# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:17:52 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-[(thiophen-3-yl)methyl]piperidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1CCN(CC1)Cc2cscc2
#
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
 T0Y  T0Y  1-[(thiophen-3-yl)methyl]piperidin-4-ol  ligand  28  13  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T0Y
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
 T0Y  C13   C  CH2   0  -0.458   3.0456   1.2157   0.5458
 T0Y  C02   C  CH1   0   0.029   3.4864  -0.2032   0.8693
 T0Y  C03   C  CH2   0  -0.480   2.2552  -1.0620   1.1373
 T0Y  C04   C  CH2   0  -0.274   1.2360  -0.9544   0.0141
 T0Y  C07   C  CR5   0   0.147  -1.5527   0.1235  -0.6200
 T0Y  C08   C  CR15  0  -0.221  -2.6552  -0.2567  -1.4421
 T0Y  C09   C  CR15  0  -0.463  -3.7741  -0.5571  -0.7287
 T0Y  C11   C  CR15  0  -0.528  -1.8772   0.0951   0.7032
 T0Y  C12   C  CH2   0  -0.278   1.9941   1.2501  -0.5531
 T0Y  N05   N  NT    0  -0.423   0.8474   0.4303  -0.1983
 T0Y  O01   O  OH1   0  -0.676   4.2341  -0.6834  -0.2337
 T0Y  S10   S  S2    0   0.200  -3.5030  -0.3900   0.9550
 T0Y  H131  H  HCH2  0   0.226   2.6312   1.6611   1.4539
 T0Y  H132  H  HCH2  0   0.236   3.9051   1.8254   0.2559
 T0Y  H021  H  HCH1  0   0.212   4.1125  -0.1865   1.7724
 T0Y  H031  H  HCH2  0   0.235   2.5422  -2.1081   1.2809
 T0Y  H032  H  HCH2  0   0.225   1.7959  -0.7331   2.0739
 T0Y  H041  H  HCH2  0   0.193   1.6430  -1.3998  -0.9099
 T0Y  H042  H  HCH2  0   0.239   0.3499  -1.5357   0.2764
 T0Y  H061  H  HCH2  0   0.210  -0.0081  -0.0068  -2.0934
 T0Y  H062  H  HCH2  0   0.251  -0.2937   1.6009  -1.4644
 T0Y  H081  H  HCR5  0   0.259  -2.6083  -0.3044  -2.5218
 T0Y  H091  H  HCR5  0   0.292  -4.7363  -0.8714  -1.1022
 T0Y  H111  H  HCR5  0   0.284  -1.2359   0.3254   1.5399
 T0Y  H121  H  HCH2  0   0.234   1.6529   2.2788  -0.6925
 T0Y  H122  H  HCH2  0   0.191   2.4397   0.9355  -1.5114
 T0Y  H011  H  HOH1  0   0.446   4.4492  -1.6072  -0.0710
 T0Y  C06   C  CH2   0  -0.308  -0.2204   0.5504  -1.1650

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
 T0Y  C02  O01   single    1.416  0.020  1.416
 T0Y  C03  C02   single    1.525  0.020  1.525
 T0Y  C04  C03   single    1.520  0.020  1.520
 T0Y  N05  C04   single    1.454  0.020  1.454
 T0Y  C07  C06   single    1.501  0.020  1.501
 T0Y  C08  C07   aromatic  1.427  0.020  1.427
 T0Y  C09  C08   aromatic  1.361  0.020  1.361
 T0Y  S10  C09   aromatic  1.714  0.020  1.714
 T0Y  C11  S10   aromatic  1.715  0.020  1.715
 T0Y  C06  N05   single    1.445  0.020  1.445
 T0Y  C12  N05   single    1.453  0.020  1.453
 T0Y  C13  C12   single    1.521  0.020  1.521
 T0Y  C02  C13   single    1.521  0.020  1.521
 T0Y  C07  C11   aromatic  1.363  0.020  1.363
 T0Y  C13  H131  single    0.970  0.020  1.090
 T0Y  C13  H132  single    0.970  0.020  1.090
 T0Y  C02  H021  single    0.970  0.020  1.090
 T0Y  C03  H031  single    0.970  0.020  1.090
 T0Y  C03  H032  single    0.970  0.020  1.090
 T0Y  C04  H041  single    0.970  0.020  1.090
 T0Y  C04  H042  single    0.970  0.020  1.090
 T0Y  C06  H061  single    0.970  0.020  1.090
 T0Y  C06  H062  single    0.970  0.020  1.090
 T0Y  C08  H081  single    0.930  0.020  1.080
 T0Y  C09  H091  single    0.930  0.020  1.080
 T0Y  C11  H111  single    0.930  0.020  1.080
 T0Y  C12  H121  single    0.970  0.020  1.090
 T0Y  C12  H122  single    0.970  0.020  1.090
 T0Y  O01  H011  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
 T0Y  H132  C13  H131  106.93  3.000
 T0Y  H132  C13  C12   109.84  3.000
 T0Y  H131  C13  C12   109.20  3.000
 T0Y  H132  C13  C02   110.42  3.000
 T0Y  H131  C13  C02   108.26  3.000
 T0Y  C12   C13  C02   112.03  3.000
 T0Y  H021  C02  O01   110.14  3.000
 T0Y  H021  C02  C03   108.91  3.000
 T0Y  O01   C02  C03   111.85  3.000
 T0Y  H021  C02  C13   109.01  3.000
 T0Y  C03   C02  C13   109.20  3.000
 T0Y  O01   C02  C13   107.68  3.000
 T0Y  H032  C03  H031  106.57  3.000
 T0Y  H032  C03  C04   109.25  3.000
 T0Y  H031  C03  C04   109.90  3.000
 T0Y  H032  C03  C02   108.67  3.000
 T0Y  H031  C03  C02   110.47  3.000
 T0Y  C04   C03  C02   111.81  3.000
 T0Y  H042  C04  H041  106.59  3.000
 T0Y  H042  C04  N05   108.99  3.000
 T0Y  H041  C04  N05   111.14  3.000
 T0Y  H042  C04  C03   109.21  3.000
 T0Y  H041  C04  C03   110.04  3.000
 T0Y  N05   C04  C03   110.77  3.000
 T0Y  C11   C07  C08   111.70  3.000
 T0Y  C11   C07  C06   124.73  3.000
 T0Y  C08   C07  C06   123.53  3.000
 T0Y  H081  C08  C09   123.31  3.000
 T0Y  H081  C08  C07   123.59  3.000
 T0Y  C09   C08  C07   113.09  3.000
 T0Y  H091  C09  S10   120.64  3.000
 T0Y  H091  C09  C08   128.04  3.000
 T0Y  S10   C09  C08   111.32  3.000
 T0Y  H111  C11  S10   120.66  3.000
 T0Y  H111  C11  C07   127.36  3.000
 T0Y  S10   C11  C07   111.98  3.000
 T0Y  H122  C12  H121  106.49  3.000
 T0Y  H122  C12  N05   111.72  3.000
 T0Y  H121  C12  N05   108.41  3.000
 T0Y  H122  C12  C13   110.00  3.000
 T0Y  H121  C12  C13   109.22  3.000
 T0Y  N05   C12  C13   110.87  3.000
 T0Y  C12   N05  C06   111.89  3.000
 T0Y  C12   N05  C04   111.22  3.000
 T0Y  C06   N05  C04   111.98  3.000
 T0Y  H011  O01  C02   108.16  3.000
 T0Y  C11   S10  C09    91.91  3.000
 T0Y  H062  C06  H061  105.50  3.000
 T0Y  H062  C06  N05   108.19  3.000
 T0Y  H061  C06  N05   112.25  3.000
 T0Y  H062  C06  C07   108.22  3.000
 T0Y  H061  C06  C07   109.42  3.000
 T0Y  N05   C06  C07   112.91  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
 T0Y  CONST_01  S10   C09  C08  C07     0.00   0.0  0
 T0Y  CONST_02  C09   S10  C11  C07     0.00   0.0  0
 T0Y  CONST_03  S10   C11  C07  C08     0.00   0.0  0
 T0Y  CONST_04  C11   S10  C09  C08     0.00   0.0  0
 T0Y  CONST_05  C11   C07  C08  C09     0.00   0.0  0
 T0Y  CONST_06  C09   C08  C07  C06   180.00   0.0  0
 T0Y  CONST_07  S10   C11  C07  C06   180.00   0.0  0
 T0Y  CONST_08  H091  C09  C08  C07   180.00   0.0  0
 T0Y  CONST_09  H111  C11  C07  C08   180.00   0.0  0
 T0Y  CONST_10  H081  C08  C07  C11   180.00   0.0  0
 T0Y  Var_01    C04   N05  C12  C13   -59.60  30.0  1
 T0Y  Var_02    N05   C04  C03  C02   -56.59  30.0  1
 T0Y  Var_03    N05   C12  C13  C02    56.10  30.0  1
 T0Y  Var_04    C12   N05  C04  C03    59.91  30.0  1
 T0Y  Var_05    C07   C06  N05  C04    74.21  30.0  2
 T0Y  Var_06    N05   C06  C07  C08  -159.46  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
 T0Y  chir_01  C02  O01  C03  C13  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
 T0Y  plan-1  C07   0.020
 T0Y  plan-1  C08   0.020
 T0Y  plan-1  C09   0.020
 T0Y  plan-1  C11   0.020
 T0Y  plan-1  S10   0.020
 T0Y  plan-1  H081  0.020
 T0Y  plan-1  H091  0.020
 T0Y  plan-1  H111  0.020
 T0Y  plan-1  C06   0.020

