# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:07:27 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: (4S)-N4-(6-methoxyquinolin-8-yl)pentane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(N[C@@H](C)CCCN)c2ncccc2c1
#
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
 1PQ  1PQ  (4S)-N4-(6-methoxyquinolin-8-yl)pentane-1,4-diamine  ligand  40  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1PQ
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
 1PQ  C1   C  CH3   0  -0.436   3.9974  -2.9992  -0.9903
 1PQ  O1   O  O2    0  -0.474   2.6428  -2.7816  -0.6513
 1PQ  C2   C  CR6   0   0.411   2.2403  -1.5225  -0.4005
 1PQ  C3   C  CR16  0  -0.483   0.8744  -1.4110  -0.0543
 1PQ  C4   C  CR6   0   0.386   0.3028  -0.1861   0.2247
 1PQ  N1   N  NH1   0  -0.681  -1.0057  -0.0080   0.5235
 1PQ  C5   C  CH1   0  -0.088  -1.9190  -1.0750   0.8754
 1PQ  C6   C  CH3   0  -0.657  -1.6270  -1.6481   2.2613
 1PQ  C7   C  CH2   0  -0.438  -3.3529  -0.5622   0.7850
 1PQ  C8   C  CH2   0  -0.423  -3.7746  -0.1062  -0.6046
 1PQ  C9   C  CH2   0  -0.271  -5.2346   0.3196  -0.6493
 1PQ  N2   N  NH2   0  -0.801  -5.6067   0.7717  -1.9822
 1PQ  C10  C  CR66  0   0.104   1.1422   0.9851   0.1737
 1PQ  N3   N  N     0  -0.434   0.5779   2.1701   0.4682
 1PQ  C11  C  CR16  0  -0.085   1.3152   3.2512   0.4310
 1PQ  C12  C  CR16  0  -0.330   2.6802   3.2330   0.0946
 1PQ  C13  C  CR16  0  -0.203   3.2695   2.0341  -0.2025
 1PQ  C14  C  CR66  0   0.124   2.5053   0.8471  -0.1707
 1PQ  C15  C  CR16  0  -0.523   3.0593  -0.4202  -0.4628
 1PQ  H1   H  HCH3  0   0.228   4.2773  -2.4735  -1.9067
 1PQ  H2   H  HCH3  0   0.228   4.6718  -2.6894  -0.1877
 1PQ  H3   H  HCH3  0   0.260   4.1090  -4.0687  -1.1509
 1PQ  H4   H  HCR6  0   0.268   0.2854  -2.3182  -0.0168
 1PQ  H5   H  HNH1  0   0.378  -1.2418   0.9221   0.8370
 1PQ  H6   H  HCH1  0   0.232  -1.8058  -1.8735   0.1337
 1PQ  H7   H  HCH3  0   0.222  -1.7668  -0.8846   3.0288
 1PQ  H8   H  HCH3  0   0.228  -2.2969  -2.4792   2.4851
 1PQ  H9   H  HCH3  0   0.236  -0.6039  -2.0178   2.3369
 1PQ  H10  H  HCH2  0   0.232  -4.0146  -1.3658   1.1220
 1PQ  H11  H  HCH2  0   0.220  -3.4857   0.2556   1.5032
 1PQ  H12  H  HCH2  0   0.219  -3.1508   0.7256  -0.9419
 1PQ  H13  H  HCH2  0   0.213  -3.6151  -0.9238  -1.3169
 1PQ  H14  H  HCH2  0   0.187  -5.8567  -0.5078  -0.2765
 1PQ  H15  H  HCH2  0   0.211  -5.3855   1.1493   0.0472
 1PQ  H16  H  HNH2  0   0.337  -5.5666  -0.0126  -2.6218
 1PQ  H17  H  HNH2  0   0.345  -6.5736   1.0701  -1.9793
 1PQ  H19  H  HCR6  0   0.259   0.8286   4.1889   0.6760
 1PQ  H20  H  HCR6  0   0.268   3.2445   4.1555   0.0750
 1PQ  H21  H  HCR6  0   0.266   4.3200   1.9833  -0.4617
 1PQ  H22  H  HCR6  0   0.270   4.1064  -0.4868  -0.7241

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
 1PQ  C13  C12  aromatic  1.368  0.020  1.368
 1PQ  C13  C14  aromatic  1.412  0.020  1.412
 1PQ  C12  C11  aromatic  1.406  0.020  1.406
 1PQ  C15  C14  aromatic  1.414  0.020  1.414
 1PQ  C15  C2   aromatic  1.375  0.020  1.375
 1PQ  C14  C10  aromatic  1.413  0.020  1.413
 1PQ  O1   C2   single    1.345  0.020  1.345
 1PQ  O1   C1   single    1.413  0.020  1.413
 1PQ  C2   C3   aromatic  1.414  0.020  1.414
 1PQ  C11  N3   aromatic  1.309  0.020  1.309
 1PQ  C10  N3   aromatic  1.345  0.020  1.345
 1PQ  C10  C4   aromatic  1.442  0.020  1.442
 1PQ  N2   C9   single    1.456  0.020  1.456
 1PQ  C3   C4   aromatic  1.380  0.020  1.380
 1PQ  C4   N1   single    1.354  0.020  1.354
 1PQ  C6   C5   single    1.528  0.020  1.528
 1PQ  N1   C5   single    1.448  0.020  1.448
 1PQ  C9   C8   single    1.521  0.020  1.521
 1PQ  C5   C7   single    1.526  0.020  1.526
 1PQ  C8   C7   single    1.522  0.020  1.522
 1PQ  C1   H1   single    0.970  0.020  1.090
 1PQ  C1   H2   single    0.970  0.020  1.090
 1PQ  C1   H3   single    0.970  0.020  1.090
 1PQ  C3   H4   single    0.930  0.020  1.080
 1PQ  N1   H5   single    0.890  0.020  1.040
 1PQ  C5   H6   single    0.970  0.020  1.090
 1PQ  C6   H7   single    0.970  0.020  1.090
 1PQ  C6   H8   single    0.970  0.020  1.090
 1PQ  C6   H9   single    0.970  0.020  1.090
 1PQ  C7   H10  single    0.970  0.020  1.090
 1PQ  C7   H11  single    0.970  0.020  1.090
 1PQ  C8   H12  single    0.970  0.020  1.090
 1PQ  C8   H13  single    0.970  0.020  1.090
 1PQ  C9   H14  single    0.970  0.020  1.090
 1PQ  C9   H15  single    0.970  0.020  1.090
 1PQ  N2   H16  single    0.890  0.020  1.040
 1PQ  N2   H17  single    0.890  0.020  1.040
 1PQ  C11  H19  single    0.930  0.020  1.080
 1PQ  C12  H20  single    0.930  0.020  1.080
 1PQ  C13  H21  single    0.930  0.020  1.080
 1PQ  C15  H22  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
 1PQ  H3   C1   H2   108.90  3.000
 1PQ  H3   C1   H1   108.85  3.000
 1PQ  H2   C1   H1   108.74  3.000
 1PQ  H3   C1   O1   106.58  3.000
 1PQ  H2   C1   O1   111.82  3.000
 1PQ  H1   C1   O1   111.87  3.000
 1PQ  C2   O1   C1   118.40  3.000
 1PQ  C15  C2   C3   121.56  3.000
 1PQ  C3   C2   O1   114.12  3.000
 1PQ  C15  C2   O1   124.32  3.000
 1PQ  H4   C3   C4   120.77  3.000
 1PQ  H4   C3   C2   117.92  3.000
 1PQ  C4   C3   C2   121.32  3.000
 1PQ  C10  C4   N1   117.62  3.000
 1PQ  N1   C4   C3   124.17  3.000
 1PQ  C10  C4   C3   118.20  3.000
 1PQ  H5   N1   C5   117.13  3.000
 1PQ  H5   N1   C4   114.56  3.000
 1PQ  C5   N1   C4   124.49  3.000
 1PQ  H6   C5   C7   107.58  3.000
 1PQ  H6   C5   C6   108.72  3.000
 1PQ  C7   C5   C6   111.06  3.000
 1PQ  H6   C5   N1   107.91  3.000
 1PQ  C7   C5   N1   109.32  3.000
 1PQ  C6   C5   N1   112.10  3.000
 1PQ  H9   C6   H8   107.68  3.000
 1PQ  H9   C6   H7   107.98  3.000
 1PQ  H8   C6   H7   108.06  3.000
 1PQ  H9   C6   C5   111.67  3.000
 1PQ  H8   C6   C5   110.76  3.000
 1PQ  H7   C6   C5   110.55  3.000
 1PQ  H11  C7   H10  105.84  3.000
 1PQ  H11  C7   C8   109.93  3.000
 1PQ  H10  C7   C8   109.49  3.000
 1PQ  H11  C7   C5   109.01  3.000
 1PQ  H10  C7   C5   107.66  3.000
 1PQ  C8   C7   C5   114.53  3.000
 1PQ  H13  C8   H12  106.50  3.000
 1PQ  H13  C8   C9   109.22  3.000
 1PQ  H12  C8   C9   109.00  3.000
 1PQ  H13  C8   C7   109.24  3.000
 1PQ  H12  C8   C7   110.59  3.000
 1PQ  C9   C8   C7   112.12  3.000
 1PQ  H15  C9   H14  106.06  3.000
 1PQ  H15  C9   N2   108.19  3.000
 1PQ  H14  C9   N2   113.53  3.000
 1PQ  H15  C9   C8   109.02  3.000
 1PQ  H14  C9   C8   108.80  3.000
 1PQ  N2   C9   C8   111.04  3.000
 1PQ  H17  N2   H16  105.55  3.000
 1PQ  H17  N2   C9   109.46  3.000
 1PQ  H16  N2   C9   109.13  3.000
 1PQ  C14  C10  N3   122.97  3.000
 1PQ  N3   C10  C4   117.62  3.000
 1PQ  C14  C10  C4   119.41  3.000
 1PQ  C11  N3   C10  119.02  3.000
 1PQ  H19  C11  C12  120.06  3.000
 1PQ  H19  C11  N3   117.06  3.000
 1PQ  C12  C11  N3   122.88  3.000
 1PQ  H20  C12  C13  121.24  3.000
 1PQ  H20  C12  C11  119.99  3.000
 1PQ  C13  C12  C11  118.77  3.000
 1PQ  H21  C13  C14  119.39  3.000
 1PQ  H21  C13  C12  120.71  3.000
 1PQ  C14  C13  C12  119.90  3.000
 1PQ  C15  C14  C13  122.47  3.000
 1PQ  C15  C14  C10  121.07  3.000
 1PQ  C13  C14  C10  116.46  3.000
 1PQ  H22  C15  C14  118.99  3.000
 1PQ  H22  C15  C2   122.58  3.000
 1PQ  C14  C15  C2   118.43  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
 1PQ  CONST_01  C13  C14  C15  C2   180.00   0.0  0
 1PQ  CONST_02  C10  C14  C15  C2     0.00   0.0  0
 1PQ  CONST_03  C10  C4   C3   C2     0.00   0.0  0
 1PQ  CONST_04  C14  C15  C2   C3     0.00   0.0  0
 1PQ  CONST_05  C14  C10  C4   C3     0.00   0.0  0
 1PQ  CONST_06  N3   C10  C4   C3   180.00   0.0  0
 1PQ  CONST_07  C13  C14  C10  C4   180.00   0.0  0
 1PQ  CONST_08  C15  C14  C10  C4     0.00   0.0  0
 1PQ  CONST_09  C11  N3   C10  C4   180.00   0.0  0
 1PQ  CONST_10  C15  C2   C3   C4     0.00   0.0  0
 1PQ  CONST_11  C12  C13  C14  C10    0.00   0.0  0
 1PQ  CONST_12  C12  C11  N3   C10    0.00   0.0  0
 1PQ  CONST_13  C13  C12  C11  N3     0.00   0.0  0
 1PQ  CONST_14  C13  C14  C10  N3     0.00   0.0  0
 1PQ  CONST_15  C15  C14  C10  N3   180.00   0.0  0
 1PQ  CONST_16  C14  C13  C12  C11    0.00   0.0  0
 1PQ  CONST_17  C14  C10  N3   C11    0.00   0.0  0
 1PQ  CONST_18  C15  C14  C13  C12  180.00   0.0  0
 1PQ  CONST_19  C14  C15  C2   O1   180.00   0.0  0
 1PQ  CONST_20  C4   C3   C2   O1   180.00   0.0  0
 1PQ  CONST_21  N1   C4   C3   C2   180.00   0.0  0
 1PQ  CONST_22  C14  C10  C4   N1   180.00   0.0  0
 1PQ  CONST_23  N3   C10  C4   N1     0.00   0.0  0
 1PQ  CONST_24  H22  C15  C2   C3   180.00   0.0  0
 1PQ  CONST_25  H21  C13  C14  C10  180.00   0.0  0
 1PQ  CONST_26  H19  C11  N3   C10  180.00   0.0  0
 1PQ  CONST_27  H4   C3   C4   C10  180.00   0.0  0
 1PQ  CONST_28  H20  C12  C11  N3   180.00   0.0  0
 1PQ  CONST_29  C5   N1   C4   C3     0.00   0.0  0
 1PQ  CONST_30  C10  C4   N1   C5   180.00   0.0  0
 1PQ  CONST_31  H5   N1   C4   C3   180.00   0.0  0
 1PQ  Var_01    C15  C2   O1   C1     0.61  30.0  2
 1PQ  Var_02    H1   C1   O1   C2   -61.11  30.0  3
 1PQ  Var_03    C9   C8   C7   C5   176.77  30.0  1
 1PQ  Var_04    N2   C9   C8   C7   179.06  30.0  2
 1PQ  Var_05    H16  N2   C9   C8    66.35  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
 1PQ  chir_01  C5  C6  N1  C7  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
 1PQ  plan-1  O1   0.020
 1PQ  plan-1  C2   0.020
 1PQ  plan-1  C3   0.020
 1PQ  plan-1  C4   0.020
 1PQ  plan-1  N1   0.020
 1PQ  plan-1  C10  0.020
 1PQ  plan-1  N3   0.020
 1PQ  plan-1  C11  0.020
 1PQ  plan-1  C12  0.020
 1PQ  plan-1  C13  0.020
 1PQ  plan-1  C14  0.020
 1PQ  plan-1  C15  0.020
 1PQ  plan-1  H4   0.020
 1PQ  plan-1  H19  0.020
 1PQ  plan-1  H20  0.020
 1PQ  plan-1  H21  0.020
 1PQ  plan-1  H22  0.020
 1PQ  plan-2  C4   0.020
 1PQ  plan-2  N1   0.020
 1PQ  plan-2  C5   0.020
 1PQ  plan-2  H5   0.020

