# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 13:36:18 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-[4-cyano-2-[[(2~{R})-2-(4-fluoranylnaphthalen-1-yl)propanoyl]amino]phenyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C(=O)Nc1cc(ccc1CCCC(O)=O)C#N)c2ccc(F)c3ccccc23
#
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
 7UR  7UR  '4-[4-cyano-2-[[(2~{R})-2-(4-fluoranylnaphthalen-1-yl)propanoyl]amino]phenyl]butanoic acid'  ligand  50  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7UR
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
 7UR  C10  C  CR16   0  -0.248  -2.0833  -2.8228  -0.4504
 7UR  C15  C  CR16   0  -0.325  -3.2798  -1.9395   1.8878
 7UR  C17  C  CH2    0  -0.518  -2.1719   0.3076   1.7029
 7UR  C20  C  C      0   0.416  -3.5213   3.9033   0.8351
 7UR  C24  C  CH3    0  -0.668   0.9933  -0.4608  -3.2576
 7UR  C26  C  CR16   0  -0.336   1.4409   1.7914   0.5424
 7UR  C28  C  CR16   0  -0.259   2.8964   2.8087   2.1708
 7UR  C02  C  C      0   0.516   4.9457   0.9157  -0.2783
 7UR  C03  C  C1     0  -0.420   4.8148   0.1392  -1.3835
 7UR  C04  C  C1     0  -0.345   3.5224  -0.1182  -1.8825
 7UR  C05  C  C      0   0.161   2.3976   0.3937  -1.2930
 7UR  C06  C  CH1    0  -0.534   1.0188   0.0956  -1.8311
 7UR  C07  C  C      0   0.555   0.3178  -0.9170  -0.9301
 7UR  N08  N  NH1    0  -0.759  -1.0038  -0.6823  -0.7385
 7UR  C09  C  CR6    0   0.289  -1.8462  -1.5366   0.0078
 7UR  C11  C  CR6    0  -0.018  -2.9198  -3.6687   0.2715
 7UR  C12  C  CSP    0   0.054  -3.1620  -4.9930  -0.2000
 7UR  N13  N  NS     0  -0.252  -3.3576  -6.0638  -0.5782
 7UR  C14  C  CR16   0  -0.224  -3.5281  -3.2243   1.4447
 7UR  C16  C  CR6    0   0.153  -2.4306  -1.0785   1.1944
 7UR  C18  C  CH2    0  -0.416  -3.0521   1.3649   1.0272
 7UR  C19  C  CH2    0  -0.590  -2.6799   2.7735   1.4582
 7UR  O21  O  OC    -1  -0.629  -3.2921   5.0530   1.2642
 7UR  O22  O  O      0  -0.607  -4.3469   3.5918  -0.0450
 7UR  O23  O  O      0  -0.448   0.8920  -1.8788  -0.4591
 7UR  C25  C  CR6    0   0.158   2.5435   1.2147  -0.1329
 7UR  C27  C  CR16   0  -0.234   1.6088   2.5627   1.6603
 7UR  C29  C  CR16   0  -0.282   3.9917   2.2798   1.5458
 7UR  C30  C  CR6    0  -0.122   3.8389   1.4786   0.3909
 7UR  H1   H  HCR6   0   0.286  -1.6315  -3.1606  -1.3732
 7UR  H2   H  HCR6   0   0.269  -3.7421  -1.5991   2.8056
 7UR  H3   H  HCH2   0   0.257  -2.3465   0.3340   2.7808
 7UR  H4   H  HCH2   0   0.237  -1.1167   0.5554   1.5581
 7UR  H5   H  HCH3   0   0.258  -0.0364  -0.5537  -3.6016
 7UR  H6   H  HCH3   0   0.255   1.5119   0.2116  -3.9403
 7UR  H7   H  HCH3   0   0.242   1.4565  -1.4447  -3.3243
 7UR  H8   H  HCR6   0   0.225   0.4381   1.6329   0.1720
 7UR  H9   H  HCR6   0   0.265   3.0178   3.4185   3.0559
 7UR  H10  H  H      0   0.281   5.6854  -0.2763  -1.8734
 7UR  H11  H  H      0   0.268   3.4431  -0.7416  -2.7621
 7UR  H12  H  HCH1   0   0.281   0.4419   1.0256  -1.8478
 7UR  H13  H  HNH1   0   0.415  -1.4074   0.1546  -1.1315
 7UR  H14  H  HCR6   0   0.283  -4.1839  -3.8792   2.0014
 7UR  H15  H  HCH2   0   0.212  -2.9782   1.2840  -0.0604
 7UR  H16  H  HCH2   0   0.230  -4.0979   1.1595   1.2672
 7UR  H17  H  HCH2   0   0.224  -1.6274   2.9641   1.2117
 7UR  H18  H  HCH2   0   0.225  -2.7351   2.8562   2.5492
 7UR  H20  H  HCR6   0   0.264   0.7458   2.9893   2.1552
 7UR  H21  H  HCR6   0   0.264   4.9799   2.4730   1.9398
 7UR  F01  F  F      0  -0.306   6.1676   1.1727   0.2133

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
 7UR  C28  C29  aromatic  1.367  0.020  1.367
 7UR  C28  C27  aromatic  1.407  0.020  1.407
 7UR  C29  C30  aromatic  1.414  0.020  1.414
 7UR  F01  C02  single    1.342  0.020  1.342
 7UR  C27  C26  aromatic  1.368  0.020  1.368
 7UR  C30  C02  aromatic  1.411  0.020  1.411
 7UR  C30  C25  aromatic  1.422  0.020  1.422
 7UR  C02  C03  aromatic  1.357  0.020  1.357
 7UR  C26  C25  aromatic  1.416  0.020  1.416
 7UR  C25  C05  aromatic  1.429  0.020  1.429
 7UR  C03  C04  aromatic  1.409  0.020  1.409
 7UR  O22  C20  deloc     1.246  0.020  1.246
 7UR  C05  C04  aromatic  1.369  0.020  1.369
 7UR  C05  C06  single    1.510  0.020  1.510
 7UR  C20  C19  single    1.540  0.020  1.540
 7UR  C20  O21  deloc     1.248  0.020  1.248
 7UR  C19  C18  single    1.519  0.020  1.519
 7UR  C06  C24  single    1.531  0.020  1.531
 7UR  C06  C07  single    1.526  0.020  1.526
 7UR  N08  C07  single    1.356  0.020  1.356
 7UR  N08  C09  single    1.413  0.020  1.413
 7UR  C18  C17  single    1.533  0.020  1.533
 7UR  C07  O23  double    1.215  0.020  1.215
 7UR  C09  C10  aromatic  1.386  0.020  1.386
 7UR  C09  C16  aromatic  1.400  0.020  1.400
 7UR  C17  C16  single    1.499  0.020  1.499
 7UR  C10  C11  aromatic  1.392  0.020  1.392
 7UR  C16  C15  aromatic  1.394  0.020  1.394
 7UR  C11  C12  single    1.426  0.020  1.426
 7UR  C11  C14  aromatic  1.394  0.020  1.394
 7UR  C12  N13  triple    1.152  0.020  1.152
 7UR  C15  C14  aromatic  1.382  0.020  1.382
 7UR  C10  H1   single    0.930  0.020  1.080
 7UR  C15  H2   single    0.930  0.020  1.080
 7UR  C17  H3   single    0.970  0.020  1.090
 7UR  C17  H4   single    0.970  0.020  1.090
 7UR  C24  H5   single    0.970  0.020  1.090
 7UR  C24  H6   single    0.970  0.020  1.090
 7UR  C24  H7   single    0.970  0.020  1.090
 7UR  C26  H8   single    0.930  0.020  1.080
 7UR  C28  H9   single    0.930  0.020  1.080
 7UR  C03  H10  single    0.930  0.020  1.080
 7UR  C04  H11  single    0.930  0.020  1.080
 7UR  C06  H12  single    0.970  0.020  1.090
 7UR  N08  H13  single    0.860  0.020  1.020
 7UR  C14  H14  single    0.930  0.020  1.080
 7UR  C18  H15  single    0.970  0.020  1.090
 7UR  C18  H16  single    0.970  0.020  1.090
 7UR  C19  H17  single    0.970  0.020  1.090
 7UR  C19  H18  single    0.970  0.020  1.090
 7UR  C27  H20  single    0.930  0.020  1.080
 7UR  C29  H21  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
 7UR  H1   C10  C11  120.26  3.000
 7UR  H1   C10  C09  120.04  3.000
 7UR  C11  C10  C09  119.70  3.000
 7UR  H2   C15  C16  119.19  3.000
 7UR  H2   C15  C14  119.18  3.000
 7UR  C16  C15  C14  121.62  3.000
 7UR  H4   C17  H3   106.23  3.000
 7UR  H4   C17  C18  109.84  3.000
 7UR  H3   C17  C18  109.06  3.000
 7UR  H4   C17  C16  109.34  3.000
 7UR  H3   C17  C16  109.24  3.000
 7UR  C18  C17  C16  112.91  3.000
 7UR  O22  C20  O21  126.48  3.000
 7UR  O21  C20  C19  115.86  3.000
 7UR  O22  C20  C19  117.66  3.000
 7UR  H7   C24  H6   108.46  3.000
 7UR  H7   C24  H5   107.78  3.000
 7UR  H6   C24  H5   107.73  3.000
 7UR  H7   C24  C06  112.21  3.000
 7UR  H6   C24  C06  110.58  3.000
 7UR  H5   C24  C06  109.93  3.000
 7UR  H8   C26  C27  118.46  3.000
 7UR  H8   C26  C25  119.96  3.000
 7UR  C27  C26  C25  121.58  3.000
 7UR  H9   C28  C29  120.14  3.000
 7UR  H9   C28  C27  119.88  3.000
 7UR  C29  C28  C27  119.97  3.000
 7UR  C30  C02  C03  122.62  3.000
 7UR  C03  C02  F01  119.72  3.000
 7UR  C30  C02  F01  117.66  3.000
 7UR  H10  C03  C04  120.50  3.000
 7UR  H10  C03  C02  120.72  3.000
 7UR  C04  C03  C02  118.78  3.000
 7UR  H11  C04  C05  120.38  3.000
 7UR  H11  C04  C03  117.44  3.000
 7UR  C05  C04  C03  122.18  3.000
 7UR  C25  C05  C06  119.74  3.000
 7UR  C06  C05  C04  121.52  3.000
 7UR  C25  C05  C04  118.73  3.000
 7UR  H12  C06  C07  109.31  3.000
 7UR  H12  C06  C05  108.60  3.000
 7UR  C07  C06  C05  109.88  3.000
 7UR  H12  C06  C24  106.60  3.000
 7UR  C07  C06  C24  107.53  3.000
 7UR  C05  C06  C24  114.77  3.000
 7UR  O23  C07  N08  122.88  3.000
 7UR  O23  C07  C06  122.48  3.000
 7UR  N08  C07  C06  114.60  3.000
 7UR  H13  N08  C09  117.96  3.000
 7UR  H13  N08  C07  118.59  3.000
 7UR  C09  N08  C07  123.44  3.000
 7UR  C16  C09  N08  119.92  3.000
 7UR  C16  C09  C10  120.84  3.000
 7UR  N08  C09  C10  119.24  3.000
 7UR  C14  C11  C12  120.00  3.000
 7UR  C14  C11  C10  120.33  3.000
 7UR  C12  C11  C10  119.66  3.000
 7UR  N13  C12  C11  180.00  3.000
 7UR  H14  C14  C11  120.32  3.000
 7UR  H14  C14  C15  120.48  3.000
 7UR  C11  C14  C15  119.20  3.000
 7UR  C09  C16  C17  121.21  3.000
 7UR  C17  C16  C15  120.50  3.000
 7UR  C09  C16  C15  118.28  3.000
 7UR  H16  C18  H15  105.63  3.000
 7UR  H16  C18  C19  110.28  3.000
 7UR  H15  C18  C19  109.53  3.000
 7UR  H16  C18  C17  108.85  3.000
 7UR  H15  C18  C17  110.41  3.000
 7UR  C19  C18  C17  111.95  3.000
 7UR  H18  C19  H17  105.00  3.000
 7UR  H18  C19  C18  109.89  3.000
 7UR  H17  C19  C18  109.41  3.000
 7UR  H18  C19  C20  108.66  3.000
 7UR  H17  C19  C20  107.79  3.000
 7UR  C18  C19  C20  115.56  3.000
 7UR  C30  C25  C05  119.92  3.000
 7UR  C05  C25  C26  122.81  3.000
 7UR  C30  C25  C26  117.27  3.000
 7UR  H20  C27  C28  119.67  3.000
 7UR  H20  C27  C26  119.85  3.000
 7UR  C28  C27  C26  120.49  3.000
 7UR  H21  C29  C30  119.85  3.000
 7UR  H21  C29  C28  119.76  3.000
 7UR  C30  C29  C28  120.39  3.000
 7UR  C29  C30  C25  120.30  3.000
 7UR  C25  C30  C02  117.77  3.000
 7UR  C29  C30  C02  121.93  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
 7UR  CONST_01  C15  C16  C09  C10     0.00   0.0  0
 7UR  CONST_02  C15  C14  C11  C10     0.00   0.0  0
 7UR  CONST_03  C29  C28  C27  C26     0.00   0.0  0
 7UR  CONST_04  C29  C30  C25  C26     0.00   0.0  0
 7UR  CONST_05  C02  C30  C25  C26   180.00   0.0  0
 7UR  CONST_06  C04  C05  C25  C26   180.00   0.0  0
 7UR  CONST_07  C02  C30  C29  C28   180.00   0.0  0
 7UR  CONST_08  C25  C30  C29  C28     0.00   0.0  0
 7UR  CONST_09  C25  C26  C27  C28     0.00   0.0  0
 7UR  CONST_10  C05  C25  C30  C02     0.00   0.0  0
 7UR  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 7UR  CONST_12  C29  C30  C02  C03   180.00   0.0  0
 7UR  CONST_13  C25  C30  C02  C03     0.00   0.0  0
 7UR  CONST_14  C25  C05  C04  C03     0.00   0.0  0
 7UR  CONST_15  C30  C02  C03  C04     0.00   0.0  0
 7UR  CONST_16  C30  C25  C05  C04     0.00   0.0  0
 7UR  CONST_17  C29  C30  C25  C05   180.00   0.0  0
 7UR  CONST_18  C27  C26  C25  C05   180.00   0.0  0
 7UR  CONST_19  C14  C11  C10  C09     0.00   0.0  0
 7UR  CONST_20  C14  C15  C16  C09     0.00   0.0  0
 7UR  CONST_21  C16  C09  C10  C11     0.00   0.0  0
 7UR  CONST_22  C16  C15  C14  C11     0.00   0.0  0
 7UR  CONST_23  C30  C29  C28  C27     0.00   0.0  0
 7UR  CONST_24  C30  C25  C26  C27     0.00   0.0  0
 7UR  CONST_25  C17  C16  C09  C10   180.00   0.0  0
 7UR  CONST_26  N08  C09  C16  C15   180.00   0.0  0
 7UR  CONST_27  C12  C11  C14  C15   180.00   0.0  0
 7UR  CONST_28  C14  C15  C16  C17   180.00   0.0  0
 7UR  CONST_29  C06  C05  C25  C26     0.00   0.0  0
 7UR  CONST_30  C29  C30  C02  F01     0.00   0.0  0
 7UR  CONST_31  C25  C30  C02  F01   180.00   0.0  0
 7UR  CONST_32  C04  C03  C02  F01   180.00   0.0  0
 7UR  CONST_33  C06  C05  C04  C03   180.00   0.0  0
 7UR  CONST_34  C30  C25  C05  C06   180.00   0.0  0
 7UR  CONST_35  C11  C10  C09  N08   180.00   0.0  0
 7UR  CONST_36  C12  C11  C10  C09   180.00   0.0  0
 7UR  CONST_37  H14  C14  C11  C10   180.00   0.0  0
 7UR  CONST_38  H9   C28  C27  C26   180.00   0.0  0
 7UR  CONST_39  H8   C26  C27  C28   180.00   0.0  0
 7UR  CONST_40  H21  C29  C30  C02     0.00   0.0  0
 7UR  CONST_41  H11  C04  C03  C02   180.00   0.0  0
 7UR  CONST_42  H10  C03  C04  C05   180.00   0.0  0
 7UR  CONST_43  H2   C15  C16  C09   180.00   0.0  0
 7UR  CONST_44  H1   C10  C11  C14   180.00   0.0  0
 7UR  CONST_45  H20  C27  C26  C25   180.00   0.0  0
 7UR  CONST_49  C09  N08  C07  C06   180.00   0.0  0
 7UR  CONST_50  O23  C07  N08  C09     0.00   0.0  0
 7UR  Var_01    C18  C17  C16  C15   -97.09  30.0  3
 7UR  Var_02    C19  C18  C17  C16  -174.43  30.0  1
 7UR  Var_03    C20  C19  C18  C17  -179.58  30.0  2
 7UR  Var_04    O22  C20  C19  C18    -6.06  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
 7UR  chir_01  C06  C05  C24  C07  negativ

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
 7UR  plan-1  C10  0.020
 7UR  plan-1  C15  0.020
 7UR  plan-1  C17  0.020
 7UR  plan-1  N08  0.020
 7UR  plan-1  C09  0.020
 7UR  plan-1  C11  0.020
 7UR  plan-1  C12  0.020
 7UR  plan-1  N13  0.020
 7UR  plan-1  C14  0.020
 7UR  plan-1  C16  0.020
 7UR  plan-1  H1   0.020
 7UR  plan-1  H2   0.020
 7UR  plan-1  H14  0.020
 7UR  plan-2  C26  0.020
 7UR  plan-2  C28  0.020
 7UR  plan-2  C02  0.020
 7UR  plan-2  C03  0.020
 7UR  plan-2  C04  0.020
 7UR  plan-2  C05  0.020
 7UR  plan-2  C06  0.020
 7UR  plan-2  C25  0.020
 7UR  plan-2  C27  0.020
 7UR  plan-2  C29  0.020
 7UR  plan-2  C30  0.020
 7UR  plan-2  H8   0.020
 7UR  plan-2  H9   0.020
 7UR  plan-2  H10  0.020
 7UR  plan-2  H11  0.020
 7UR  plan-2  H20  0.020
 7UR  plan-2  H21  0.020
 7UR  plan-2  F01  0.020
 7UR  plan-3  C06  0.020
 7UR  plan-3  C07  0.020
 7UR  plan-3  N08  0.020
 7UR  plan-3  C09  0.020
 7UR  plan-3  O23  0.020
 7UR  plan-3  H13  0.020
 7UR  plan-4  C20  0.020
 7UR  plan-4  C19  0.020
 7UR  plan-4  O21  0.020
 7UR  plan-4  O22  0.020

