# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 09:14:41 2021
#   Inital geometry file: a 76 line input string
#   Ligand name: 2-[(2~{R})-piperidin-2-yl]-1~{H}-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC[C@@H](NC1)c2[nH]c3ccccc3c2
#
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
 QME  QME  2-[(2~{R})-piperidin-2-yl]-1~{H}-indole  ligand  31  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QME
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
 QME  C5   C  CH2   0  -0.426  -1.9869  -17.7361  28.2842
 QME  C7   C  CR56  0   0.078  -5.5733  -17.5395  25.3697
 QME  C8   C  CR56  0   0.330  -4.4687  -16.8158  24.8675
 QME  C10  C  CH2   0  -0.315  -2.7029  -15.6190  30.1296
 QME  C13  C  CH2   0  -0.438  -1.2875  -16.1884  30.1345
 QME  C15  C  CR16  0  -0.287  -5.4246  -16.7694  22.6970
 QME  C1   C  CR5   0   0.412  -4.1136  -17.1855  27.0484
 QME  C11  C  CR16  0  -0.351  -6.6164  -17.8742  24.4980
 QME  C12  C  CR16  0  -0.313  -4.3797  -16.4238  23.5335
 QME  C14  C  CR16  0  -0.272  -6.5330  -17.4882  23.1742
 QME  C2   C  CH1   0  -0.209  -3.3877  -17.1123  28.3519
 QME  C3   C  CR15  0  -0.475  -5.3193  -17.7600  26.7590
 QME  C9   C  CH2   0  -0.444  -1.2906  -17.6302  29.6378
 QME  N4   N  NR15  0  -0.737  -3.6051  -16.6188  25.9072
 QME  N6   N  NH1   0  -0.577  -3.3828  -15.7359  28.8462
 QME  H1   H  HCH2  0   0.239  -2.0635  -18.7799  27.9696
 QME  H2   H  HCH2  0   0.212  -1.3860  -17.2211  27.5260
 QME  H3   H  HCH2  0   0.237  -2.6959  -14.5660  30.4182
 QME  H4   H  HCH2  0   0.216  -3.3067  -16.1433  30.8790
 QME  H5   H  HCH2  0   0.228  -0.8639  -16.1273  31.1400
 QME  H6   H  HCH2  0   0.215  -0.6513  -15.5777  29.4852
 QME  H8   H  HCR6  0   0.244  -7.4768  -18.4267  24.8556
 QME  H9   H  HCR6  0   0.257  -3.5256  -15.8703  23.1641
 QME  H10  H  HCR6  0   0.245  -7.3327  -17.7411  22.4901
 QME  H11  H  HCH1  0   0.247  -3.9756  -17.7004  29.0659
 QME  H12  H  HCR5  0   0.247  -5.9494  -18.2813  27.4631
 QME  H13  H  HCH2  0   0.217  -1.8100  -18.2657  30.3636
 QME  H14  H  HCH2  0   0.234  -0.2708  -18.0141  29.5644
 QME  H15  H  HNR5  0   0.404  -2.7159  -16.1525  25.8331
 QME  H16  H  HNH1  0   0.335  -2.9114  -15.1380  28.1750
 QME  H7   H  HCR6  0   0.248  -5.3884  -16.4800  21.6546

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
 QME  C15  C14  aromatic  1.405  0.020  1.405
 QME  C15  C12  aromatic  1.382  0.020  1.382
 QME  C14  C11  aromatic  1.381  0.020  1.381
 QME  C12  C8   aromatic  1.393  0.020  1.393
 QME  C11  C7   aromatic  1.400  0.020  1.400
 QME  C8   C7   aromatic  1.413  0.020  1.413
 QME  C8   N4   aromatic  1.366  0.020  1.366
 QME  C7   C3   aromatic  1.429  0.020  1.429
 QME  N4   C1   aromatic  1.372  0.020  1.372
 QME  C3   C1   aromatic  1.367  0.020  1.367
 QME  C1   C2   single    1.494  0.020  1.494
 QME  C2   C5   single    1.535  0.020  1.535
 QME  C2   N6   single    1.462  0.020  1.462
 QME  C5   C9   single    1.526  0.020  1.526
 QME  N6   C10  single    1.457  0.020  1.457
 QME  C9   C13  single    1.525  0.020  1.525
 QME  C10  C13  single    1.526  0.020  1.526
 QME  C5   H1   single    0.970  0.020  1.090
 QME  C5   H2   single    0.970  0.020  1.090
 QME  C10  H3   single    0.970  0.020  1.090
 QME  C10  H4   single    0.970  0.020  1.090
 QME  C13  H5   single    0.970  0.020  1.090
 QME  C13  H6   single    0.970  0.020  1.090
 QME  C15  H7   single    0.930  0.020  1.080
 QME  C11  H8   single    0.930  0.020  1.080
 QME  C12  H9   single    0.930  0.020  1.080
 QME  C14  H10  single    0.930  0.020  1.080
 QME  C2   H11  single    0.970  0.020  1.090
 QME  C3   H12  single    0.930  0.020  1.080
 QME  C9   H13  single    0.970  0.020  1.090
 QME  C9   H14  single    0.970  0.020  1.090
 QME  N4   H15  single    0.860  0.020  1.020
 QME  N6   H16  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
 QME  H2   C5   H1   106.74  3.000
 QME  H2   C5   C9   109.32  3.000
 QME  H1   C5   C9   110.71  3.000
 QME  H2   C5   C2   109.87  3.000
 QME  H1   C5   C2   109.69  3.000
 QME  C9   C5   C2   110.44  3.000
 QME  C3   C7   C11  134.48  3.000
 QME  C3   C7   C8   106.59  3.000
 QME  C11  C7   C8   118.93  3.000
 QME  N4   C8   C12  130.38  3.000
 QME  N4   C8   C7   107.32  3.000
 QME  C12  C8   C7   122.30  3.000
 QME  H4   C10  H3   106.51  3.000
 QME  H4   C10  N6   107.87  3.000
 QME  H3   C10  N6   108.25  3.000
 QME  H4   C10  C13  109.29  3.000
 QME  H3   C10  C13  110.67  3.000
 QME  N6   C10  C13  113.94  3.000
 QME  H6   C13  H5   106.81  3.000
 QME  H6   C13  C9   109.59  3.000
 QME  H5   C13  C9   110.69  3.000
 QME  H6   C13  C10  109.21  3.000
 QME  H5   C13  C10  109.98  3.000
 QME  C9   C13  C10  110.48  3.000
 QME  H7   C15  C14  119.37  3.000
 QME  H7   C15  C12  119.38  3.000
 QME  C14  C15  C12  121.25  3.000
 QME  N4   C1   C3   108.94  3.000
 QME  C3   C1   C2   129.36  3.000
 QME  N4   C1   C2   121.70  3.000
 QME  H8   C11  C14  120.45  3.000
 QME  H8   C11  C7   120.55  3.000
 QME  C14  C11  C7   119.00  3.000
 QME  H9   C12  C15  121.17  3.000
 QME  H9   C12  C8   121.39  3.000
 QME  C15  C12  C8   117.44  3.000
 QME  H10  C14  C11  119.72  3.000
 QME  H10  C14  C15  119.20  3.000
 QME  C11  C14  C15  121.08  3.000
 QME  H11  C2   N6   106.66  3.000
 QME  H11  C2   C1   106.35  3.000
 QME  N6   C2   C1   110.04  3.000
 QME  H11  C2   C5   107.47  3.000
 QME  N6   C2   C5   113.22  3.000
 QME  C1   C2   C5   112.65  3.000
 QME  H12  C3   C1   125.45  3.000
 QME  H12  C3   C7   127.23  3.000
 QME  C1   C3   C7   107.32  3.000
 QME  H14  C9   H13  106.45  3.000
 QME  H14  C9   C13  110.63  3.000
 QME  H13  C9   C13  109.48  3.000
 QME  H14  C9   C5   110.01  3.000
 QME  H13  C9   C5   109.34  3.000
 QME  C13  C9   C5   110.82  3.000
 QME  H15  N4   C1   125.45  3.000
 QME  H15  N4   C8   124.70  3.000
 QME  C1   N4   C8   109.83  3.000
 QME  H16  N6   C2   109.42  3.000
 QME  H16  N6   C10  108.57  3.000
 QME  C2   N6   C10  112.01  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
 QME  CONST_01  C15  C14  C11  C7     0.00   0.0  0
 QME  CONST_02  C15  C12  C8   C7     0.00   0.0  0
 QME  CONST_03  C1   N4   C8   C7     0.00   0.0  0
 QME  CONST_04  N4   C1   C3   C7     0.00   0.0  0
 QME  CONST_05  C14  C15  C12  C8     0.00   0.0  0
 QME  CONST_06  C14  C11  C7   C8     0.00   0.0  0
 QME  CONST_07  C1   C3   C7   C8     0.00   0.0  0
 QME  CONST_08  C3   C1   N4   C8     0.00   0.0  0
 QME  CONST_09  N4   C8   C12  C15  180.00   0.0  0
 QME  CONST_10  C12  C8   N4   C1   180.00   0.0  0
 QME  CONST_11  C11  C7   C3   C1   180.00   0.0  0
 QME  CONST_12  C12  C15  C14  C11    0.00   0.0  0
 QME  CONST_13  C12  C8   C7   C11    0.00   0.0  0
 QME  CONST_14  N4   C8   C7   C11  180.00   0.0  0
 QME  CONST_15  C3   C7   C8   C12  180.00   0.0  0
 QME  CONST_16  C3   C7   C11  C14  180.00   0.0  0
 QME  CONST_17  N4   C8   C7   C3     0.00   0.0  0
 QME  CONST_18  C2   C1   C3   C7   180.00   0.0  0
 QME  CONST_19  C2   C1   N4   C8   180.00   0.0  0
 QME  CONST_20  H10  C14  C11  C7   180.00   0.0  0
 QME  CONST_21  H9   C12  C8   C7   180.00   0.0  0
 QME  CONST_22  H15  N4   C8   C7   180.00   0.0  0
 QME  CONST_23  H7   C15  C12  C8   180.00   0.0  0
 QME  CONST_24  H8   C11  C7   C8   180.00   0.0  0
 QME  CONST_25  H12  C3   C7   C8   180.00   0.0  0
 QME  Var_01    C10  C13  C9   C5    53.18  30.0  1
 QME  Var_02    C2   C5   C9   C13  -53.51  30.0  1
 QME  Var_03    C2   N6   C10  C13   53.92  30.0  1
 QME  Var_04    N6   C10  C13  C9   -53.80  30.0  1

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
 QME  chir_01  C2  C1  C5  N6  negativ

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
 QME  plan-1  C7   0.020
 QME  plan-1  C8   0.020
 QME  plan-1  C15  0.020
 QME  plan-1  C1   0.020
 QME  plan-1  C11  0.020
 QME  plan-1  C12  0.020
 QME  plan-1  C14  0.020
 QME  plan-1  C2   0.020
 QME  plan-1  C3   0.020
 QME  plan-1  N4   0.020
 QME  plan-1  H8   0.020
 QME  plan-1  H9   0.020
 QME  plan-1  H10  0.020
 QME  plan-1  H12  0.020
 QME  plan-1  H15  0.020
 QME  plan-1  H7   0.020

