# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 14:13:59 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 3-[5-(3-nitrophenyl)thiophen-2-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1sc(cc1)c2cccc(c2)[N+]([O-])=O
#
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
 53N  53N  '3-[5-(3-nitrophenyl)thiophen-2-yl]propanoic acid'  ligand  29  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_53N
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
 53N  C5    C  CR16   0  -0.360   2.2573   0.2149   0.1807
 53N  C6    C  CR6    0   0.169   1.7089  -1.0530  -0.0039
 53N  C7    C  CR5    0  -0.221   0.2656  -1.2456  -0.1051
 53N  C15   C  CR15   0  -0.219  -1.8526  -2.2027  -0.0410
 53N  C17   C  CR16   0  -0.304   2.5761  -2.1478  -0.0816
 53N  C1    C  CR6    0   0.284   3.6317   0.3575   0.2797
 53N  N2    N  N      1   0.329   4.1836   1.6934   0.4688
 53N  O3    O  O     -1  -0.376   3.4192   2.6289   0.4778
 53N  O4    O  O      0  -0.374   5.3791   1.7982   0.6063
 53N  S8    S  S2     0   0.209  -0.7848   0.0334  -0.6095
 53N  C9    C  CR5    0  -0.135  -2.1933  -0.9489  -0.4575
 53N  C11   C  CH2    0  -0.575  -3.9952   0.5942   0.3654
 53N  C12   C  C      0   0.416  -5.3932   1.2049   0.1560
 53N  O13   O  OC    -1  -0.626  -5.8746   1.8080   1.1368
 53N  O14   O  O      0  -0.605  -5.9220   1.0695  -0.9642
 53N  C16   C  CR15   0  -0.226  -0.4592  -2.3745   0.1581
 53N  C18   C  CR16   0  -0.228   3.9459  -1.9834   0.0341
 53N  C19   C  CR16   0  -0.285   4.4956  -0.7241   0.2148
 53N  H5    H  HCR6   0   0.291   1.6155   1.0812   0.2641
 53N  H10   H  HCH2   0   0.246  -3.5757   0.1053  -1.6926
 53N  H10A  H  HCH2   0   0.245  -4.2533  -1.2209  -0.7753
 53N  H15   H  HCR5   0   0.261  -2.5847  -2.9811   0.1244
 53N  H17   H  HCR6   0   0.273   2.1777  -3.1395  -0.2499
 53N  H11   H  HCH2   0   0.230  -3.9603   0.1038   1.3423
 53N  H11A  H  HCH2   0   0.231  -3.2748   1.4181   0.4290
 53N  H16   H  HCR5   0   0.265  -0.0172  -3.2979   0.5057
 53N  H18   H  HCR6   0   0.282   4.5973  -2.8438  -0.0286
 53N  H19   H  HCR6   0   0.300   5.5653  -0.6012   0.2946
 53N  C10   C  CH2    0  -0.495  -3.5517  -0.3865  -0.7181

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
 53N  C5   C6    aromatic  1.394  0.020  1.394
 53N  C5   C1    aromatic  1.385  0.020  1.385
 53N  C6   C7    single    1.460  0.020  1.460
 53N  C6   C17   aromatic  1.399  0.020  1.399
 53N  C7   S8    aromatic  1.730  0.020  1.730
 53N  C7   C16   aromatic  1.367  0.020  1.367
 53N  C10  C9    single    1.493  0.020  1.493
 53N  C10  C11   single    1.527  0.020  1.527
 53N  C15  C9    aromatic  1.364  0.020  1.364
 53N  C15  C16   aromatic  1.418  0.020  1.418
 53N  C17  C18   aromatic  1.384  0.020  1.384
 53N  C1   N2    single    1.458  0.020  1.458
 53N  C1   C19   aromatic  1.386  0.020  1.386
 53N  N2   O3    single    1.208  0.020  1.208
 53N  N2   O4    double    1.208  0.020  1.208
 53N  S8   C9    aromatic  1.724  0.020  1.724
 53N  C11  C12   single    1.540  0.020  1.540
 53N  C12  O13   deloc     1.248  0.020  1.248
 53N  C12  O14   deloc     1.246  0.020  1.246
 53N  C18  C19   aromatic  1.386  0.020  1.386
 53N  C5   H5    single    0.930  0.020  1.080
 53N  C10  H10   single    0.970  0.020  1.090
 53N  C10  H10A  single    0.970  0.020  1.090
 53N  C15  H15   single    0.930  0.020  1.080
 53N  C17  H17   single    0.930  0.020  1.080
 53N  C11  H11   single    0.970  0.020  1.090
 53N  C11  H11A  single    0.970  0.020  1.090
 53N  C16  H16   single    0.930  0.020  1.080
 53N  C18  H18   single    0.930  0.020  1.080
 53N  C19  H19   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
 53N  H5    C5   C1   120.05  3.000
 53N  H5    C5   C6   120.37  3.000
 53N  C1    C5   C6   119.57  3.000
 53N  C17   C6   C7   120.39  3.000
 53N  C17   C6   C5   118.39  3.000
 53N  C7    C6   C5   121.22  3.000
 53N  C16   C7   S8   110.16  3.000
 53N  C16   C7   C6   128.30  3.000
 53N  S8    C7   C6   121.53  3.000
 53N  H15   C15  C16  123.82  3.000
 53N  H15   C15  C9   122.63  3.000
 53N  C16   C15  C9   113.55  3.000
 53N  H17   C17  C18  119.10  3.000
 53N  H17   C17  C6   119.84  3.000
 53N  C18   C17  C6   121.05  3.000
 53N  C19   C1   N2   119.03  3.000
 53N  C19   C1   C5   122.33  3.000
 53N  N2    C1   C5   118.64  3.000
 53N  O4    N2   O3   123.93  3.000
 53N  O4    N2   C1   117.97  3.000
 53N  O3    N2   C1   118.10  3.000
 53N  C9    S8   C7    92.81  3.000
 53N  S8    C9   C15  110.27  3.000
 53N  S8    C9   C10  120.88  3.000
 53N  C15   C9   C10  128.80  3.000
 53N  H11A  C11  H11  105.32  3.000
 53N  H11A  C11  C12  107.84  3.000
 53N  H11   C11  C12  109.17  3.000
 53N  H11A  C11  C10  109.44  3.000
 53N  H11   C11  C10  109.67  3.000
 53N  C12   C11  C10  114.95  3.000
 53N  O14   C12  O13  126.53  3.000
 53N  O14   C12  C11  117.68  3.000
 53N  O13   C12  C11  115.78  3.000
 53N  H16   C16  C15  123.39  3.000
 53N  H16   C16  C7   123.39  3.000
 53N  C15   C16  C7   113.20  3.000
 53N  H18   C18  C19  119.46  3.000
 53N  H18   C18  C17  119.79  3.000
 53N  C19   C18  C17  120.75  3.000
 53N  H19   C19  C18  120.40  3.000
 53N  H19   C19  C1   121.69  3.000
 53N  C18   C19  C1   117.91  3.000
 53N  H10A  C10  H10  106.46  3.000
 53N  H10A  C10  C11  109.95  3.000
 53N  H10   C10  C11  109.73  3.000
 53N  H10A  C10  C9   107.81  3.000
 53N  H10   C10  C9   110.21  3.000
 53N  C11   C10  C9   112.47  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
 53N  CONST_03  C18  C17  C6   C5      0.00   0.0  0
 53N  CONST_04  C18  C19  C1   C5      0.00   0.0  0
 53N  CONST_05  C19  C1   C5   C6      0.00   0.0  0
 53N  CONST_06  C9   S8   C7   C6    180.00   0.0  0
 53N  CONST_07  C15  C16  C7   C6    180.00   0.0  0
 53N  CONST_08  C19  C18  C17  C6      0.00   0.0  0
 53N  CONST_09  C1   C5   C6   C7    180.00   0.0  0
 53N  CONST_10  C18  C17  C6   C7    180.00   0.0  0
 53N  CONST_11  C15  C9   S8   C7      0.00   0.0  0
 53N  CONST_12  C9   C15  C16  C7      0.00   0.0  0
 53N  CONST_13  S8   C7   C16  C15     0.00   0.0  0
 53N  CONST_14  C1   C5   C6   C17     0.00   0.0  0
 53N  CONST_17  C1   C19  C18  C17     0.00   0.0  0
 53N  CONST_18  C16  C15  C9   S8      0.00   0.0  0
 53N  CONST_19  C16  C7   S8   C9      0.00   0.0  0
 53N  CONST_20  N2   C1   C5   C6    180.00   0.0  0
 53N  CONST_21  C10  C9   S8   C7    180.00   0.0  0
 53N  CONST_22  C16  C15  C9   C10   180.00   0.0  0
 53N  CONST_23  C18  C19  C1   N2    180.00   0.0  0
 53N  CONST_24  H17  C17  C6   C5    180.00   0.0  0
 53N  CONST_25  H19  C19  C1   C5    180.00   0.0  0
 53N  CONST_26  H16  C16  C7   C6      0.00   0.0  0
 53N  CONST_27  H18  C18  C17  C6    180.00   0.0  0
 53N  CONST_28  H5   C5   C6   C7      0.00   0.0  0
 53N  CONST_29  H15  C15  C16  C7    180.00   0.0  0
 53N  CONST_30  O3   N2   C1   C5      0.00   0.0  0
 53N  CONST_31  O4   N2   C1   C5    180.00   0.0  0
 53N  CONST_32  C19  C1   N2   O3    180.00   0.0  0
 53N  CONST_33  C19  C1   N2   O4      0.00   0.0  0
 53N  Var_01    C11  C10  C9   C15   106.66  30.0  2
 53N  Var_02    C12  C11  C10  C9   -179.75  30.0  3
 53N  Var_03    O13  C12  C11  C10   167.30  30.0  3

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
 53N  plan-1  C6   0.020
 53N  plan-1  C7   0.020
 53N  plan-1  C15  0.020
 53N  plan-1  S8   0.020
 53N  plan-1  C9   0.020
 53N  plan-1  C16  0.020
 53N  plan-1  H15  0.020
 53N  plan-1  H16  0.020
 53N  plan-1  C10  0.020
 53N  plan-2  C5   0.020
 53N  plan-2  C6   0.020
 53N  plan-2  C7   0.020
 53N  plan-2  C17  0.020
 53N  plan-2  C1   0.020
 53N  plan-2  N2   0.020
 53N  plan-2  C18  0.020
 53N  plan-2  C19  0.020
 53N  plan-2  H5   0.020
 53N  plan-2  H17  0.020
 53N  plan-2  H18  0.020
 53N  plan-2  H19  0.020
 53N  plan-3  C1   0.020
 53N  plan-3  N2   0.020
 53N  plan-3  O3   0.020
 53N  plan-3  O4   0.020
 53N  plan-4  C11  0.020
 53N  plan-4  C12  0.020
 53N  plan-4  O13  0.020
 53N  plan-4  O14  0.020

