# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 07:59:12 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: piperidin-1-yl(quinoxalin-6-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N1CCCCC1)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
 CX5  CX5  piperidin-1-yl(quinoxalin-6-yl)methanone  ligand  33  18  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CX5
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
 CX5  C1   C  CR16  0  -0.313  -0.8531  -0.1097  -0.8120
 CX5  C2   C  CR6   0  -0.076  -0.0623   0.6891  -0.0280
 CX5  C3   C  CR16  0  -0.264  -0.6215   1.3889   1.0670
 CX5  C4   C  CR16  0  -0.296  -1.9446   1.2538   1.3801
 CX5  C6   C  CR66  0   0.229  -2.7781   0.4380   0.5858
 CX5  C7   C  CR16  0  -0.112  -4.8107  -0.4394   0.1148
 CX5  C8   C  CR16  0  -0.113  -4.2586  -1.1203  -0.9988
 CX5  C9   C  C     0   0.523   1.3670   0.9597  -0.3894
 CX5  C11  C  CH2   0  -0.318   1.9753  -1.4039   0.0638
 CX5  C13  C  CH2   0  -0.435   4.5372  -0.0215   0.1970
 CX5  C14  C  CH2   0  -0.446   4.3621  -1.3765   0.8744
 CX5  C5   C  CR66  0   0.247  -2.2267  -0.2436  -0.5244
 CX5  N1   N  N     0  -0.377  -4.0919   0.3211   0.8899
 CX5  N2   N  N     0  -0.379  -2.9987  -1.0270  -1.3140
 CX5  C10  C  CH2   0  -0.427   2.9046  -1.6088   1.2560
 CX5  N3   N  NT    0  -0.441   2.1940  -0.0917  -0.5322
 CX5  C12  C  CH2   0  -0.319   3.5679   0.1181  -0.9695
 CX5  O1   O  O     0  -0.486   1.7028   2.1218  -0.5815
 CX5  H1   H  HCR6  0   0.279  -0.4507  -0.6451  -1.6637
 CX5  H2   H  HCR6  0   0.273   0.0124   2.0269   1.6686
 CX5  H3   H  HCR6  0   0.274  -2.3753   1.7709   2.2277
 CX5  H4   H  HCR6  0   0.281  -5.8654  -0.5452   0.3410
 CX5  H5   H  HCR6  0   0.281  -4.8936  -1.7436  -1.6175
 CX5  H7   H  HCH2  0   0.272   0.9400  -1.5137   0.3736
 CX5  H8   H  HCH2  0   0.227   4.3582   0.7860   0.9130
 CX5  H9   H  HCH2  0   0.240   5.5592   0.0974  -0.1688
 CX5  H10  H  HCH2  0   0.218   4.6864  -2.1648   0.1868
 CX5  H11  H  HCH2  0   0.240   5.0018  -1.4493   1.7559
 CX5  H12  H  HCH2  0   0.224   2.6114  -0.9209   2.0554
 CX5  H13  H  HCH2  0   0.242   2.7626  -2.6208   1.6411
 CX5  H14  H  HCH2  0   0.264   3.6523   1.0916  -1.4449
 CX5  H15  H  HCH2  0   0.244   3.7897  -0.6398  -1.7275
 CX5  H6   H  HCH2  0   0.244   2.1650  -2.1648  -0.6988

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
 CX5  C12  C13  single    1.523  0.020  1.523
 CX5  C12  N3   single    1.457  0.020  1.457
 CX5  C13  C14  single    1.525  0.020  1.525
 CX5  C7   N1   aromatic  1.302  0.020  1.302
 CX5  C7   C8   aromatic  1.417  0.020  1.417
 CX5  N1   C6   aromatic  1.354  0.020  1.354
 CX5  C8   N2   aromatic  1.302  0.020  1.302
 CX5  C6   C4   aromatic  1.411  0.020  1.411
 CX5  C6   C5   aromatic  1.415  0.020  1.415
 CX5  C4   C3   aromatic  1.366  0.020  1.366
 CX5  C14  C10  single    1.524  0.020  1.524
 CX5  N2   C5   aromatic  1.354  0.020  1.354
 CX5  C5   C1   aromatic  1.410  0.020  1.410
 CX5  C3   C2   aromatic  1.415  0.020  1.415
 CX5  N3   C11  single    1.458  0.020  1.458
 CX5  N3   C9   single    1.345  0.020  1.345
 CX5  C1   C2   aromatic  1.370  0.020  1.370
 CX5  C2   C9   single    1.499  0.020  1.499
 CX5  C11  C10  single    1.525  0.020  1.525
 CX5  C9   O1   double    1.225  0.020  1.225
 CX5  C1   H1   single    0.930  0.020  1.080
 CX5  C3   H2   single    0.930  0.020  1.080
 CX5  C4   H3   single    0.930  0.020  1.080
 CX5  C7   H4   single    0.930  0.020  1.080
 CX5  C8   H5   single    0.930  0.020  1.080
 CX5  C11  H6   single    0.970  0.020  1.090
 CX5  C11  H7   single    0.970  0.020  1.090
 CX5  C13  H8   single    0.970  0.020  1.090
 CX5  C13  H9   single    0.970  0.020  1.090
 CX5  C14  H10  single    0.970  0.020  1.090
 CX5  C14  H11  single    0.970  0.020  1.090
 CX5  C10  H12  single    0.970  0.020  1.090
 CX5  C10  H13  single    0.970  0.020  1.090
 CX5  C12  H14  single    0.970  0.020  1.090
 CX5  C12  H15  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
 CX5  H1   C1   C5   118.38  3.000
 CX5  H1   C1   C2   121.56  3.000
 CX5  C5   C1   C2   120.06  3.000
 CX5  C9   C2   C3   118.31  3.000
 CX5  C9   C2   C1   121.17  3.000
 CX5  C3   C2   C1   120.20  3.000
 CX5  H2   C3   C4   119.88  3.000
 CX5  H2   C3   C2   119.37  3.000
 CX5  C4   C3   C2   120.75  3.000
 CX5  H3   C4   C6   118.82  3.000
 CX5  H3   C4   C3   121.18  3.000
 CX5  C6   C4   C3   120.00  3.000
 CX5  N1   C6   C5   120.86  3.000
 CX5  C5   C6   C4   119.35  3.000
 CX5  N1   C6   C4   119.78  3.000
 CX5  H4   C7   N1   118.03  3.000
 CX5  H4   C7   C8   119.75  3.000
 CX5  N1   C7   C8   122.23  3.000
 CX5  H5   C8   N2   118.04  3.000
 CX5  H5   C8   C7   119.78  3.000
 CX5  N2   C8   C7   122.19  3.000
 CX5  O1   C9   N3   123.80  3.000
 CX5  O1   C9   C2   118.07  3.000
 CX5  N3   C9   C2   118.08  3.000
 CX5  H7   C11  H6   107.09  3.000
 CX5  H7   C11  N3   110.52  3.000
 CX5  H6   C11  N3   108.36  3.000
 CX5  H7   C11  C10  110.13  3.000
 CX5  H6   C11  C10  110.23  3.000
 CX5  N3   C11  C10  110.43  3.000
 CX5  H9   C13  H8   106.98  3.000
 CX5  H9   C13  C12  109.22  3.000
 CX5  H8   C13  C12  109.24  3.000
 CX5  H9   C13  C14  110.67  3.000
 CX5  H8   C13  C14  110.26  3.000
 CX5  C12  C13  C14  110.40  3.000
 CX5  H11  C14  H10  106.59  3.000
 CX5  H11  C14  C10  110.37  3.000
 CX5  H10  C14  C10  109.31  3.000
 CX5  H11  C14  C13  110.53  3.000
 CX5  H10  C14  C13  109.06  3.000
 CX5  C10  C14  C13  110.87  3.000
 CX5  N2   C5   C6   120.95  3.000
 CX5  N2   C5   C1   119.44  3.000
 CX5  C6   C5   C1   119.61  3.000
 CX5  C7   N1   C6   116.90  3.000
 CX5  C5   N2   C8   116.87  3.000
 CX5  H13  C10  H12  106.86  3.000
 CX5  H13  C10  C14  110.72  3.000
 CX5  H12  C10  C14  110.06  3.000
 CX5  H13  C10  C11  108.72  3.000
 CX5  H12  C10  C11  108.85  3.000
 CX5  C14  C10  C11  111.49  3.000
 CX5  C12  N3   C11  113.19  3.000
 CX5  C11  N3   C9   124.60  3.000
 CX5  C12  N3   C9   119.93  3.000
 CX5  H15  C12  H14  107.55  3.000
 CX5  H15  C12  N3   107.41  3.000
 CX5  H14  C12  N3   109.49  3.000
 CX5  H15  C12  C13  109.75  3.000
 CX5  H14  C12  C13  111.58  3.000
 CX5  N3   C12  C13  110.92  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
 CX5  CONST_01  N1   C6   C5   C1   180.00   0.0  0
 CX5  CONST_02  C4   C6   C5   C1     0.00   0.0  0
 CX5  CONST_03  C8   N2   C5   C1   180.00   0.0  0
 CX5  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 CX5  CONST_05  C6   C4   C3   C2     0.00   0.0  0
 CX5  CONST_06  C6   C5   C1   C2     0.00   0.0  0
 CX5  CONST_07  N2   C5   C1   C2   180.00   0.0  0
 CX5  CONST_08  N1   C6   C4   C3   180.00   0.0  0
 CX5  CONST_09  C5   C6   C4   C3     0.00   0.0  0
 CX5  CONST_10  C5   C1   C2   C3     0.00   0.0  0
 CX5  CONST_11  C7   N1   C6   C4   180.00   0.0  0
 CX5  CONST_12  N2   C5   C6   C4   180.00   0.0  0
 CX5  CONST_13  C8   C7   N1   C6     0.00   0.0  0
 CX5  CONST_14  C8   N2   C5   C6     0.00   0.0  0
 CX5  CONST_15  C5   C6   N1   C7     0.00   0.0  0
 CX5  CONST_16  C5   N2   C8   C7     0.00   0.0  0
 CX5  CONST_17  N2   C8   C7   N1     0.00   0.0  0
 CX5  CONST_18  N2   C5   C6   N1     0.00   0.0  0
 CX5  CONST_19  C9   C2   C3   C4   180.00   0.0  0
 CX5  CONST_20  C5   C1   C2   C9   180.00   0.0  0
 CX5  CONST_21  C12  N3   C9   C2   180.00   0.0  0
 CX5  CONST_23  H2   C3   C2   C1   180.00   0.0  0
 CX5  CONST_24  H3   C4   C3   C2   180.00   0.0  0
 CX5  CONST_25  H1   C1   C2   C3   180.00   0.0  0
 CX5  CONST_26  H4   C7   N1   C6   180.00   0.0  0
 CX5  CONST_27  H5   C8   N2   C5   180.00   0.0  0
 CX5  CONST_29  O1   C9   N3   C12    0.00   0.0  0
 CX5  Var_01    C13  C12  N3   C11  -59.11  30.0  1
 CX5  Var_02    C13  C14  C10  C11   52.67  30.0  1
 CX5  Var_03    N3   C12  C13  C14   55.65  30.0  1
 CX5  Var_04    N3   C11  C10  C14  -54.13  30.0  1
 CX5  Var_05    C12  C13  C14  C10  -53.00  30.0  1
 CX5  Var_06    C12  N3   C11  C10   57.87  30.0  1
 CX5  Var_07    N3   C9   C2   C1   -57.54  30.0  2

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
 CX5  plan-1  C1   0.020
 CX5  plan-1  C2   0.020
 CX5  plan-1  C3   0.020
 CX5  plan-1  C4   0.020
 CX5  plan-1  C6   0.020
 CX5  plan-1  C7   0.020
 CX5  plan-1  C8   0.020
 CX5  plan-1  C9   0.020
 CX5  plan-1  C5   0.020
 CX5  plan-1  N1   0.020
 CX5  plan-1  N2   0.020
 CX5  plan-1  H1   0.020
 CX5  plan-1  H2   0.020
 CX5  plan-1  H3   0.020
 CX5  plan-1  H4   0.020
 CX5  plan-1  H5   0.020
 CX5  plan-2  C2   0.020
 CX5  plan-2  C9   0.020
 CX5  plan-2  C11  0.020
 CX5  plan-2  N3   0.020
 CX5  plan-2  C12  0.020
 CX5  plan-2  O1   0.020

