# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 01:04:39 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 8-(3-nitrophenyl)-6-(pyridin-4-ylmethyl)quinoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccc(c1)c2cc(Cc3ccncc3)cc4cccnc24
#
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
 988  988  8-(3-nitrophenyl)-6-(pyridin-4-ylmethyl)quinoline  ligand  41  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_988
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
 988  C1    C  CR16   0  -0.190  -1.4117   4.0674   0.8982
 988  C2    C  CR66   0   0.110  -1.1913   2.6762   0.8076
 988  C3    C  CR66   0   0.153   0.0196   2.2394   0.2171
 988  N4    N  N      0  -0.419   0.9527   3.1082  -0.2289
 988  C5    C  CR16   0  -0.080   0.7161   4.3894  -0.1261
 988  C6    C  CR16   0  -0.325  -0.4613   4.9286   0.4288
 988  C13   C  CR16   0  -0.414  -2.1262   1.7329   1.2884
 988  C15   C  CR6    0   0.158  -1.8739   0.3915   1.2005
 988  C17   C  CR16   0  -0.339  -0.6671  -0.0394   0.6040
 988  C19   C  CR6    0   0.057   0.2653   0.8387   0.1118
 988  C22   C  CR6    0   0.094   1.5049   0.3238  -0.5048
 988  C24   C  CR16   0  -0.332   2.2557  -0.6349   0.1646
 988  C25   C  CR6    0   0.273   3.3953  -1.1521  -0.4348
 988  C26   C  CR16   0  -0.277   3.8159  -0.7420  -1.6899
 988  C27   C  CR16   0  -0.241   3.0617   0.2128  -2.3528
 988  C28   C  CR16   0  -0.254   1.9224   0.7438  -1.7693
 988  C35   C  CH2    0  -0.595  -2.8571  -0.6321   1.7052
 988  C37   C  CR6    0   0.219  -3.3520  -1.5264   0.6005
 988  C39   C  CR16   0  -0.391  -3.0693  -2.8856   0.5789
 988  C40   C  CR16   0  -0.057  -3.5381  -3.6585  -0.4746
 988  N41   N  N      0  -0.411  -4.2542  -3.1716  -1.4795
 988  C42   C  CR16   0  -0.060  -4.5266  -1.8697  -1.4573
 988  C43   C  CR16   0  -0.354  -4.1025  -1.0147  -0.4543
 988  N50   N  N      1   0.327   4.1730  -2.1527   0.2811
 988  O52   O  O     -1  -0.379   3.7840  -2.5054   1.3698
 988  O54   O  O      0  -0.377   5.1700  -2.5835  -0.2485
 988  H1    H  HCR6   0   0.275  -2.3298   4.4340   1.3406
 988  H5    H  HCR6   0   0.265   1.4879   5.0576  -0.4935
 988  H6    H  HCR6   0   0.274  -0.5931   6.0003   0.4806
 988  H13   H  HCR6   0   0.263  -3.0491   2.0896   1.7316
 988  H17   H  HCR6   0   0.261  -0.4846  -1.1045   0.5117
 988  H24   H  HCR6   0   0.295   1.9559  -0.9599   1.1510
 988  H26   H  HCR6   0   0.299   4.7034  -1.1504  -2.1503
 988  H27   H  HCR6   0   0.279   3.3642   0.5414  -3.3373
 988  H28   H  HCR6   0   0.270   1.3419   1.4772  -2.3103
 988  H35   H  HCH2   0   0.280  -2.3890  -1.2409   2.4823
 988  H35A  H  HCH2   0   0.283  -3.7038  -0.1219   2.1685
 988  H39   H  HCR6   0   0.268  -2.4933  -3.3459   1.3717
 988  H40   H  HCR6   0   0.264  -3.3207  -4.7208  -0.5029
 988  H42   H  HCR6   0   0.263  -5.1139  -1.4842  -2.2835
 988  H43   H  HCR6   0   0.264  -4.3562   0.0372  -0.5003

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
 988  C1   C2    aromatic  1.411  0.020  1.411
 988  C1   C6    aromatic  1.366  0.020  1.366
 988  C1   H1    single    0.930  0.020  1.080
 988  C2   C3    aromatic  1.416  0.020  1.416
 988  C2   C13   aromatic  1.412  0.020  1.412
 988  C3   N4    aromatic  1.351  0.020  1.351
 988  C3   C19   aromatic  1.426  0.020  1.426
 988  N4   C5    aromatic  1.307  0.020  1.307
 988  C5   C6    aromatic  1.409  0.020  1.409
 988  C5   H5    single    0.930  0.020  1.080
 988  C6   H6    single    0.930  0.020  1.080
 988  C13  C15   aromatic  1.368  0.020  1.368
 988  C13  H13   single    0.930  0.020  1.080
 988  C15  C17   aromatic  1.413  0.020  1.413
 988  C15  C35   single    1.506  0.020  1.506
 988  C17  C19   aromatic  1.372  0.020  1.372
 988  C17  H17   single    0.930  0.020  1.080
 988  C19  C22   single    1.477  0.020  1.477
 988  C22  C24   aromatic  1.390  0.020  1.390
 988  C22  C28   aromatic  1.396  0.020  1.396
 988  C24  C25   aromatic  1.388  0.020  1.388
 988  C24  H24   single    0.930  0.020  1.080
 988  C25  C26   aromatic  1.386  0.020  1.386
 988  C25  N50   single    1.456  0.020  1.456
 988  C26  C27   aromatic  1.386  0.020  1.386
 988  C26  H26   single    0.930  0.020  1.080
 988  C27  C28   aromatic  1.386  0.020  1.386
 988  C27  H27   single    0.930  0.020  1.080
 988  C28  H28   single    0.930  0.020  1.080
 988  C35  C37   single    1.505  0.020  1.505
 988  C35  H35   single    0.970  0.020  1.090
 988  C35  H35A  single    0.970  0.020  1.090
 988  C37  C39   aromatic  1.388  0.020  1.388
 988  C37  C43   aromatic  1.392  0.020  1.392
 988  C39  C40   aromatic  1.388  0.020  1.388
 988  C39  H39   single    0.930  0.020  1.080
 988  C40  N41   aromatic  1.327  0.020  1.327
 988  C40  H40   single    0.930  0.020  1.080
 988  N41  C42   aromatic  1.330  0.020  1.330
 988  C42  C43   aromatic  1.384  0.020  1.384
 988  C42  H42   single    0.930  0.020  1.080
 988  C43  H43   single    0.930  0.020  1.080
 988  N50  O52   single    1.209  0.020  1.209
 988  N50  O54   double    1.208  0.020  1.208

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
 988  H1    C1   C6   121.12  3.000
 988  H1    C1   C2   119.49  3.000
 988  C6    C1   C2   119.39  3.000
 988  C13   C2   C3   120.13  3.000
 988  C13   C2   C1   122.21  3.000
 988  C3    C2   C1   117.66  3.000
 988  C19   C3   N4   119.24  3.000
 988  C19   C3   C2   118.75  3.000
 988  N4    C3   C2   122.00  3.000
 988  C5    N4   C3   118.66  3.000
 988  H5    C5   C6   119.48  3.000
 988  H5    C5   N4   116.64  3.000
 988  C6    C5   N4   123.88  3.000
 988  H6    C6   C5   120.01  3.000
 988  H6    C6   C1   121.59  3.000
 988  C5    C6   C1   118.40  3.000
 988  H13   C13  C15  120.40  3.000
 988  H13   C13  C2   118.87  3.000
 988  C15   C13  C2   120.73  3.000
 988  C35   C15  C17  119.44  3.000
 988  C35   C15  C13  121.63  3.000
 988  C17   C15  C13  118.92  3.000
 988  H17   C17  C19  118.93  3.000
 988  H17   C17  C15  118.61  3.000
 988  C19   C17  C15  122.44  3.000
 988  C22   C19  C17  119.80  3.000
 988  C22   C19  C3   121.18  3.000
 988  C17   C19  C3   119.02  3.000
 988  C28   C22  C24  118.83  3.000
 988  C28   C22  C19  121.61  3.000
 988  C24   C22  C19  119.52  3.000
 988  H24   C24  C25  120.65  3.000
 988  H24   C24  C22  119.82  3.000
 988  C25   C24  C22  119.52  3.000
 988  N50   C25  C26  119.13  3.000
 988  N50   C25  C24  118.85  3.000
 988  C26   C25  C24  122.02  3.000
 988  H26   C26  C27  120.26  3.000
 988  H26   C26  C25  121.58  3.000
 988  C27   C26  C25  118.16  3.000
 988  H27   C27  C28  119.81  3.000
 988  H27   C27  C26  119.53  3.000
 988  C28   C27  C26  120.67  3.000
 988  H28   C28  C27  119.40  3.000
 988  H28   C28  C22  119.79  3.000
 988  C27   C28  C22  120.79  3.000
 988  H35A  C35  H35  106.91  3.000
 988  H35A  C35  C37  109.52  3.000
 988  H35   C35  C37  109.38  3.000
 988  H35A  C35  C15  109.32  3.000
 988  H35   C35  C15  109.71  3.000
 988  C37   C35  C15  111.87  3.000
 988  C43   C37  C39  117.25  3.000
 988  C43   C37  C35  121.00  3.000
 988  C39   C37  C35  121.75  3.000
 988  H39   C39  C40  119.91  3.000
 988  H39   C39  C37  120.87  3.000
 988  C40   C39  C37  119.22  3.000
 988  H40   C40  N41  116.62  3.000
 988  H40   C40  C39  119.83  3.000
 988  N41   C40  C39  123.56  3.000
 988  C42   N41  C40  117.21  3.000
 988  H42   C42  C43  119.89  3.000
 988  H42   C42  N41  116.49  3.000
 988  C43   C42  N41  123.62  3.000
 988  H43   C43  C42  119.82  3.000
 988  H43   C43  C37  121.03  3.000
 988  C42   C43  C37  119.15  3.000
 988  O54   N50  O52  123.80  3.000
 988  O54   N50  C25  118.06  3.000
 988  O52   N50  C25  118.14  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
 988  CONST_01  N4   C3   C2   C1     0.00   0.0  0
 988  CONST_02  C19  C3   C2   C1   180.00   0.0  0
 988  CONST_03  C15  C13  C2   C1   180.00   0.0  0
 988  CONST_04  N4   C5   C6   C1     0.00   0.0  0
 988  CONST_05  C5   C6   C1   C2     0.00   0.0  0
 988  CONST_06  C5   N4   C3   C2     0.00   0.0  0
 988  CONST_07  C17  C19  C3   C2     0.00   0.0  0
 988  CONST_08  C22  C19  C3   C2   180.00   0.0  0
 988  CONST_09  C17  C15  C13  C2     0.00   0.0  0
 988  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 988  CONST_11  C15  C13  C2   C3     0.00   0.0  0
 988  CONST_12  C6   C5   N4   C3     0.00   0.0  0
 988  CONST_13  C15  C17  C19  C3     0.00   0.0  0
 988  CONST_16  C13  C2   C3   N4   180.00   0.0  0
 988  CONST_17  C17  C19  C3   N4   180.00   0.0  0
 988  CONST_18  C22  C19  C3   N4     0.00   0.0  0
 988  CONST_19  C19  C3   N4   C5   180.00   0.0  0
 988  CONST_20  C13  C2   C1   C6   180.00   0.0  0
 988  CONST_21  C19  C3   C2   C13    0.00   0.0  0
 988  CONST_22  C19  C17  C15  C13    0.00   0.0  0
 988  CONST_23  C22  C19  C17  C15  180.00   0.0  0
 988  CONST_26  C25  C24  C22  C19  180.00   0.0  0
 988  CONST_27  C27  C28  C22  C19  180.00   0.0  0
 988  CONST_28  C26  C25  C24  C22    0.00   0.0  0
 988  CONST_29  C26  C27  C28  C22    0.00   0.0  0
 988  CONST_30  C27  C28  C22  C24    0.00   0.0  0
 988  CONST_31  C27  C26  C25  C24    0.00   0.0  0
 988  CONST_32  C28  C22  C24  C25    0.00   0.0  0
 988  CONST_33  C28  C27  C26  C25    0.00   0.0  0
 988  CONST_34  N41  C40  C39  C37    0.00   0.0  0
 988  CONST_35  N41  C42  C43  C37    0.00   0.0  0
 988  CONST_36  C42  C43  C37  C39    0.00   0.0  0
 988  CONST_37  C42  N41  C40  C39    0.00   0.0  0
 988  CONST_38  C43  C37  C39  C40    0.00   0.0  0
 988  CONST_39  C43  C42  N41  C40    0.00   0.0  0
 988  CONST_40  C35  C15  C13  C2   180.00   0.0  0
 988  CONST_41  C35  C15  C17  C19  180.00   0.0  0
 988  CONST_42  N50  C25  C24  C22  180.00   0.0  0
 988  CONST_43  N50  C25  C26  C27  180.00   0.0  0
 988  CONST_44  C40  C39  C37  C35  180.00   0.0  0
 988  CONST_45  C42  C43  C37  C35  180.00   0.0  0
 988  CONST_46  H13  C13  C2   C1     0.00   0.0  0
 988  CONST_47  H5   C5   C6   C1   180.00   0.0  0
 988  CONST_48  H6   C6   C1   C2   180.00   0.0  0
 988  CONST_49  H1   C1   C2   C3   180.00   0.0  0
 988  CONST_50  H17  C17  C19  C3   180.00   0.0  0
 988  CONST_51  H24  C24  C22  C19    0.00   0.0  0
 988  CONST_52  H28  C28  C22  C19    0.00   0.0  0
 988  CONST_53  H27  C27  C28  C22  180.00   0.0  0
 988  CONST_54  H26  C26  C25  C24  180.00   0.0  0
 988  CONST_55  H40  C40  C39  C37  180.00   0.0  0
 988  CONST_56  H42  C42  C43  C37  180.00   0.0  0
 988  CONST_57  H43  C43  C37  C39  180.00   0.0  0
 988  CONST_58  H39  C39  C40  N41  180.00   0.0  0
 988  CONST_59  O52  N50  C25  C24    0.00   0.0  0
 988  CONST_60  O54  N50  C25  C24  180.00   0.0  0
 988  CONST_61  O52  N50  C25  C26  180.00   0.0  0
 988  CONST_62  O54  N50  C25  C26    0.00   0.0  0
 988  Var_01    C37  C35  C15  C13  118.24  30.0  2
 988  Var_02    C39  C37  C35  C15  114.80  30.0  2

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
 988  plan-1  C19  0.020
 988  plan-1  C22  0.020
 988  plan-1  C24  0.020
 988  plan-1  C25  0.020
 988  plan-1  C26  0.020
 988  plan-1  C27  0.020
 988  plan-1  C28  0.020
 988  plan-1  N50  0.020
 988  plan-1  H24  0.020
 988  plan-1  H26  0.020
 988  plan-1  H27  0.020
 988  plan-1  H28  0.020
 988  plan-2  C35  0.020
 988  plan-2  C37  0.020
 988  plan-2  C39  0.020
 988  plan-2  C40  0.020
 988  plan-2  N41  0.020
 988  plan-2  C42  0.020
 988  plan-2  C43  0.020
 988  plan-2  H39  0.020
 988  plan-2  H40  0.020
 988  plan-2  H42  0.020
 988  plan-2  H43  0.020
 988  plan-3  C1   0.020
 988  plan-3  C2   0.020
 988  plan-3  C3   0.020
 988  plan-3  N4   0.020
 988  plan-3  C5   0.020
 988  plan-3  C6   0.020
 988  plan-3  C13  0.020
 988  plan-3  C15  0.020
 988  plan-3  C17  0.020
 988  plan-3  C19  0.020
 988  plan-3  C22  0.020
 988  plan-3  C35  0.020
 988  plan-3  H1   0.020
 988  plan-3  H5   0.020
 988  plan-3  H6   0.020
 988  plan-3  H13  0.020
 988  plan-3  H17  0.020
 988  plan-4  C25  0.020
 988  plan-4  N50  0.020
 988  plan-4  O52  0.020
 988  plan-4  O54  0.020

