# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:19:06 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-benzamido-4-[(2~{R})-1,2,3,4-tetrahydronaphthalen-2-yl]thiophene-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(NC(=O)c2ccccc2)scc1[C@@H]3CCc4ccccc4C3
#
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
 49I  49I  "2-benzamido-4-[(2~{R})-1,2,3,4-tetrahydronaphthalen-2-yl]thiophene-3-carboxylic acid"  ligand  45  27  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_49I
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
 49I  C1   C  CR16   0  -0.303   2.8049   -7.0678  16.8558
 49I  C5   C  CR16   0  -0.262   1.6600   -6.9823  18.9598
 49I  C4   C  CR16   0  -0.297   2.7839   -7.5111  19.5720
 49I  C3   C  CR66   0   0.070   3.9323   -7.8255  18.8427
 49I  C2   C  CR66   0   0.078   3.9420   -7.6038  17.4632
 49I  C6   C  CR16   0  -0.260   1.6712   -6.7572  17.5877
 49I  C7   C  C      0  -0.476   5.1343   -7.9513  16.6088
 49I  C8   C  CR16   0  -0.342   6.4102   -8.1729  17.4190
 49I  O3   O  O      0  -0.470  11.5078   -9.9414  13.9084
 49I  C16  C  C      0   0.535  10.7199  -10.8770  13.8435
 49I  C17  C  CR6    0  -0.046  11.0244  -12.1026  13.0505
 49I  C18  C  CR16   0  -0.265  12.3431  -12.3061  12.6461
 49I  C19  C  CR16   0  -0.241  12.6850  -13.4198  11.8958
 49I  C20  C  CR16   0  -0.249  11.7108  -14.3398  11.5303
 49I  C21  C  CR16   0  -0.238  10.3931  -14.1390  11.9193
 49I  C22  C  CR16   0  -0.293  10.0505  -13.0284  12.6758
 49I  C13  C  CR5    0   0.106   9.0483   -9.8188  15.2312
 49I  C14  C  CR5    0  -0.227   7.8140   -9.8401  15.8555
 49I  C15  C  C      0   0.450   6.9119  -11.0470  15.7114
 49I  O2   O  O      0  -0.610   7.4047  -12.0492  15.1147
 49I  C11  C  CR5    0   0.280   7.5831   -8.6073  16.5745
 49I  C12  C  CR15   0  -0.600   8.6317   -7.7486  16.4453
 49I  S1   S  S2     0   0.226   9.9183   -8.3576  15.4829
 49I  C9   C  C      0  -0.430   6.1323   -9.0589  18.6317
 49I  C10  C  C      0  -0.509   5.1444   -8.3658  19.5596
 49I  H1   H  HCR6   0   0.237   2.8160   -6.8915  15.7857
 49I  H2   H  HCR6   0   0.245   0.7809   -6.7476  19.5466
 49I  H3   H  HCR6   0   0.239   2.7765   -7.6874  20.6421
 49I  H4   H  HCR6   0   0.245   0.8021   -6.3421  17.0932
 49I  H5   H  H      0   0.236   5.2994   -7.1548  15.8780
 49I  H6   H  H      0   0.260   4.9117   -8.8547  16.0400
 49I  H7   H  HCR6   0   0.232   6.6966   -7.1935  17.8223
 49I  H9   H  HCR6   0   0.258  13.1054  -11.5907  12.9237
 49I  H10  H  HCR6   0   0.261  13.7135  -13.5691  11.5945
 49I  H11  H  HCR6   0   0.263  11.9762  -15.2076  10.9407
 49I  H12  H  HCR6   0   0.263   9.6269  -14.8460  11.6300
 49I  H13  H  HCR6   0   0.251   9.0115  -12.8910  12.9466
 49I  H14  H  HNH1   0   0.454   8.8437  -11.6461  14.5393
 49I  H15  H  HCR5   0   0.277   8.7151   -6.7654  16.8845
 49I  H16  H  H      0   0.240   5.7393  -10.0199  18.3049
 49I  H17  H  H      0   0.225   7.0613   -9.2553  19.1716
 49I  H18  H  H      0   0.244   4.8260   -9.0489  20.3511
 49I  H19  H  H      0   0.237   5.6474   -7.5363  20.0693
 49I  N1   N  NH1    0  -0.754   9.5355  -10.8618  14.4830
 49I  O1   O  OC    -1  -0.539   5.7616  -11.0029  16.1645

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
 49I  C21  C20  aromatic  1.388  0.020  1.388
 49I  C21  C22  aromatic  1.387  0.020  1.387
 49I  C20  C19  aromatic  1.389  0.020  1.389
 49I  C22  C17  aromatic  1.395  0.020  1.395
 49I  C19  C18  aromatic  1.386  0.020  1.386
 49I  C17  C18  aromatic  1.394  0.020  1.394
 49I  C17  C16  single    1.491  0.020  1.491
 49I  O2   C15  deloc     1.266  0.020  1.266
 49I  C16  N1   single    1.346  0.020  1.346
 49I  C16  O3   double    1.225  0.020  1.225
 49I  N1   C13  single    1.373  0.020  1.373
 49I  C15  O1   deloc     1.237  0.020  1.237
 49I  C15  C14  single    1.514  0.020  1.514
 49I  C13  C14  aromatic  1.383  0.020  1.383
 49I  C13  S1   aromatic  1.719  0.020  1.719
 49I  C14  C11  aromatic  1.446  0.020  1.446
 49I  S1   C12  aromatic  1.718  0.020  1.718
 49I  C11  C12  aromatic  1.361  0.020  1.361
 49I  C11  C8   single    1.509  0.020  1.509
 49I  C7   C8   single    1.528  0.020  1.528
 49I  C7   C2   single    1.507  0.020  1.507
 49I  C1   C2   aromatic  1.396  0.020  1.396
 49I  C1   C6   aromatic  1.385  0.020  1.385
 49I  C8   C9   single    1.527  0.020  1.527
 49I  C2   C3   aromatic  1.397  0.020  1.397
 49I  C6   C5   aromatic  1.391  0.020  1.391
 49I  C9   C10  single    1.522  0.020  1.522
 49I  C3   C10  single    1.508  0.020  1.508
 49I  C3   C4   aromatic  1.396  0.020  1.396
 49I  C5   C4   aromatic  1.385  0.020  1.385
 49I  C1   H1   single    0.930  0.020  1.080
 49I  C5   H2   single    0.930  0.020  1.080
 49I  C4   H3   single    0.930  0.020  1.080
 49I  C6   H4   single    0.930  0.020  1.080
 49I  C7   H5   single    0.970  0.020  1.090
 49I  C7   H6   single    0.970  0.020  1.090
 49I  C8   H7   single    0.970  0.020  1.090
 49I  C18  H9   single    0.930  0.020  1.080
 49I  C19  H10  single    0.930  0.020  1.080
 49I  C20  H11  single    0.930  0.020  1.080
 49I  C21  H12  single    0.930  0.020  1.080
 49I  C22  H13  single    0.930  0.020  1.080
 49I  N1   H14  single    0.860  0.020  1.020
 49I  C12  H15  single    0.930  0.020  1.080
 49I  C9   H16  single    0.970  0.020  1.090
 49I  C9   H17  single    0.970  0.020  1.090
 49I  C10  H18  single    0.970  0.020  1.090
 49I  C10  H19  single    0.970  0.020  1.090

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
 49I  H1   C1   C6   119.57  3.000
 49I  H1   C1   C2   118.90  3.000
 49I  C6   C1   C2   121.53  3.000
 49I  H2   C5   C6   120.42  3.000
 49I  H2   C5   C4   120.14  3.000
 49I  C6   C5   C4   119.44  3.000
 49I  H3   C4   C3   118.97  3.000
 49I  H3   C4   C5   119.52  3.000
 49I  C3   C4   C5   121.51  3.000
 49I  C10  C3   C2   121.36  3.000
 49I  C10  C3   C4   119.57  3.000
 49I  C2   C3   C4   119.06  3.000
 49I  C7   C2   C3   121.90  3.000
 49I  C3   C2   C1   119.00  3.000
 49I  C7   C2   C1   119.09  3.000
 49I  H4   C6   C5   120.41  3.000
 49I  H4   C6   C1   120.12  3.000
 49I  C5   C6   C1   119.46  3.000
 49I  H6   C7   H5   106.59  3.000
 49I  H6   C7   C8   109.09  3.000
 49I  H5   C7   C8   109.52  3.000
 49I  H6   C7   C2   108.97  3.000
 49I  H5   C7   C2   109.29  3.000
 49I  C8   C7   C2   113.17  3.000
 49I  H7   C8   C9   105.87  3.000
 49I  H7   C8   C11  105.06  3.000
 49I  C9   C8   C11  114.76  3.000
 49I  H7   C8   C7   106.47  3.000
 49I  C9   C8   C7   110.69  3.000
 49I  C11  C8   C7   113.21  3.000
 49I  N1   C16  C17  116.21  3.000
 49I  N1   C16  O3   122.15  3.000
 49I  C17  C16  O3   121.64  3.000
 49I  C22  C17  C18  119.05  3.000
 49I  C18  C17  C16  117.86  3.000
 49I  C22  C17  C16  123.07  3.000
 49I  H9   C18  C19  119.78  3.000
 49I  H9   C18  C17  119.71  3.000
 49I  C19  C18  C17  120.51  3.000
 49I  H10  C19  C20  120.14  3.000
 49I  H10  C19  C18  119.75  3.000
 49I  C20  C19  C18  120.12  3.000
 49I  H11  C20  C21  120.09  3.000
 49I  H11  C20  C19  120.16  3.000
 49I  C21  C20  C19  119.75  3.000
 49I  H12  C21  C22  119.62  3.000
 49I  H12  C21  C20  120.18  3.000
 49I  C22  C21  C20  120.21  3.000
 49I  H13  C22  C21  118.37  3.000
 49I  H13  C22  C17  121.25  3.000
 49I  C21  C22  C17  120.36  3.000
 49I  S1   C13  C14  113.49  3.000
 49I  S1   C13  N1   123.09  3.000
 49I  C14  C13  N1   123.42  3.000
 49I  C11  C14  C15  129.21  3.000
 49I  C11  C14  C13  110.72  3.000
 49I  C15  C14  C13  120.07  3.000
 49I  O2   C15  C14  116.36  3.000
 49I  C14  C15  O1   119.40  3.000
 49I  O2   C15  O1   124.24  3.000
 49I  C12  C11  C14  111.57  3.000
 49I  C12  C11  C8   118.05  3.000
 49I  C14  C11  C8   130.38  3.000
 49I  H15  C12  S1   119.51  3.000
 49I  H15  C12  C11  126.51  3.000
 49I  S1   C12  C11  113.98  3.000
 49I  C12  S1   C13   90.25  3.000
 49I  H17  C9   H16  107.26  3.000
 49I  H17  C9   C10  109.42  3.000
 49I  H16  C9   C10  110.53  3.000
 49I  H17  C9   C8   110.00  3.000
 49I  H16  C9   C8   109.85  3.000
 49I  C10  C9   C8   109.75  3.000
 49I  H19  C10  H18  105.66  3.000
 49I  H19  C10  C9   109.29  3.000
 49I  H18  C10  C9   110.24  3.000
 49I  H19  C10  C3   108.59  3.000
 49I  H18  C10  C3   109.51  3.000
 49I  C9   C10  C3   113.26  3.000
 49I  H14  N1   C13  107.78  3.000
 49I  H14  N1   C16  126.74  3.000
 49I  C13  N1   C16  125.43  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
 49I  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 49I  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 49I  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 49I  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 49I  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 49I  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 49I  CONST_07  C20  C21  C22  C17     0.00   0.0  0
 49I  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 49I  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 49I  CONST_10  C21  C22  C17  C18     0.00   0.0  0
 49I  CONST_11  C22  C21  C20  C19     0.00   0.0  0
 49I  CONST_12  C22  C17  C18  C19     0.00   0.0  0
 49I  CONST_13  C12  C11  C14  C13     0.00   0.0  0
 49I  CONST_14  C11  C12  S1   C13     0.00   0.0  0
 49I  CONST_15  C12  S1   C13  C14     0.00   0.0  0
 49I  CONST_16  S1   C12  C11  C14     0.00   0.0  0
 49I  CONST_17  S1   C13  C14  C11     0.00   0.0  0
 49I  CONST_18  C13  C14  C11  C8    180.00   0.0  0
 49I  CONST_19  S1   C12  C11  C8    180.00   0.0  0
 49I  CONST_20  C15  C14  C11  C8      0.00   0.0  0
 49I  CONST_21  C21  C22  C17  C16   180.00   0.0  0
 49I  CONST_22  C19  C18  C17  C16   180.00   0.0  0
 49I  CONST_23  C11  C14  C13  N1    180.00   0.0  0
 49I  CONST_24  C12  S1   C13  N1    180.00   0.0  0
 49I  CONST_25  S1   C13  C14  C15   180.00   0.0  0
 49I  CONST_26  C12  C11  C14  C15   180.00   0.0  0
 49I  CONST_27  H2   C5   C6   C1    180.00   0.0  0
 49I  CONST_28  H1   C1   C6   C5    180.00   0.0  0
 49I  CONST_29  H4   C6   C5   C4    180.00   0.0  0
 49I  CONST_30  H1   C1   C2   C3    180.00   0.0  0
 49I  CONST_31  H2   C5   C4   C3    180.00   0.0  0
 49I  CONST_32  H4   C6   C1   C2    180.00   0.0  0
 49I  CONST_33  H3   C4   C3   C2    180.00   0.0  0
 49I  CONST_34  H3   C4   C5   C6    180.00   0.0  0
 49I  CONST_35  H1   C1   C2   C7      0.00   0.0  0
 49I  CONST_36  H15  C12  C11  C8      0.00   0.0  0
 49I  CONST_37  H12  C21  C22  C17   180.00   0.0  0
 49I  CONST_38  H10  C19  C18  C17   180.00   0.0  0
 49I  CONST_39  H11  C20  C19  C18   180.00   0.0  0
 49I  CONST_40  H13  C22  C17  C18   180.00   0.0  0
 49I  CONST_41  H12  C21  C20  C19   180.00   0.0  0
 49I  CONST_42  H13  C22  C21  C20   180.00   0.0  0
 49I  CONST_43  H9   C18  C19  C20   180.00   0.0  0
 49I  CONST_44  H10  C19  C20  C21   180.00   0.0  0
 49I  CONST_45  H11  C20  C21  C22   180.00   0.0  0
 49I  CONST_46  H9   C18  C17  C22   180.00   0.0  0
 49I  CONST_47  H15  C12  S1   C13   180.00   0.0  0
 49I  CONST_48  H15  C12  C11  C14   180.00   0.0  0
 49I  CONST_49  H3   C4   C3   C10     0.00   0.0  0
 49I  CONST_50  C13  N1   C16  C17   180.00   0.0  0
 49I  CONST_51  C14  C13  N1   C16   180.00   0.0  0
 49I  CONST_52  S1   C13  N1   C16     0.00   0.0  0
 49I  CONST_53  H14  N1   C13  C14     0.00   0.0  0
 49I  CONST_54  H14  N1   C13  S1    180.00   0.0  0
 49I  CONST_55  C13  N1   C16  O3      0.00   0.0  0
 49I  CONST_56  H14  N1   C16  C17     0.00   0.0  0
 49I  CONST_57  H14  N1   C16  O3    180.00   0.0  0
 49I  Var_01    C8   C7   C2   C1    164.84  30.0  1
 49I  Var_02    C9   C10  C3   C4    161.95  30.0  1
 49I  Var_03    C8   C7   C2   C3    -16.36  30.0  1
 49I  Var_04    C8   C9   C10  C3     48.55  30.0  1
 49I  Var_05    C9   C10  C3   C2    -19.46  30.0  1
 49I  Var_06    H5   C7   C2   C1     42.50  30.0  1
 49I  Var_07    H6   C7   C2   C1    -73.61  30.0  1
 49I  Var_08    H18  C10  C3   C4     38.46  30.0  1
 49I  Var_09    H19  C10  C3   C4    -76.45  30.0  1
 49I  Var_10    H5   C7   C2   C3   -138.69  30.0  1
 49I  Var_11    H6   C7   C2   C3    105.19  30.0  1
 49I  Var_12    H16  C9   C10  C3    -72.75  30.0  1
 49I  Var_13    H17  C9   C10  C3    169.34  30.0  1
 49I  Var_14    H18  C10  C3   C2   -142.95  30.0  1
 49I  Var_15    H19  C10  C3   C2    102.13  30.0  1
 49I  Var_16    H18  C10  C9   C8    171.64  30.0  1
 49I  Var_17    H19  C10  C9   C8    -72.65  30.0  1
 49I  Var_18    C13  C14  C15  O1   -173.04  30.0  2
 49I  Var_19    C11  C14  C15  O1      6.09  30.0  2
 49I  Var_20    C22  C17  C16  O3   -163.48  30.0  2
 49I  Var_21    C18  C17  C16  O3     15.08  30.0  2
 49I  Var_22    N1   C16  C17  C18  -164.75  30.0  2
 49I  Var_23    N1   C16  C17  C22    16.69  30.0  2
 49I  Var_24    O2   C15  C14  C13     6.65  30.0  2
 49I  Var_25    C11  C14  C15  O2   -174.23  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
 49I  chir_01  C8  C11  C7  C9  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
 49I  plan-1  C8   0.020
 49I  plan-1  C13  0.020
 49I  plan-1  C14  0.020
 49I  plan-1  C15  0.020
 49I  plan-1  C11  0.020
 49I  plan-1  C12  0.020
 49I  plan-1  S1   0.020
 49I  plan-1  H15  0.020
 49I  plan-1  N1   0.020
 49I  plan-2  C16  0.020
 49I  plan-2  C17  0.020
 49I  plan-2  C18  0.020
 49I  plan-2  C19  0.020
 49I  plan-2  C20  0.020
 49I  plan-2  C21  0.020
 49I  plan-2  C22  0.020
 49I  plan-2  H9   0.020
 49I  plan-2  H10  0.020
 49I  plan-2  H11  0.020
 49I  plan-2  H12  0.020
 49I  plan-2  H13  0.020
 49I  plan-3  C1   0.020
 49I  plan-3  C5   0.020
 49I  plan-3  C4   0.020
 49I  plan-3  C3   0.020
 49I  plan-3  C2   0.020
 49I  plan-3  C6   0.020
 49I  plan-3  C7   0.020
 49I  plan-3  C10  0.020
 49I  plan-3  H1   0.020
 49I  plan-3  H2   0.020
 49I  plan-3  H3   0.020
 49I  plan-3  H4   0.020
 49I  plan-4  O3   0.020
 49I  plan-4  C16  0.020
 49I  plan-4  C17  0.020
 49I  plan-4  C13  0.020
 49I  plan-4  H14  0.020
 49I  plan-4  N1   0.020
 49I  plan-5  C14  0.020
 49I  plan-5  C15  0.020
 49I  plan-5  O2   0.020
 49I  plan-5  O1   0.020

