# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:03:30 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 3-[(2R)-piperidin-2-yl]-1-(1,3-thiazol-2-yl)propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC[C@H]1CCCCN1)c2sccn2
#
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
 5TP  5TP  3-[(2R)-piperidin-2-yl]-1-(1,3-thiazol-2-yl)propan-1-one  peptide  31  15  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_5TP
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
 5TP  N11   N  NH1   0  -0.580   2.7425   0.8929  -0.6057
 5TP  C21   C  CH1   0  -0.090   2.5619  -0.1920   0.3518
 5TP  C31   C  CH2   0  -0.419   3.7433  -1.1650   0.3739
 5TP  C41   C  CH2   0  -0.441   5.0574  -0.4252   0.6047
 5TP  C51   C  CH2   0  -0.439   5.2247   0.7044  -0.4061
 5TP  C61   C  CH2   0  -0.310   3.9943   1.6081  -0.4066
 5TP  C1'   C  CH2   0  -0.428   1.2513  -0.9223   0.0861
 5TP  C2'   C  CH2   0  -0.556   0.0403  -0.0094   0.1811
 5TP  S1    S  S2    0   0.289  -4.0275  -0.6460  -0.1829
 5TP  O2    O  O     0  -0.390  -1.3680  -1.8755  -0.3614
 5TP  C52   C  CR15  0  -0.492  -4.7779   0.8440   0.1548
 5TP  C22   C  CR5   0  -0.061  -2.4962   0.0999   0.0821
 5TP  C2'1  C  C     0   0.398  -1.2642  -0.7066  -0.0587
 5TP  C42   C  CR15  0  -0.017  -3.8366   1.7902   0.4419
 5TP  N3    N  N     0  -0.365  -2.5522   1.3571   0.3977
 5TP  H21   H  HCH1  0   0.211   2.5015   0.2753   1.3451
 5TP  H31   H  HCH2  0   0.223   3.5892  -1.9170   1.1530
 5TP  H32   H  HCH2  0   0.206   3.7813  -1.7049  -0.5804
 5TP  H41   H  HCH2  0   0.211   5.0619  -0.0088   1.6181
 5TP  H42   H  HCH2  0   0.229   5.9003  -1.1179   0.5511
 5TP  H51   H  HCH2  0   0.224   6.1216   1.2907  -0.1891
 5TP  H52   H  HCH2  0   0.211   5.3591   0.2828  -1.4083
 5TP  H61   H  HCH2  0   0.231   4.0827   2.3736  -1.1806
 5TP  H62   H  HCH2  0   0.212   3.9337   2.1397   0.5498
 5TP  H1'1  H  HCH2  0   0.225   1.2949  -1.3905  -0.9028
 5TP  H1'2  H  HCH2  0   0.236   1.1605  -1.7381   0.8075
 5TP  H2'1  H  HCH2  0   0.272  -0.0063   0.4740   1.1626
 5TP  H2'2  H  HCH2  0   0.281   0.1177   0.8170  -0.5313
 5TP  H43   H  HCR5  0   0.281  -4.0535   2.8187   0.6909
 5TP  H2    H  HNH1  0   0.330   2.7360   0.5025  -1.5435
 5TP  H5    H  HCR5  0   0.319  -5.8497   0.9612   0.1304

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
 5TP  N11  C21   single    1.458  0.020  1.458
 5TP  N11  C61   single    1.455  0.020  1.455
 5TP  C21  C31   single    1.531  0.020  1.531
 5TP  C21  C1'   single    1.524  0.020  1.524
 5TP  C21  H21   single    0.970  0.020  1.090
 5TP  C31  C41   single    1.526  0.020  1.526
 5TP  C31  H31   single    0.970  0.020  1.090
 5TP  C31  H32   single    0.970  0.020  1.090
 5TP  C41  C51   single    1.525  0.020  1.525
 5TP  C41  H41   single    0.970  0.020  1.090
 5TP  C41  H42   single    0.970  0.020  1.090
 5TP  C51  C61   single    1.527  0.020  1.527
 5TP  C51  H51   single    0.970  0.020  1.090
 5TP  C51  H52   single    0.970  0.020  1.090
 5TP  C61  H61   single    0.970  0.020  1.090
 5TP  C61  H62   single    0.970  0.020  1.090
 5TP  C1'  C2'   single    1.519  0.020  1.519
 5TP  C1'  H1'1  single    0.970  0.020  1.090
 5TP  C1'  H1'2  single    0.970  0.020  1.090
 5TP  C2'  H2'1  single    0.970  0.020  1.090
 5TP  C2'  H2'2  single    0.970  0.020  1.090
 5TP  S1   C52   aromatic  1.702  0.020  1.702
 5TP  S1   C22   aromatic  1.724  0.020  1.724
 5TP  O2   C2'1  double    1.212  0.020  1.212
 5TP  C52  C42   aromatic  1.365  0.020  1.365
 5TP  C52  H5    single    0.930  0.020  1.080
 5TP  C22  C2'1  single    1.479  0.020  1.479
 5TP  C22  N3    aromatic  1.297  0.020  1.297
 5TP  C42  N3    aromatic  1.356  0.020  1.356
 5TP  C42  H43   single    0.930  0.020  1.080
 5TP  C2'  C2'1  single    1.498  0.020  1.498
 5TP  N11  H2    single    0.890  0.020  1.040

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
 5TP  H2    N11   C61   108.70  3.000
 5TP  H2    N11   C21   108.63  3.000
 5TP  C61   N11   C21   112.48  3.000
 5TP  H21   C21   C1'   108.31  3.000
 5TP  H21   C21   C31   107.43  3.000
 5TP  C1'   C21   C31   111.20  3.000
 5TP  H21   C21   N11   106.49  3.000
 5TP  C1'   C21   N11   110.40  3.000
 5TP  C31   C21   N11   112.76  3.000
 5TP  H32   C31   H31   106.63  3.000
 5TP  H32   C31   C41   109.90  3.000
 5TP  H31   C31   C41   110.30  3.000
 5TP  H32   C31   C21   109.08  3.000
 5TP  H31   C31   C21   109.79  3.000
 5TP  C41   C31   C21   111.02  3.000
 5TP  H42   C41   H41   106.46  3.000
 5TP  H42   C41   C51   110.64  3.000
 5TP  H41   C41   C51   109.33  3.000
 5TP  H42   C41   C31   110.47  3.000
 5TP  H41   C41   C31   109.13  3.000
 5TP  C51   C41   C31   110.70  3.000
 5TP  H52   C51   H51   106.69  3.000
 5TP  H52   C51   C61   109.05  3.000
 5TP  H51   C51   C61   110.11  3.000
 5TP  H52   C51   C41   109.56  3.000
 5TP  H51   C51   C41   110.83  3.000
 5TP  C61   C51   C41   110.51  3.000
 5TP  H62   C61   H61   106.43  3.000
 5TP  H62   C61   C51   109.36  3.000
 5TP  H61   C61   C51   110.49  3.000
 5TP  H62   C61   N11   108.07  3.000
 5TP  H61   C61   N11   108.48  3.000
 5TP  C51   C61   N11   113.73  3.000
 5TP  H1'2  C1'   H1'1  106.28  3.000
 5TP  H1'2  C1'   C2'   109.94  3.000
 5TP  H1'1  C1'   C2'   110.19  3.000
 5TP  H1'2  C1'   C21   108.31  3.000
 5TP  H1'1  C1'   C21   109.16  3.000
 5TP  C2'   C1'   C21   112.74  3.000
 5TP  H2'2  C2'   H2'1  104.67  3.000
 5TP  H2'2  C2'   C2'1  107.99  3.000
 5TP  H2'1  C2'   C2'1  108.16  3.000
 5TP  C2'1  C2'   C1'   113.85  3.000
 5TP  H2'2  C2'   C1'   110.91  3.000
 5TP  H2'1  C2'   C1'   110.81  3.000
 5TP  C22   S1    C52    88.99  3.000
 5TP  H5    C52   C42   127.93  3.000
 5TP  H5    C52   S1    121.92  3.000
 5TP  C42   C52   S1    110.15  3.000
 5TP  N3    C22   C2'1  125.97  3.000
 5TP  N3    C22   S1    114.73  3.000
 5TP  C2'1  C22   S1    119.30  3.000
 5TP  C22   C2'1  O2    118.57  3.000
 5TP  C22   C2'1  C2'   117.14  3.000
 5TP  O2    C2'1  C2'   124.28  3.000
 5TP  H43   C42   N3    120.12  3.000
 5TP  H43   C42   C52   124.74  3.000
 5TP  N3    C42   C52   115.13  3.000
 5TP  C42   N3    C22   111.00  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
 5TP  CONST_01  N3    C42   C52   S1       0.00   0.0  0
 5TP  CONST_02  C42   N3    C22   S1       0.00   0.0  0
 5TP  CONST_03  N3    C22   S1    C52      0.00   0.0  0
 5TP  CONST_04  C22   N3    C42   C52      0.00   0.0  0
 5TP  CONST_05  C42   C52   S1    C22      0.00   0.0  0
 5TP  CONST_06  C2'1  C22   S1    C52    180.00   0.0  0
 5TP  CONST_07  C42   N3    C22   C2'1   180.00   0.0  0
 5TP  CONST_08  H43   C42   C52   S1     180.00   0.0  0
 5TP  CONST_09  H5    C52   S1    C22    180.00   0.0  0
 5TP  Var_01    C41   C51   C61   N11    -53.62  30.0  1
 5TP  Var_02    C51   C61   N11   C21     54.21  30.0  1
 5TP  Var_03    C51   C41   C31   C21    -53.24  30.0  1
 5TP  Var_04    C61   C51   C41   C31     52.70  30.0  1
 5TP  Var_05    S1    C22   C2'1  C2'    179.94  30.0  2
 5TP  Var_06    C2'1  C2'   C1'   C21   -179.25  30.0  3
 5TP  Var_07    C22   C2'1  C2'   C1'    177.07  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
 5TP  chir_01  C21  N11  C31  C1'  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
 5TP  plan-1  S1    0.020
 5TP  plan-1  C52   0.020
 5TP  plan-1  C22   0.020
 5TP  plan-1  C2'1  0.020
 5TP  plan-1  C42   0.020
 5TP  plan-1  N3    0.020
 5TP  plan-1  H43   0.020
 5TP  plan-1  H5    0.020
 5TP  plan-2  C2'   0.020
 5TP  plan-2  O2    0.020
 5TP  plan-2  C22   0.020
 5TP  plan-2  C2'1  0.020

