# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 03:37:56 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-[(1S)-1-amino-3-methylbutyl]-6-(pyridin-4-yl)quinoline-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)c1cc(C#N)c2cc(ccc2n1)c3ccncc3
#
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
 5P6  5P6  "2-[(1S)-1-amino-3-methylbutyl]-6-(pyridin-4-yl)quinoline-4-carbonitrile"  ligand  44  24  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5P6
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
 5P6  C13  C  CR6   0   0.170  -36.7355  19.5088  -0.9398
 5P6  C18  C  CH2   0  -0.409  -35.6514  16.5701   6.8473
 5P6  C17  C  CH3   0  -0.657  -38.0651  15.9637   7.3576
 5P6  C16  C  CH3   0  -0.645  -37.1367  18.1856   8.0373
 5P6  C15  C  CR6   0   0.258  -35.8541  16.0717   4.4116
 5P6  C19  C  CH1   0  -0.154  -35.4124  15.5271   5.7513
 5P6  C11  C  CR66  0   0.144  -36.6978  17.1421   2.0013
 5P6  C12  C  CR6   0   0.106  -36.3508  18.8451   0.3196
 5P6  C2   C  CR16  0  -0.295  -35.2418  19.3228   1.0619
 5P6  C3   C  CR16  0  -0.276  -34.8777  18.7390   2.2400
 5P6  C4   C  CR16  0  -0.372  -38.0726  19.6827  -1.2911
 5P6  C5   C  CR16  0  -0.374  -35.7779  19.9949  -1.8277
 5P6  C6   C  CR16  0  -0.344  -36.9568  15.4911   3.7453
 5P6  C7   C  CR16  0  -0.400  -37.0593  17.7659   0.7918
 5P6  C8   C  CR16  0  -0.058  -38.3802  20.3164  -2.4841
 5P6  C9   C  CR16  0  -0.058  -36.1926  20.6105  -2.9978
 5P6  C10  C  CR6   0   0.134  -37.3728  16.0229   2.5532
 5P6  C14  C  CR66  0   0.167  -35.5972  17.6327   2.7456
 5P6  N21  N  NS    0  -0.224  -39.3817  14.9710   1.3234
 5P6  N22  N  N     0  -0.402  -37.4671  20.7760  -3.3317
 5P6  N23  N  N     0  -0.417  -35.2082  17.0957   3.9199
 5P6  N24  N  NH2   0  -0.792  -33.9924  15.2054   5.7022
 5P6  H39  H  HCH2  0   0.226  -35.3330  16.1354   7.8023
 5P6  H40  H  HCH2  0   0.227  -34.9860  17.4152   6.6479
 5P6  H36  H  HCH3  0   0.228  -39.0723  16.3620   7.4910
 5P6  H37  H  HCH3  0   0.227  -38.1260  15.1857   6.5953
 5P6  H38  H  HCH3  0   0.216  -37.7721  15.4851   8.2953
 5P6  H33  H  HCH3  0   0.225  -38.1438  18.5950   8.1307
 5P6  H34  H  HCH3  0   0.213  -36.8409  17.8083   9.0194
 5P6  H35  H  HCH3  0   0.224  -36.4657  19.0067   7.7803
 5P6  H41  H  HCH1  0   0.232  -36.0287  14.6439   5.9685
 5P6  H42  H  HCH1  0   0.221  -37.4028  17.5113   6.0364
 5P6  H25  H  HCR6  0   0.270  -34.6896  20.1808   0.7012
 5P6  H26  H  HCR6  0   0.272  -34.0403  19.1139   2.8134
 5P6  H27  H  HCR6  0   0.272  -38.8717  19.3534  -0.6401
 5P6  H28  H  HCR6  0   0.272  -34.7194  19.8844  -1.6320
 5P6  H29  H  HCR6  0   0.295  -37.4628  14.6369   4.1757
 5P6  H30  H  HCR6  0   0.272  -37.8956  17.3776   0.2227
 5P6  H31  H  HCR6  0   0.266  -39.4181  20.4634  -2.7619
 5P6  H32  H  HCR6  0   0.266  -35.4542  20.9845  -3.6984
 5P6  H1   H  HNH2  0   0.350  -33.7018  14.8802   6.6168
 5P6  H43  H  HNH2  0   0.347  -33.8427  14.4248   5.0743
 5P6  C20  C  CH1   0  -0.248  -37.0872  17.0759   6.9919
 5P6  C1   C  CSP   0   0.024  -38.4859  15.4416   1.8725

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
 5P6  N22  C9   aromatic  1.328  0.020  1.328
 5P6  N22  C8   aromatic  1.328  0.020  1.328
 5P6  C9   C5   aromatic  1.386  0.020  1.386
 5P6  C8   C4   aromatic  1.385  0.020  1.385
 5P6  C5   C13  aromatic  1.393  0.020  1.393
 5P6  C4   C13  aromatic  1.393  0.020  1.393
 5P6  C13  C12  single    1.475  0.020  1.475
 5P6  C12  C7   aromatic  1.375  0.020  1.375
 5P6  C12  C2   aromatic  1.417  0.020  1.417
 5P6  C7   C11  aromatic  1.408  0.020  1.408
 5P6  C2   C3   aromatic  1.364  0.020  1.364
 5P6  N21  C1   triple    1.151  0.020  1.151
 5P6  C11  C10  aromatic  1.419  0.020  1.419
 5P6  C11  C14  aromatic  1.416  0.020  1.416
 5P6  C1   C10  single    1.428  0.020  1.428
 5P6  C3   C14  aromatic  1.413  0.020  1.413
 5P6  C10  C6   aromatic  1.370  0.020  1.370
 5P6  C14  N23  aromatic  1.349  0.020  1.349
 5P6  C6   C15  aromatic  1.413  0.020  1.413
 5P6  N23  C15  aromatic  1.307  0.020  1.307
 5P6  C15  C19  single    1.512  0.020  1.512
 5P6  N24  C19  single    1.457  0.020  1.457
 5P6  C19  C18  single    1.532  0.020  1.532
 5P6  C18  C20  single    1.529  0.020  1.529
 5P6  C20  C17  single    1.525  0.020  1.525
 5P6  C20  C16  single    1.525  0.020  1.525
 5P6  C18  H39  single    0.970  0.020  1.090
 5P6  C18  H40  single    0.970  0.020  1.090
 5P6  C17  H36  single    0.970  0.020  1.090
 5P6  C17  H37  single    0.970  0.020  1.090
 5P6  C17  H38  single    0.970  0.020  1.090
 5P6  C16  H33  single    0.970  0.020  1.090
 5P6  C16  H34  single    0.970  0.020  1.090
 5P6  C16  H35  single    0.970  0.020  1.090
 5P6  C19  H41  single    0.970  0.020  1.090
 5P6  C20  H42  single    0.970  0.020  1.090
 5P6  C2   H25  single    0.930  0.020  1.080
 5P6  C3   H26  single    0.930  0.020  1.080
 5P6  C4   H27  single    0.930  0.020  1.080
 5P6  C5   H28  single    0.930  0.020  1.080
 5P6  C6   H29  single    0.930  0.020  1.080
 5P6  C7   H30  single    0.930  0.020  1.080
 5P6  C8   H31  single    0.930  0.020  1.080
 5P6  C9   H32  single    0.930  0.020  1.080
 5P6  N24  H1   single    0.890  0.020  1.040
 5P6  N24  H43  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
 5P6  C5   C13  C4   117.08  3.000
 5P6  C4   C13  C12  121.46  3.000
 5P6  C5   C13  C12  121.46  3.000
 5P6  H40  C18  H39  106.76  3.000
 5P6  H40  C18  C20  109.44  3.000
 5P6  H39  C18  C20  108.75  3.000
 5P6  H40  C18  C19  107.50  3.000
 5P6  H39  C18  C19  107.94  3.000
 5P6  C20  C18  C19  116.07  3.000
 5P6  H38  C17  H37  107.59  3.000
 5P6  H38  C17  H36  107.60  3.000
 5P6  H37  C17  H36  107.11  3.000
 5P6  H38  C17  C20  110.68  3.000
 5P6  H37  C17  C20  112.85  3.000
 5P6  H36  C17  C20  110.79  3.000
 5P6  H35  C16  H34  107.76  3.000
 5P6  H35  C16  H33  107.78  3.000
 5P6  H34  C16  H33  107.60  3.000
 5P6  H35  C16  C20  111.47  3.000
 5P6  H34  C16  C20  110.85  3.000
 5P6  H33  C16  C20  111.20  3.000
 5P6  N23  C15  C6   122.02  3.000
 5P6  N23  C15  C19  118.11  3.000
 5P6  C6   C15  C19  119.85  3.000
 5P6  H41  C19  N24  112.08  3.000
 5P6  H41  C19  C15  107.50  3.000
 5P6  N24  C19  C15  109.54  3.000
 5P6  H41  C19  C18  108.57  3.000
 5P6  N24  C19  C18  109.06  3.000
 5P6  C15  C19  C18  110.07  3.000
 5P6  C14  C11  C10  116.01  3.000
 5P6  C14  C11  C7   119.83  3.000
 5P6  C10  C11  C7   124.16  3.000
 5P6  C7   C12  C2   119.20  3.000
 5P6  C2   C12  C13  119.98  3.000
 5P6  C7   C12  C13  120.82  3.000
 5P6  H25  C2   C3   119.40  3.000
 5P6  H25  C2   C12  119.46  3.000
 5P6  C3   C2   C12  121.12  3.000
 5P6  H26  C3   C14  118.40  3.000
 5P6  H26  C3   C2   121.06  3.000
 5P6  C14  C3   C2   120.54  3.000
 5P6  H27  C4   C8   119.56  3.000
 5P6  H27  C4   C13  121.27  3.000
 5P6  C8   C4   C13  119.16  3.000
 5P6  H28  C5   C9   119.40  3.000
 5P6  H28  C5   C13  121.42  3.000
 5P6  C9   C5   C13  119.17  3.000
 5P6  H29  C6   C10  120.70  3.000
 5P6  H29  C6   C15  120.11  3.000
 5P6  C10  C6   C15  119.19  3.000
 5P6  H30  C7   C12  119.91  3.000
 5P6  H30  C7   C11  119.38  3.000
 5P6  C12  C7   C11  120.70  3.000
 5P6  H31  C8   N22  116.60  3.000
 5P6  H31  C8   C4   119.67  3.000
 5P6  N22  C8   C4   123.73  3.000
 5P6  H32  C9   N22  116.62  3.000
 5P6  H32  C9   C5   119.67  3.000
 5P6  N22  C9   C5   123.71  3.000
 5P6  C6   C10  C1   119.56  3.000
 5P6  C6   C10  C11  120.02  3.000
 5P6  C1   C10  C11  120.42  3.000
 5P6  N23  C14  C3   118.45  3.000
 5P6  N23  C14  C11  122.94  3.000
 5P6  C3   C14  C11  118.60  3.000
 5P6  C9   N22  C8   117.15  3.000
 5P6  C14  N23  C15  119.81  3.000
 5P6  H43  N24  H1   105.66  3.000
 5P6  H43  N24  C19  109.58  3.000
 5P6  H1   N24  C19  108.66  3.000
 5P6  H42  C20  C16  107.40  3.000
 5P6  H42  C20  C17  108.29  3.000
 5P6  C16  C20  C17  110.20  3.000
 5P6  H42  C20  C18  108.62  3.000
 5P6  C16  C20  C18  109.63  3.000
 5P6  C17  C20  C18  112.55  3.000
 5P6  N21  C1   C10  180.00  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
 5P6  CONST_01  N22  C9   C5   C13     0.00   0.0  0
 5P6  CONST_02  N22  C8   C4   C13     0.00   0.0  0
 5P6  CONST_03  C11  C7   C12  C13   180.00   0.0  0
 5P6  CONST_04  C3   C2   C12  C13   180.00   0.0  0
 5P6  CONST_05  C11  C10  C6   C15     0.00   0.0  0
 5P6  CONST_06  C11  C14  N23  C15     0.00   0.0  0
 5P6  CONST_07  C3   C14  N23  C15   180.00   0.0  0
 5P6  CONST_08  C2   C12  C7   C11     0.00   0.0  0
 5P6  CONST_09  C2   C3   C14  C11     0.00   0.0  0
 5P6  CONST_10  C9   C5   C13  C12   180.00   0.0  0
 5P6  CONST_11  C8   C4   C13  C12   180.00   0.0  0
 5P6  CONST_12  C10  C11  C7   C12   180.00   0.0  0
 5P6  CONST_13  C14  C11  C7   C12     0.00   0.0  0
 5P6  CONST_14  C14  C3   C2   C12     0.00   0.0  0
 5P6  CONST_17  N23  C14  C3   C2    180.00   0.0  0
 5P6  CONST_18  C7   C12  C2   C3      0.00   0.0  0
 5P6  CONST_19  C7   C11  C14  C3      0.00   0.0  0
 5P6  CONST_20  C10  C11  C14  C3    180.00   0.0  0
 5P6  CONST_21  C9   N22  C8   C4      0.00   0.0  0
 5P6  CONST_22  C9   C5   C13  C4      0.00   0.0  0
 5P6  CONST_24  C8   N22  C9   C5      0.00   0.0  0
 5P6  CONST_25  C8   C4   C13  C5      0.00   0.0  0
 5P6  CONST_27  C7   C11  C10  C6    180.00   0.0  0
 5P6  CONST_28  C14  C11  C10  C6      0.00   0.0  0
 5P6  CONST_29  C14  N23  C15  C6      0.00   0.0  0
 5P6  CONST_30  N23  C14  C11  C7    180.00   0.0  0
 5P6  CONST_31  N23  C14  C11  C10     0.00   0.0  0
 5P6  CONST_32  N23  C15  C6   C10     0.00   0.0  0
 5P6  CONST_33  C1   C10  C6   C15   180.00   0.0  0
 5P6  CONST_34  C10  C6   C15  C19   180.00   0.0  0
 5P6  CONST_35  C14  N23  C15  C19   180.00   0.0  0
 5P6  CONST_36  C7   C11  C10  C1      0.00   0.0  0
 5P6  CONST_37  C14  C11  C10  C1    180.00   0.0  0
 5P6  CONST_38  H32  C9   C5   C13   180.00   0.0  0
 5P6  CONST_39  H31  C8   C4   C13   180.00   0.0  0
 5P6  CONST_40  H30  C7   C12  C13     0.00   0.0  0
 5P6  CONST_41  H25  C2   C12  C13     0.00   0.0  0
 5P6  CONST_42  H29  C6   C10  C11   180.00   0.0  0
 5P6  CONST_43  H26  C3   C14  C11   180.00   0.0  0
 5P6  CONST_44  H28  C5   C13  C12     0.00   0.0  0
 5P6  CONST_45  H27  C4   C13  C12     0.00   0.0  0
 5P6  CONST_46  H26  C3   C2   C12   180.00   0.0  0
 5P6  CONST_47  H30  C7   C12  C2    180.00   0.0  0
 5P6  CONST_48  H28  C5   C13  C4    180.00   0.0  0
 5P6  CONST_49  H27  C4   C13  C5    180.00   0.0  0
 5P6  CONST_50  H25  C2   C12  C7    180.00   0.0  0
 5P6  CONST_51  H32  C9   N22  C8    180.00   0.0  0
 5P6  CONST_52  H31  C8   N22  C9    180.00   0.0  0
 5P6  CONST_53  H30  C7   C11  C10     0.00   0.0  0
 5P6  CONST_54  H30  C7   C11  C14   180.00   0.0  0
 5P6  CONST_55  H25  C2   C3   C14   180.00   0.0  0
 5P6  CONST_56  H28  C5   C9   N22   180.00   0.0  0
 5P6  CONST_57  H27  C4   C8   N22   180.00   0.0  0
 5P6  CONST_58  H26  C3   C14  N23     0.00   0.0  0
 5P6  CONST_59  H29  C6   C15  N23   180.00   0.0  0
 5P6  Var_01    C19  C18  C20  C17    61.70  30.0  1
 5P6  Var_02    C19  C18  C20  C16  -175.28  30.0  1
 5P6  Var_03    H36  C17  C20  C18   177.82  30.0  3
 5P6  Var_04    H37  C17  C20  C18   -62.09  30.0  3
 5P6  Var_05    H38  C17  C20  C18    58.55  30.0  3
 5P6  Var_06    H33  C16  C20  C18   177.59  30.0  3
 5P6  Var_07    H34  C16  C20  C18   -62.75  30.0  3
 5P6  Var_08    H35  C16  C20  C18    57.28  30.0  3
 5P6  Var_09    H39  C18  C20  C17   -60.18  30.0  1
 5P6  Var_10    H40  C18  C20  C17  -176.46  30.0  1
 5P6  Var_11    H33  C16  C20  C17   -58.01  30.0  3
 5P6  Var_12    H34  C16  C20  C17    61.65  30.0  3
 5P6  Var_13    H35  C16  C20  C17  -178.32  30.0  3
 5P6  Var_14    H39  C18  C20  C16    62.84  30.0  1
 5P6  Var_15    H40  C18  C20  C16   -53.44  30.0  1
 5P6  Var_16    H36  C17  C20  C16    55.11  30.0  3
 5P6  Var_17    H37  C17  C20  C16   175.21  30.0  3
 5P6  Var_18    H38  C17  C20  C16   -64.16  30.0  3
 5P6  Var_19    H42  C20  C18  C19   -58.20  30.0  3

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
 5P6  chir_01  C19  C15  N24  C18  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
 5P6  plan-1  C13  0.020
 5P6  plan-1  C12  0.020
 5P6  plan-1  C4   0.020
 5P6  plan-1  C5   0.020
 5P6  plan-1  C8   0.020
 5P6  plan-1  C9   0.020
 5P6  plan-1  N22  0.020
 5P6  plan-1  H27  0.020
 5P6  plan-1  H28  0.020
 5P6  plan-1  H31  0.020
 5P6  plan-1  H32  0.020
 5P6  plan-2  C13  0.020
 5P6  plan-2  C15  0.020
 5P6  plan-2  C19  0.020
 5P6  plan-2  C11  0.020
 5P6  plan-2  C12  0.020
 5P6  plan-2  C2   0.020
 5P6  plan-2  C3   0.020
 5P6  plan-2  C6   0.020
 5P6  plan-2  C7   0.020
 5P6  plan-2  C10  0.020
 5P6  plan-2  C14  0.020
 5P6  plan-2  N21  0.020
 5P6  plan-2  N23  0.020
 5P6  plan-2  H25  0.020
 5P6  plan-2  H26  0.020
 5P6  plan-2  H29  0.020
 5P6  plan-2  H30  0.020
 5P6  plan-2  C1   0.020

