# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 19:03:02 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-[2-[[(2~{R})-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-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(Br)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
 8VL  8VL  '4-[2-[[(2~{R})-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-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_8VL
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
 8VL  C10  C   CR16   0  -0.246  -2.9237  -2.8129  -0.4643
 8VL  C15  C   CR16   0  -0.325  -4.2156  -1.9756   1.8395
 8VL  C17  C   CH2    0  -0.516  -3.1794   0.3073   1.6899
 8VL  C20  C   C      0   0.416  -4.6885   3.8341   0.7993
 8VL  C24  C   CH3    0  -0.668   0.2783  -0.4212  -3.0823
 8VL  C26  C   CR16   0  -0.331   0.3476   1.9890   0.6261
 8VL  C28  C   CR16   0  -0.247   1.6027   3.1082   2.3394
 8VL  C02  C   C      0  -0.226   3.9523   1.1896   0.1508
 8VL  C03  C   C1     0  -0.214   3.9076   0.3710  -0.9388
 8VL  C04  C   C1     0  -0.366   2.6711   0.0586  -1.5322
 8VL  C05  C   C      0   0.186   1.4927   0.5604  -1.0534
 8VL  C06  C   CH1    0  -0.537   0.1703   0.1906  -1.6830
 8VL  C07  C   C      0   0.556  -0.5525  -0.8179  -0.7945
 8VL  C09  C   CR6    0   0.285  -2.7384  -1.5227   0.0059
 8VL  C11  C   CR6    0  -0.019  -3.7582  -3.6859   0.2271
 8VL  C12  C   CSP    0   0.054  -3.9491  -5.0139  -0.2574
 8VL  C14  C   CR16   0  -0.222  -4.4133  -3.2646   1.3835
 8VL  C16  C   CR6    0   0.154  -3.3724  -1.0865   1.1744
 8VL  C18  C   CH2    0  -0.413  -4.0886   1.3239   0.9905
 8VL  C19  C   CH2    0  -0.592  -3.7976   2.7482   1.4309
 8VL  C25  C   CR6    0   0.107   1.5279   1.4273   0.0811
 8VL  C27  C   CR16   0  -0.242   0.3773   2.8029   1.7244
 8VL  C29  C   CR16   0  -0.318   2.7679   2.5964   1.8390
 8VL  C30  C   CR6    0   0.201   2.7701   1.7485   0.7063
 8VL  N08  N   NH1    0  -0.758  -1.8933  -0.6436  -0.7104
 8VL  N13  N   NS     0  -0.252  -4.1070  -6.0866  -0.6479
 8VL  O21  O   OC    -1  -0.629  -4.5386   4.9896   1.2476
 8VL  O22  O   O      0  -0.607  -5.4726   3.4864  -0.1049
 8VL  O23  O   O      0  -0.449   0.0295  -1.7310  -0.2422
 8VL  H1   H   HCR6   0   0.286  -2.4310  -3.1329  -1.3726
 8VL  H2   H   HCR6   0   0.269  -4.7147  -1.6532   2.7444
 8VL  H3   H   HCH2   0   0.256  -3.3807   0.3258   2.7633
 8VL  H4   H   HCH2   0   0.238  -2.1333   0.6004   1.5686
 8VL  H6   H   HCH3   0   0.256   0.8138   0.2491  -3.7538
 8VL  H7   H   HCH3   0   0.242   0.7924  -1.3817  -3.0709
 8VL  H8   H   HCR6   0   0.231  -0.6080   1.7846   0.1645
 8VL  H9   H   HCR6   0   0.268   1.6263   3.7525   3.2079
 8VL  H10  H   H      0   0.283   4.8104  -0.0519  -1.3582
 8VL  H11  H   H      0   0.269   2.6832  -0.6005  -2.3889
 8VL  H12  H   HCH1   0   0.287  -0.4381   1.0944  -1.7792
 8VL  H13  H   HCR6   0   0.283  -5.0666  -3.9405   1.9177
 8VL  H14  H   HCH2   0   0.213  -3.9790   1.2464  -0.0942
 8VL  H15  H   HCH2   0   0.229  -5.1297   1.0688   1.2022
 8VL  H16  H   HCH2   0   0.225  -2.7539   2.9973   1.1992
 8VL  H17  H   HCH2   0   0.224  -3.8725   2.8251   2.5210
 8VL  H18  H   HCR6   0   0.264  -0.5421   3.2160   2.1188
 8VL  H19  H   HCR6   0   0.261   3.6987   2.8490   2.3266
 8VL  H20  H   HNH1   0   0.416  -2.3136   0.1465  -1.1767
 8VL  BR1  BR  BR     0  -0.040   5.6452   1.5624   0.9078
 8VL  H5   H   HCH3   0   0.259  -0.7166  -0.5817  -3.4964

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
 8VL  BR1  C02  single    1.891  0.020  1.891
 8VL  C28  C29  aromatic  1.368  0.020  1.368
 8VL  C28  C27  aromatic  1.405  0.020  1.405
 8VL  C29  C30  aromatic  1.415  0.020  1.415
 8VL  C27  C26  aromatic  1.367  0.020  1.367
 8VL  C30  C02  aromatic  1.421  0.020  1.421
 8VL  C30  C25  aromatic  1.427  0.020  1.427
 8VL  C02  C03  aromatic  1.364  0.020  1.364
 8VL  C26  C25  aromatic  1.416  0.020  1.416
 8VL  C25  C05  aromatic  1.428  0.020  1.428
 8VL  C03  C04  aromatic  1.407  0.020  1.407
 8VL  O22  C20  deloc     1.246  0.020  1.246
 8VL  C05  C04  aromatic  1.367  0.020  1.367
 8VL  C05  C06  single    1.511  0.020  1.511
 8VL  C20  C19  single    1.540  0.020  1.540
 8VL  C20  O21  deloc     1.248  0.020  1.248
 8VL  C19  C18  single    1.519  0.020  1.519
 8VL  C06  C24  single    1.531  0.020  1.531
 8VL  C06  C07  single    1.526  0.020  1.526
 8VL  C18  C17  single    1.533  0.020  1.533
 8VL  N08  C07  single    1.355  0.020  1.355
 8VL  N08  C09  single    1.414  0.020  1.414
 8VL  C07  O23  double    1.216  0.020  1.216
 8VL  C09  C10  aromatic  1.386  0.020  1.386
 8VL  C09  C16  aromatic  1.399  0.020  1.399
 8VL  C17  C16  single    1.499  0.020  1.499
 8VL  C10  C11  aromatic  1.392  0.020  1.392
 8VL  C16  C15  aromatic  1.394  0.020  1.394
 8VL  C11  C12  single    1.426  0.020  1.426
 8VL  C11  C14  aromatic  1.394  0.020  1.394
 8VL  C15  C14  aromatic  1.381  0.020  1.381
 8VL  C12  N13  triple    1.152  0.020  1.152
 8VL  C10  H1   single    0.930  0.020  1.080
 8VL  C15  H2   single    0.930  0.020  1.080
 8VL  C17  H3   single    0.970  0.020  1.090
 8VL  C17  H4   single    0.970  0.020  1.090
 8VL  C24  H5   single    0.970  0.020  1.090
 8VL  C24  H6   single    0.970  0.020  1.090
 8VL  C24  H7   single    0.970  0.020  1.090
 8VL  C26  H8   single    0.930  0.020  1.080
 8VL  C28  H9   single    0.930  0.020  1.080
 8VL  C03  H10  single    0.930  0.020  1.080
 8VL  C04  H11  single    0.930  0.020  1.080
 8VL  C06  H12  single    0.970  0.020  1.090
 8VL  C14  H13  single    0.930  0.020  1.080
 8VL  C18  H14  single    0.970  0.020  1.090
 8VL  C18  H15  single    0.970  0.020  1.090
 8VL  C19  H16  single    0.970  0.020  1.090
 8VL  C19  H17  single    0.970  0.020  1.090
 8VL  C27  H18  single    0.930  0.020  1.080
 8VL  C29  H19  single    0.930  0.020  1.080
 8VL  N08  H20  single    0.860  0.020  1.020

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
 8VL  H1   C10  C11  120.31  3.000
 8VL  H1   C10  C09  119.97  3.000
 8VL  C11  C10  C09  119.72  3.000
 8VL  H2   C15  C16  119.19  3.000
 8VL  H2   C15  C14  119.20  3.000
 8VL  C16  C15  C14  121.61  3.000
 8VL  H4   C17  H3   106.32  3.000
 8VL  H4   C17  C18  109.83  3.000
 8VL  H3   C17  C18  109.14  3.000
 8VL  H4   C17  C16  109.54  3.000
 8VL  H3   C17  C16  109.27  3.000
 8VL  C18  C17  C16  112.55  3.000
 8VL  O22  C20  O21  126.46  3.000
 8VL  O21  C20  C19  115.84  3.000
 8VL  O22  C20  C19  117.69  3.000
 8VL  H7   C24  H6   108.48  3.000
 8VL  H7   C24  H5   107.76  3.000
 8VL  H6   C24  H5   107.77  3.000
 8VL  H7   C24  C06  112.09  3.000
 8VL  H6   C24  C06  110.62  3.000
 8VL  H5   C24  C06  109.99  3.000
 8VL  H8   C26  C27  118.35  3.000
 8VL  H8   C26  C25  119.83  3.000
 8VL  C27  C26  C25  121.81  3.000
 8VL  H9   C28  C29  119.88  3.000
 8VL  H9   C28  C27  120.00  3.000
 8VL  C29  C28  C27  120.12  3.000
 8VL  BR1  C02  C30  120.71  3.000
 8VL  C30  C02  C03  121.42  3.000
 8VL  BR1  C02  C03  117.87  3.000
 8VL  H10  C03  C04  118.90  3.000
 8VL  H10  C03  C02  121.15  3.000
 8VL  C04  C03  C02  119.95  3.000
 8VL  H11  C04  C05  120.73  3.000
 8VL  H11  C04  C03  117.38  3.000
 8VL  C05  C04  C03  121.89  3.000
 8VL  C25  C05  C06  120.08  3.000
 8VL  C06  C05  C04  121.24  3.000
 8VL  C25  C05  C04  118.67  3.000
 8VL  H12  C06  C07  109.50  3.000
 8VL  H12  C06  C05  108.74  3.000
 8VL  C07  C06  C05  109.50  3.000
 8VL  H12  C06  C24  106.80  3.000
 8VL  C07  C06  C24  107.54  3.000
 8VL  C05  C06  C24  114.65  3.000
 8VL  O23  C07  N08  122.84  3.000
 8VL  O23  C07  C06  122.29  3.000
 8VL  N08  C07  C06  114.83  3.000
 8VL  N08  C09  C16  119.99  3.000
 8VL  C16  C09  C10  120.87  3.000
 8VL  N08  C09  C10  119.13  3.000
 8VL  C14  C11  C12  120.01  3.000
 8VL  C14  C11  C10  120.28  3.000
 8VL  C12  C11  C10  119.71  3.000
 8VL  N13  C12  C11  180.00  3.000
 8VL  H13  C14  C11  120.32  3.000
 8VL  H13  C14  C15  120.44  3.000
 8VL  C11  C14  C15  119.24  3.000
 8VL  C09  C16  C17  121.26  3.000
 8VL  C17  C16  C15  120.46  3.000
 8VL  C09  C16  C15  118.27  3.000
 8VL  H15  C18  H14  105.74  3.000
 8VL  H15  C18  C19  110.20  3.000
 8VL  H14  C18  C19  109.57  3.000
 8VL  H15  C18  C17  108.78  3.000
 8VL  H14  C18  C17  110.26  3.000
 8VL  C19  C18  C17  112.09  3.000
 8VL  H17  C19  H16  105.02  3.000
 8VL  H17  C19  C18  109.95  3.000
 8VL  H16  C19  C18  109.50  3.000
 8VL  H17  C19  C20  108.61  3.000
 8VL  H16  C19  C20  107.67  3.000
 8VL  C18  C19  C20  115.56  3.000
 8VL  C30  C25  C05  120.39  3.000
 8VL  C05  C25  C26  121.73  3.000
 8VL  C30  C25  C26  117.88  3.000
 8VL  H18  C27  C28  119.90  3.000
 8VL  H18  C27  C26  120.09  3.000
 8VL  C28  C27  C26  120.00  3.000
 8VL  H19  C29  C30  119.99  3.000
 8VL  H19  C29  C28  118.77  3.000
 8VL  C30  C29  C28  121.24  3.000
 8VL  C29  C30  C25  118.96  3.000
 8VL  C25  C30  C02  117.67  3.000
 8VL  C29  C30  C02  123.37  3.000
 8VL  H20  N08  C09  118.15  3.000
 8VL  H20  N08  C07  118.97  3.000
 8VL  C09  N08  C07  122.88  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
 8VL  CONST_01  C15  C16  C09  C10     0.00   0.0  0
 8VL  CONST_02  C15  C14  C11  C10     0.00   0.0  0
 8VL  CONST_03  C29  C28  C27  C26     0.00   0.0  0
 8VL  CONST_04  C29  C30  C25  C26     0.00   0.0  0
 8VL  CONST_05  C02  C30  C25  C26   180.00   0.0  0
 8VL  CONST_06  C04  C05  C25  C26   180.00   0.0  0
 8VL  CONST_07  C02  C30  C29  C28   180.00   0.0  0
 8VL  CONST_08  C25  C30  C29  C28     0.00   0.0  0
 8VL  CONST_09  C25  C26  C27  C28     0.00   0.0  0
 8VL  CONST_10  C05  C25  C30  C02     0.00   0.0  0
 8VL  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 8VL  CONST_12  C29  C30  C02  C03   180.00   0.0  0
 8VL  CONST_13  C25  C30  C02  C03     0.00   0.0  0
 8VL  CONST_14  C25  C05  C04  C03     0.00   0.0  0
 8VL  CONST_15  C30  C02  C03  C04     0.00   0.0  0
 8VL  CONST_16  C30  C25  C05  C04     0.00   0.0  0
 8VL  CONST_17  C29  C30  C25  C05   180.00   0.0  0
 8VL  CONST_18  C27  C26  C25  C05   180.00   0.0  0
 8VL  CONST_19  C14  C11  C10  C09     0.00   0.0  0
 8VL  CONST_20  C14  C15  C16  C09     0.00   0.0  0
 8VL  CONST_21  C16  C09  C10  C11     0.00   0.0  0
 8VL  CONST_22  C16  C15  C14  C11     0.00   0.0  0
 8VL  CONST_23  C30  C29  C28  C27     0.00   0.0  0
 8VL  CONST_24  C30  C25  C26  C27     0.00   0.0  0
 8VL  CONST_25  C17  C16  C09  C10   180.00   0.0  0
 8VL  CONST_26  N08  C09  C16  C15   180.00   0.0  0
 8VL  CONST_27  C12  C11  C14  C15   180.00   0.0  0
 8VL  CONST_28  C14  C15  C16  C17   180.00   0.0  0
 8VL  CONST_29  C06  C05  C25  C26     0.00   0.0  0
 8VL  CONST_30  C06  C05  C04  C03   180.00   0.0  0
 8VL  CONST_31  BR1  C02  C03  C04   180.00   0.0  0
 8VL  CONST_32  C30  C25  C05  C06   180.00   0.0  0
 8VL  CONST_33  C12  C11  C10  C09   180.00   0.0  0
 8VL  CONST_34  N08  C09  C10  C11   180.00   0.0  0
 8VL  CONST_35  BR1  C02  C30  C25   180.00   0.0  0
 8VL  CONST_36  BR1  C02  C30  C29     0.00   0.0  0
 8VL  CONST_37  H13  C14  C11  C10   180.00   0.0  0
 8VL  CONST_38  H9   C28  C27  C26   180.00   0.0  0
 8VL  CONST_39  H8   C26  C27  C28   180.00   0.0  0
 8VL  CONST_40  H19  C29  C30  C02     0.00   0.0  0
 8VL  CONST_41  H11  C04  C03  C02   180.00   0.0  0
 8VL  CONST_42  H10  C03  C04  C05   180.00   0.0  0
 8VL  CONST_43  H2   C15  C16  C09   180.00   0.0  0
 8VL  CONST_44  H1   C10  C11  C14   180.00   0.0  0
 8VL  CONST_45  H18  C27  C26  C25   180.00   0.0  0
 8VL  CONST_49  C09  N08  C07  C06   180.00   0.0  0
 8VL  CONST_50  O23  C07  N08  C09     0.00   0.0  0
 8VL  Var_01    C18  C17  C16  C15   -96.30  30.0  3
 8VL  Var_02    C19  C18  C17  C16  -174.87  30.0  1
 8VL  Var_03    C20  C19  C18  C17  -178.70  30.0  1
 8VL  Var_04    O22  C20  C19  C18    -6.91  30.0  2

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
 8VL  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
 8VL  plan-1  C10  0.020
 8VL  plan-1  C15  0.020
 8VL  plan-1  C17  0.020
 8VL  plan-1  C09  0.020
 8VL  plan-1  C11  0.020
 8VL  plan-1  C12  0.020
 8VL  plan-1  C14  0.020
 8VL  plan-1  C16  0.020
 8VL  plan-1  N08  0.020
 8VL  plan-1  N13  0.020
 8VL  plan-1  H1   0.020
 8VL  plan-1  H2   0.020
 8VL  plan-1  H13  0.020
 8VL  plan-2  C26  0.020
 8VL  plan-2  C28  0.020
 8VL  plan-2  C02  0.020
 8VL  plan-2  C03  0.020
 8VL  plan-2  C04  0.020
 8VL  plan-2  C05  0.020
 8VL  plan-2  C06  0.020
 8VL  plan-2  C25  0.020
 8VL  plan-2  C27  0.020
 8VL  plan-2  C29  0.020
 8VL  plan-2  C30  0.020
 8VL  plan-2  H8   0.020
 8VL  plan-2  H9   0.020
 8VL  plan-2  H10  0.020
 8VL  plan-2  H11  0.020
 8VL  plan-2  H18  0.020
 8VL  plan-2  H19  0.020
 8VL  plan-2  BR1  0.020
 8VL  plan-3  C06  0.020
 8VL  plan-3  C07  0.020
 8VL  plan-3  C09  0.020
 8VL  plan-3  N08  0.020
 8VL  plan-3  O23  0.020
 8VL  plan-3  H20  0.020
 8VL  plan-4  C20  0.020
 8VL  plan-4  C19  0.020
 8VL  plan-4  O21  0.020
 8VL  plan-4  O22  0.020

