# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 17:43:09 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-(quinolin-3-ylmethyl)piperidine-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)N1CCC(CC1)Cc2cnc3ccccc3c2
#
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
 PF7  PF7  '4-(quinolin-3-ylmethyl)piperidine-1-carboxylic acid'  ligand  37  20  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PF7
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
 PF7  O19   O  O      0  -0.645  50.2470  -15.3488  -34.0687
 PF7  C18   C  C      0   0.517  50.1775  -15.4671  -35.3108
 PF7  N15   N  NT     0  -0.473  49.1460  -14.7525  -35.9659
 PF7  C16   C  CH2    0  -0.295  48.0030  -14.3052  -35.2008
 PF7  C17   C  CH2    0  -0.416  46.9161  -15.3745  -35.1178
 PF7  C12   C  CH1    0  -0.233  46.4958  -15.8396  -36.5108
 PF7  C13   C  CH2    0  -0.422  47.7259  -16.2344  -37.3277
 PF7  C14   C  CH2    0  -0.300  48.7777  -15.1283  -37.3131
 PF7  C11   C  CH2    0  -0.506  45.4839  -16.9913  -36.4622
 PF7  C9    C  CR6    0   0.058  44.1904  -16.6113  -35.8071
 PF7  C10   C  CR16   0  -0.256  43.8484  -16.9926  -34.5386
 PF7  C3    C  CR6    0   0.089  42.6297  -16.5593  -33.9709
 PF7  C4    C  C1     0  -0.314  42.2215  -16.9145  -32.6655
 PF7  C5    C  C1     0  -0.256  41.0319  -16.4582  -32.1648
 PF7  C6    C  C1     0  -0.262  40.2005  -15.6298  -32.9478
 PF7  C1    C  C1     0  -0.292  40.5711  -15.2732  -34.2167
 PF7  C2    C  CR6    0   0.195  41.7940  -15.7298  -34.7572
 PF7  N7    N  N      0  -0.428  42.1332  -15.3624  -36.0174
 PF7  C8    C  CR16   0  -0.112  43.2681  -15.7859  -36.4998
 PF7  OXT   O  OC    -1  -0.646  50.9561  -16.1254  -36.0336
 PF7  H161  H  HCH2   0   0.233  48.3250  -14.0064  -34.2068
 PF7  H162  H  HCH2   0   0.204  47.5864  -13.4130  -35.6847
 PF7  H141  H  HCH2   0   0.204  48.3750  -14.2458  -37.8266
 PF7  H142  H  HCH2   0   0.233  49.6661  -15.4349  -37.8594
 PF7  H171  H  HCH2   0   0.208  47.2965  -16.2286  -34.5448
 PF7  H172  H  HCH2   0   0.223  46.0560  -14.9826  -34.5679
 PF7  H12   H  HCH1   0   0.216  46.0197  -14.9895  -37.0202
 PF7  H131  H  HCH2   0   0.210  48.1642  -17.1506  -36.9150
 PF7  H132  H  HCH2   0   0.220  47.4325  -16.4601  -38.3576
 PF7  H111  H  HCH2   0   0.247  45.2862  -17.3302  -37.4841
 PF7  H112  H  HCH2   0   0.241  45.9299  -17.8392  -35.9344
 PF7  H10   H  HCR6   0   0.261  44.5073  -17.6286  -33.9573
 PF7  H8    H  HCR6   0   0.255  43.5053  -15.4760  -37.5145
 PF7  H4    H  H      0   0.261  42.8620  -17.5519  -32.0681
 PF7  H5    H  H      0   0.262  40.7250  -16.7316  -31.1640
 PF7  H6    H  H      0   0.261  39.2637  -15.2749  -32.5387
 PF7  H1    H  H      0   0.259  39.9413  -14.6376  -34.8261

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
 PF7  O19  C18   deloc     1.250  0.020  1.250
 PF7  C18  N15   single    1.416  0.020  1.416
 PF7  C18  OXT   deloc     1.250  0.020  1.250
 PF7  N15  C16   single    1.446  0.020  1.446
 PF7  N15  C14   single    1.446  0.020  1.446
 PF7  C16  C17   single    1.527  0.020  1.527
 PF7  C17  C12   single    1.528  0.020  1.528
 PF7  C12  C13   single    1.528  0.020  1.528
 PF7  C12  C11   single    1.534  0.020  1.534
 PF7  C13  C14   single    1.526  0.020  1.526
 PF7  C11  C9    single    1.499  0.020  1.499
 PF7  C9   C10   aromatic  1.368  0.020  1.368
 PF7  C9   C8    aromatic  1.418  0.020  1.418
 PF7  C10  C3    aromatic  1.412  0.020  1.412
 PF7  C3   C4    aromatic  1.413  0.020  1.413
 PF7  C3   C2    aromatic  1.416  0.020  1.416
 PF7  C4   C5    aromatic  1.369  0.020  1.369
 PF7  C5   C6    aromatic  1.411  0.020  1.411
 PF7  C6   C1    aromatic  1.369  0.020  1.369
 PF7  C1   C2    aromatic  1.413  0.020  1.413
 PF7  C2   N7    aromatic  1.356  0.020  1.356
 PF7  N7   C8    aromatic  1.304  0.020  1.304
 PF7  C16  H161  single    0.970  0.020  1.090
 PF7  C16  H162  single    0.970  0.020  1.090
 PF7  C14  H141  single    0.970  0.020  1.090
 PF7  C14  H142  single    0.970  0.020  1.090
 PF7  C17  H171  single    0.970  0.020  1.090
 PF7  C17  H172  single    0.970  0.020  1.090
 PF7  C12  H12   single    0.970  0.020  1.090
 PF7  C13  H131  single    0.970  0.020  1.090
 PF7  C13  H132  single    0.970  0.020  1.090
 PF7  C11  H111  single    0.970  0.020  1.090
 PF7  C11  H112  single    0.970  0.020  1.090
 PF7  C10  H10   single    0.930  0.020  1.080
 PF7  C8   H8    single    0.930  0.020  1.080
 PF7  C4   H4    single    0.930  0.020  1.080
 PF7  C5   H5    single    0.930  0.020  1.080
 PF7  C6   H6    single    0.930  0.020  1.080
 PF7  C1   H1    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
 PF7  OXT   C18  N15   116.88  3.000
 PF7  OXT   C18  O19   126.16  3.000
 PF7  N15   C18  O19   116.92  3.000
 PF7  C14   N15  C16   111.83  3.000
 PF7  C14   N15  C18   119.04  3.000
 PF7  C16   N15  C18   119.15  3.000
 PF7  H162  C16  H161  106.99  3.000
 PF7  H162  C16  C17   108.85  3.000
 PF7  H161  C16  C17   110.72  3.000
 PF7  H162  C16  N15   108.56  3.000
 PF7  H161  C16  N15   109.56  3.000
 PF7  C17   C16  N15   112.01  3.000
 PF7  H172  C17  H171  106.80  3.000
 PF7  H172  C17  C12   110.56  3.000
 PF7  H171  C17  C12   109.56  3.000
 PF7  H172  C17  C16   109.65  3.000
 PF7  H171  C17  C16   109.08  3.000
 PF7  C12   C17  C16   111.07  3.000
 PF7  H12   C12  C11   108.03  3.000
 PF7  H12   C12  C13   107.49  3.000
 PF7  C11   C12  C13   110.73  3.000
 PF7  H12   C12  C17   107.83  3.000
 PF7  C11   C12  C17   112.42  3.000
 PF7  C13   C12  C17   110.16  3.000
 PF7  H132  C13  H131  106.81  3.000
 PF7  H132  C13  C14   110.07  3.000
 PF7  H131  C13  C14   109.05  3.000
 PF7  H132  C13  C12   109.91  3.000
 PF7  H131  C13  C12   109.66  3.000
 PF7  C14   C13  C12   111.24  3.000
 PF7  H142  C14  H141  106.95  3.000
 PF7  H142  C14  C13   110.73  3.000
 PF7  H141  C14  C13   108.98  3.000
 PF7  H142  C14  N15   109.47  3.000
 PF7  H141  C14  N15   108.68  3.000
 PF7  C13   C14  N15   111.88  3.000
 PF7  H112  C11  H111  106.51  3.000
 PF7  H112  C11  C9    109.73  3.000
 PF7  H111  C11  C9    109.30  3.000
 PF7  H112  C11  C12   109.16  3.000
 PF7  H111  C11  C12   108.79  3.000
 PF7  C9    C11  C12   113.13  3.000
 PF7  C8    C9   C10   116.90  3.000
 PF7  C8    C9   C11   119.69  3.000
 PF7  C10   C9   C11   123.39  3.000
 PF7  H10   C10  C3    119.25  3.000
 PF7  H10   C10  C9    120.56  3.000
 PF7  C3    C10  C9    120.19  3.000
 PF7  C2    C3   C4    119.33  3.000
 PF7  C2    C3   C10   117.76  3.000
 PF7  C4    C3   C10   122.92  3.000
 PF7  H4    C4   C5    120.55  3.000
 PF7  H4    C4   C3    119.11  3.000
 PF7  C5    C4   C3    120.34  3.000
 PF7  H5    C5   C6    119.64  3.000
 PF7  H5    C5   C4    120.04  3.000
 PF7  C6    C5   C4    120.32  3.000
 PF7  H6    C6   C1    119.95  3.000
 PF7  H6    C6   C5    119.53  3.000
 PF7  C1    C6   C5    120.51  3.000
 PF7  H1    C1   C2    118.56  3.000
 PF7  H1    C1   C6    121.13  3.000
 PF7  C2    C1   C6    120.31  3.000
 PF7  N7    C2   C1    118.98  3.000
 PF7  N7    C2   C3    121.83  3.000
 PF7  C1    C2   C3    119.19  3.000
 PF7  C8    N7   C2    118.27  3.000
 PF7  H8    C8   N7    116.27  3.000
 PF7  H8    C8   C9    118.68  3.000
 PF7  N7    C8   C9    125.05  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
 PF7  CONST_01  C4   C3   C10  C9    180.00   0.0  0
 PF7  CONST_02  C2   C3   C10  C9      0.00   0.0  0
 PF7  CONST_03  C2   N7   C8   C9      0.00   0.0  0
 PF7  CONST_04  N7   C8   C9   C10     0.00   0.0  0
 PF7  CONST_05  C5   C4   C3   C10   180.00   0.0  0
 PF7  CONST_06  C1   C2   C3   C10   180.00   0.0  0
 PF7  CONST_07  N7   C2   C3   C10     0.00   0.0  0
 PF7  CONST_08  C8   C9   C10  C3      0.00   0.0  0
 PF7  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 PF7  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 PF7  CONST_11  C8   N7   C2   C3      0.00   0.0  0
 PF7  CONST_12  C1   C2   C3   C4      0.00   0.0  0
 PF7  CONST_13  N7   C2   C3   C4    180.00   0.0  0
 PF7  CONST_14  C1   C6   C5   C4      0.00   0.0  0
 PF7  CONST_15  C2   C3   C4   C5      0.00   0.0  0
 PF7  CONST_16  C2   C1   C6   C5      0.00   0.0  0
 PF7  CONST_17  N7   C2   C1   C6    180.00   0.0  0
 PF7  CONST_18  C8   N7   C2   C1    180.00   0.0  0
 PF7  CONST_19  C3   C10  C9   C11   180.00   0.0  0
 PF7  CONST_20  N7   C8   C9   C11   180.00   0.0  0
 PF7  CONST_21  H8   C8   C9   C10   180.00   0.0  0
 PF7  CONST_22  H4   C4   C3   C10     0.00   0.0  0
 PF7  CONST_23  H5   C5   C4   C3    180.00   0.0  0
 PF7  CONST_24  H1   C1   C2   C3    180.00   0.0  0
 PF7  CONST_25  H10  C10  C3   C4      0.00   0.0  0
 PF7  CONST_26  H6   C6   C5   C4    180.00   0.0  0
 PF7  Var_01    C12  C17  C16  N15   -55.19  30.0  1
 PF7  Var_02    C12  C13  C14  N15    55.08  30.0  1
 PF7  Var_03    C13  C14  N15  C16   -58.19  30.0  1
 PF7  Var_04    C14  N15  C16  C17    58.32  30.0  1
 PF7  Var_05    C10  C9   C11  C12  -104.12  30.0  2
 PF7  Var_06    C16  N15  C18  O19   -20.01  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
 PF7  chir_01  C12  C17  C13  C11  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
 PF7  plan-1  C11  0.020
 PF7  plan-1  C9   0.020
 PF7  plan-1  C10  0.020
 PF7  plan-1  C3   0.020
 PF7  plan-1  C4   0.020
 PF7  plan-1  C5   0.020
 PF7  plan-1  C6   0.020
 PF7  plan-1  C1   0.020
 PF7  plan-1  C2   0.020
 PF7  plan-1  N7   0.020
 PF7  plan-1  C8   0.020
 PF7  plan-1  H10  0.020
 PF7  plan-1  H8   0.020
 PF7  plan-1  H4   0.020
 PF7  plan-1  H5   0.020
 PF7  plan-1  H6   0.020
 PF7  plan-1  H1   0.020
 PF7  plan-2  O19  0.020
 PF7  plan-2  C18  0.020
 PF7  plan-2  N15  0.020
 PF7  plan-2  OXT  0.020

