# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:40:39 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: [(3S)-3-methylpiperidin-1-yl](quinoxalin-6-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCCN(C1)C(=O)c2ccc3nccnc3c2
#
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
 MQS  MQS  '[(3S)-3-methylpiperidin-1-yl](quinoxalin-6-yl)methanone'  ligand  36  19  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MQS
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
 MQS  C1   C  CR16  0  -0.313  -1.1605  -0.1839   0.8020
 MQS  C2   C  CR6   0  -0.078  -0.3894   0.6751   0.0630
 MQS  C3   C  CR16  0  -0.265  -0.9750   1.4549  -0.9617
 MQS  C4   C  CR16  0  -0.296  -2.3049   1.3394  -1.2532
 MQS  C5   C  CR66  0   0.247  -2.5401  -0.3009   0.5370
 MQS  C6   C  CR66  0   0.229  -3.1180   0.4612  -0.5050
 MQS  N1   N  N     0  -0.377  -4.4380   0.3620  -0.7881
 MQS  C7   C  CR16  0  -0.112  -5.1368  -0.4590  -0.0576
 MQS  C8   C  CR16  0  -0.113  -4.5582  -1.2200   0.9885
 MQS  N2   N  N     0  -0.379  -3.2918  -1.1453   1.2820
 MQS  C9   C  C     0   0.524   1.0463   0.9212   0.4160
 MQS  C10  C  CH2   0  -0.430   2.5830  -1.5654  -1.3827
 MQS  C11  C  CH2   0  -0.318   1.6430  -1.4118  -0.1926
 MQS  N3   N  NT    0  -0.446   1.8754  -0.1368   0.4729
 MQS  C12  C  CH2   0  -0.289   3.2471   0.0355   0.9264
 MQS  C13  C  CH1   0  -0.243   4.2414  -0.0558  -0.2281
 MQS  C14  C  CH2   0  -0.426   4.0379  -1.3735  -0.9725
 MQS  O1   O  O     0  -0.487   1.3851   2.0676   0.6830
 MQS  C15  C  CH3   0  -0.658   5.6668   0.0963   0.2822
 MQS  H1   H  HCR6  0   0.279  -0.7356  -0.7804   1.6005
 MQS  H2   H  HCR6  0   0.273  -0.3561   2.1397  -1.5261
 MQS  H3   H  HCR6  0   0.274  -2.7567   1.9180  -2.0485
 MQS  H4   H  HCR6  0   0.281  -6.1959  -0.5527  -0.2682
 MQS  H5   H  HCR6  0   0.281  -5.1778  -1.8915   1.5714
 MQS  H7   H  HCH2  0   0.225   2.3100  -0.8314  -2.1473
 MQS  H8   H  HCH2  0   0.273   0.6103  -1.4881  -0.5198
 MQS  H9   H  HCH2  0   0.244   1.8130  -2.2158   0.5295
 MQS  H10  H  HCH2  0   0.261   3.3377   0.9855   1.4481
 MQS  H11  H  HCH2  0   0.239   3.4580  -0.7589   1.6517
 MQS  H12  H  HCH1  0   0.228   4.0280   0.7686  -0.9193
 MQS  H13  H  HCH2  0   0.213   4.3467  -2.2016  -0.3236
 MQS  H14  H  HCH2  0   0.237   4.6876  -1.4099  -1.8507
 MQS  H15  H  HCH3  0   0.218   5.9064  -0.6715   1.0216
 MQS  H16  H  HCH3  0   0.232   6.3846   0.0044  -0.5340
 MQS  H17  H  HCH3  0   0.230   5.8215   1.0691   0.7520
 MQS  H6   H  HCH2  0   0.242   2.4339  -2.5536  -1.8228

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
 MQS  C15  C13  single    1.522  0.020  1.522
 MQS  C13  C12  single    1.526  0.020  1.526
 MQS  C13  C14  single    1.527  0.020  1.527
 MQS  C12  N3   single    1.455  0.020  1.455
 MQS  C14  C10  single    1.524  0.020  1.524
 MQS  C7   N1   aromatic  1.302  0.020  1.302
 MQS  C7   C8   aromatic  1.417  0.020  1.417
 MQS  N1   C6   aromatic  1.354  0.020  1.354
 MQS  C8   N2   aromatic  1.302  0.020  1.302
 MQS  C6   C4   aromatic  1.411  0.020  1.411
 MQS  C6   C5   aromatic  1.414  0.020  1.414
 MQS  C4   C3   aromatic  1.366  0.020  1.366
 MQS  N2   C5   aromatic  1.354  0.020  1.354
 MQS  C5   C1   aromatic  1.410  0.020  1.410
 MQS  N3   C11  single    1.457  0.020  1.457
 MQS  N3   C9   single    1.345  0.020  1.345
 MQS  C3   C2   aromatic  1.415  0.020  1.415
 MQS  C1   C2   aromatic  1.371  0.020  1.371
 MQS  C10  C11  single    1.524  0.020  1.524
 MQS  C2   C9   single    1.499  0.020  1.499
 MQS  C9   O1   double    1.225  0.020  1.225
 MQS  C1   H1   single    0.930  0.020  1.080
 MQS  C3   H2   single    0.930  0.020  1.080
 MQS  C4   H3   single    0.930  0.020  1.080
 MQS  C7   H4   single    0.930  0.020  1.080
 MQS  C8   H5   single    0.930  0.020  1.080
 MQS  C10  H6   single    0.970  0.020  1.090
 MQS  C10  H7   single    0.970  0.020  1.090
 MQS  C11  H8   single    0.970  0.020  1.090
 MQS  C11  H9   single    0.970  0.020  1.090
 MQS  C12  H10  single    0.970  0.020  1.090
 MQS  C12  H11  single    0.970  0.020  1.090
 MQS  C13  H12  single    0.970  0.020  1.090
 MQS  C14  H13  single    0.970  0.020  1.090
 MQS  C14  H14  single    0.970  0.020  1.090
 MQS  C15  H15  single    0.970  0.020  1.090
 MQS  C15  H16  single    0.970  0.020  1.090
 MQS  C15  H17  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
 MQS  H1   C1   C5   118.47  3.000
 MQS  H1   C1   C2   121.45  3.000
 MQS  C5   C1   C2   120.08  3.000
 MQS  C9   C2   C3   118.47  3.000
 MQS  C9   C2   C1   120.98  3.000
 MQS  C3   C2   C1   120.21  3.000
 MQS  H2   C3   C4   119.93  3.000
 MQS  H2   C3   C2   119.34  3.000
 MQS  C4   C3   C2   120.73  3.000
 MQS  H3   C4   C6   118.79  3.000
 MQS  H3   C4   C3   121.19  3.000
 MQS  C6   C4   C3   120.01  3.000
 MQS  N2   C5   C6   120.96  3.000
 MQS  N2   C5   C1   119.45  3.000
 MQS  C6   C5   C1   119.58  3.000
 MQS  N1   C6   C5   120.86  3.000
 MQS  C5   C6   C4   119.36  3.000
 MQS  N1   C6   C4   119.77  3.000
 MQS  C7   N1   C6   116.89  3.000
 MQS  H4   C7   C8   119.74  3.000
 MQS  H4   C7   N1   118.02  3.000
 MQS  C8   C7   N1   122.24  3.000
 MQS  H5   C8   N2   118.06  3.000
 MQS  H5   C8   C7   119.75  3.000
 MQS  N2   C8   C7   122.19  3.000
 MQS  C8   N2   C5   116.86  3.000
 MQS  O1   C9   N3   123.80  3.000
 MQS  O1   C9   C2   118.04  3.000
 MQS  N3   C9   C2   118.11  3.000
 MQS  H7   C10  H6   106.93  3.000
 MQS  H7   C10  C14  109.99  3.000
 MQS  H6   C10  C14  110.66  3.000
 MQS  H7   C10  C11  108.91  3.000
 MQS  H6   C10  C11  108.76  3.000
 MQS  C14  C10  C11  111.47  3.000
 MQS  H9   C11  H8   107.16  3.000
 MQS  H9   C11  N3   108.47  3.000
 MQS  H8   C11  N3   110.54  3.000
 MQS  H9   C11  C10  110.22  3.000
 MQS  H8   C11  C10  110.13  3.000
 MQS  N3   C11  C10  110.27  3.000
 MQS  C12  N3   C11  113.35  3.000
 MQS  C11  N3   C9   124.80  3.000
 MQS  C12  N3   C9   120.07  3.000
 MQS  H11  C12  H10  107.44  3.000
 MQS  H11  C12  C13  109.38  3.000
 MQS  H10  C12  C13  111.15  3.000
 MQS  H11  C12  N3   107.56  3.000
 MQS  H10  C12  N3   109.36  3.000
 MQS  C13  C12  N3   111.79  3.000
 MQS  H12  C13  C15  108.57  3.000
 MQS  H12  C13  C14  108.38  3.000
 MQS  C15  C13  C14  111.99  3.000
 MQS  H12  C13  C12  107.76  3.000
 MQS  C14  C13  C12  109.49  3.000
 MQS  C15  C13  C12  110.52  3.000
 MQS  H14  C14  H13  106.44  3.000
 MQS  H14  C14  C13  109.96  3.000
 MQS  H13  C14  C13  109.00  3.000
 MQS  H14  C14  C10  110.31  3.000
 MQS  H13  C14  C10  109.46  3.000
 MQS  C13  C14  C10  111.54  3.000
 MQS  H17  C15  H16  107.69  3.000
 MQS  H17  C15  H15  107.69  3.000
 MQS  H16  C15  H15  107.63  3.000
 MQS  H17  C15  C13  111.48  3.000
 MQS  H16  C15  C13  110.92  3.000
 MQS  H15  C15  C13  111.24  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
 MQS  CONST_01  N1   C6   C5   C1   180.00   0.0  0
 MQS  CONST_02  C4   C6   C5   C1     0.00   0.0  0
 MQS  CONST_03  C8   N2   C5   C1   180.00   0.0  0
 MQS  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 MQS  CONST_05  C6   C4   C3   C2     0.00   0.0  0
 MQS  CONST_06  C6   C5   C1   C2     0.00   0.0  0
 MQS  CONST_07  N2   C5   C1   C2   180.00   0.0  0
 MQS  CONST_08  N1   C6   C4   C3   180.00   0.0  0
 MQS  CONST_09  C5   C6   C4   C3     0.00   0.0  0
 MQS  CONST_10  C5   C1   C2   C3     0.00   0.0  0
 MQS  CONST_11  C7   N1   C6   C4   180.00   0.0  0
 MQS  CONST_12  N2   C5   C6   C4   180.00   0.0  0
 MQS  CONST_13  C7   N1   C6   C5     0.00   0.0  0
 MQS  CONST_14  C7   C8   N2   C5     0.00   0.0  0
 MQS  CONST_15  C8   C7   N1   C6     0.00   0.0  0
 MQS  CONST_16  C8   N2   C5   C6     0.00   0.0  0
 MQS  CONST_17  N2   C8   C7   N1     0.00   0.0  0
 MQS  CONST_18  N2   C5   C6   N1     0.00   0.0  0
 MQS  CONST_19  C9   C2   C3   C4   180.00   0.0  0
 MQS  CONST_20  C9   C2   C1   C5   180.00   0.0  0
 MQS  CONST_21  C12  N3   C9   C2   180.00   0.0  0
 MQS  CONST_23  H2   C3   C2   C1   180.00   0.0  0
 MQS  CONST_24  H3   C4   C3   C2   180.00   0.0  0
 MQS  CONST_25  H1   C1   C2   C3   180.00   0.0  0
 MQS  CONST_26  H5   C8   N2   C5   180.00   0.0  0
 MQS  CONST_27  H4   C7   N1   C6   180.00   0.0  0
 MQS  CONST_29  O1   C9   N3   C12    0.00   0.0  0
 MQS  Var_01    C12  N3   C11  C10  -57.45  30.0  1
 MQS  Var_02    C13  C12  N3   C11   58.84  30.0  1
 MQS  Var_03    C13  C14  C10  C11  -53.10  30.0  1
 MQS  Var_04    C14  C10  C11  N3    54.07  30.0  1
 MQS  Var_05    N3   C9   C2   C1    57.04  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
 MQS  chir_01  C13  C15  C12  C14  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
 MQS  plan-1  C1   0.020
 MQS  plan-1  C2   0.020
 MQS  plan-1  C3   0.020
 MQS  plan-1  C4   0.020
 MQS  plan-1  C5   0.020
 MQS  plan-1  C6   0.020
 MQS  plan-1  N1   0.020
 MQS  plan-1  C7   0.020
 MQS  plan-1  C8   0.020
 MQS  plan-1  N2   0.020
 MQS  plan-1  C9   0.020
 MQS  plan-1  H1   0.020
 MQS  plan-1  H2   0.020
 MQS  plan-1  H3   0.020
 MQS  plan-1  H4   0.020
 MQS  plan-1  H5   0.020
 MQS  plan-2  C2   0.020
 MQS  plan-2  C9   0.020
 MQS  plan-2  C11  0.020
 MQS  plan-2  N3   0.020
 MQS  plan-2  C12  0.020
 MQS  plan-2  O1   0.020

