# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:07:10 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 8-(naphthalen-1-yl)quinoline-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2cccc(c3cccc4ccccc34)c2n1
#
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
 59Y  59Y  '8-(naphthalen-1-yl)quinoline-2-carboxylic acid'  ligand  35  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_59Y
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
 59Y  C1   C  CR6    0  -0.029  -0.0500  -1.6512  -0.0896
 59Y  C2   C  CR16   0  -0.302  -0.0862  -2.9809   0.2508
 59Y  C3   C  CR16   0  -0.247  -1.2862  -3.6089   0.6419
 59Y  C11  C  CR16   0  -0.196  -3.6255  -0.7366   0.3712
 59Y  C12  C  CR16   0  -0.307  -3.5532   0.5765   0.0117
 59Y  C13  C  CR6    0   0.013  -2.3094   1.1161  -0.4009
 59Y  C15  C  C      0   0.380  -2.2354   2.5861  -0.8319
 59Y  C16  C  CR66   0   0.114   3.1402   0.4473  -0.0680
 59Y  C17  C  CR66   0   0.122   1.9072  -0.1141   0.3580
 59Y  C18  C  CR16   0  -0.330   1.4144   0.2328   1.6383
 59Y  C19  C  CR16   0  -0.259   2.1005   1.0979   2.4465
 59Y  C20  C  CR16   0  -0.261   3.3179   1.6645   2.0163
 59Y  C21  C  CR16   0  -0.314   3.8250   1.3430   0.7877
 59Y  C4   C  CR16   0  -0.327  -2.4514  -2.8958   0.6939
 59Y  C5   C  CR6    0   0.095   1.2246  -1.0197  -0.5032
 59Y  C6   C  CR16   0  -0.330   3.6656   0.0966  -1.3341
 59Y  C7   C  CR16   0  -0.321   1.7761  -1.3435  -1.7166
 59Y  C8   C  CR16   0  -0.246   2.9990  -0.7832  -2.1388
 59Y  C9   C  CR66   0   0.145  -1.2558  -0.8944  -0.0613
 59Y  C10  C  CR66   0   0.094  -2.4568  -1.5280   0.3447
 59Y  N14  N  N      0  -0.393  -1.2130   0.4032  -0.4336
 59Y  O22  O  O      0  -0.590  -3.2800   3.2454  -0.6589
 59Y  O23  O  OC    -1  -0.578  -1.1613   2.9800  -1.3070
 59Y  H1   H  HCR6   0   0.256   0.8277  -3.5615   0.2323
 59Y  H2   H  HCR6   0   0.261  -1.2741  -4.6583   0.9049
 59Y  H3   H  HCR6   0   0.263  -4.5647  -1.1818   0.6776
 59Y  H4   H  HCR6   0   0.257  -4.4283   1.2089   0.0256
 59Y  H7   H  HCR6   0   0.256   3.8495   2.3504   2.6628
 59Y  H8   H  HCR6   0   0.254   4.7639   1.7693   0.4549
 59Y  H9   H  HCR6   0   0.260  -3.3779  -3.3667   0.9996
 59Y  H10  H  HCR6   0   0.254   4.6056   0.5319  -1.6506
 59Y  H11  H  HCR6   0   0.250   1.2581  -2.0353  -2.3691
 59Y  H12  H  HCR6   0   0.257   3.4023  -1.0546  -3.1057
 59Y  H5   H  HCR6   0   0.245   0.4840  -0.1975   1.9838
 59Y  H6   H  HCR6   0   0.256   1.7087   1.3501   3.4234

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
 59Y  O22  C15  deloc     1.247  0.020  1.247
 59Y  O23  C15  deloc     1.239  0.020  1.239
 59Y  C15  C13  single    1.534  0.020  1.534
 59Y  C13  C12  aromatic  1.417  0.020  1.417
 59Y  C13  N14  aromatic  1.308  0.020  1.308
 59Y  C12  C11  aromatic  1.363  0.020  1.363
 59Y  N14  C9   aromatic  1.351  0.020  1.351
 59Y  C11  C10  aromatic  1.412  0.020  1.412
 59Y  C8   C6   aromatic  1.366  0.020  1.366
 59Y  C8   C7   aromatic  1.410  0.020  1.410
 59Y  C6   C16  aromatic  1.415  0.020  1.415
 59Y  C9   C10  aromatic  1.417  0.020  1.417
 59Y  C9   C1   aromatic  1.424  0.020  1.424
 59Y  C7   C5   aromatic  1.372  0.020  1.372
 59Y  C16  C21  aromatic  1.415  0.020  1.415
 59Y  C16  C17  aromatic  1.420  0.020  1.420
 59Y  C10  C4   aromatic  1.412  0.020  1.412
 59Y  C21  C20  aromatic  1.367  0.020  1.367
 59Y  C5   C17  aromatic  1.424  0.020  1.424
 59Y  C5   C1   single    1.481  0.020  1.481
 59Y  C17  C18  aromatic  1.415  0.020  1.415
 59Y  C20  C19  aromatic  1.410  0.020  1.410
 59Y  C1   C2   aromatic  1.373  0.020  1.373
 59Y  C18  C19  aromatic  1.368  0.020  1.368
 59Y  C4   C3   aromatic  1.367  0.020  1.367
 59Y  C2   C3   aromatic  1.410  0.020  1.410
 59Y  C2   H1   single    0.930  0.020  1.080
 59Y  C3   H2   single    0.930  0.020  1.080
 59Y  C11  H3   single    0.930  0.020  1.080
 59Y  C12  H4   single    0.930  0.020  1.080
 59Y  C18  H5   single    0.930  0.020  1.080
 59Y  C19  H6   single    0.930  0.020  1.080
 59Y  C20  H7   single    0.930  0.020  1.080
 59Y  C21  H8   single    0.930  0.020  1.080
 59Y  C4   H9   single    0.930  0.020  1.080
 59Y  C6   H10  single    0.930  0.020  1.080
 59Y  C7   H11  single    0.930  0.020  1.080
 59Y  C8   H12  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
 59Y  C9   C1   C5   120.50  3.000
 59Y  C5   C1   C2   120.31  3.000
 59Y  C9   C1   C2   119.18  3.000
 59Y  H1   C2   C3   118.97  3.000
 59Y  H1   C2   C1   119.52  3.000
 59Y  C3   C2   C1   121.51  3.000
 59Y  H2   C3   C4   120.41  3.000
 59Y  H2   C3   C2   119.34  3.000
 59Y  C4   C3   C2   120.25  3.000
 59Y  H3   C11  C10  119.51  3.000
 59Y  H3   C11  C12  121.08  3.000
 59Y  C10  C11  C12  119.41  3.000
 59Y  H4   C12  C13  119.47  3.000
 59Y  H4   C12  C11  121.18  3.000
 59Y  C13  C12  C11  119.35  3.000
 59Y  N14  C13  C15  118.35  3.000
 59Y  N14  C13  C12  122.36  3.000
 59Y  C15  C13  C12  119.28  3.000
 59Y  O23  C15  O22  127.68  3.000
 59Y  O23  C15  C13  117.02  3.000
 59Y  O22  C15  C13  115.30  3.000
 59Y  C6   C16  C21  121.22  3.000
 59Y  C21  C16  C17  119.26  3.000
 59Y  C6   C16  C17  119.52  3.000
 59Y  C5   C17  C18  122.43  3.000
 59Y  C18  C17  C16  118.48  3.000
 59Y  C5   C17  C16  119.09  3.000
 59Y  H5   C18  C19  119.61  3.000
 59Y  H5   C18  C17  119.41  3.000
 59Y  C19  C18  C17  120.99  3.000
 59Y  H6   C19  C20  119.62  3.000
 59Y  H6   C19  C18  119.93  3.000
 59Y  C20  C19  C18  120.44  3.000
 59Y  H7   C20  C21  120.24  3.000
 59Y  H7   C20  C19  119.77  3.000
 59Y  C21  C20  C19  119.99  3.000
 59Y  H8   C21  C20  120.32  3.000
 59Y  H8   C21  C16  118.85  3.000
 59Y  C20  C21  C16  120.84  3.000
 59Y  H9   C4   C10  119.19  3.000
 59Y  H9   C4   C3   120.86  3.000
 59Y  C10  C4   C3   119.95  3.000
 59Y  C7   C5   C17  119.50  3.000
 59Y  C17  C5   C1   120.98  3.000
 59Y  C7   C5   C1   119.50  3.000
 59Y  H10  C6   C8   120.68  3.000
 59Y  H10  C6   C16  118.94  3.000
 59Y  C8   C6   C16  120.38  3.000
 59Y  H11  C7   C8   119.23  3.000
 59Y  H11  C7   C5   119.44  3.000
 59Y  C8   C7   C5   121.33  3.000
 59Y  H12  C8   C7   119.41  3.000
 59Y  H12  C8   C6   120.40  3.000
 59Y  C7   C8   C6   120.18  3.000
 59Y  N14  C9   C10  122.37  3.000
 59Y  C10  C9   C1   119.05  3.000
 59Y  N14  C9   C1   118.58  3.000
 59Y  C9   C10  C4   120.05  3.000
 59Y  C4   C10  C11  122.80  3.000
 59Y  C9   C10  C11  117.15  3.000
 59Y  C9   N14  C13  119.35  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
 59Y  CONST_01  C13  N14  C9   C1   180.00   0.0  0
 59Y  CONST_02  C11  C10  C9   C1   180.00   0.0  0
 59Y  CONST_03  C4   C10  C9   C1     0.00   0.0  0
 59Y  CONST_04  C8   C7   C5   C1   180.00   0.0  0
 59Y  CONST_05  C16  C17  C5   C1   180.00   0.0  0
 59Y  CONST_06  C18  C17  C5   C1     0.00   0.0  0
 59Y  CONST_07  C4   C3   C2   C1     0.00   0.0  0
 59Y  CONST_08  N14  C9   C1   C2   180.00   0.0  0
 59Y  CONST_09  C10  C9   C1   C2     0.00   0.0  0
 59Y  CONST_12  C10  C4   C3   C2     0.00   0.0  0
 59Y  CONST_13  C11  C10  C4   C3   180.00   0.0  0
 59Y  CONST_14  C9   C10  C4   C3     0.00   0.0  0
 59Y  CONST_15  C9   C1   C2   C3     0.00   0.0  0
 59Y  CONST_16  C5   C1   C2   C3   180.00   0.0  0
 59Y  CONST_17  N14  C13  C12  C11    0.00   0.0  0
 59Y  CONST_18  N14  C9   C10  C11    0.00   0.0  0
 59Y  CONST_19  C9   N14  C13  C12    0.00   0.0  0
 59Y  CONST_20  C9   C10  C11  C12    0.00   0.0  0
 59Y  CONST_21  C4   C10  C11  C12  180.00   0.0  0
 59Y  CONST_22  C10  C11  C12  C13    0.00   0.0  0
 59Y  CONST_23  C10  C9   N14  C13    0.00   0.0  0
 59Y  CONST_24  C7   C8   C6   C16    0.00   0.0  0
 59Y  CONST_25  C19  C20  C21  C16    0.00   0.0  0
 59Y  CONST_26  C7   C5   C17  C16    0.00   0.0  0
 59Y  CONST_27  C19  C18  C17  C16    0.00   0.0  0
 59Y  CONST_28  C8   C6   C16  C17    0.00   0.0  0
 59Y  CONST_29  C20  C21  C16  C17    0.00   0.0  0
 59Y  CONST_30  C8   C7   C5   C17    0.00   0.0  0
 59Y  CONST_32  C20  C19  C18  C17    0.00   0.0  0
 59Y  CONST_33  C6   C16  C17  C18  180.00   0.0  0
 59Y  CONST_34  C21  C16  C17  C18    0.00   0.0  0
 59Y  CONST_35  C7   C5   C17  C18  180.00   0.0  0
 59Y  CONST_36  C21  C20  C19  C18    0.00   0.0  0
 59Y  CONST_37  C5   C17  C18  C19  180.00   0.0  0
 59Y  CONST_38  C6   C16  C21  C20  180.00   0.0  0
 59Y  CONST_39  C8   C6   C16  C21  180.00   0.0  0
 59Y  CONST_40  C5   C17  C16  C21  180.00   0.0  0
 59Y  CONST_41  N14  C9   C10  C4   180.00   0.0  0
 59Y  CONST_42  C6   C8   C7   C5     0.00   0.0  0
 59Y  CONST_43  C6   C16  C17  C5     0.00   0.0  0
 59Y  CONST_44  N14  C9   C1   C5     0.00   0.0  0
 59Y  CONST_45  C10  C9   C1   C5   180.00   0.0  0
 59Y  CONST_47  C15  C13  C12  C11  180.00   0.0  0
 59Y  CONST_48  C9   N14  C13  C15  180.00   0.0  0
 59Y  CONST_49  H11  C7   C5   C1     0.00   0.0  0
 59Y  CONST_50  H2   C3   C2   C1   180.00   0.0  0
 59Y  CONST_51  H9   C4   C3   C2   180.00   0.0  0
 59Y  CONST_52  H3   C11  C12  C13  180.00   0.0  0
 59Y  CONST_53  H12  C8   C6   C16  180.00   0.0  0
 59Y  CONST_54  H7   C20  C21  C16  180.00   0.0  0
 59Y  CONST_55  H5   C18  C17  C16  180.00   0.0  0
 59Y  CONST_56  H10  C6   C16  C17  180.00   0.0  0
 59Y  CONST_57  H8   C21  C16  C17  180.00   0.0  0
 59Y  CONST_58  H6   C19  C18  C17  180.00   0.0  0
 59Y  CONST_59  H1   C2   C3   C4   180.00   0.0  0
 59Y  CONST_60  H4   C12  C11  C10  180.00   0.0  0
 59Y  Var_01    O22  C15  C13  C12    6.77  30.0  3

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
 59Y  plan-1  C1   0.020
 59Y  plan-1  C2   0.020
 59Y  plan-1  C3   0.020
 59Y  plan-1  C11  0.020
 59Y  plan-1  C12  0.020
 59Y  plan-1  C13  0.020
 59Y  plan-1  C15  0.020
 59Y  plan-1  C4   0.020
 59Y  plan-1  C5   0.020
 59Y  plan-1  C9   0.020
 59Y  plan-1  C10  0.020
 59Y  plan-1  N14  0.020
 59Y  plan-1  H1   0.020
 59Y  plan-1  H2   0.020
 59Y  plan-1  H3   0.020
 59Y  plan-1  H4   0.020
 59Y  plan-1  H9   0.020
 59Y  plan-2  C1   0.020
 59Y  plan-2  C16  0.020
 59Y  plan-2  C17  0.020
 59Y  plan-2  C18  0.020
 59Y  plan-2  C19  0.020
 59Y  plan-2  C20  0.020
 59Y  plan-2  C21  0.020
 59Y  plan-2  C5   0.020
 59Y  plan-2  C6   0.020
 59Y  plan-2  C7   0.020
 59Y  plan-2  C8   0.020
 59Y  plan-2  H7   0.020
 59Y  plan-2  H8   0.020
 59Y  plan-2  H10  0.020
 59Y  plan-2  H11  0.020
 59Y  plan-2  H12  0.020
 59Y  plan-2  H5   0.020
 59Y  plan-2  H6   0.020
 59Y  plan-3  C13  0.020
 59Y  plan-3  C15  0.020
 59Y  plan-3  O22  0.020
 59Y  plan-3  O23  0.020

