# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 14:17:34 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (S)-[(1S)-1-(5-chloro-1-benzothiophen-3-yl)-2-{[(E)-2-(3,4-difluorophenyl)ethenyl]amino}-2-oxoethyl]methylphosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[P](O)(=O)[C@H](C(=O)N/C=C/c1ccc(F)c(F)c1)c2csc3ccc(Cl)cc23
#
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
 N7O  N7O  '(S)-[(1S)-1-(5-chloro-1-benzothiophen-3-yl)-2-{[(E)-2-(3,4-difluorophenyl)ethenyl]amino}-2-oxoethyl]methylphosphinic acid'  ligand  43  28  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N7O
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
 N7O  C10   C   C1    0  -0.401   2.8595   0.7818  -0.4431
 N7O  C13   C   CR16  0  -0.394   6.4397   0.2528  -1.4106
 N7O  C20   C   CR15  0  -0.571  -2.2813   1.3647  -1.6244
 N7O  C22   C   CR56  0  -0.212  -3.4433  -0.8121  -1.7244
 N7O  C24   C   CR16  0  -0.227  -4.3422  -2.8766  -0.9423
 N7O  C28   C   CR56  0   0.200  -2.9926  -0.4888  -0.4349
 N7O  P02   P   P     0   1.252  -1.5874   3.1548   0.9298
 N7O  O03   O   O     0  -0.703  -0.6630   3.6869  -0.1150
 N7O  O04   O   OH1   0  -0.736  -3.0764   3.7072   0.6897
 N7O  C05   C   CH1   0  -0.782  -1.7333   1.3213   0.8775
 N7O  C06   C   C     0   0.570  -0.4004   0.6315   1.1656
 N7O  O07   O   O     0  -0.445  -0.2828  -0.1849   2.0576
 N7O  N08   N   NH1   0  -0.659   0.6091   0.9763   0.3286
 N7O  C09   C   C1    0   0.039   1.8653   0.3996   0.3646
 N7O  C11   C   CR6   0   0.171   4.2004   0.2070  -0.4695
 N7O  C12   C   CR16  0  -0.315   5.1478   0.7536  -1.3377
 N7O  C14   C   CR6   0   0.376   6.7976  -0.8082  -0.6089
 N7O  F15   F   F     0  -0.305   8.0349  -1.3142  -0.6509
 N7O  C16   C   CR6   0   0.436   5.8682  -1.3630   0.2574
 N7O  F17   F   F     0  -0.308   6.2378  -2.3943   1.0247
 N7O  C18   C   CR16  0  -0.501   4.5862  -0.8724   0.3344
 N7O  C19   C   CR5   0   0.251  -2.3235   0.7881  -0.3992
 N7O  S21   S   S2    0   0.246  -3.0404   0.4305  -2.8585
 N7O  C23   C   CR16  0  -0.278  -4.1190  -2.0008  -1.9843
 N7O  C25   C   CR6   0  -0.034  -3.8895  -2.5575   0.3420
 N7O  CL26  CL  CL    0  -0.124  -4.1833  -3.6816   1.6287
 N7O  C27   C   CR16  0  -0.294  -3.2190  -1.3858   0.6144
 N7O  H10   H   H     0   0.265   2.6836   1.5881  -1.1488
 N7O  H13   H   HCR6  0   0.293   7.1638   0.6867  -2.0875
 N7O  H20   H   HCR5  0   0.306  -1.8361   2.3104  -1.8934
 N7O  H24   H   HCR6  0   0.286  -4.8641  -3.8068  -1.1193
 N7O  H01   H   HCH3  0   0.301  -1.1200   4.6238   2.7545
 N7O  H01A  H   HCH3  0   0.287  -1.8500   3.1141   3.3335
 N7O  H01B  H   HCH3  0   0.288  -0.1472   3.1514   2.8483
 N7O  H05   H   HCH1  0   0.339  -2.3970   1.0546   1.7060
 N7O  HN08  H   HNH1  0   0.417   0.4488   1.7226  -0.3374
 N7O  H09   H   H     0   0.289   1.9733  -0.3905   1.0948
 N7O  H12   H   HCR6  0   0.269   4.8744   1.5898  -1.9680
 N7O  H18   H   HCR6  0   0.284   3.8990  -1.3440   1.0255
 N7O  H23   H   HCR6  0   0.282  -4.4634  -2.2428  -2.9808
 N7O  H27   H   HCR6  0   0.274  -2.8754  -1.1702   1.6173
 N7O  H15   H   HOH1  0   0.496  -3.7291   3.4952   1.3699
 N7O  C01   C   CH3   0  -0.927  -1.1399   3.5417   2.6263

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
 N7O  C10  C09   double    1.337  0.020  1.337
 N7O  C10  C11   single    1.459  0.020  1.459
 N7O  C10  H10   single    0.930  0.020  1.080
 N7O  C13  C12   aromatic  1.387  0.020  1.387
 N7O  C13  C14   aromatic  1.377  0.020  1.377
 N7O  C13  H13   single    0.930  0.020  1.080
 N7O  C20  C19   aromatic  1.355  0.020  1.355
 N7O  C20  S21   aromatic  1.724  0.020  1.724
 N7O  C20  H20   single    0.930  0.020  1.080
 N7O  C22  C28   aromatic  1.404  0.020  1.404
 N7O  C22  S21   aromatic  1.730  0.020  1.730
 N7O  C22  C23   aromatic  1.392  0.020  1.392
 N7O  C24  C23   aromatic  1.379  0.020  1.379
 N7O  C24  C25   aromatic  1.399  0.020  1.399
 N7O  C24  H24   single    0.930  0.020  1.080
 N7O  C28  C19   aromatic  1.442  0.020  1.442
 N7O  C28  C27   aromatic  1.399  0.020  1.399
 N7O  C01  P02   single    1.797  0.020  1.797
 N7O  C01  H01   single    0.970  0.020  1.090
 N7O  C01  H01A  single    0.970  0.020  1.090
 N7O  C01  H01B  single    0.970  0.020  1.090
 N7O  P02  O03   double    1.493  0.020  1.493
 N7O  P02  O04   single    1.606  0.020  1.606
 N7O  P02  C05   single    1.840  0.020  1.840
 N7O  C05  C06   single    1.528  0.020  1.528
 N7O  C05  C19   single    1.504  0.020  1.504
 N7O  C05  H05   single    0.970  0.020  1.090
 N7O  C06  O07   double    1.215  0.020  1.215
 N7O  C06  N08   single    1.356  0.020  1.356
 N7O  N08  C09   single    1.383  0.020  1.383
 N7O  N08  HN08  single    0.860  0.020  1.020
 N7O  C09  H09   single    0.930  0.020  1.080
 N7O  C11  C12   aromatic  1.396  0.020  1.396
 N7O  C11  C18   aromatic  1.400  0.020  1.400
 N7O  C12  H12   single    0.930  0.020  1.080
 N7O  C14  F15   single    1.337  0.020  1.337
 N7O  C14  C16   aromatic  1.386  0.020  1.386
 N7O  C16  F17   single    1.337  0.020  1.337
 N7O  C16  C18   aromatic  1.375  0.020  1.375
 N7O  C18  H18   single    0.930  0.020  1.080
 N7O  C23  H23   single    0.930  0.020  1.080
 N7O  C25  CL26  single    1.734  0.020  1.734
 N7O  C25  C27   aromatic  1.377  0.020  1.377
 N7O  C27  H27   single    0.930  0.020  1.080
 N7O  O04  H15   single    0.850  0.020  0.980

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
 N7O  H10   C10  C11   115.44  3.000
 N7O  H10   C10  C09   118.98  3.000
 N7O  C11   C10  C09   125.58  3.000
 N7O  H13   C13  C14   119.95  3.000
 N7O  H13   C13  C12   120.75  3.000
 N7O  C14   C13  C12   119.30  3.000
 N7O  H20   C20  S21   118.56  3.000
 N7O  H20   C20  C19   127.68  3.000
 N7O  S21   C20  C19   113.77  3.000
 N7O  C23   C22  S21   127.17  3.000
 N7O  C23   C22  C28   121.61  3.000
 N7O  S21   C22  C28   111.22  3.000
 N7O  H24   C24  C25   120.19  3.000
 N7O  H24   C24  C23   120.05  3.000
 N7O  C25   C24  C23   119.77  3.000
 N7O  C27   C28  C19   128.63  3.000
 N7O  C27   C28  C22   119.30  3.000
 N7O  C19   C28  C22   112.07  3.000
 N7O  C05   P02  O04   105.37  3.000
 N7O  C05   P02  O03   112.60  3.000
 N7O  O04   P02  O03   110.29  3.000
 N7O  C05   P02  C01   105.14  3.000
 N7O  O04   P02  C01   107.34  3.000
 N7O  O03   P02  C01   115.45  3.000
 N7O  H15   O04  P02   116.45  3.000
 N7O  H05   C05  C19   108.55  3.000
 N7O  H05   C05  C06   106.04  3.000
 N7O  C19   C05  C06   110.01  3.000
 N7O  H05   C05  P02   105.63  3.000
 N7O  C19   C05  P02   114.11  3.000
 N7O  C06   C05  P02   112.04  3.000
 N7O  N08   C06  O07   123.51  3.000
 N7O  N08   C06  C05   114.72  3.000
 N7O  O07   C06  C05   121.74  3.000
 N7O  HN08  N08  C09   117.92  3.000
 N7O  HN08  N08  C06   118.38  3.000
 N7O  C09   N08  C06   123.66  3.000
 N7O  H09   C09  N08   114.40  3.000
 N7O  H09   C09  C10   122.87  3.000
 N7O  N08   C09  C10   122.73  3.000
 N7O  C18   C11  C12   118.15  3.000
 N7O  C18   C11  C10   123.13  3.000
 N7O  C12   C11  C10   118.72  3.000
 N7O  H12   C12  C11   119.54  3.000
 N7O  H12   C12  C13   118.92  3.000
 N7O  C11   C12  C13   121.54  3.000
 N7O  C16   C14  F15   119.24  3.000
 N7O  C16   C14  C13   119.86  3.000
 N7O  F15   C14  C13   120.90  3.000
 N7O  C18   C16  F17   120.05  3.000
 N7O  C18   C16  C14   121.15  3.000
 N7O  F17   C16  C14   118.80  3.000
 N7O  H18   C18  C16   118.18  3.000
 N7O  H18   C18  C11   121.83  3.000
 N7O  C16   C18  C11   119.99  3.000
 N7O  C05   C19  C28   121.13  3.000
 N7O  C05   C19  C20   127.19  3.000
 N7O  C28   C19  C20   111.65  3.000
 N7O  C22   S21  C20    91.29  3.000
 N7O  H23   C23  C24   120.15  3.000
 N7O  H23   C23  C22   121.18  3.000
 N7O  C24   C23  C22   118.67  3.000
 N7O  C27   C25  CL26  119.17  3.000
 N7O  C27   C25  C24   122.23  3.000
 N7O  CL26  C25  C24   118.60  3.000
 N7O  H27   C27  C25   120.50  3.000
 N7O  H27   C27  C28   121.08  3.000
 N7O  C25   C27  C28   118.43  3.000
 N7O  H01B  C01  H01A  108.72  3.000
 N7O  H01B  C01  H01   108.36  3.000
 N7O  H01A  C01  H01   108.98  3.000
 N7O  H01B  C01  P02   110.01  3.000
 N7O  H01A  C01  P02   111.47  3.000
 N7O  H01   C01  P02   109.24  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
 N7O  CONST_01  C18   C11  C12  C13     0.00   0.0  0
 N7O  CONST_02  C18   C16  C14  C13     0.00   0.0  0
 N7O  CONST_03  C22   C28  C19  C20     0.00   0.0  0
 N7O  CONST_04  C27   C28  C19  C20   180.00   0.0  0
 N7O  CONST_05  C28   C22  S21  C20     0.00   0.0  0
 N7O  CONST_06  C23   C22  S21  C20   180.00   0.0  0
 N7O  CONST_07  C25   C27  C28  C22     0.00   0.0  0
 N7O  CONST_08  C19   C20  S21  C22     0.00   0.0  0
 N7O  CONST_09  C25   C24  C23  C22     0.00   0.0  0
 N7O  CONST_10  C28   C22  C23  C24     0.00   0.0  0
 N7O  CONST_11  S21   C22  C23  C24   180.00   0.0  0
 N7O  CONST_12  C28   C27  C25  C24     0.00   0.0  0
 N7O  CONST_13  S21   C20  C19  C28     0.00   0.0  0
 N7O  CONST_14  C14   C13  C12  C11     0.00   0.0  0
 N7O  CONST_15  C14   C16  C18  C11     0.00   0.0  0
 N7O  CONST_16  C16   C14  C13  C12     0.00   0.0  0
 N7O  CONST_17  C16   C18  C11  C12     0.00   0.0  0
 N7O  CONST_18  S21   C22  C28  C19     0.00   0.0  0
 N7O  CONST_19  C23   C22  C28  C19   180.00   0.0  0
 N7O  CONST_20  C25   C27  C28  C19   180.00   0.0  0
 N7O  CONST_21  C27   C28  C22  S21   180.00   0.0  0
 N7O  CONST_22  C27   C28  C22  C23     0.00   0.0  0
 N7O  CONST_23  C27   C25  C24  C23     0.00   0.0  0
 N7O  CONST_24  C13   C12  C11  C10   180.00   0.0  0
 N7O  CONST_25  C16   C18  C11  C10   180.00   0.0  0
 N7O  CONST_26  F17   C16  C14  C13   180.00   0.0  0
 N7O  CONST_27  C05   C19  C28  C22   180.00   0.0  0
 N7O  CONST_28  CL26  C25  C27  C28   180.00   0.0  0
 N7O  CONST_29  S21   C20  C19  C05   180.00   0.0  0
 N7O  CONST_30  C27   C28  C19  C05     0.00   0.0  0
 N7O  CONST_31  F17   C16  C18  C11   180.00   0.0  0
 N7O  CONST_32  F15   C14  C13  C12   180.00   0.0  0
 N7O  CONST_33  C18   C16  C14  F15   180.00   0.0  0
 N7O  CONST_34  CL26  C25  C24  C23   180.00   0.0  0
 N7O  CONST_35  H27   C27  C28  C22   180.00   0.0  0
 N7O  CONST_36  H20   C20  S21  C22   180.00   0.0  0
 N7O  CONST_37  H24   C24  C23  C22   180.00   0.0  0
 N7O  CONST_38  H23   C23  C22  C28   180.00   0.0  0
 N7O  CONST_39  H13   C13  C12  C11   180.00   0.0  0
 N7O  CONST_40  H18   C18  C11  C12   180.00   0.0  0
 N7O  CONST_41  H12   C12  C13  C14   180.00   0.0  0
 N7O  CONST_42  C09   N08  C06  C05   180.00   0.0  0
 N7O  CONST_43  C09   N08  C06  O07     0.00   0.0  0
 N7O  CONST_44  HN08  N08  C06  C05     0.00   0.0  0
 N7O  Var_01    C12   C11  C10  C09  -177.47  30.0  2
 N7O  Var_02    C11   C10  C09  N08  -179.21   0.0  2
 N7O  Var_03    C06   N08  C09  C10  -177.94  30.0  1
 N7O  Var_04    H01   C01  P02  O03    60.14  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
 N7O  chir_02  C05  P02  C06  C19  positiv
 N7O  chir_03  P02  O03  O04  C05  both

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
 N7O  plan-1  C10   0.020
 N7O  plan-1  C13   0.020
 N7O  plan-1  C11   0.020
 N7O  plan-1  C12   0.020
 N7O  plan-1  C14   0.020
 N7O  plan-1  F15   0.020
 N7O  plan-1  C16   0.020
 N7O  plan-1  F17   0.020
 N7O  plan-1  C18   0.020
 N7O  plan-1  H13   0.020
 N7O  plan-1  H12   0.020
 N7O  plan-1  H18   0.020
 N7O  plan-2  C20   0.020
 N7O  plan-2  C22   0.020
 N7O  plan-2  C24   0.020
 N7O  plan-2  C28   0.020
 N7O  plan-2  C05   0.020
 N7O  plan-2  C19   0.020
 N7O  plan-2  S21   0.020
 N7O  plan-2  C23   0.020
 N7O  plan-2  C25   0.020
 N7O  plan-2  CL26  0.020
 N7O  plan-2  C27   0.020
 N7O  plan-2  H20   0.020
 N7O  plan-2  H24   0.020
 N7O  plan-2  H23   0.020
 N7O  plan-2  H27   0.020
 N7O  plan-3  C05   0.020
 N7O  plan-3  C06   0.020
 N7O  plan-3  O07   0.020
 N7O  plan-3  N08   0.020
 N7O  plan-3  C09   0.020
 N7O  plan-3  HN08  0.020
 N7O  plan-4  C10   0.020
 N7O  plan-4  N08   0.020
 N7O  plan-4  C09   0.020
 N7O  plan-4  C11   0.020
 N7O  plan-4  H10   0.020
 N7O  plan-4  H09   0.020

