# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 17:51:47 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2S,4R)-1-[(2R,3S)-3-amino-2-hydroxy-4-phenylbutyl]-4-[(pyridin-3-ylmethyl)sulfanyl]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)SCc3cccnc3
#
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
 P0Y  P0Y  '(2S,4R)-1-[(2R,3S)-3-amino-2-hydroxy-4-phenylbutyl]-4-[(pyridin-3-ylmethyl)sulfanyl]piperidine-2-carboxylic acid'  peptide  58  29  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_P0Y
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
 P0Y  N    N  NH2   0  -0.785   -4.3621   1.0958   0.1171
 P0Y  CA1  C  CH1   0  -0.139   -4.1332  -0.3397   0.1193
 P0Y  CC   C  CH1   0   0.067   -2.6811  -0.5999  -0.3119
 P0Y  O1   O  OH1   0  -0.664   -2.4207  -1.9743  -0.5119
 P0Y  CB1  C  CH2   0  -0.510   -5.1297  -1.1334  -0.7492
 P0Y  CG   C  CR6   0   0.128   -6.5509  -0.8822  -0.3342
 P0Y  CD1  C  CR16  0  -0.321   -7.3466   0.0487  -0.9990
 P0Y  CD2  C  CR16  0  -0.302   -7.0918  -1.5467   0.7668
 P0Y  CE1  C  CR16  0  -0.241   -8.6467   0.3066  -0.5811
 P0Y  CE2  C  CR16  0  -0.241   -8.3886  -1.2920   1.1898
 P0Y  CZ   C  CR16  0  -0.274   -9.1719  -0.3622   0.5158
 P0Y  CM   C  CH2   0  -0.315   -1.6912   0.0299   0.6627
 P0Y  N11  N  NT    0  -0.426   -0.3244   0.0491   0.1473
 P0Y  C21  C  CH1   0  -0.152    0.3207   1.3350   0.3007
 P0Y  C31  C  CH2   0  -0.431    1.7391   1.3359  -0.2959
 P0Y  C41  C  CH1   0  -0.396    2.5742   0.2168   0.3056
 P0Y  C51  C  CH2   0  -0.418    1.8589  -1.1050   0.0956
 P0Y  C61  C  CH2   0  -0.290    0.4702  -1.0340   0.7072
 P0Y  C    C  C     0   0.519   -0.4431   2.4117  -0.4512
 P0Y  O    O  O     0  -0.428   -1.0635   2.2362  -1.4683
 P0Y  N12  N  N     0  -0.401    8.6751   0.4061   0.6122
 P0Y  C22  C  CR16  0  -0.080    7.3901   0.2230   0.8798
 P0Y  C32  C  CR6   0   0.025    6.6004  -0.7514   0.2749
 P0Y  C42  C  CR16  0  -0.176    7.2059  -1.5689  -0.6710
 P0Y  C52  C  CR16  0  -0.319    8.5495  -1.3866  -0.9603
 P0Y  C62  C  CR16  0  -0.071    9.2398  -0.3863  -0.2932
 P0Y  S    S  S2    0   0.005    4.2249   0.2793  -0.4576
 P0Y  H    H  HNH2  0   0.338   -4.3178   1.4475  -0.8329
 P0Y  HA1  H  HCH1  0   0.226   -4.2496  -0.6800   1.1572
 P0Y  HC   H  HCH1  0   0.220   -2.5287  -0.1338  -1.2909
 P0Y  HOR  H  HOH1  0   0.441   -2.5367  -2.4315   0.3284
 P0Y  HB2  H  HCH2  0   0.235   -4.9910  -0.8478  -1.7971
 P0Y  HB3  H  HCH2  0   0.242   -4.9145  -2.2008  -0.6788
 P0Y  HD1  H  HCR6  0   0.247   -6.9477   0.5727  -1.8599
 P0Y  HD2  H  HCR6  0   0.245   -6.4881  -2.2752   1.2964
 P0Y  HE1  H  HCR6  0   0.253   -9.2492   1.0313  -1.1137
 P0Y  HE2  H  HCR6  0   0.252   -8.7904  -1.8212   2.0448
 P0Y  HZ   H  HCR6  0   0.253  -10.1850  -0.1644   0.8413
 P0Y  HM1  H  HCH2  0   0.252   -2.0412   1.0388   0.8830
 P0Y  HM2  H  HCH2  0   0.221   -1.7370  -0.5043   1.6243
 P0Y  H1   H  HCH1  0   0.241    0.4009   1.6384   1.3582
 P0Y  H31  H  HCH2  0   0.249    1.6731   1.1992  -1.3798
 P0Y  H32  H  HCH2  0   0.267    2.2040   2.3050  -0.1072
 P0Y  H41  H  HCH1  0   0.272    2.7034   0.4017   1.3778
 P0Y  H51  H  HCH2  0   0.229    1.7877  -1.3151  -0.9749
 P0Y  H52  H  HCH2  0   0.250    2.4060  -1.9290   0.5576
 P0Y  H61  H  HCH2  0   0.196    0.5666  -0.9373   1.8031
 P0Y  H62  H  HCH2  0   0.247   -0.0515  -1.9718   0.5212
 P0Y  H42  H  HCR6  0   0.272    6.6345  -2.3421  -1.1700
 P0Y  H53  H  HCR6  0   0.273    9.0555  -2.0068  -1.6874
 P0Y  H63  H  HCR6  0   0.265   10.2914  -0.2188  -0.4970
 P0Y  H2   H  HNH2  0   0.353   -5.2974   1.2988   0.4471
 P0Y  OXT  O  OH1   0  -0.590   -0.2916   3.6011   0.1187
 P0Y  HXT  H  HOH1  0   0.482   -0.7241   4.2841  -0.4162
 P0Y  CE   C  CH2   0  -0.630    5.1478  -0.8731   0.6120
 P0Y  H21  H  HCR6  0   0.261    6.9506   0.8827   1.6228
 P0Y  H11  H  HCH2  0   0.287    4.8009  -1.8946   0.4556
 P0Y  H2A  H  HCH2  0   0.288    4.9651  -0.6041   1.6536

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
 P0Y  N    CA1  single    1.454  0.020  1.454
 P0Y  N    H    single    0.860  0.020  0.860
 P0Y  CA1  CC   single    1.537  0.020  1.537
 P0Y  CA1  CB1  single    1.542  0.020  1.542
 P0Y  CA1  HA1  single    0.970  0.020  1.090
 P0Y  CC   O1   single    1.413  0.020  1.413
 P0Y  CC   CM   single    1.525  0.020  1.525
 P0Y  CC   HC   single    0.970  0.020  1.090
 P0Y  O1   HOR  single    0.850  0.020  0.980
 P0Y  CB1  CG   single    1.502  0.020  1.502
 P0Y  CB1  HB2  single    0.970  0.020  1.090
 P0Y  CB1  HB3  single    0.970  0.020  1.090
 P0Y  CG   CD1  aromatic  1.393  0.020  1.393
 P0Y  CG   CD2  aromatic  1.395  0.020  1.395
 P0Y  CD1  CE1  aromatic  1.390  0.020  1.390
 P0Y  CD1  HD1  single    0.930  0.020  1.080
 P0Y  CD2  CE2  aromatic  1.388  0.020  1.388
 P0Y  CD2  HD2  single    0.930  0.020  1.080
 P0Y  CE1  CZ   aromatic  1.388  0.020  1.388
 P0Y  CE1  HE1  single    0.930  0.020  1.080
 P0Y  CE2  CZ   aromatic  1.390  0.020  1.390
 P0Y  CE2  HE2  single    0.930  0.020  1.080
 P0Y  CZ   HZ   single    0.930  0.020  1.080
 P0Y  CM   HM1  single    0.970  0.020  1.090
 P0Y  CM   HM2  single    0.970  0.020  1.090
 P0Y  CM   N11  single    1.461  0.020  1.461
 P0Y  N11  C21  single    1.447  0.020  1.447
 P0Y  N11  C61  single    1.455  0.020  1.455
 P0Y  C21  C31  single    1.539  0.020  1.539
 P0Y  C21  C    single    1.519  0.020  1.519
 P0Y  C21  H1   single    0.970  0.020  1.090
 P0Y  C31  C41  single    1.520  0.020  1.520
 P0Y  C31  H31  single    0.970  0.020  1.090
 P0Y  C31  H32  single    0.970  0.020  1.090
 P0Y  C41  C51  single    1.518  0.020  1.518
 P0Y  C41  H41  single    0.970  0.020  1.090
 P0Y  C41  S    single    1.820  0.020  1.820
 P0Y  C51  C61  single    1.519  0.020  1.519
 P0Y  C51  H51  single    0.970  0.020  1.090
 P0Y  C51  H52  single    0.970  0.020  1.090
 P0Y  C61  H61  single    0.970  0.020  1.090
 P0Y  C61  H62  single    0.970  0.020  1.090
 P0Y  C    O    double    1.231  0.020  1.231
 P0Y  N12  C22  aromatic  1.325  0.020  1.325
 P0Y  N12  C62  aromatic  1.329  0.020  1.329
 P0Y  C22  C32  aromatic  1.393  0.020  1.393
 P0Y  C22  H21  single    0.930  0.020  1.080
 P0Y  C32  C42  aromatic  1.389  0.020  1.389
 P0Y  C32  CE   single    1.496  0.020  1.496
 P0Y  C42  C52  aromatic  1.386  0.020  1.386
 P0Y  C42  H42  single    0.930  0.020  1.080
 P0Y  C52  C62  aromatic  1.386  0.020  1.386
 P0Y  C52  H53  single    0.930  0.020  1.080
 P0Y  C62  H63  single    0.930  0.020  1.080
 P0Y  CE   S    single    1.823  0.020  1.823
 P0Y  CE   H11  single    0.970  0.020  1.090
 P0Y  CE   H2A  single    0.970  0.020  1.090
 P0Y  N    H2   single    0.890  0.020  1.040
 P0Y  C    OXT  single    1.328  0.020  1.328
 P0Y  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
 P0Y  H2   N    H    106.04  3.000
 P0Y  H2   N    CA1  110.06  3.000
 P0Y  H    N    CA1  109.70  3.000
 P0Y  HA1  CA1  CB1  107.71  3.000
 P0Y  HA1  CA1  CC   108.23  3.000
 P0Y  CB1  CA1  CC   111.43  3.000
 P0Y  HA1  CA1  N    106.90  3.000
 P0Y  CB1  CA1  N    113.94  3.000
 P0Y  CC   CA1  N    108.39  3.000
 P0Y  HC   CC   CM   107.77  3.000
 P0Y  HC   CC   O1   105.18  3.000
 P0Y  CM   CC   O1   111.86  3.000
 P0Y  HC   CC   CA1  108.08  3.000
 P0Y  CM   CC   CA1  111.34  3.000
 P0Y  O1   CC   CA1  112.24  3.000
 P0Y  HOR  O1   CC   108.42  3.000
 P0Y  HB3  CB1  HB2  106.97  3.000
 P0Y  HB3  CB1  CG   109.42  3.000
 P0Y  HB2  CB1  CG   109.92  3.000
 P0Y  HB3  CB1  CA1  109.87  3.000
 P0Y  HB2  CB1  CA1  108.84  3.000
 P0Y  CG   CB1  CA1  111.71  3.000
 P0Y  CD2  CG   CD1  118.25  3.000
 P0Y  CD2  CG   CB1  120.35  3.000
 P0Y  CD1  CG   CB1  121.35  3.000
 P0Y  HD1  CD1  CE1  119.57  3.000
 P0Y  HD1  CD1  CG   119.45  3.000
 P0Y  CE1  CD1  CG   120.98  3.000
 P0Y  HD2  CD2  CE2  119.66  3.000
 P0Y  HD2  CD2  CG   119.32  3.000
 P0Y  CE2  CD2  CG   121.03  3.000
 P0Y  HE1  CE1  CZ   120.05  3.000
 P0Y  HE1  CE1  CD1  119.80  3.000
 P0Y  CZ   CE1  CD1  120.15  3.000
 P0Y  HE2  CE2  CZ   120.04  3.000
 P0Y  HE2  CE2  CD2  119.85  3.000
 P0Y  CZ   CE2  CD2  120.11  3.000
 P0Y  HZ   CZ   CE2  120.26  3.000
 P0Y  HZ   CZ   CE1  120.25  3.000
 P0Y  CE2  CZ   CE1  119.49  3.000
 P0Y  HM2  CM   HM1  105.02  3.000
 P0Y  HM2  CM   N11  110.70  3.000
 P0Y  HM1  CM   N11  111.06  3.000
 P0Y  N11  CM   CC   112.78  3.000
 P0Y  HM2  CM   CC   109.32  3.000
 P0Y  HM1  CM   CC   107.63  3.000
 P0Y  C61  N11  C21  112.16  3.000
 P0Y  C61  N11  CM   111.43  3.000
 P0Y  C21  N11  CM   113.05  3.000
 P0Y  H1   C21  C    108.43  3.000
 P0Y  H1   C21  C31  107.72  3.000
 P0Y  C    C21  C31  105.73  3.000
 P0Y  H1   C21  N11  112.24  3.000
 P0Y  C    C21  N11  110.69  3.000
 P0Y  C31  C21  N11  111.74  3.000
 P0Y  H32  C31  H31  107.93  3.000
 P0Y  H32  C31  C41  110.57  3.000
 P0Y  H31  C31  C41  109.45  3.000
 P0Y  H32  C31  C21  109.04  3.000
 P0Y  H31  C31  C21  109.16  3.000
 P0Y  C41  C31  C21  110.64  3.000
 P0Y  H41  C41  S    107.32  3.000
 P0Y  S    C41  C51  113.55  3.000
 P0Y  H41  C41  C51  109.76  3.000
 P0Y  S    C41  C31  107.88  3.000
 P0Y  H41  C41  C31  109.13  3.000
 P0Y  C51  C41  C31  109.11  3.000
 P0Y  H52  C51  H51  107.58  3.000
 P0Y  H52  C51  C61  108.85  3.000
 P0Y  H51  C51  C61  110.11  3.000
 P0Y  H52  C51  C41  111.26  3.000
 P0Y  H51  C51  C41  109.49  3.000
 P0Y  C61  C51  C41  109.54  3.000
 P0Y  H62  C61  H61  106.66  3.000
 P0Y  H62  C61  C51  109.20  3.000
 P0Y  H61  C61  C51  108.90  3.000
 P0Y  H62  C61  N11  108.27  3.000
 P0Y  H61  C61  N11  111.36  3.000
 P0Y  C51  C61  N11  112.27  3.000
 P0Y  OXT  C    O    123.50  3.000
 P0Y  OXT  C    C21  111.42  3.000
 P0Y  O    C    C21  125.01  3.000
 P0Y  C62  N12  C22  117.85  3.000
 P0Y  H21  C22  C32  119.51  3.000
 P0Y  H21  C22  N12  116.52  3.000
 P0Y  C32  C22  N12  123.97  3.000
 P0Y  CE   C32  C42  121.92  3.000
 P0Y  CE   C32  C22  120.64  3.000
 P0Y  C42  C32  C22  117.41  3.000
 P0Y  H42  C42  C52  120.60  3.000
 P0Y  H42  C42  C32  120.25  3.000
 P0Y  C52  C42  C32  119.15  3.000
 P0Y  H53  C52  C62  120.29  3.000
 P0Y  H53  C52  C42  121.22  3.000
 P0Y  C62  C52  C42  118.49  3.000
 P0Y  H63  C62  C52  120.26  3.000
 P0Y  H63  C62  N12  116.62  3.000
 P0Y  C52  C62  N12  123.12  3.000
 P0Y  CE   S    C41  101.04  3.000
 P0Y  HXT  OXT  C    110.09  3.000
 P0Y  H2A  CE   H11  108.34  3.000
 P0Y  H2A  CE   S    108.63  3.000
 P0Y  H11  CE   S    110.31  3.000
 P0Y  H2A  CE   C32  110.95  3.000
 P0Y  H11  CE   C32  110.67  3.000
 P0Y  S    CE   C32  107.93  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
 P0Y  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 P0Y  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 P0Y  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 P0Y  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 P0Y  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 P0Y  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 P0Y  CONST_07  C42  C32  C22  N12     0.00   0.0  0
 P0Y  CONST_08  C42  C52  C62  N12     0.00   0.0  0
 P0Y  CONST_09  C52  C62  N12  C22     0.00   0.0  0
 P0Y  CONST_10  C52  C42  C32  C22     0.00   0.0  0
 P0Y  CONST_11  C62  N12  C22  C32     0.00   0.0  0
 P0Y  CONST_12  C62  C52  C42  C32     0.00   0.0  0
 P0Y  CONST_13  CE1  CD1  CG   CB1   180.00   0.0  0
 P0Y  CONST_14  CE2  CD2  CG   CB1   180.00   0.0  0
 P0Y  CONST_15  CE   C32  C22  N12   180.00   0.0  0
 P0Y  CONST_16  CE   C32  C42  C52   180.00   0.0  0
 P0Y  CONST_17  HE1  CE1  CD1  CG    180.00   0.0  0
 P0Y  CONST_18  HE2  CE2  CD2  CG    180.00   0.0  0
 P0Y  CONST_19  HD2  CD2  CG   CD1   180.00   0.0  0
 P0Y  CONST_20  HZ   CZ   CE1  CD1   180.00   0.0  0
 P0Y  CONST_21  HD1  CD1  CG   CD2   180.00   0.0  0
 P0Y  CONST_22  H53  C52  C62  N12   180.00   0.0  0
 P0Y  CONST_23  H63  C62  N12  C22   180.00   0.0  0
 P0Y  CONST_24  H42  C42  C32  C22   180.00   0.0  0
 P0Y  CONST_25  H21  C22  C32  C42   180.00   0.0  0
 P0Y  CONST_26  HXT  OXT  C    C21   180.00   0.0  0
 P0Y  Var_01    C41  C51  C61  N11    57.83  30.0  1
 P0Y  Var_02    C51  C61  N11  C21   -57.04  30.0  1
 P0Y  Var_03    CD1  CG   CB1  CA1    97.34  30.0  2
 P0Y  Var_04    C21  N11  CM   CC    132.44  30.0  3
 P0Y  Var_05    C32  CE   S    C41  -169.81  30.0  1
 P0Y  Var_06    S    CE   C32  C22    85.99  30.0  2

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
 P0Y  chir_01  CA1  N    CC   CB1  positiv
 P0Y  chir_02  CC   O1   CA1  CM   negativ
 P0Y  chir_03  C21  N11  C    C31  positiv
 P0Y  chir_04  C41  S    C51  C31  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
 P0Y  plan-1  CB1  0.020
 P0Y  plan-1  CG   0.020
 P0Y  plan-1  CD1  0.020
 P0Y  plan-1  CD2  0.020
 P0Y  plan-1  CE1  0.020
 P0Y  plan-1  CE2  0.020
 P0Y  plan-1  CZ   0.020
 P0Y  plan-1  HD1  0.020
 P0Y  plan-1  HD2  0.020
 P0Y  plan-1  HE1  0.020
 P0Y  plan-1  HE2  0.020
 P0Y  plan-1  HZ   0.020
 P0Y  plan-2  N12  0.020
 P0Y  plan-2  C22  0.020
 P0Y  plan-2  C32  0.020
 P0Y  plan-2  C42  0.020
 P0Y  plan-2  C52  0.020
 P0Y  plan-2  C62  0.020
 P0Y  plan-2  H42  0.020
 P0Y  plan-2  H53  0.020
 P0Y  plan-2  H63  0.020
 P0Y  plan-2  CE   0.020
 P0Y  plan-2  H21  0.020
 P0Y  plan-3  C21  0.020
 P0Y  plan-3  C    0.020
 P0Y  plan-3  O    0.020
 P0Y  plan-3  OXT  0.020
 P0Y  plan-3  HXT  0.020

