# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 01:23:37 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-(2-methyl-1H-indol-3-yl)-2-[(2R)-2-methylpiperidin-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCCCN1CC(=O)c2c(C)[nH]c3ccccc23
#
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
 QS4  QS4  1-(2-methyl-1H-indol-3-yl)-2-[(2R)-2-methylpiperidin-1-yl]ethan-1-one  ligand  42  20  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QS4
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
 QS4  C4   C  CH2   0  -0.448   5.1600   0.9039  -0.1549
 QS4  C14  C  CR16  0  -0.285  -5.2392   1.2768  -1.0300
 QS4  C5   C  CH2   0  -0.435   4.0161   1.9091  -0.1479
 QS4  C6   C  CH2   0  -0.285   2.7911   1.3284   0.5407
 QS4  C8   C  C     0   0.303  -0.0534   0.3033  -0.3156
 QS4  C9   C  CR5   0  -0.182  -1.4092  -0.0708   0.0578
 QS4  C10  C  CR5   0   0.350  -1.8407  -1.0733   0.9216
 QS4  C12  C  CR56  0   0.330  -3.6949  -0.1022   0.1159
 QS4  C13  C  CR16  0  -0.300  -5.0175   0.2353  -0.1485
 QS4  N1   N  NT    0  -0.412   2.3965   0.0728  -0.0750
 QS4  N2   N  NR15  0  -0.722  -3.1913  -1.0743   0.9407
 QS4  C3   C  CH2   0  -0.424   4.6864  -0.4227  -0.7376
 QS4  C1   C  CH3   0  -0.682   3.7547  -1.4825   1.3726
 QS4  C2   C  CH1   0  -0.105   3.4380  -0.9525  -0.0303
 QS4  O1   O  O     0  -0.425   0.1427   1.1581  -1.1621
 QS4  C15  C  CR16  0  -0.256  -4.1662   1.9552  -1.6239
 QS4  C16  C  CR16  0  -0.371  -2.8537   1.6095  -1.3556
 QS4  C17  C  CR56  0   0.111  -2.5989   0.5577  -0.4674
 QS4  H1   H  HCH2  0   0.231   6.0052   1.2861  -0.7317
 QS4  H2   H  HCH2  0   0.214   5.5269   0.7590   0.8660
 QS4  H4   H  HCH2  0   0.226   4.3120   2.8326   0.3549
 QS4  H5   H  HCH2  0   0.212   3.7514   2.1744  -1.1757
 QS4  H6   H  HCH2  0   0.190   2.9961   1.2133   1.6187
 QS4  H7   H  HCH2  0   0.238   1.9631   2.0331   0.4620
 QS4  H8   H  HCH3  0   0.269  -0.4572  -1.5795   2.4789
 QS4  H9   H  HCH3  0   0.276  -1.8008  -2.6993   2.3023
 QS4  H10  H  HCH3  0   0.270  -0.4835  -2.7182   1.1398
 QS4  H13  H  HCR6  0   0.264  -5.8381  -0.2954   0.3169
 QS4  H15  H  HNR5  0   0.415  -3.7489  -1.7121   1.4868
 QS4  H16  H  HCH2  0   0.220   4.4509  -0.2841  -1.7972
 QS4  H17  H  HCH2  0   0.226   5.4786  -1.1734  -0.6857
 QS4  H18  H  HCH3  0   0.229   2.8671  -1.8982   1.8530
 QS4  H19  H  HCH3  0   0.231   4.4946  -2.2822   1.3155
 QS4  H20  H  HCH3  0   0.223   4.1544  -0.7115   2.0328
 QS4  H21  H  HCH1  0   0.232   3.0659  -1.7982  -0.6192
 QS4  H22  H  HCR6  0   0.249  -4.3692   2.7703  -2.3070
 QS4  H23  H  HCR6  0   0.248  -2.0446   2.1474  -1.8261
 QS4  C7   C  CH2   0  -0.404   1.1137  -0.3925   0.3717
 QS4  H3   H  HCR6  0   0.253  -6.2537   1.5732  -1.2617
 QS4  C11  C  CH3   0  -0.767  -1.1063  -2.0667   1.7522
 QS4  H11  H  HCH2  0   0.231   0.9757  -0.3037   1.4617
 QS4  H12  H  HCH2  0   0.265   1.0272  -1.4615   0.1533

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
 QS4  C5   C4   single    1.523  0.020  1.523
 QS4  C5   C6   single    1.520  0.020  1.520
 QS4  C4   C3   single    1.524  0.020  1.524
 QS4  C6   N1   single    1.453  0.020  1.453
 QS4  C1   C2   single    1.533  0.020  1.533
 QS4  C3   C2   single    1.530  0.020  1.530
 QS4  N1   C2   single    1.462  0.020  1.462
 QS4  N1   C7   single    1.436  0.020  1.436
 QS4  C7   C8   single    1.523  0.020  1.523
 QS4  O1   C8   double    1.219  0.020  1.219
 QS4  C8   C9   single    1.455  0.020  1.455
 QS4  C11  C10  single    1.489  0.020  1.489
 QS4  C9   C10  aromatic  1.392  0.020  1.392
 QS4  C9   C17  aromatic  1.444  0.020  1.444
 QS4  C10  N2   aromatic  1.351  0.020  1.351
 QS4  C17  C16  aromatic  1.400  0.020  1.400
 QS4  C17  C12  aromatic  1.406  0.020  1.406
 QS4  C16  C15  aromatic  1.384  0.020  1.384
 QS4  N2   C12  aromatic  1.371  0.020  1.371
 QS4  C12  C13  aromatic  1.390  0.020  1.390
 QS4  C15  C14  aromatic  1.402  0.020  1.402
 QS4  C13  C14  aromatic  1.382  0.020  1.382
 QS4  C4   H1   single    0.970  0.020  1.090
 QS4  C4   H2   single    0.970  0.020  1.090
 QS4  C14  H3   single    0.930  0.020  1.080
 QS4  C5   H4   single    0.970  0.020  1.090
 QS4  C5   H5   single    0.970  0.020  1.090
 QS4  C6   H6   single    0.970  0.020  1.090
 QS4  C6   H7   single    0.970  0.020  1.090
 QS4  C11  H8   single    0.970  0.020  1.090
 QS4  C11  H9   single    0.970  0.020  1.090
 QS4  C11  H10  single    0.970  0.020  1.090
 QS4  C7   H11  single    0.970  0.020  1.090
 QS4  C7   H12  single    0.970  0.020  1.090
 QS4  C13  H13  single    0.930  0.020  1.080
 QS4  N2   H15  single    0.860  0.020  1.020
 QS4  C3   H16  single    0.970  0.020  1.090
 QS4  C3   H17  single    0.970  0.020  1.090
 QS4  C1   H18  single    0.970  0.020  1.090
 QS4  C1   H19  single    0.970  0.020  1.090
 QS4  C1   H20  single    0.970  0.020  1.090
 QS4  C2   H21  single    0.970  0.020  1.090
 QS4  C15  H22  single    0.930  0.020  1.080
 QS4  C16  H23  single    0.930  0.020  1.080

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
 QS4  H2   C4   H1   106.22  3.000
 QS4  H2   C4   C3   110.21  3.000
 QS4  H1   C4   C3   110.06  3.000
 QS4  H2   C4   C5   109.57  3.000
 QS4  H1   C4   C5   110.65  3.000
 QS4  C3   C4   C5   110.05  3.000
 QS4  H3   C14  C15  119.63  3.000
 QS4  H3   C14  C13  119.56  3.000
 QS4  C15  C14  C13  120.81  3.000
 QS4  H5   C5   H4   107.03  3.000
 QS4  H5   C5   C6   108.85  3.000
 QS4  H4   C5   C6   109.43  3.000
 QS4  H5   C5   C4   109.72  3.000
 QS4  H4   C5   C4   110.90  3.000
 QS4  C6   C5   C4   110.81  3.000
 QS4  H7   C6   H6   106.20  3.000
 QS4  H7   C6   N1   108.77  3.000
 QS4  H6   C6   N1   111.98  3.000
 QS4  H7   C6   C5   109.42  3.000
 QS4  H6   C6   C5   109.43  3.000
 QS4  N1   C6   C5   110.91  3.000
 QS4  O1   C8   C9   120.56  3.000
 QS4  C9   C8   C7   118.74  3.000
 QS4  O1   C8   C7   120.71  3.000
 QS4  C17  C9   C10  106.48  3.000
 QS4  C17  C9   C8   124.21  3.000
 QS4  C10  C9   C8   129.29  3.000
 QS4  N2   C10  C9   108.62  3.000
 QS4  N2   C10  C11  119.01  3.000
 QS4  C9   C10  C11  132.37  3.000
 QS4  C17  C12  N2   107.22  3.000
 QS4  N2   C12  C13  129.50  3.000
 QS4  C17  C12  C13  123.28  3.000
 QS4  H13  C13  C12  121.36  3.000
 QS4  H13  C13  C14  121.46  3.000
 QS4  C12  C13  C14  117.18  3.000
 QS4  C2   N1   C7   113.55  3.000
 QS4  C7   N1   C6   113.00  3.000
 QS4  C2   N1   C6   113.55  3.000
 QS4  H15  N2   C12  124.86  3.000
 QS4  H15  N2   C10  124.14  3.000
 QS4  C12  N2   C10  111.00  3.000
 QS4  H17  C3   H16  106.80  3.000
 QS4  H17  C3   C2   109.37  3.000
 QS4  H16  C3   C2   108.42  3.000
 QS4  H17  C3   C4   110.77  3.000
 QS4  H16  C3   C4   109.08  3.000
 QS4  C2   C3   C4   112.23  3.000
 QS4  H20  C1   H19  107.53  3.000
 QS4  H20  C1   H18  107.50  3.000
 QS4  H19  C1   H18  107.18  3.000
 QS4  H20  C1   C2   112.65  3.000
 QS4  H19  C1   C2   110.23  3.000
 QS4  H18  C1   C2   111.50  3.000
 QS4  H21  C2   C1   107.17  3.000
 QS4  H21  C2   C3   107.22  3.000
 QS4  C1   C2   C3   111.99  3.000
 QS4  H21  C2   N1   106.43  3.000
 QS4  C3   C2   N1   108.92  3.000
 QS4  C1   C2   N1   114.69  3.000
 QS4  H22  C15  C16  119.23  3.000
 QS4  H22  C15  C14  119.22  3.000
 QS4  C16  C15  C14  121.54  3.000
 QS4  H23  C16  C17  120.96  3.000
 QS4  H23  C16  C15  120.13  3.000
 QS4  C17  C16  C15  118.91  3.000
 QS4  C16  C17  C12  118.29  3.000
 QS4  C12  C17  C9   106.68  3.000
 QS4  C16  C17  C9   135.03  3.000
 QS4  H12  C7   H11  105.43  3.000
 QS4  H12  C7   N1   108.97  3.000
 QS4  H11  C7   N1   113.17  3.000
 QS4  H12  C7   C8   107.20  3.000
 QS4  H11  C7   C8   108.27  3.000
 QS4  N1   C7   C8   113.34  3.000
 QS4  H10  C11  H9   107.53  3.000
 QS4  H10  C11  H8   107.56  3.000
 QS4  H9   C11  H8   107.63  3.000
 QS4  H10  C11  C10  111.56  3.000
 QS4  H9   C11  C10  110.79  3.000
 QS4  H8   C11  C10  111.57  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
 QS4  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 QS4  CONST_02  C17  C12  C13  C14     0.00   0.0  0
 QS4  CONST_03  N2   C12  C13  C14   180.00   0.0  0
 QS4  CONST_04  C12  N2   C10  C9      0.00   0.0  0
 QS4  CONST_05  C15  C16  C17  C9    180.00   0.0  0
 QS4  CONST_06  N2   C12  C17  C9      0.00   0.0  0
 QS4  CONST_07  C13  C12  C17  C9    180.00   0.0  0
 QS4  CONST_08  C16  C17  C9   C10   180.00   0.0  0
 QS4  CONST_09  C12  C17  C9   C10     0.00   0.0  0
 QS4  CONST_10  C17  C12  N2   C10     0.00   0.0  0
 QS4  CONST_11  C13  C12  N2   C10   180.00   0.0  0
 QS4  CONST_12  C15  C16  C17  C12     0.00   0.0  0
 QS4  CONST_13  C15  C14  C13  C12     0.00   0.0  0
 QS4  CONST_14  C16  C17  C12  C13     0.00   0.0  0
 QS4  CONST_15  C16  C15  C14  C13     0.00   0.0  0
 QS4  CONST_16  C17  C9   C10  N2      0.00   0.0  0
 QS4  CONST_17  C16  C17  C12  N2    180.00   0.0  0
 QS4  CONST_18  C17  C9   C10  C11   180.00   0.0  0
 QS4  CONST_19  C12  N2   C10  C11   180.00   0.0  0
 QS4  CONST_20  N2   C10  C9   C8    180.00   0.0  0
 QS4  CONST_21  C16  C17  C9   C8      0.00   0.0  0
 QS4  CONST_22  C12  C17  C9   C8    180.00   0.0  0
 QS4  CONST_23  H23  C16  C15  C14   180.00   0.0  0
 QS4  CONST_24  H15  N2   C10  C9    180.00   0.0  0
 QS4  CONST_25  H3   C14  C13  C12   180.00   0.0  0
 QS4  CONST_26  H22  C15  C14  C13   180.00   0.0  0
 QS4  CONST_27  H13  C13  C12  N2      0.00   0.0  0
 QS4  Var_01    N1   C6   C5   C4    -55.46  30.0  1
 QS4  Var_02    C2   C3   C4   C5    -53.58  30.0  1
 QS4  Var_03    C2   N1   C6   C5     59.48  30.0  1
 QS4  Var_04    C3   C4   C5   C6     52.77  30.0  1
 QS4  Var_05    C8   C7   N1   C6     79.75  30.0  3
 QS4  Var_06    C10  C9   C8   C7     -4.93  30.0  2
 QS4  Var_07    N1   C7   C8   C9   -179.48  30.0  2
 QS4  Var_08    H8   C11  C10  C9     60.28  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
 QS4  chir_01  C2  C1  C3  N1  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
 QS4  plan-1  C14  0.020
 QS4  plan-1  C8   0.020
 QS4  plan-1  C9   0.020
 QS4  plan-1  C10  0.020
 QS4  plan-1  C12  0.020
 QS4  plan-1  C13  0.020
 QS4  plan-1  N2   0.020
 QS4  plan-1  C15  0.020
 QS4  plan-1  C16  0.020
 QS4  plan-1  C17  0.020
 QS4  plan-1  H13  0.020
 QS4  plan-1  H15  0.020
 QS4  plan-1  H22  0.020
 QS4  plan-1  H23  0.020
 QS4  plan-1  H3   0.020
 QS4  plan-1  C11  0.020
 QS4  plan-2  C8   0.020
 QS4  plan-2  C9   0.020
 QS4  plan-2  O1   0.020
 QS4  plan-2  C7   0.020

