   H  HCH2  0   0.237   4.8803   0.0834   1.7675
 SZ0  H6   H  HCH2  0   0.249   4.5374  -1.5830   1.3480
 SZ0  H7   H  HCR6  0   0.237   6.9716   1.1109   1.0832
 SZ0  H8   H  HCR6  0   0.241   5.8885  -2.7373  -0.4277
 SZ0  H9   H  HCR6  0   0.250   9.2430   0.8326   0.1691
 SZ0  H10  H  HCR6  0   0.249   8.1522  -3.0157  -1.3550
 SZ0  H11  H  HCR6  0   0.250   9.8453  -1.2314  -1.0587
 SZ0  H12  H  HCH2  0   0.229   1.7280   1.2142  -1.0451
 SZ0  H13  H  HCH2  0   0.234   1.4462  -0.4451  -1.4768
 SZ0  H14  H  HCH1  0   0.253  -0.7535   1.6973  -1.5171
 SZ0  H15  H  HCH2  0   0.267  -1.8630   1.7085   1.3247
 SZ0  H16  H  HCH2  0   0.286  -2.4869   2.5860  -0.0803
 SZ0  H17  H  HCH1  0   0.321  -3.0344   0.4629  -1.2136
 SZ0  H18  H  HCH2  0   0.254  -1.9610  -0.8874   1.3199
 SZ0  H19  H  HCH2  0   0.267  -2.6270  -1.7114  -0.0951
 SZ0  H20  H  HCH2  0   0.207  -0.8655  -0.8966  -1.5293
 SZ0  H21  H  HCH2  0   0.258  -0.1793  -1.7063  -0.1270
 SZ0  H23  H  HCR6  0   0.302  -5.0167  -2.1221   1.6592
 SZ0  H24  H  HCR6  0   0.302  -5.8596   0.2324  -1.8579
 SZ0  H25  H  HCR6  0   0.284  -7.0828  -1.7197  -2.7460
 SZ0  H2   H  HNH2  0   0.337   4.1715   1.8585   0.1228
 SZ0  OXT  O  OH1   0  -0.587  -0.0948   3.8671  -0.6495
 SZ0  HXT  H  HOH1  0   0.485   0.3538   4.6400  -0.2735
 SZ0  H22  H  HCR6  0   0.284  -6.2866  -3.9618   0.6041

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
 SZ0  N    C1   single    1.451  0.020  1.451
 SZ0  N    H    single    0.860  0.020  0.860
 SZ0  N    H2   single    0.890  0.020  1.040
 SZ0  C1   C2   single    1.543  0.020  1.543
 SZ0  C1   C3   single    1.535  0.020  1.535
 SZ0  C1   H1   single    0.970  0.020  1.090
 SZ0  C2   O1   single    1.414  0.020  1.414
 SZ0  C2   C10  single    1.527  0.020  1.527
 SZ0  C2   H3   single    0.970  0.020  1.090
 SZ0  O1   H4   single    0.850  0.020  0.980
 SZ0  C3   C4   single    1.501  0.020  1.501
 SZ0  C3   H5   single    0.970  0.020  1.090
 SZ0  C3   H6   single    0.970  0.020  1.090
 SZ0  C4   C5   aromatic  1.393  0.020  1.393
 SZ0  C4   C6   aromatic  1.394  0.020  1.394
 SZ0  C5   C7   aromatic  1.389  0.020  1.389
 SZ0  C5   H7   single    0.930  0.020  1.080
 SZ0  C6   C8   aromatic  1.389  0.020  1.389
 SZ0  C6   H8   single    0.930  0.020  1.080
 SZ0  C7   C9   aromatic  1.389  0.020  1.389
 SZ0  C7   H9   single    0.930  0.020  1.080
 SZ0  C8   C9   aromatic  1.389  0.020  1.389
 SZ0  C8   H10  single    0.930  0.020  1.080
 SZ0  C9   H11  single    0.930  0.020  1.080
 SZ0  C10  H12  single    0.970  0.020  1.090
 SZ0  C10  H13  single    0.970  0.020  1.090
 SZ0  C10  N2   single    1.461  0.020  1.461
 SZ0  N2   C11  single    1.446  0.020  1.446
 SZ0  N2   C15  single    1.454  0.020  1.454
 SZ0  C11  C12  single    1.539  0.020  1.539
 SZ0  C11  C    single    1.520  0.020  1.520
 SZ0  C11  H14  single    0.970  0.020  1.090
 SZ0  C12  C13  single    1.521  0.020  1.521
 SZ0  C12  H15  single    0.970  0.020  1.090
 SZ0  C12  H16  single    0.970  0.020  1.090
 SZ0  C13  C14  single    1.517  0.020  1.517
 SZ0  C13  H17  single    0.970  0.020  1.090
 SZ0  C13  S1   single    1.803  0.020  1.803
 SZ0  C14  C15  single    1.519  0.020  1.519
 SZ0  C14  H18  single    0.970  0.020  1.090
 SZ0  C14  H19  single    0.970  0.020  1.090
 SZ0  C15  H20  single    0.970  0.020  1.090
 SZ0  C15  H21  single    0.970  0.020  1.090
 SZ0  C    O    double    1.231  0.020  1.231
 SZ0  C    OXT  single    1.326  0.020  1.326
 SZ0  N3   C17  aromatic  1.326  0.020  1.326
 SZ0  N3   C21  aromatic  1.327  0.020  1.327
 SZ0  C17  C18  aromatic  1.389  0.020  1.389
 SZ0  C17  H22  single    0.930  0.020  1.080
 SZ0  C18  C19  aromatic  1.383  0.020  1.383
 SZ0  C18  H23  single    0.930  0.020  1.080
 SZ0  C19  C20  aromatic  1.385  0.020  1.385
 SZ0  C19  S1   single    1.783  0.020  1.783
 SZ0  C20  C21  aromatic  1.388  0.020  1.388
 SZ0  C20  H24  single    0.930  0.020  1.080
 SZ0  C21  H25  single    0.930  0.020  1.080
 SZ0  S1   O3   double    1.461  0.020  1.461
 SZ0  S1   O4   double    1.461  0.020  1.461
 SZ0  OXT  HXT  single    0.850  0.020  0.980

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
 SZ0  H2   N    H    107.00  3.000
 SZ0  H2   N    C1   110.43  3.000
 SZ0  H    N    C1   111.69  3.000
 SZ0  H1   C1   C3   108.02  3.000
 SZ0  H1   C1   C2   107.87  3.000
 SZ0  C3   C1   C2   110.75  3.000
 SZ0  H1   C1   N    107.04  3.000
 SZ0  C3   C1   N    108.73  3.000
 SZ0  C2   C1   N    114.20  3.000
 SZ0  H3   C2   C10  107.88  3.000
 SZ0  H3   C2   O1   105.56  3.000
 SZ0  C10  C2   O1   111.05  3.000
 SZ0  H3   C2   C1   108.31  3.000
 SZ0  C10  C2   C1   112.00  3.000
 SZ0  O1   C2   C1   111.71  3.000
 SZ0  H4   O1   C2   108.33  3.000
 SZ0  H6   C3   H5   106.53  3.000
 SZ0  H6   C3   C4   109.41  3.000
 SZ0  H5   C3   C4   110.00  3.000
 SZ0  H6   C3   C1   109.56  3.000
 SZ0  H5   C3   C1   108.61  3.000
 SZ0  C4   C3   C1   112.56  3.000
 SZ0  C6   C4   C5   118.27  3.000
 SZ0  C6   C4   C3   120.24  3.000
 SZ0  C5   C4   C3   121.49  3.000
 SZ0  H7   C5   C7   119.70  3.000
 SZ0  H7   C5   C4   119.33  3.000
 SZ0  C7   C5   C4   120.97  3.000
 SZ0  H8   C6   C8   119.51  3.000
 SZ0  H8   C6   C4   119.42  3.000
 SZ0  C8   C6   C4   121.07  3.000
 SZ0  H9   C7   C9   119.98  3.000
 SZ0  H9   C7   C5   119.84  3.000
 SZ0  C9   C7   C5   120.18  3.000
 SZ0  H10  C8   C9   120.07  3.000
 SZ0  H10  C8   C6   119.87  3.000
 SZ0  C9   C8   C6   120.06  3.000
 SZ0  H11  C9   C8   120.28  3.000
 SZ0  H11  C9   C7   120.27  3.000
 SZ0  C8   C9   C7   119.45  3.000
 SZ0  H13  C10  H12  104.91  3.000
 SZ0  H13  C10  N2   110.55  3.000
 SZ0  H12  C10  N2   110.16  3.000
 SZ0  N2   C10  C2   112.53  3.000
 SZ0  H13  C10  C2   109.43  3.000
 SZ0  H12  C10  C2   108.97  3.000
 SZ0  C15  N2   C11  111.95  3.000
 SZ0  C15  N2   C10  111.05  3.000
 SZ0  C11  N2   C10  113.72  3.000
 SZ0  H14  C11  C    108.32  3.000
 SZ0  H14  C11  C12  107.86  3.000
 SZ0  C    C11  C12  105.62  3.000
 SZ0  H14  C11  N2   112.45  3.000
 SZ0  C    C11  N2   110.95  3.000
 SZ0  C12  C11  N2   111.33  3.000
 SZ0  H16  C12  H15  108.38  3.000
 SZ0  H16  C12  C13  110.85  3.000
 SZ0  H15  C12  C13  109.95  3.000
 SZ0  H16  C12  C11  109.01  3.000
 SZ0  H15  C12  C11  109.08  3.000
 SZ0  C13  C12  C11  109.54  3.000
 SZ0  H17  C13  S1   104.86  3.000
 SZ0  S1   C13  C14  112.17  3.000
 SZ0  H17  C13  C14  110.49  3.000
 SZ0  S1   C13  C12  108.77  3.000
 SZ0  H17  C13  C12  109.96  3.000
 SZ0  C14  C13  C12  110.43  3.000
 SZ0  H19  C14  H18  108.15  3.000
 SZ0  H19  C14  C15  108.37  3.000
 SZ0  H18  C14  C15  109.91  3.000
 SZ0  H19  C14  C13  111.43  3.000
 SZ0  H18  C14  C13  110.40  3.000
 SZ0  C15  C14  C13  108.55  3.000
 SZ0  H21  C15  H20  106.74  3.000
 SZ0  H21  C15  C14  108.42  3.000
 SZ0  H20  C15  C14  108.89  3.000
 SZ0  H21  C15  N2   108.48  3.000
 SZ0  H20  C15  N2   111.58  3.000
 SZ0  C14  C15  N2   112.53  3.000
 SZ0  OXT  C    O    123.75  3.000
 SZ0  OXT  C    C11  111.17  3.000
 SZ0  O    C    C11  125.02  3.000
 SZ0  C21  N3   C17  118.30  3.000
 SZ0  H22  C17  C18  119.75  3.000
 SZ0  H22  C17  N3   116.84  3.000
 SZ0  C18  C17  N3   123.42  3.000
 SZ0  H23  C18  C19  122.44  3.000
 SZ0  H23  C18  C17  120.30  3.000
 SZ0  C19  C18  C17  117.26  3.000
 SZ0  S1   C19  C20  119.44  3.000
 SZ0  S1   C19  C18  120.21  3.000
 SZ0  C20  C19  C18  120.35  3.000
 SZ0  H24  C20  C21  120.18  3.000
 SZ0  H24  C20  C19  122.54  3.000
 SZ0  C21  C20  C19  117.28  3.000
 SZ0  H25  C21  C20  119.76  3.000
 SZ0  H25  C21  N3   116.85  3.000
 SZ0  C20  C21  N3   123.39  3.000
 SZ0  O4   S1   O3   118.92  3.000
 SZ0  O4   S1   C19  107.70  3.000
 SZ0  O3   S1   C19  108.18  3.000
 SZ0  O4   S1   C13  108.40  3.000
 SZ0  O3   S1   C13  109.10  3.000
 SZ0  C19  S1   C13  103.44  3.000
 SZ0  HXT  OXT  C    110.15  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
 SZ0  CONST_01  C9   C7   C5   C4     0.00   0.0  0
 SZ0  CONST_02  C9   C8   C6   C4     0.00   0.0  0
 SZ0  CONST_03  C8   C6   C4   C5     0.00   0.0  0
 SZ0  CONST_04  C8   C9   C7   C5     0.00   0.0  0
 SZ0  CONST_05  C7   C5   C4   C6     0.00   0.0  0
 SZ0  CONST_06  C7   C9   C8   C6     0.00   0.0  0
 SZ0  CONST_07  C19  C18  C17  N3     0.00   0.0  0
 SZ0  CONST_08  C19  C20  C21  N3     0.00   0.0  0
 SZ0  CONST_09  C20  C21  N3   C17    0.00   0.0  0
 SZ0  CONST_10  C20  C19  C18  C17    0.00   0.0  0
 SZ0  CONST_11  C21  N3   C17  C18    0.00   0.0  0
 SZ0  CONST_12  C21  C20  C19  C18    0.00   0.0  0
 SZ0  CONST_13  C7   C5   C4   C3   180.00   0.0  0
 SZ0  CONST_14  C8   C6   C4   C3   180.00   0.0  0
 SZ0  CONST_15  S1   C19  C18  C17  180.00   0.0  0
 SZ0  CONST_16  S1   C19  C20  C21  180.00   0.0  0
 SZ0  CONST_17  H9   C7   C5   C4   180.00   0.0  0
 SZ0  CONST_18  H10  C8   C6   C4   180.00   0.0  0
 SZ0  CONST_19  H8   C6   C4   C5   180.00   0.0  0
 SZ0  CONST_20  H11  C9   C7   C5   180.00   0.0  0
 SZ0  CONST_21  H7   C5   C4   C6   180.00   0.0  0
 SZ0  CONST_22  H23  C18  C17  N3   180.00   0.0  0
 SZ0  CONST_23  H24  C20  C21  N3   180.00   0.0  0
 SZ0  CONST_24  H25  C21  N3   C17  180.00   0.0  0
 SZ0  CONST_25  H22  C17  C18  C19  180.00   0.0  0
 SZ0  CONST_26  HXT  OXT  C    C11  180.00   0.0  0
 SZ0  Var_01    C13  C14  C15  N2    57.21  30.0  1
 SZ0  Var_02    C14  C15  N2   C11  -58.19  30.0  1
 SZ0  Var_03    C18  C19  S1   C13   98.97  30.0  2
 SZ0  Var_04    C5   C4   C3   C1    97.05  30.0  2
 SZ0  Var_05    C11  N2   C10  C2   131.84  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
 SZ0  chir_01  C1   N   C2   C3   positiv
 SZ0  chir_02  C2   O1  C1   C10  negativ
 SZ0  chir_03  C11  N2  C    C12  positiv
 SZ0  chir_04  C13  S1  C14  C12  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
 SZ0  plan-1  C3   0.020
 SZ0  plan-1  C4   0.020
 SZ0  plan-1  C5   0.020
 SZ0  plan-1  C6   0.020
 SZ0  plan-1  C7   0.020
 SZ0  plan-1  C8   0.020
 SZ0  plan-1  C9   0.020
 SZ0  plan-1  H7   0.020
 SZ0  plan-1  H8   0.020
 SZ0  plan-1  H9   0.020
 SZ0  plan-1  H10  0.020
 SZ0  plan-1  H11  0.020
 SZ0  plan-2  N3   0.020
 SZ0  plan-2  C17  0.020
 SZ0  plan-2  C18  0.020
 SZ0  plan-2  C19  0.020
 SZ0  plan-2  C20  0.020
 SZ0  plan-2  C21  0.020
 SZ0  plan-2  S1   0.020
 SZ0  plan-2  H23  0.020
 SZ0  plan-2  H24  0.020
 SZ0  plan-2  H25  0.020
 SZ0  plan-2  H22  0.020
 SZ0  plan-3  C11  0.020
 SZ0  plan-3  C    0.020
 SZ0  plan-3  O    0.020
 SZ0  plan-3  OXT  0.020
 SZ0  plan-3  HXT  0.020

