# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:44:19 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: [(3R)-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
 MQR  MQR  '[(3R)-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_MQR
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
 MQR  O1   O  O     0  -0.486   1.3824  -2.1016   0.5024
 MQR  C1   C  CR16  0  -0.313  -1.1681   0.1292   0.8048
 MQR  C2   C  CR6   0  -0.078  -0.3950  -0.6655  -0.0009
 MQR  C3   C  CR16  0  -0.264  -0.9787  -1.3601  -1.0864
 MQR  C4   C  CR16  0  -0.296  -2.3087  -1.2241  -1.3684
 MQR  C5   C  CR66  0   0.247  -2.5481   0.2637   0.5496
 MQR  C6   C  CR66  0   0.229  -3.1243  -0.4128  -0.5510
 MQR  N1   N  N     0  -0.377  -4.4447  -0.2951  -0.8245
 MQR  C7   C  CR16  0  -0.112  -5.1461   0.4607  -0.0290
 MQR  C8   C  CR16  0  -0.113  -4.5691   1.1355   1.0757
 MQR  N2   N  N     0  -0.379  -3.3023   1.0418   1.3613
 MQR  C9   C  C     0   0.523   1.0410  -0.9382   0.3300
 MQR  C10  C  CH2   0  -0.429   2.5651   1.6485  -1.3004
 MQR  C11  C  CH2   0  -0.319   1.6402   1.4306  -0.1082
 MQR  N3   N  NT    0  -0.445   1.8682   0.1136   0.4722
 MQR  C12  C  CH2   0  -0.290   3.2440  -0.0960   0.8976
 MQR  C13  C  CH1   0  -0.243   4.2224   0.0514  -0.2650
 MQR  C14  C  CH2   0  -0.426   4.0230   1.4147  -0.9244
 MQR  C15  C  CH3   0  -0.658   5.6538  -0.1452   0.2118
 MQR  H2   H  HCR6  0   0.273  -0.3581  -1.9942  -1.7057
 MQR  H3   H  HCR6  0   0.274  -2.7588  -1.7363  -2.2088
 MQR  H4   H  HCR6  0   0.281  -6.2056   0.5674  -0.2312
 MQR  H5   H  HCR6  0   0.281  -5.1904   1.7544   1.7126
 MQR  H6   H  HCH2  0   0.224   2.2702   0.9691  -2.1062
 MQR  H7   H  HCH2  0   0.242   2.4221   2.6645  -1.6744
 MQR  H8   H  HCH2  0   0.244   1.8295   2.1849   0.6611
 MQR  H9   H  HCH2  0   0.273   0.6034   1.5385  -0.4136
 MQR  H10  H  HCH2  0   0.239   3.4713   0.6569   1.6609
 MQR  H11  H  HCH2  0   0.261   3.3334  -1.0738   1.3655
 MQR  H12  H  HCH1  0   0.228   3.9900  -0.7295  -0.9992
 MQR  H13  H  HCH2  0   0.237   4.6624   1.5008  -1.8064
 MQR  H14  H  HCH2  0   0.213   4.3475   2.1954  -0.2263
 MQR  H15  H  HCH3  0   0.230   5.8004  -1.1395   0.6374
 MQR  H16  H  HCH3  0   0.232   6.3579  -0.0318  -0.6136
 MQR  H17  H  HCH3  0   0.218   5.9209   0.5870   0.9772
 MQR  H1   H  HCR6  0   0.279  -0.7464   0.6598   1.6501

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
 MQR  C10  C11  single    1.525  0.020  1.525
 MQR  C10  C14  single    1.524  0.020  1.524
 MQR  C11  N3   single    1.457  0.020  1.457
 MQR  C14  C13  single    1.527  0.020  1.527
 MQR  N1   C7   aromatic  1.302  0.020  1.302
 MQR  N1   C6   aromatic  1.354  0.020  1.354
 MQR  C7   C8   aromatic  1.417  0.020  1.417
 MQR  C4   C6   aromatic  1.411  0.020  1.411
 MQR  C4   C3   aromatic  1.366  0.020  1.366
 MQR  C6   C5   aromatic  1.415  0.020  1.415
 MQR  C8   N2   aromatic  1.302  0.020  1.302
 MQR  C3   C2   aromatic  1.415  0.020  1.415
 MQR  C5   N2   aromatic  1.354  0.020  1.354
 MQR  C5   C1   aromatic  1.410  0.020  1.410
 MQR  N3   C12  single    1.455  0.020  1.455
 MQR  N3   C9   single    1.346  0.020  1.346
 MQR  C2   C1   aromatic  1.371  0.020  1.371
 MQR  C2   C9   single    1.499  0.020  1.499
 MQR  C13  C12  single    1.527  0.020  1.527
 MQR  C13  C15  single    1.521  0.020  1.521
 MQR  C9   O1   double    1.225  0.020  1.225
 MQR  C1   H1   single    0.930  0.020  1.080
 MQR  C3   H2   single    0.930  0.020  1.080
 MQR  C4   H3   single    0.930  0.020  1.080
 MQR  C7   H4   single    0.930  0.020  1.080
 MQR  C8   H5   single    0.930  0.020  1.080
 MQR  C10  H6   single    0.970  0.020  1.090
 MQR  C10  H7   single    0.970  0.020  1.090
 MQR  C11  H8   single    0.970  0.020  1.090
 MQR  C11  H9   single    0.970  0.020  1.090
 MQR  C12  H10  single    0.970  0.020  1.090
 MQR  C12  H11  single    0.970  0.020  1.090
 MQR  C13  H12  single    0.970  0.020  1.090
 MQR  C14  H13  single    0.970  0.020  1.090
 MQR  C14  H14  single    0.970  0.020  1.090
 MQR  C15  H15  single    0.970  0.020  1.090
 MQR  C15  H16  single    0.970  0.020  1.090
 MQR  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
 MQR  H1   C1   C5   118.40  3.000
 MQR  H1   C1   C2   121.53  3.000
 MQR  C5   C1   C2   120.07  3.000
 MQR  C9   C2   C3   118.39  3.000
 MQR  C9   C2   C1   121.08  3.000
 MQR  C3   C2   C1   120.20  3.000
 MQR  H2   C3   C4   119.90  3.000
 MQR  H2   C3   C2   119.36  3.000
 MQR  C4   C3   C2   120.74  3.000
 MQR  H3   C4   C6   118.78  3.000
 MQR  H3   C4   C3   121.20  3.000
 MQR  C6   C4   C3   120.01  3.000
 MQR  N2   C5   C6   120.96  3.000
 MQR  N2   C5   C1   119.44  3.000
 MQR  C6   C5   C1   119.60  3.000
 MQR  N1   C6   C5   120.86  3.000
 MQR  C5   C6   C4   119.35  3.000
 MQR  N1   C6   C4   119.78  3.000
 MQR  C7   N1   C6   116.90  3.000
 MQR  H4   C7   C8   119.76  3.000
 MQR  H4   C7   N1   118.01  3.000
 MQR  C8   C7   N1   122.22  3.000
 MQR  H5   C8   N2   118.03  3.000
 MQR  H5   C8   C7   119.77  3.000
 MQR  N2   C8   C7   122.19  3.000
 MQR  C8   N2   C5   116.86  3.000
 MQR  N3   C9   C2   118.05  3.000
 MQR  C2   C9   O1   118.10  3.000
 MQR  N3   C9   O1   123.80  3.000
 MQR  H7   C10  H6   106.86  3.000
 MQR  H7   C10  C14  110.64  3.000
 MQR  H6   C10  C14  110.14  3.000
 MQR  H7   C10  C11  108.74  3.000
 MQR  H6   C10  C11  108.88  3.000
 MQR  C14  C10  C11  111.45  3.000
 MQR  H9   C11  H8   107.12  3.000
 MQR  H9   C11  N3   110.56  3.000
 MQR  H8   C11  N3   108.42  3.000
 MQR  H9   C11  C10  110.18  3.000
 MQR  H8   C11  C10  110.27  3.000
 MQR  N3   C11  C10  110.22  3.000
 MQR  C12  N3   C11  113.24  3.000
 MQR  C12  N3   C9   119.97  3.000
 MQR  C11  N3   C9   124.62  3.000
 MQR  H11  C12  H10  107.52  3.000
 MQR  H11  C12  C13  111.20  3.000
 MQR  H10  C12  C13  109.34  3.000
 MQR  H11  C12  N3   109.45  3.000
 MQR  H10  C12  N3   107.51  3.000
 MQR  C13  C12  N3   111.68  3.000
 MQR  H12  C13  C15  108.49  3.000
 MQR  H12  C13  C14  108.60  3.000
 MQR  C15  C13  C14  111.93  3.000
 MQR  H12  C13  C12  107.77  3.000
 MQR  C15  C13  C12  110.60  3.000
 MQR  C14  C13  C12  109.34  3.000
 MQR  H14  C14  H13  106.54  3.000
 MQR  H14  C14  C13  108.78  3.000
 MQR  H13  C14  C13  110.02  3.000
 MQR  H14  C14  C10  109.33  3.000
 MQR  H13  C14  C10  110.40  3.000
 MQR  C13  C14  C10  111.62  3.000
 MQR  H17  C15  H16  107.62  3.000
 MQR  H17  C15  H15  107.73  3.000
 MQR  H16  C15  H15  107.64  3.000
 MQR  H17  C15  C13  111.28  3.000
 MQR  H16  C15  C13  110.90  3.000
 MQR  H15  C15  C13  111.49  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
 MQR  CONST_01  N1   C6   C5   C1   180.00   0.0  0
 MQR  CONST_02  C4   C6   C5   C1     0.00   0.0  0
 MQR  CONST_03  C8   N2   C5   C1   180.00   0.0  0
 MQR  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 MQR  CONST_05  C6   C4   C3   C2     0.00   0.0  0
 MQR  CONST_06  C6   C5   C1   C2     0.00   0.0  0
 MQR  CONST_07  N2   C5   C1   C2   180.00   0.0  0
 MQR  CONST_08  N1   C6   C4   C3   180.00   0.0  0
 MQR  CONST_09  C5   C6   C4   C3     0.00   0.0  0
 MQR  CONST_10  C5   C1   C2   C3     0.00   0.0  0
 MQR  CONST_11  C7   N1   C6   C4   180.00   0.0  0
 MQR  CONST_12  N2   C5   C6   C4   180.00   0.0  0
 MQR  CONST_13  C7   N1   C6   C5     0.00   0.0  0
 MQR  CONST_14  C7   C8   N2   C5     0.00   0.0  0
 MQR  CONST_15  C8   C7   N1   C6     0.00   0.0  0
 MQR  CONST_16  C8   N2   C5   C6     0.00   0.0  0
 MQR  CONST_17  N2   C8   C7   N1     0.00   0.0  0
 MQR  CONST_18  N2   C5   C6   N1     0.00   0.0  0
 MQR  CONST_19  C9   C2   C3   C4   180.00   0.0  0
 MQR  CONST_20  C9   C2   C1   C5   180.00   0.0  0
 MQR  CONST_22  C12  N3   C9   C2   180.00   0.0  0
 MQR  CONST_23  H2   C3   C2   C1   180.00   0.0  0
 MQR  CONST_24  H3   C4   C3   C2   180.00   0.0  0
 MQR  CONST_25  H1   C1   C2   C3   180.00   0.0  0
 MQR  CONST_26  H5   C8   N2   C5   180.00   0.0  0
 MQR  CONST_27  H4   C7   N1   C6   180.00   0.0  0
 MQR  CONST_29  C12  N3   C9   O1     0.00   0.0  0
 MQR  Var_01    C12  N3   C11  C10   57.70  30.0  1
 MQR  Var_02    C13  C14  C10  C11   53.01  30.0  1
 MQR  Var_03    C13  C12  N3   C11  -59.30  30.0  1
 MQR  Var_04    C14  C10  C11  N3   -54.02  30.0  1
 MQR  Var_05    N3   C9   C2   C1   -57.03  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
 MQR  chir_01  C13  C14  C12  C15  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
 MQR  plan-1  C1   0.020
 MQR  plan-1  C2   0.020
 MQR  plan-1  C3   0.020
 MQR  plan-1  C4   0.020
 MQR  plan-1  C5   0.020
 MQR  plan-1  C6   0.020
 MQR  plan-1  N1   0.020
 MQR  plan-1  C7   0.020
 MQR  plan-1  C8   0.020
 MQR  plan-1  N2   0.020
 MQR  plan-1  C9   0.020
 MQR  plan-1  H2   0.020
 MQR  plan-1  H3   0.020
 MQR  plan-1  H4   0.020
 MQR  plan-1  H5   0.020
 MQR  plan-1  H1   0.020
 MQR  plan-2  O1   0.020
 MQR  plan-2  C2   0.020
 MQR  plan-2  C9   0.020
 MQR  plan-2  C11  0.020
 MQR  plan-2  N3   0.020
 MQR  plan-2  C12  0.020

