# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 18:27:18 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 2,2'-(2-phenyl-4,5,6,7-tetrahydro-2H-isophosphindole-1,3-diyl)dipyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCc2c(C1)c([p](c3ccccc3)c2c4ccccn4)c5ccccn5
#
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
 AUP  AUP  2,2'-(2-phenyl-4,5,6,7-tetrahydro-2H-isophosphindole-1,3-diyl)dipyridine  ligand  48  27  .  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_AUP
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
 AUP  C1   C  CR5   0   0.163   0.8126  -1.7512  -0.1015
 AUP  C2   C  CR5   0   0.169  -0.6496  -1.8005  -0.1718
 AUP  C3   C  CH2   0  -0.517  -1.3607  -3.0615  -0.5808
 AUP  C4   C  CH2   0  -0.445  -0.4517  -4.0689  -1.2737
 AUP  C5   C  CH2   0  -0.446   0.8405  -4.2417  -0.4944
 AUP  C6   C  CH2   0  -0.498   1.6372  -2.9425  -0.5010
 AUP  C7   C  CR5   0  -0.365   1.3013  -0.5620   0.3522
 AUP  P    P  P     0   0.592  -0.0464   0.4854   0.9251
 AUP  C9   C  CR5   0  -0.372  -1.2593  -0.6524   0.2350
 AUP  N14  N  N     0  -0.423  -3.4468  -0.7986  -0.7442
 AUP  C15  C  CR16  0  -0.077  -4.7304  -0.4737  -0.7774
 AUP  C16  C  CR16  0  -0.329  -5.3418   0.3484   0.1584
 AUP  C17  C  CR16  0  -0.156  -4.5586   0.8486   1.1870
 AUP  C18  C  CR16  0  -0.339  -3.2171   0.5109   1.2343
 AUP  C19  C  CR6   0   0.216  -2.6846  -0.3221   0.2441
 AUP  C24  C  CR16  0  -0.262  -0.1030   4.0952  -1.9444
 AUP  C25  C  CR16  0  -0.234  -0.2133   4.2842  -0.5752
 AUP  C26  C  CR16  0  -0.316  -0.1901   3.1875   0.2803
 AUP  C27  C  CR6   0  -0.149  -0.0574   1.9011  -0.2318
 AUP  C28  C  CR16  0  -0.237   0.0505   1.7174  -1.6106
 AUP  C29  C  CR16  0  -0.237   0.0289   2.8097  -2.4624
 AUP  N35  N  N     0  -0.425   3.5868  -0.7054  -0.3542
 AUP  C36  C  CR6   0   0.215   2.6933  -0.1395   0.4627
 AUP  C37  C  CR16  0  -0.338   3.0692   0.8603   1.3687
 AUP  C38  C  CR16  0  -0.157   4.3884   1.2722   1.4157
 AUP  C39  C  CR16  0  -0.330   5.3094   0.6764   0.5664
 AUP  C40  C  CR16  0  -0.078   4.8500  -0.3093  -0.2943
 AUP  H31  H  HCH2  0   0.267  -2.2164  -2.8129  -1.2049
 AUP  H32  H  HCH2  0   0.244  -1.7750  -3.5214   0.3239
 AUP  H41  H  HCH2  0   0.222  -0.2231  -3.7317  -2.2897
 AUP  H42  H  HCH2  0   0.239  -0.9803  -5.0189  -1.3717
 AUP  H51  H  HCH2  0   0.221   0.6119  -4.5404   0.5339
 AUP  H52  H  HCH2  0   0.238   1.4514  -5.0382  -0.9234
 AUP  H61  H  HCH2  0   0.249   2.5157  -3.0183   0.1402
 AUP  H62  H  HCH2  0   0.245   2.0279  -2.7719  -1.5087
 AUP  H16  H  HCR6  0   0.271  -6.3937   0.5843   0.0790
 AUP  H17  H  HCR6  0   0.273  -4.9857   1.4892   1.9474
 AUP  H18  H  HCR6  0   0.268  -2.5935   0.8779   2.0392
 AUP  H24  H  HCR6  0   0.263  -0.1196   4.9465  -2.6125
 AUP  H25  H  HCR6  0   0.261  -0.3184   5.2820  -0.1696
 AUP  H26  H  HCR6  0   0.258  -0.2768   3.3374   1.3497
 AUP  H28  H  HCR6  0   0.262   0.1504   0.7169  -2.0151
 AUP  H29  H  HCR6  0   0.261   0.1120   2.6623  -3.5314
 AUP  H37  H  HCR6  0   0.268   2.3409   1.3003   2.0381
 AUP  H38  H  HCR6  0   0.273   4.6928   2.0450   2.1094
 AUP  H39  H  HCR6  0   0.270   6.3514   0.9643   0.5671
 AUP  H40  H  HCR6  0   0.259   5.5371  -0.8000  -0.9752
 AUP  H15  H  HCR6  0   0.261  -5.3073  -0.8862  -1.5980

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
 AUP  C1   C2   aromatic  1.465  0.020  1.465
 AUP  C1   C6   single    1.503  0.020  1.503
 AUP  C1   C7   aromatic  1.363  0.020  1.363
 AUP  C2   C3   single    1.504  0.020  1.504
 AUP  C2   C9   aromatic  1.362  0.020  1.362
 AUP  C3   C4   single    1.523  0.020  1.523
 AUP  C3   H31  single    0.970  0.020  1.090
 AUP  C3   H32  single    0.970  0.020  1.090
 AUP  C4   C5   single    1.519  0.020  1.519
 AUP  C4   H41  single    0.970  0.020  1.090
 AUP  C4   H42  single    0.970  0.020  1.090
 AUP  C5   C6   single    1.524  0.020  1.524
 AUP  C5   H51  single    0.970  0.020  1.090
 AUP  C5   H52  single    0.970  0.020  1.090
 AUP  C6   H61  single    0.970  0.020  1.090
 AUP  C6   H62  single    0.970  0.020  1.090
 AUP  C7   P    aromatic  1.800  0.020  1.800
 AUP  C7   C36  single    1.459  0.020  1.459
 AUP  P    C9   aromatic  1.801  0.020  1.801
 AUP  P    C27  single    1.828  0.020  1.828
 AUP  C9   C19  single    1.463  0.020  1.463
 AUP  N14  C15  aromatic  1.324  0.020  1.324
 AUP  N14  C19  aromatic  1.336  0.020  1.336
 AUP  C15  C16  aromatic  1.388  0.020  1.388
 AUP  C15  H15  single    0.930  0.020  1.080
 AUP  C16  C17  aromatic  1.386  0.020  1.386
 AUP  C16  H16  single    0.930  0.020  1.080
 AUP  C17  C18  aromatic  1.384  0.020  1.384
 AUP  C17  H17  single    0.930  0.020  1.080
 AUP  C18  C19  aromatic  1.399  0.020  1.399
 AUP  C18  H18  single    0.930  0.020  1.080
 AUP  C24  C25  aromatic  1.387  0.020  1.387
 AUP  C24  C29  aromatic  1.392  0.020  1.392
 AUP  C24  H24  single    0.930  0.020  1.080
 AUP  C25  C26  aromatic  1.391  0.020  1.391
 AUP  C25  H25  single    0.930  0.020  1.080
 AUP  C26  C27  aromatic  1.391  0.020  1.391
 AUP  C26  H26  single    0.930  0.020  1.080
 AUP  C27  C28  aromatic  1.395  0.020  1.395
 AUP  C28  C29  aromatic  1.385  0.020  1.385
 AUP  C28  H28  single    0.930  0.020  1.080
 AUP  C29  H29  single    0.930  0.020  1.080
 AUP  N35  C36  aromatic  1.336  0.020  1.336
 AUP  N35  C40  aromatic  1.325  0.020  1.325
 AUP  C36  C37  aromatic  1.401  0.020  1.401
 AUP  C37  C38  aromatic  1.383  0.020  1.383
 AUP  C37  H37  single    0.930  0.020  1.080
 AUP  C38  C39  aromatic  1.387  0.020  1.387
 AUP  C38  H38  single    0.930  0.020  1.080
 AUP  C39  C40  aromatic  1.387  0.020  1.387
 AUP  C39  H39  single    0.930  0.020  1.080
 AUP  C40  H40  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
 AUP  C7   C1   C6   125.67  3.000
 AUP  C7   C1   C2   113.77  3.000
 AUP  C6   C1   C2   120.55  3.000
 AUP  C9   C2   C3   125.18  3.000
 AUP  C9   C2   C1   113.84  3.000
 AUP  C3   C2   C1   120.87  3.000
 AUP  H32  C3   H31  105.79  3.000
 AUP  H32  C3   C4   108.87  3.000
 AUP  H31  C3   C4   111.07  3.000
 AUP  H32  C3   C2   107.81  3.000
 AUP  H31  C3   C2   109.65  3.000
 AUP  C4   C3   C2   113.32  3.000
 AUP  H42  C4   H41  106.61  3.000
 AUP  H42  C4   C5   111.04  3.000
 AUP  H41  C4   C5   109.49  3.000
 AUP  H42  C4   C3   109.11  3.000
 AUP  H41  C4   C3   110.06  3.000
 AUP  C5   C4   C3   110.45  3.000
 AUP  H52  C5   H51  106.67  3.000
 AUP  H52  C5   C6   109.13  3.000
 AUP  H51  C5   C6   110.23  3.000
 AUP  H52  C5   C4   110.94  3.000
 AUP  H51  C5   C4   109.59  3.000
 AUP  C6   C5   C4   110.22  3.000
 AUP  H62  C6   H61  105.35  3.000
 AUP  H62  C6   C5   108.88  3.000
 AUP  H61  C6   C5   111.06  3.000
 AUP  H62  C6   C1   108.49  3.000
 AUP  H61  C6   C1   109.93  3.000
 AUP  C5   C6   C1   112.81  3.000
 AUP  C36  C7   P    121.44  3.000
 AUP  C36  C7   C1   128.30  3.000
 AUP  P    C7   C1   110.18  3.000
 AUP  C27  P    C9   104.05  3.000
 AUP  C27  P    C7   104.69  3.000
 AUP  C9   P    C7    90.84  3.000
 AUP  C19  C9   P    120.74  3.000
 AUP  C19  C9   C2   128.92  3.000
 AUP  P    C9   C2   110.22  3.000
 AUP  C19  N14  C15  118.94  3.000
 AUP  H15  C15  C16  120.08  3.000
 AUP  H15  C15  N14  116.17  3.000
 AUP  C16  C15  N14  123.75  3.000
 AUP  H16  C16  C17  121.71  3.000
 AUP  H16  C16  C15  120.57  3.000
 AUP  C17  C16  C15  117.72  3.000
 AUP  H17  C17  C18  120.20  3.000
 AUP  H17  C17  C16  120.80  3.000
 AUP  C18  C17  C16  119.01  3.000
 AUP  H18  C18  C19  120.59  3.000
 AUP  H18  C18  C17  120.08  3.000
 AUP  C19  C18  C17  119.33  3.000
 AUP  C18  C19  N14  121.25  3.000
 AUP  C18  C19  C9   120.63  3.000
 AUP  N14  C19  C9   118.08  3.000
 AUP  H24  C24  C29  119.87  3.000
 AUP  H24  C24  C25  120.07  3.000
 AUP  C29  C24  C25  120.05  3.000
 AUP  H25  C25  C26  119.87  3.000
 AUP  H25  C25  C24  120.23  3.000
 AUP  C26  C25  C24  119.90  3.000
 AUP  H26  C26  C27  119.94  3.000
 AUP  H26  C26  C25  119.78  3.000
 AUP  C27  C26  C25  120.28  3.000
 AUP  C28  C27  C26  119.54  3.000
 AUP  C28  C27  P    121.53  3.000
 AUP  C26  C27  P    118.93  3.000
 AUP  H28  C28  C29  119.99  3.000
 AUP  H28  C28  C27  119.84  3.000
 AUP  C29  C28  C27  120.17  3.000
 AUP  H29  C29  C28  119.92  3.000
 AUP  H29  C29  C24  120.03  3.000
 AUP  C28  C29  C24  120.05  3.000
 AUP  C40  N35  C36  118.89  3.000
 AUP  C37  C36  N35  121.22  3.000
 AUP  C37  C36  C7   120.78  3.000
 AUP  N35  C36  C7   117.97  3.000
 AUP  H37  C37  C38  119.98  3.000
 AUP  H37  C37  C36  120.63  3.000
 AUP  C38  C37  C36  119.38  3.000
 AUP  H38  C38  C39  120.82  3.000
 AUP  H38  C38  C37  120.19  3.000
 AUP  C39  C38  C37  118.99  3.000
 AUP  H39  C39  C40  120.60  3.000
 AUP  H39  C39  C38  121.68  3.000
 AUP  C40  C39  C38  117.72  3.000
 AUP  H40  C40  C39  120.08  3.000
 AUP  H40  C40  N35  116.12  3.000
 AUP  C39  C40  N35  123.80  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
 AUP  CONST_01  P    C9   C2   C1     0.00   0.0  0
 AUP  CONST_02  C19  C9   C2   C1   180.00   0.0  0
 AUP  CONST_03  C9   P    C7   C1     0.00   0.0  0
 AUP  CONST_07  P    C7   C1   C2     0.00   0.0  0
 AUP  CONST_08  C36  C7   C1   C2   180.00   0.0  0
 AUP  CONST_09  C7   P    C9   C2     0.00   0.0  0
 AUP  CONST_13  C9   C2   C1   C7     0.00   0.0  0
 AUP  CONST_14  C19  C9   P    C7   180.00   0.0  0
 AUP  CONST_17  C40  N35  C36  C7   180.00   0.0  0
 AUP  CONST_18  C38  C37  C36  C7   180.00   0.0  0
 AUP  CONST_23  C25  C26  C27  P    180.00   0.0  0
 AUP  CONST_24  C29  C28  C27  P    180.00   0.0  0
 AUP  CONST_25  C36  C7   P    C9   180.00   0.0  0
 AUP  CONST_28  C15  N14  C19  C9   180.00   0.0  0
 AUP  CONST_29  C17  C18  C19  C9   180.00   0.0  0
 AUP  CONST_30  C17  C16  C15  N14    0.00   0.0  0
 AUP  CONST_31  C17  C18  C19  N14    0.00   0.0  0
 AUP  CONST_32  C18  C19  N14  C15    0.00   0.0  0
 AUP  CONST_33  C18  C17  C16  C15    0.00   0.0  0
 AUP  CONST_34  C19  N14  C15  C16    0.00   0.0  0
 AUP  CONST_35  C19  C18  C17  C16    0.00   0.0  0
 AUP  CONST_37  C27  C26  C25  C24    0.00   0.0  0
 AUP  CONST_38  C27  C28  C29  C24    0.00   0.0  0
 AUP  CONST_39  C28  C29  C24  C25    0.00   0.0  0
 AUP  CONST_40  C28  C27  C26  C25    0.00   0.0  0
 AUP  CONST_41  C29  C24  C25  C26    0.00   0.0  0
 AUP  CONST_42  C29  C28  C27  C26    0.00   0.0  0
 AUP  CONST_44  C38  C37  C36  N35    0.00   0.0  0
 AUP  CONST_45  C38  C39  C40  N35    0.00   0.0  0
 AUP  CONST_46  C39  C40  N35  C36    0.00   0.0  0
 AUP  CONST_47  C39  C38  C37  C36    0.00   0.0  0
 AUP  CONST_48  C40  N35  C36  C37    0.00   0.0  0
 AUP  CONST_49  C40  C39  C38  C37    0.00   0.0  0
 AUP  CONST_50  C19  C9   C2   C3     0.00   0.0  0
 AUP  CONST_51  C36  C7   C1   C6     0.00   0.0  0
 AUP  CONST_52  H37  C37  C36  C7     0.00   0.0  0
 AUP  CONST_53  H26  C26  C27  P      0.00   0.0  0
 AUP  CONST_54  H28  C28  C27  P      0.00   0.0  0
 AUP  CONST_55  H18  C18  C19  C9     0.00   0.0  0
 AUP  CONST_56  H16  C16  C15  N14  180.00   0.0  0
 AUP  CONST_57  H17  C17  C16  C15  180.00   0.0  0
 AUP  CONST_58  H15  C15  C16  C17  180.00   0.0  0
 AUP  CONST_59  H29  C29  C24  C25  180.00   0.0  0
 AUP  CONST_60  H24  C24  C25  C26  180.00   0.0  0
 AUP  CONST_61  H25  C25  C26  C27  180.00   0.0  0
 AUP  CONST_62  H39  C39  C40  N35  180.00   0.0  0
 AUP  CONST_63  H40  C40  N35  C36  180.00   0.0  0
 AUP  CONST_64  H38  C38  C37  C36  180.00   0.0  0
 AUP  Var_01    C4   C3   C2   C1   -16.77  30.0  1
 AUP  Var_02    C4   C5   C6   C1    50.13  30.0  1
 AUP  Var_03    C5   C6   C1   C2   -19.69  30.0  1
 AUP  Var_04    C5   C4   C3   C2    47.19  30.0  1
 AUP  Var_05    C6   C5   C4   C3   -65.07  30.0  1

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
 AUP  plan-1  C9   0.020
 AUP  plan-1  N14  0.020
 AUP  plan-1  C15  0.020
 AUP  plan-1  C16  0.020
 AUP  plan-1  C17  0.020
 AUP  plan-1  C18  0.020
 AUP  plan-1  C19  0.020
 AUP  plan-1  H16  0.020
 AUP  plan-1  H17  0.020
 AUP  plan-1  H18  0.020
 AUP  plan-1  H15  0.020
 AUP  plan-2  P    0.020
 AUP  plan-2  C24  0.020
 AUP  plan-2  C25  0.020
 AUP  plan-2  C26  0.020
 AUP  plan-2  C27  0.020
 AUP  plan-2  C28  0.020
 AUP  plan-2  C29  0.020
 AUP  plan-2  H24  0.020
 AUP  plan-2  H25  0.020
 AUP  plan-2  H26  0.020
 AUP  plan-2  H28  0.020
 AUP  plan-2  H29  0.020
 AUP  plan-3  C1   0.020
 AUP  plan-3  C2   0.020
 AUP  plan-3  C3   0.020
 AUP  plan-3  C6   0.020
 AUP  plan-3  C7   0.020
 AUP  plan-3  P    0.020
 AUP  plan-3  C9   0.020
 AUP  plan-3  C19  0.020
 AUP  plan-3  C27  0.020
 AUP  plan-3  C36  0.020
 AUP  plan-4  C7   0.020
 AUP  plan-4  N35  0.020
 AUP  plan-4  C36  0.020
 AUP  plan-4  C37  0.020
 AUP  plan-4  C38  0.020
 AUP  plan-4  C39  0.020
 AUP  plan-4  C40  0.020
 AUP  plan-4  H37  0.020
 AUP  plan-4  H38  0.020
 AUP  plan-4  H39  0.020
 AUP  plan-4  H40  0.020

