# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 09:39:11 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-[(2-oxo-2-piperidin-1-ylethyl)sulfanyl]-6-(trifluoromethyl)pyrimidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(nc(SCC(=O)N2CCCCC2)n1)C(F)(F)F
#
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
 B1V  B1V  2-[(2-oxo-2-piperidin-1-ylethyl)sulfanyl]-6-(trifluoromethyl)pyrimidin-4-ol  ligand  35  21  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B1V
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
 B1V  F27   F  F     0  -0.305  -1.2452   1.5013   4.6505
 B1V  C24   C  CT    0   1.060  -0.6028   0.3317   4.6599
 B1V  F25   F  F     0  -0.305  -1.5110  -0.6223   4.8730
 B1V  F26   F  F     0  -0.295   0.2317   0.3361   5.6983
 B1V  C9    C  CR6   0   0.031   0.1132   0.1064   3.3520
 B1V  N11   N  N     0  -0.453  -0.6907   0.0801   2.2964
 B1V  C7    C  CR16  0  -0.426   1.4741  -0.0519   3.2877
 B1V  C5    C  CR6   0   0.551   1.9781  -0.2510   1.9953
 B1V  O13   O  OH1   0  -0.582   3.2754  -0.4141   1.8407
 B1V  N3    N  N     0  -0.453   1.1995  -0.2817   0.9312
 B1V  C1    C  CR6   0   0.249  -0.1005  -0.1144   1.1290
 B1V  S14   S  S2    0   0.105  -1.2114  -0.1414  -0.2194
 B1V  C15   C  CH2   0  -0.724  -0.0722  -0.4044  -1.6000
 B1V  C16   C  C     0   0.587  -0.9196  -0.4431  -2.8593
 B1V  O23   O  O     0  -0.498  -2.1357  -0.3194  -2.7719
 B1V  N17   N  NT    0  -0.446  -0.2735  -0.6308  -4.0198
 B1V  C18   C  CH2   0  -0.328   1.1737  -0.6433  -4.1729
 B1V  C19   C  CH2   0  -0.428   1.6414   0.6210  -4.8841
 B1V  C20   C  CH2   0  -0.446   0.9186   0.7942  -6.2162
 B1V  C21   C  CH2   0  -0.433  -0.5947   0.7080  -6.0402
 B1V  C22   C  CH2   0  -0.317  -0.9842  -0.5593  -5.2885
 B1V  H7    H  HCR6  0   0.305   2.1253  -0.0300   4.1482
 B1V  H13   H  HOH1  0   0.487   3.4814  -0.5484   0.9041
 B1V  H151  H  HCH2  0   0.321   0.4728  -1.3385  -1.4596
 B1V  H152  H  HCH2  0   0.315   0.6597   0.4036  -1.6337
 B1V  H181  H  HCH2  0   0.276   1.6656  -0.7556  -3.2100
 B1V  H182  H  HCH2  0   0.251   1.4432  -1.5257  -4.7612
 B1V  H191  H  HCH2  0   0.242   2.7211   0.5667  -5.0370
 B1V  H192  H  HCH2  0   0.226   1.4541   1.4827  -4.2360
 B1V  H201  H  HCH2  0   0.220   1.2464   0.0105  -6.9073
 B1V  H202  H  HCH2  0   0.240   1.1939   1.7469  -6.6728
 B1V  H211  H  HCH2  0   0.240  -1.0949   0.7157  -7.0108
 B1V  H212  H  HCH2  0   0.227  -0.9601   1.5781  -5.4868
 B1V  H221  H  HCH2  0   0.242  -0.7154  -1.4416  -5.8776
 B1V  H222  H  HCH2  0   0.266  -2.0548  -0.6011  -5.1090

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
 B1V  F27  C24   single    1.334  0.020  1.334
 B1V  C24  F25   single    1.334  0.020  1.334
 B1V  C24  F26   single    1.332  0.020  1.332
 B1V  C24  C9    single    1.508  0.020  1.508
 B1V  C9   N11   aromatic  1.327  0.020  1.327
 B1V  C9   C7    aromatic  1.372  0.020  1.372
 B1V  N11  C1    aromatic  1.323  0.020  1.323
 B1V  C7   C5    aromatic  1.401  0.020  1.401
 B1V  C7   H7    single    0.930  0.020  1.080
 B1V  C5   O13   single    1.317  0.020  1.317
 B1V  C5   N3    aromatic  1.319  0.020  1.319
 B1V  O13  H13   single    0.850  0.020  0.980
 B1V  N3   C1    aromatic  1.326  0.020  1.326
 B1V  C1   S14   single    1.747  0.020  1.747
 B1V  S14  C15   single    1.809  0.020  1.809
 B1V  C15  C16   single    1.518  0.020  1.518
 B1V  C15  H151  single    0.970  0.020  1.090
 B1V  C15  H152  single    0.970  0.020  1.090
 B1V  C16  O23   double    1.225  0.020  1.225
 B1V  C16  N17   single    1.341  0.020  1.341
 B1V  N17  C18   single    1.455  0.020  1.455
 B1V  N17  C22   single    1.456  0.020  1.456
 B1V  C18  C19   single    1.524  0.020  1.524
 B1V  C18  H181  single    0.970  0.020  1.090
 B1V  C18  H182  single    0.970  0.020  1.090
 B1V  C19  C20   single    1.525  0.020  1.525
 B1V  C19  H191  single    0.970  0.020  1.090
 B1V  C19  H192  single    0.970  0.020  1.090
 B1V  C20  C21   single    1.526  0.020  1.526
 B1V  C20  H201  single    0.970  0.020  1.090
 B1V  C20  H202  single    0.970  0.020  1.090
 B1V  C21  C22   single    1.524  0.020  1.524
 B1V  C21  H211  single    0.970  0.020  1.090
 B1V  C21  H212  single    0.970  0.020  1.090
 B1V  C22  H221  single    0.970  0.020  1.090
 B1V  C22  H222  single    0.970  0.020  1.090

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
 B1V  C9    C24  F26   112.28  3.000
 B1V  C9    C24  F25   110.79  3.000
 B1V  F26   C24  F25   107.71  3.000
 B1V  C9    C24  F27   110.70  3.000
 B1V  F26   C24  F27   107.71  3.000
 B1V  F25   C24  F27   107.46  3.000
 B1V  C7    C9   N11   124.15  3.000
 B1V  C7    C9   C24   121.94  3.000
 B1V  N11   C9   C24   113.91  3.000
 B1V  C1    N11  C9    115.77  3.000
 B1V  H7    C7   C5    121.40  3.000
 B1V  H7    C7   C9    123.98  3.000
 B1V  C5    C7   C9    114.61  3.000
 B1V  N3    C5   O13   118.95  3.000
 B1V  N3    C5   C7    122.34  3.000
 B1V  O13   C5   C7    118.70  3.000
 B1V  H13   O13  C5    109.90  3.000
 B1V  C1    N3   C5    117.11  3.000
 B1V  S14   C1   N3    120.43  3.000
 B1V  S14   C1   N11   113.56  3.000
 B1V  N3    C1   N11   126.01  3.000
 B1V  C15   S14  C1    101.00  3.000
 B1V  H152  C15  H151  107.65  3.000
 B1V  H152  C15  C16   111.57  3.000
 B1V  H151  C15  C16   111.33  3.000
 B1V  H152  C15  S14   109.78  3.000
 B1V  H151  C15  S14   109.94  3.000
 B1V  C16   C15  S14   106.57  3.000
 B1V  N17   C16  O23   123.63  3.000
 B1V  N17   C16  C15   116.89  3.000
 B1V  O23   C16  C15   119.48  3.000
 B1V  C22   N17  C18   113.21  3.000
 B1V  C22   N17  C16   120.78  3.000
 B1V  C18   N17  C16   124.84  3.000
 B1V  H182  C18  H181  106.35  3.000
 B1V  H182  C18  C19   110.03  3.000
 B1V  H181  C18  C19   111.10  3.000
 B1V  H182  C18  N17   107.97  3.000
 B1V  H181  C18  N17   110.96  3.000
 B1V  C19   C18  N17   110.31  3.000
 B1V  H192  C19  H191  106.94  3.000
 B1V  H192  C19  C20   110.28  3.000
 B1V  H191  C19  C20   110.61  3.000
 B1V  H192  C19  C18   108.92  3.000
 B1V  H191  C19  C18   109.12  3.000
 B1V  C20   C19  C18   110.87  3.000
 B1V  H202  C20  H201  106.57  3.000
 B1V  H202  C20  C21   110.34  3.000
 B1V  H201  C20  C21   109.22  3.000
 B1V  H202  C20  C19   110.17  3.000
 B1V  H201  C20  C19   109.15  3.000
 B1V  C21   C20  C19   111.27  3.000
 B1V  H212  C21  H211  106.92  3.000
 B1V  H212  C21  C22   109.05  3.000
 B1V  H211  C21  C22   109.10  3.000
 B1V  H212  C21  C20   110.16  3.000
 B1V  H211  C21  C20   110.57  3.000
 B1V  C22   C21  C20   110.93  3.000
 B1V  H222  C22  H221  107.46  3.000
 B1V  H222  C22  C21   111.43  3.000
 B1V  H221  C22  C21   110.00  3.000
 B1V  H222  C22  N17   109.59  3.000
 B1V  H221  C22  N17   108.03  3.000
 B1V  C21   C22  N17   110.23  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
 B1V  CONST_01  N3   C1   N11  C9      0.00   0.0  0
 B1V  CONST_02  N3   C5   C7   C9      0.00   0.0  0
 B1V  CONST_03  C5   C7   C9   N11     0.00   0.0  0
 B1V  CONST_04  C5   N3   C1   N11     0.00   0.0  0
 B1V  CONST_05  C1   N11  C9   C7      0.00   0.0  0
 B1V  CONST_06  C1   N3   C5   C7      0.00   0.0  0
 B1V  CONST_07  C1   N11  C9   C24   180.00   0.0  0
 B1V  CONST_08  C5   C7   C9   C24   180.00   0.0  0
 B1V  CONST_09  S14  C1   N11  C9    180.00   0.0  0
 B1V  CONST_10  O13  C5   C7   C9    180.00   0.0  0
 B1V  CONST_11  S14  C1   N3   C5    180.00   0.0  0
 B1V  CONST_12  C1   N3   C5   O13   180.00   0.0  0
 B1V  CONST_13  H7   C7   C9   N11   180.00   0.0  0
 B1V  CONST_14  C18  N17  C16  C15     0.00   0.0  0
 B1V  CONST_15  C22  N17  C16  C15   180.00   0.0  0
 B1V  CONST_16  C18  N17  C16  O23   180.00   0.0  0
 B1V  CONST_17  C22  N17  C16  O23     0.00   0.0  0
 B1V  Var_01    C20  C19  C18  N17   -54.90  30.0  1
 B1V  Var_02    C20  C21  C22  N17    54.86  30.0  1
 B1V  Var_03    C21  C22  N17  C18   -59.69  30.0  1
 B1V  Var_04    C21  C20  C19  C18    52.16  30.0  1
 B1V  Var_05    C22  N17  C18  C19    59.74  30.0  1
 B1V  Var_06    C22  C21  C20  C19   -52.18  30.0  1
 B1V  Var_07    N11  C9   C24  F27   -60.35  30.0  2
 B1V  Var_08    C16  C15  S14  C1   -179.76  30.0  3
 B1V  Var_09    N17  C16  C15  S14   179.99  30.0  3

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
 B1V  plan-1  C24  0.020
 B1V  plan-1  C9   0.020
 B1V  plan-1  N11  0.020
 B1V  plan-1  C7   0.020
 B1V  plan-1  C5   0.020
 B1V  plan-1  O13  0.020
 B1V  plan-1  N3   0.020
 B1V  plan-1  C1   0.020
 B1V  plan-1  S14  0.020
 B1V  plan-1  H7   0.020
 B1V  plan-2  C15  0.020
 B1V  plan-2  C16  0.020
 B1V  plan-2  O23  0.020
 B1V  plan-2  N17  0.020
 B1V  plan-2  C18  0.020
 B1V  plan-2  C22  0.020

