# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 13:39:05 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)methyl]amino}-2-methoxybenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(NCC2=Cc3cc(Cl)ccc3NC2=O)ccc1C#N
#
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
 LJY  LJY  4-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)methyl]amino}-2-methoxybenzonitrile  ligand  38  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LJY
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
 LJY  C1   C   CH3   0  -0.442   4.9820  -1.5529  -2.7548
 LJY  C2   C   CR6   0   0.434   4.7640  -0.4849  -0.6472
 LJY  C3   C   CR6   0  -0.142   5.4194   0.0920   0.4608
 LJY  C4   C   CR16  0  -0.218   4.6529   0.6118   1.5047
 LJY  C5   C   CR16  0  -0.389   3.2777   0.5766   1.4757
 LJY  C6   C   CR6   0   0.461   2.6168   0.0104   0.3679
 LJY  C15  C   CR6   0  -0.047  -5.5899  -0.6938  -0.0449
 LJY  C14  C   CR16  0  -0.214  -5.7749   0.4114  -0.8785
 LJY  C13  C   CR16  0  -0.316  -4.7345   1.2855  -1.1023
 LJY  C16  C   CR16  0  -0.278  -4.3776  -0.9289   0.5596
 LJY  C10  C   CR66  0   0.036  -3.3126  -0.0482   0.3384
 LJY  C11  C   CR66  0   0.401  -3.4955   1.0624  -0.4960
 LJY  N2   N   NR16  0  -0.754  -2.4431   1.9136  -0.6993
 LJY  C12  C   CR6   0   0.534  -1.1913   1.7882  -0.1573
 LJY  O2   O   O     0  -0.466  -0.3178   2.6111  -0.3900
 LJY  C9   C   CR16  0  -0.177  -2.0215  -0.2358   0.9286
 LJY  C8   C   CR6   0  -0.159  -1.0040   0.6211   0.7055
 LJY  C7   C   CH2   0  -0.325   0.3554   0.4180   1.2980
 LJY  N1   N   NH1   0  -0.687   1.2711  -0.0326   0.2759
 LJY  C17  C   CR16  0  -0.508   3.3851  -0.5246  -0.6862
 LJY  O1   O   O2    0  -0.458   5.5638  -0.9607  -1.6051
 LJY  C18  C   CSP   0   0.047   6.8329   0.1332   0.5021
 LJY  N3   N   NS    0  -0.279   7.9864   0.1743   0.5486
 LJY  H1   H   HCH3  0   0.267   5.8082  -1.8539  -3.3930
 LJY  H2   H   HCH3  0   0.237   4.3916  -2.4354  -2.4988
 LJY  H3   H   HCH3  0   0.237   4.3519  -0.8448  -3.2975
 LJY  H4   H   HCR6  0   0.276   5.1531   1.0471   2.3595
 LJY  H5   H   HCR6  0   0.275   2.7261   0.9788   2.3125
 LJY  H6   H   HCR6  0   0.291  -6.7328   0.5842  -1.3497
 LJY  H7   H   HCR6  0   0.290  -4.8799   2.1417  -1.7487
 LJY  H8   H   HCR6  0   0.287  -4.2346  -1.7853   1.2058
 LJY  H9   H   HNR6  0   0.419  -2.5909   2.7158  -1.2981
 LJY  H10  H   HCR6  0   0.281  -1.8707  -1.0950   1.5725
 LJY  H11  H   HCH2  0   0.262   0.7106   1.3629   1.7130
 LJY  H12  H   HCH2  0   0.256   0.2945  -0.2949   2.1274
 LJY  H13  H   HNH1  0   0.397   0.8785  -0.5832  -0.4706
 LJY  H14  H   HCR6  0   0.293   2.8671  -0.9604  -1.5302
 LJY  CL   CL  CL    0  -0.124  -6.9122  -1.7795   0.2253

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
 LJY  C1   O1   single    1.418  0.020  1.418
 LJY  O1   C2   single    1.336  0.020  1.336
 LJY  N3   C18  triple    1.155  0.020  1.155
 LJY  C18  C3   single    1.415  0.020  1.415
 LJY  C2   C3   aromatic  1.411  0.020  1.411
 LJY  C2   C17  aromatic  1.380  0.020  1.380
 LJY  C3   C4   aromatic  1.395  0.020  1.395
 LJY  C17  C6   aromatic  1.410  0.020  1.410
 LJY  CL   C15  single    1.732  0.020  1.732
 LJY  C4   C5   aromatic  1.376  0.020  1.376
 LJY  C6   C5   aromatic  1.409  0.020  1.409
 LJY  C6   N1   single    1.350  0.020  1.350
 LJY  C16  C15  aromatic  1.375  0.020  1.375
 LJY  C16  C10  aromatic  1.400  0.020  1.400
 LJY  N1   C7   single    1.444  0.020  1.444
 LJY  C15  C14  aromatic  1.397  0.020  1.397
 LJY  C9   C10  single    1.432  0.020  1.432
 LJY  C9   C8   double    1.349  0.020  1.349
 LJY  C10  C11  aromatic  1.401  0.020  1.401
 LJY  C7   C8   single    1.497  0.020  1.497
 LJY  C14  C13  aromatic  1.377  0.020  1.377
 LJY  C8   C12  single    1.463  0.020  1.463
 LJY  C11  C13  aromatic  1.397  0.020  1.397
 LJY  C11  N2   single    1.369  0.020  1.369
 LJY  C12  N2   single    1.370  0.020  1.370
 LJY  C12  O2   double    1.222  0.020  1.222
 LJY  C1   H1   single    0.970  0.020  1.090
 LJY  C1   H2   single    0.970  0.020  1.090
 LJY  C1   H3   single    0.970  0.020  1.090
 LJY  C4   H4   single    0.930  0.020  1.080
 LJY  C5   H5   single    0.930  0.020  1.080
 LJY  C14  H6   single    0.930  0.020  1.080
 LJY  C13  H7   single    0.930  0.020  1.080
 LJY  C16  H8   single    0.930  0.020  1.080
 LJY  N2   H9   single    0.860  0.020  1.020
 LJY  C9   H10  single    0.930  0.020  1.080
 LJY  C7   H11  single    0.970  0.020  1.090
 LJY  C7   H12  single    0.970  0.020  1.090
 LJY  N1   H13  single    0.860  0.020  1.020
 LJY  C17  H14  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
 LJY  H3   C1   H2   109.18  3.000
 LJY  H3   C1   H1   109.05  3.000
 LJY  H2   C1   H1   108.96  3.000
 LJY  H3   C1   O1   111.64  3.000
 LJY  H2   C1   O1   111.67  3.000
 LJY  H1   C1   O1   106.26  3.000
 LJY  O1   C2   C17  124.60  3.000
 LJY  C17  C2   C3   119.88  3.000
 LJY  O1   C2   C3   115.52  3.000
 LJY  C18  C3   C4   121.07  3.000
 LJY  C4   C3   C2   118.99  3.000
 LJY  C18  C3   C2   119.93  3.000
 LJY  H4   C4   C5   119.28  3.000
 LJY  H4   C4   C3   119.14  3.000
 LJY  C5   C4   C3   121.57  3.000
 LJY  H5   C5   C6   121.29  3.000
 LJY  H5   C5   C4   118.99  3.000
 LJY  C6   C5   C4   119.72  3.000
 LJY  C17  C6   N1   118.71  3.000
 LJY  N1   C6   C5   122.29  3.000
 LJY  C17  C6   C5   119.00  3.000
 LJY  C16  C15  C14  120.97  3.000
 LJY  C14  C15  CL   119.21  3.000
 LJY  C16  C15  CL   119.83  3.000
 LJY  H6   C14  C13  119.79  3.000
 LJY  H6   C14  C15  120.26  3.000
 LJY  C13  C14  C15  119.95  3.000
 LJY  H7   C13  C11  120.30  3.000
 LJY  H7   C13  C14  119.84  3.000
 LJY  C11  C13  C14  119.87  3.000
 LJY  H8   C16  C10  119.46  3.000
 LJY  H8   C16  C15  120.95  3.000
 LJY  C10  C16  C15  119.59  3.000
 LJY  C9   C10  C11  117.84  3.000
 LJY  C11  C10  C16  119.57  3.000
 LJY  C9   C10  C16  122.59  3.000
 LJY  N2   C11  C10  118.75  3.000
 LJY  N2   C11  C13  121.20  3.000
 LJY  C10  C11  C13  120.05  3.000
 LJY  H9   N2   C12  116.12  3.000
 LJY  H9   N2   C11  117.94  3.000
 LJY  C12  N2   C11  125.94  3.000
 LJY  C8   C12  O2   123.89  3.000
 LJY  O2   C12  N2   121.06  3.000
 LJY  C8   C12  N2   115.04  3.000
 LJY  H10  C9   C8   119.78  3.000
 LJY  H10  C9   C10  118.29  3.000
 LJY  C8   C9   C10  121.93  3.000
 LJY  C7   C8   C9   122.24  3.000
 LJY  C7   C8   C12  117.25  3.000
 LJY  C9   C8   C12  120.50  3.000
 LJY  H12  C7   H11  107.07  3.000
 LJY  H12  C7   N1   111.59  3.000
 LJY  H11  C7   N1   109.44  3.000
 LJY  H12  C7   C8   109.73  3.000
 LJY  H11  C7   C8   109.19  3.000
 LJY  N1   C7   C8   109.76  3.000
 LJY  H13  N1   C7   116.61  3.000
 LJY  H13  N1   C6   117.17  3.000
 LJY  C7   N1   C6   125.03  3.000
 LJY  H14  C17  C6   118.37  3.000
 LJY  H14  C17  C2   120.80  3.000
 LJY  C6   C17  C2   120.83  3.000
 LJY  C2   O1   C1   118.98  3.000
 LJY  N3   C18  C3   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
 LJY  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 LJY  CONST_02  C5   C6   C17  C2      0.00   0.0  0
 LJY  CONST_03  C6   C17  C2   C3      0.00   0.0  0
 LJY  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 LJY  CONST_05  C17  C2   C3   C4      0.00   0.0  0
 LJY  CONST_06  C17  C6   C5   C4      0.00   0.0  0
 LJY  CONST_07  C11  C10  C16  C15     0.00   0.0  0
 LJY  CONST_08  C11  C13  C14  C15     0.00   0.0  0
 LJY  CONST_09  C10  C16  C15  C14     0.00   0.0  0
 LJY  CONST_10  C10  C11  C13  C14     0.00   0.0  0
 LJY  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 LJY  CONST_12  C16  C10  C11  C13     0.00   0.0  0
 LJY  CONST_13  C8   C12  N2   C11     0.00   0.0  0
 LJY  CONST_14  N1   C6   C17  C2    180.00   0.0  0
 LJY  CONST_15  O1   C2   C3   C4    180.00   0.0  0
 LJY  CONST_16  N1   C6   C5   C4    180.00   0.0  0
 LJY  CONST_17  C18  C3   C4   C5    180.00   0.0  0
 LJY  CONST_18  O1   C2   C17  C6    180.00   0.0  0
 LJY  CONST_19  C10  C16  C15  CL    180.00   0.0  0
 LJY  CONST_20  C13  C14  C15  CL    180.00   0.0  0
 LJY  CONST_21  C18  C3   C2   C17   180.00   0.0  0
 LJY  CONST_22  O2   C12  N2   C11   180.00   0.0  0
 LJY  CONST_23  H4   C4   C3   C2    180.00   0.0  0
 LJY  CONST_24  H14  C17  C2   C3    180.00   0.0  0
 LJY  CONST_25  H5   C5   C4   C3    180.00   0.0  0
 LJY  CONST_26  H7   C13  C14  C15   180.00   0.0  0
 LJY  CONST_27  H8   C16  C15  C14   180.00   0.0  0
 LJY  CONST_28  H6   C14  C15  C16   180.00   0.0  0
 LJY  CONST_29  H9   N2   C12  C8    180.00   0.0  0
 LJY  CONST_30  C7   N1   C6   C5      0.00   0.0  0
 LJY  CONST_31  C17  C6   N1   C7    180.00   0.0  0
 LJY  CONST_32  H13  N1   C6   C5    180.00   0.0  0
 LJY  Var_01    C3   C2   O1   C1   -179.81  30.0  2
 LJY  Var_02    C8   C7   N1   C6    162.33  30.0  3
 LJY  Var_03    N1   C7   C8   C12   -73.19  30.0  2
 LJY  Var_04    H1   C1   O1   C2    179.42  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
 LJY  plan-1  C2   0.020
 LJY  plan-1  C3   0.020
 LJY  plan-1  C4   0.020
 LJY  plan-1  C5   0.020
 LJY  plan-1  C6   0.020
 LJY  plan-1  N1   0.020
 LJY  plan-1  C17  0.020
 LJY  plan-1  O1   0.020
 LJY  plan-1  C18  0.020
 LJY  plan-1  N3   0.020
 LJY  plan-1  H4   0.020
 LJY  plan-1  H5   0.020
 LJY  plan-1  H14  0.020
 LJY  plan-2  C15  0.020
 LJY  plan-2  C14  0.020
 LJY  plan-2  C13  0.020
 LJY  plan-2  C16  0.020
 LJY  plan-2  C10  0.020
 LJY  plan-2  C11  0.020
 LJY  plan-2  N2   0.020
 LJY  plan-2  C12  0.020
 LJY  plan-2  O2   0.020
 LJY  plan-2  C9   0.020
 LJY  plan-2  C8   0.020
 LJY  plan-2  C7   0.020
 LJY  plan-2  H6   0.020
 LJY  plan-2  H7   0.020
 LJY  plan-2  H8   0.020
 LJY  plan-2  H9   0.020
 LJY  plan-2  H10  0.020
 LJY  plan-2  CL   0.020
 LJY  plan-3  C6   0.020
 LJY  plan-3  C7   0.020
 LJY  plan-3  N1   0.020
 LJY  plan-3  H13  0.020

