# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:29:40 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2R,3R)-1-benzyl-2-methylpiperidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1[C@@H](O)CCCN1Cc2ccccc2
#
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
 T1M  T1M  (2R,3R)-1-benzyl-2-methylpiperidin-3-ol  ligand  34  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T1M
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
 T1M  C10   C  CR6   0   0.086   1.7687  -0.3205   0.5122
 T1M  C13   C  CR16  0  -0.272   4.2627   0.3919  -0.5408
 T1M  C15   C  CR16  0  -0.290   1.9133   0.8384  -0.2472
 T1M  C01   C  CH3   0  -0.690  -2.5235  -1.2675   1.6950
 T1M  C02   C  CH1   0  -0.117  -1.9019  -0.0107   1.0770
 T1M  C03   C  CH1   0   0.069  -2.9182   0.7271   0.2039
 T1M  C05   C  CH2   0  -0.494  -3.1541  -0.0172  -1.1077
 T1M  C06   C  CH2   0  -0.426  -1.8383  -0.2900  -1.8244
 T1M  C07   C  CH2   0  -0.281  -0.8611  -0.9964  -0.8977
 T1M  C09   C  CH2   0  -0.314   0.4348  -0.6890   1.1188
 T1M  C11   C  CR16  0  -0.314   2.8878  -1.1179   0.7332
 T1M  C12   C  CR16  0  -0.243   4.1279  -0.7646   0.2158
 T1M  C14   C  CR16  0  -0.242   3.1494   1.1911  -0.7714
 T1M  N08   N  NT    0  -0.413  -0.6779  -0.2365   0.3223
 T1M  O04   O  OH1   0  -0.672  -2.4259   2.0333  -0.0197
 T1M  H131  H  HCR6  0   0.251   5.2261   0.6654  -0.9519
 T1M  H151  H  HCR6  0   0.250   1.0396   1.4506  -0.4358
 T1M  H011  H  HCH3  0   0.238  -1.8125  -1.7786   2.3452
 T1M  H013  H  HCH3  0   0.232  -3.3890  -1.0032   2.3044
 T1M  H012  H  HCH3  0   0.224  -2.8570  -1.9854   0.9452
 T1M  H031  H  HCH1  0   0.205  -3.8647   0.7704   0.7621
 T1M  H051  H  HCH2  0   0.223  -3.6627  -0.9622  -0.8945
 T1M  H052  H  HCH2  0   0.237  -3.8366   0.5558  -1.7431
 T1M  H061  H  HCH2  0   0.226  -2.0072  -0.8999  -2.7143
 T1M  H062  H  HCH2  0   0.218  -1.3936   0.6498  -2.1589
 T1M  H071  H  HCH2  0   0.193  -1.2076  -2.0264  -0.7037
 T1M  H072  H  HCH2  0   0.236   0.1072  -1.0910  -1.3942
 T1M  H091  H  HCH2  0   0.209   0.4200  -1.7742   1.3125
 T1M  H092  H  HCH2  0   0.249   0.3600  -0.2135   2.1029
 T1M  H111  H  HCR6  0   0.243   2.7909  -2.0283   1.3145
 T1M  H121  H  HCR6  0   0.251   4.9871  -1.3980   0.3973
 T1M  H141  H  HCR6  0   0.249   3.2444   2.0919  -1.3650
 T1M  H041  H  HOH1  0   0.444  -3.0574   2.4937  -0.5810
 T1M  H021  H  HCH1  0   0.235  -1.6409   0.6598   1.9042

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
 T1M  C02  C01   single    1.532  0.020  1.532
 T1M  C03  C02   single    1.529  0.020  1.529
 T1M  O04  C03   single    1.414  0.020  1.414
 T1M  C05  C03   single    1.526  0.020  1.526
 T1M  C06  C05   single    1.523  0.020  1.523
 T1M  C07  C06   single    1.521  0.020  1.521
 T1M  N08  C07   single    1.449  0.020  1.449
 T1M  C09  N08   single    1.441  0.020  1.441
 T1M  C10  C09   single    1.511  0.020  1.511
 T1M  C11  C10   aromatic  1.392  0.020  1.392
 T1M  C12  C11   aromatic  1.389  0.020  1.389
 T1M  C13  C12   aromatic  1.389  0.020  1.389
 T1M  C14  C13   aromatic  1.390  0.020  1.390
 T1M  C15  C14   aromatic  1.388  0.020  1.388
 T1M  C02  N08   single    1.456  0.020  1.456
 T1M  C10  C15   aromatic  1.393  0.020  1.393
 T1M  C13  H131  single    0.930  0.020  1.080
 T1M  C15  H151  single    0.930  0.020  1.080
 T1M  C01  H011  single    0.970  0.020  1.090
 T1M  C01  H013  single    0.970  0.020  1.090
 T1M  C01  H012  single    0.970  0.020  1.090
 T1M  C02  H021  single    0.970  0.020  1.090
 T1M  C03  H031  single    0.970  0.020  1.090
 T1M  C05  H051  single    0.970  0.020  1.090
 T1M  C05  H052  single    0.970  0.020  1.090
 T1M  C06  H061  single    0.970  0.020  1.090
 T1M  C06  H062  single    0.970  0.020  1.090
 T1M  C07  H071  single    0.970  0.020  1.090
 T1M  C07  H072  single    0.970  0.020  1.090
 T1M  C09  H091  single    0.970  0.020  1.090
 T1M  C09  H092  single    0.970  0.020  1.090
 T1M  C11  H111  single    0.930  0.020  1.080
 T1M  C12  H121  single    0.930  0.020  1.080
 T1M  C14  H141  single    0.930  0.020  1.080
 T1M  O04  H041  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
 T1M  C11   C10  C09   120.42  3.000
 T1M  C11   C10  C15   118.66  3.000
 T1M  C09   C10  C15   120.89  3.000
 T1M  H131  C13  C14   120.30  3.000
 T1M  H131  C13  C12   120.25  3.000
 T1M  C14   C13  C12   119.45  3.000
 T1M  H151  C15  C14   120.58  3.000
 T1M  H151  C15  C10   118.77  3.000
 T1M  C14   C15  C10   120.64  3.000
 T1M  H012  C01  H013  107.52  3.000
 T1M  H012  C01  H011  107.51  3.000
 T1M  H013  C01  H011  107.31  3.000
 T1M  H012  C01  C02   112.76  3.000
 T1M  H013  C01  C02   110.39  3.000
 T1M  H011  C01  C02   111.12  3.000
 T1M  H021  C02  N08   106.61  3.000
 T1M  H021  C02  C03   107.09  3.000
 T1M  N08   C02  C03   109.74  3.000
 T1M  H021  C02  C01   107.09  3.000
 T1M  N08   C02  C01   115.02  3.000
 T1M  C03   C02  C01   110.87  3.000
 T1M  H031  C03  O04   110.10  3.000
 T1M  H031  C03  C05   108.81  3.000
 T1M  O04   C03  C05   111.62  3.000
 T1M  H031  C03  C02   107.53  3.000
 T1M  C05   C03  C02   110.98  3.000
 T1M  O04   C03  C02   107.73  3.000
 T1M  H052  C05  H051  105.98  3.000
 T1M  H052  C05  C06   111.06  3.000
 T1M  H051  C05  C06   109.79  3.000
 T1M  H052  C05  C03   109.87  3.000
 T1M  H051  C05  C03   109.00  3.000
 T1M  C06   C05  C03   110.99  3.000
 T1M  H062  C06  H061  107.10  3.000
 T1M  H062  C06  C07   108.95  3.000
 T1M  H061  C06  C07   109.66  3.000
 T1M  H062  C06  C05   109.99  3.000
 T1M  H061  C06  C05   110.48  3.000
 T1M  C07   C06  C05   110.58  3.000
 T1M  H072  C07  H071  106.10  3.000
 T1M  H072  C07  N08   108.42  3.000
 T1M  H071  C07  N08   112.40  3.000
 T1M  H072  C07  C06   109.44  3.000
 T1M  H071  C07  C06   109.81  3.000
 T1M  N08   C07  C06   110.53  3.000
 T1M  H092  C09  H091  105.58  3.000
 T1M  H092  C09  N08   107.91  3.000
 T1M  H091  C09  N08   113.32  3.000
 T1M  H092  C09  C10   108.36  3.000
 T1M  H091  C09  C10   108.81  3.000
 T1M  N08   C09  C10   112.53  3.000
 T1M  H111  C11  C12   119.53  3.000
 T1M  H111  C11  C10   119.62  3.000
 T1M  C12   C11  C10   120.86  3.000
 T1M  H121  C12  C11   119.81  3.000
 T1M  H121  C12  C13   120.10  3.000
 T1M  C11   C12  C13   120.09  3.000
 T1M  H141  C14  C15   119.76  3.000
 T1M  H141  C14  C13   119.94  3.000
 T1M  C15   C14  C13   120.30  3.000
 T1M  C09   N08  C07   113.47  3.000
 T1M  C09   N08  C02   114.29  3.000
 T1M  C07   N08  C02   114.31  3.000
 T1M  H041  O04  C03   107.80  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
 T1M  CONST_01  C13   C12  C11  C10    0.00   0.0  0
 T1M  CONST_02  C13   C14  C15  C10    0.00   0.0  0
 T1M  CONST_03  C12   C13  C14  C15    0.00   0.0  0
 T1M  CONST_04  C12   C11  C10  C15    0.00   0.0  0
 T1M  CONST_05  C14   C15  C10  C11    0.00   0.0  0
 T1M  CONST_06  C14   C13  C12  C11    0.00   0.0  0
 T1M  CONST_07  C12   C11  C10  C09  180.00   0.0  0
 T1M  CONST_08  C14   C15  C10  C09  180.00   0.0  0
 T1M  CONST_09  H121  C12  C11  C10  180.00   0.0  0
 T1M  CONST_10  H141  C14  C15  C10  180.00   0.0  0
 T1M  CONST_11  H111  C11  C12  C13  180.00   0.0  0
 T1M  CONST_12  H151  C15  C14  C13  180.00   0.0  0
 T1M  CONST_13  H131  C13  C14  C15  180.00   0.0  0
 T1M  Var_01    C06   C07  N08  C02   58.90  30.0  1
 T1M  Var_02    C07   C06  C05  C03   53.30  30.0  1
 T1M  Var_03    N08   C07  C06  C05  -54.89  30.0  1
 T1M  Var_04    C07   N08  C09  C10   72.76  30.0  3
 T1M  Var_05    N08   C09  C10  C15   31.07  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
 T1M  chir_01  C02  C01  C03  N08  positiv
 T1M  chir_02  C03  O04  C02  C05  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
 T1M  plan-1  C10   0.020
 T1M  plan-1  C13   0.020
 T1M  plan-1  C15   0.020
 T1M  plan-1  C09   0.020
 T1M  plan-1  C11   0.020
 T1M  plan-1  C12   0.020
 T1M  plan-1  C14   0.020
 T1M  plan-1  H131  0.020
 T1M  plan-1  H151  0.020
 T1M  plan-1  H111  0.020
 T1M  plan-1  H121  0.020
 T1M  plan-1  H141  0.020

