# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 06:33:23 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-benzamido-4-[(2~{S})-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
 4OY  4OY  "2-benzamido-4-[(2~{S})-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_4OY
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
 4OY  C1   C  CR16   0  -0.305  11.0548   7.5700   -8.4939
 4OY  C5   C  CR16   0  -0.261  12.1505   5.8243   -9.7189
 4OY  C4   C  CR16   0  -0.297  11.3822   4.8912   -9.0424
 4OY  C3   C  CR6    0   0.073  10.4421   5.2786   -8.0870
 4OY  C2   C  CR6    0   0.081  10.2744   6.6373   -7.8097
 4OY  C6   C  CR16   0  -0.260  11.9856   7.1766   -9.4415
 4OY  C7   C  CH2    0  -0.475   9.2515   7.1166   -6.8111
 4OY  C8   C  CH1    0  -0.305   8.7825   6.0207   -5.8523
 4OY  O3   O  O      0  -0.471   4.2221   8.4702   -2.0613
 4OY  C16  C  C      0   0.546   5.2932   8.8304   -1.5877
 4OY  C17  C  CR6    0  -0.054   5.3587   9.6947   -0.3731
 4OY  C18  C  CR16   0  -0.265   4.1518  10.0726    0.2147
 4OY  C19  C  CR16   0  -0.240   4.1370  10.8795    1.3410
 4OY  C20  C  CR16   0  -0.249   5.3304  11.3212    1.8965
 4OY  C21  C  CR16   0  -0.236   6.5371  10.9488    1.3196
 4OY  C22  C  CR16   0  -0.294   6.5533  10.1423    0.1920
 4OY  C13  C  CR5    0   0.099   6.6077   7.6965   -3.2657
 4OY  C14  C  CR5    0  -0.210   7.8314   7.3500   -3.8021
 4OY  C15  C  C      0   0.443   9.1241   7.7931   -3.1569
 4OY  O2   O  OC    -1  -0.610   9.0156   8.5139   -2.1228
 4OY  C11  C  CR5    0   0.249   7.6698   6.5350   -4.9793
 4OY  C12  C  CR15   0  -0.616   6.3581   6.3099   -5.2640
 4OY  S1   S  S2     0   0.230   5.2789   7.0567   -4.1505
 4OY  C9   C  CH2    0  -0.433   8.4076   4.7889   -6.6699
 4OY  C10  C  CH2    0  -0.502   9.6447   4.2286   -7.3563
 4OY  H1   H  HCR6   0   0.238  10.9267   8.6244   -8.2744
 4OY  H2   H  HCR6   0   0.245  12.8723   5.5006  -10.4579
 4OY  H3   H  HCR6   0   0.240  11.5082   3.8358   -9.2581
 4OY  H4   H  HCR6   0   0.246  12.5802   7.9182   -9.9598
 4OY  H5   H  HCH2   0   0.251   9.6544   7.9574   -6.2444
 4OY  H6   H  HCH2   0   0.235   8.3809   7.5012   -7.3544
 4OY  H7   H  HCH1   0   0.238   9.6233   5.7568   -5.2079
 4OY  H8   H  HCR6   0   0.258   3.2187   9.7327   -0.2134
 4OY  H9   H  HCR6   0   0.261   3.1922  11.1644    1.7849
 4OY  H10  H  HCR6   0   0.263   5.3210  11.9526    2.7754
 4OY  H11  H  HCR6   0   0.264   7.4716  11.2882    1.7464
 4OY  H12  H  HCR6   0   0.251   7.5153   9.8788   -0.2275
 4OY  H13  H  HNH1   0   0.461   7.4226   8.7198   -1.8024
 4OY  H15  H  HCR5   0   0.277   5.9488   5.7396   -6.0837
 4OY  H16  H  HCH2   0   0.219   7.6555   5.0450   -7.4236
 4OY  H17  H  HCH2   0   0.236   7.9636   4.0211   -6.0324
 4OY  H18  H  HCH2   0   0.246   9.3649   3.4328   -8.0510
 4OY  H19  H  HCH2   0   0.241  10.2884   3.7558   -6.6066
 4OY  N1   N  NH1    0  -0.765   6.4676   8.4691   -2.1385
 4OY  O1   O  O      0  -0.546  10.1978   7.4336   -3.6581

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
 4OY  C5   C6   aromatic  1.390  0.020  1.390
 4OY  C5   C4   aromatic  1.385  0.020  1.385
 4OY  C6   C1   aromatic  1.385  0.020  1.385
 4OY  C4   C3   aromatic  1.395  0.020  1.395
 4OY  C1   C2   aromatic  1.395  0.020  1.395
 4OY  C3   C2   aromatic  1.397  0.020  1.397
 4OY  C3   C10  single    1.507  0.020  1.507
 4OY  C2   C7   single    1.508  0.020  1.508
 4OY  C10  C9   single    1.522  0.020  1.522
 4OY  C7   C8   single    1.530  0.020  1.530
 4OY  C9   C8   single    1.525  0.020  1.525
 4OY  C8   C11  single    1.505  0.020  1.505
 4OY  C12  C11  aromatic  1.361  0.020  1.361
 4OY  C12  S1   aromatic  1.721  0.020  1.721
 4OY  C11  C14  aromatic  1.441  0.020  1.441
 4OY  S1   C13  aromatic  1.720  0.020  1.720
 4OY  O1   C15  deloc     1.238  0.020  1.238
 4OY  C14  C15  single    1.511  0.020  1.511
 4OY  C14  C13  aromatic  1.380  0.020  1.380
 4OY  C15  O2   deloc     1.265  0.020  1.265
 4OY  C13  N1   single    1.374  0.020  1.374
 4OY  N1   C16  single    1.347  0.020  1.347
 4OY  O3   C16  double    1.225  0.020  1.225
 4OY  C16  C17  single    1.492  0.020  1.492
 4OY  C17  C22  aromatic  1.395  0.020  1.395
 4OY  C17  C18  aromatic  1.395  0.020  1.395
 4OY  C22  C21  aromatic  1.386  0.020  1.386
 4OY  C18  C19  aromatic  1.386  0.020  1.386
 4OY  C21  C20  aromatic  1.388  0.020  1.388
 4OY  C19  C20  aromatic  1.388  0.020  1.388
 4OY  C1   H1   single    0.930  0.020  1.080
 4OY  C5   H2   single    0.930  0.020  1.080
 4OY  C4   H3   single    0.930  0.020  1.080
 4OY  C6   H4   single    0.930  0.020  1.080
 4OY  C7   H5   single    0.970  0.020  1.090
 4OY  C7   H6   single    0.970  0.020  1.090
 4OY  C8   H7   single    0.970  0.020  1.090
 4OY  C18  H8   single    0.930  0.020  1.080
 4OY  C19  H9   single    0.930  0.020  1.080
 4OY  C20  H10  single    0.930  0.020  1.080
 4OY  C21  H11  single    0.930  0.020  1.080
 4OY  C22  H12  single    0.930  0.020  1.080
 4OY  N1   H13  single    0.860  0.020  1.020
 4OY  C12  H15  single    0.930  0.020  1.080
 4OY  C9   H16  single    0.970  0.020  1.090
 4OY  C9   H17  single    0.970  0.020  1.090
 4OY  C10  H18  single    0.970  0.020  1.090
 4OY  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
 4OY  H1   C1   C6   119.60  3.000
 4OY  H1   C1   C2   118.98  3.000
 4OY  C6   C1   C2   121.42  3.000
 4OY  H2   C5   C6   120.41  3.000
 4OY  H2   C5   C4   120.12  3.000
 4OY  C6   C5   C4   119.47  3.000
 4OY  H3   C4   C3   118.99  3.000
 4OY  H3   C4   C5   119.60  3.000
 4OY  C3   C4   C5   121.41  3.000
 4OY  C10  C3   C2   121.19  3.000
 4OY  C10  C3   C4   119.67  3.000
 4OY  C2   C3   C4   119.14  3.000
 4OY  C7   C2   C3   121.47  3.000
 4OY  C7   C2   C1   119.45  3.000
 4OY  C3   C2   C1   119.06  3.000
 4OY  H4   C6   C5   120.38  3.000
 4OY  H4   C6   C1   120.12  3.000
 4OY  C5   C6   C1   119.50  3.000
 4OY  H6   C7   H5   106.28  3.000
 4OY  H6   C7   C8   108.58  3.000
 4OY  H5   C7   C8   109.86  3.000
 4OY  H6   C7   C2   108.79  3.000
 4OY  H5   C7   C2   109.78  3.000
 4OY  C8   C7   C2   113.29  3.000
 4OY  H7   C8   C9   108.09  3.000
 4OY  H7   C8   C11  108.04  3.000
 4OY  C9   C8   C11  113.91  3.000
 4OY  H7   C8   C7   107.88  3.000
 4OY  C11  C8   C7   110.21  3.000
 4OY  C9   C8   C7   108.54  3.000
 4OY  N1   C16  C17  116.75  3.000
 4OY  C17  C16  O3   121.55  3.000
 4OY  N1   C16  O3   121.70  3.000
 4OY  C22  C17  C18  118.91  3.000
 4OY  C18  C17  C16  117.52  3.000
 4OY  C22  C17  C16  123.57  3.000
 4OY  H8   C18  C19  119.71  3.000
 4OY  H8   C18  C17  119.65  3.000
 4OY  C19  C18  C17  120.64  3.000
 4OY  H9   C19  C20  120.17  3.000
 4OY  H9   C19  C18  119.74  3.000
 4OY  C20  C19  C18  120.08  3.000
 4OY  H10  C20  C21  120.10  3.000
 4OY  H10  C20  C19  120.20  3.000
 4OY  C21  C20  C19  119.70  3.000
 4OY  H11  C21  C22  119.55  3.000
 4OY  H11  C21  C20  120.18  3.000
 4OY  C22  C21  C20  120.28  3.000
 4OY  H12  C22  C21  117.86  3.000
 4OY  H12  C22  C17  121.75  3.000
 4OY  C21  C22  C17  120.39  3.000
 4OY  S1   C13  C14  113.06  3.000
 4OY  C14  C13  N1   123.40  3.000
 4OY  S1   C13  N1   123.54  3.000
 4OY  C11  C14  C15  127.63  3.000
 4OY  C15  C14  C13  121.26  3.000
 4OY  C11  C14  C13  111.11  3.000
 4OY  O2   C15  C14  116.27  3.000
 4OY  O2   C15  O1   124.79  3.000
 4OY  C14  C15  O1   118.93  3.000
 4OY  C12  C11  C14  111.87  3.000
 4OY  C14  C11  C8   125.76  3.000
 4OY  C12  C11  C8   122.33  3.000
 4OY  H15  C12  S1   118.88  3.000
 4OY  H15  C12  C11  127.72  3.000
 4OY  S1   C12  C11  113.40  3.000
 4OY  C12  S1   C13   90.56  3.000
 4OY  H17  C9   H16  106.67  3.000
 4OY  H17  C9   C10  109.57  3.000
 4OY  H16  C9   C10  109.51  3.000
 4OY  H17  C9   C8   110.78  3.000
 4OY  H16  C9   C8   110.42  3.000
 4OY  C10  C9   C8   109.84  3.000
 4OY  H19  C10  H18  105.74  3.000
 4OY  H19  C10  C9   109.14  3.000
 4OY  H18  C10  C9   110.29  3.000
 4OY  H19  C10  C3   108.76  3.000
 4OY  H18  C10  C3   109.55  3.000
 4OY  C9   C10  C3   113.09  3.000
 4OY  H13  N1   C13  107.83  3.000
 4OY  H13  N1   C16  127.03  3.000
 4OY  C13  N1   C16  125.13  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
 4OY  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 4OY  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 4OY  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 4OY  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 4OY  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 4OY  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 4OY  CONST_07  C20  C21  C22  C17     0.00   0.0  0
 4OY  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 4OY  CONST_09  C21  C22  C17  C18     0.00   0.0  0
 4OY  CONST_10  C21  C20  C19  C18     0.00   0.0  0
 4OY  CONST_11  C22  C17  C18  C19     0.00   0.0  0
 4OY  CONST_12  C22  C21  C20  C19     0.00   0.0  0
 4OY  CONST_13  C11  C12  S1   C13     0.00   0.0  0
 4OY  CONST_14  C12  C11  C14  C13     0.00   0.0  0
 4OY  CONST_15  S1   C12  C11  C14     0.00   0.0  0
 4OY  CONST_16  C12  S1   C13  C14     0.00   0.0  0
 4OY  CONST_17  S1   C13  C14  C11     0.00   0.0  0
 4OY  CONST_18  S1   C12  C11  C8    180.00   0.0  0
 4OY  CONST_19  C13  C14  C11  C8    180.00   0.0  0
 4OY  CONST_20  C15  C14  C11  C8      0.00   0.0  0
 4OY  CONST_21  C21  C22  C17  C16   180.00   0.0  0
 4OY  CONST_22  C19  C18  C17  C16   180.00   0.0  0
 4OY  CONST_23  C12  S1   C13  N1    180.00   0.0  0
 4OY  CONST_24  C11  C14  C13  N1    180.00   0.0  0
 4OY  CONST_25  C12  C11  C14  C15   180.00   0.0  0
 4OY  CONST_26  S1   C13  C14  C15   180.00   0.0  0
 4OY  CONST_27  H2   C5   C6   C1    180.00   0.0  0
 4OY  CONST_28  H1   C1   C6   C5    180.00   0.0  0
 4OY  CONST_29  H4   C6   C5   C4    180.00   0.0  0
 4OY  CONST_30  H2   C5   C4   C3    180.00   0.0  0
 4OY  CONST_31  H1   C1   C2   C3    180.00   0.0  0
 4OY  CONST_32  H4   C6   C1   C2    180.00   0.0  0
 4OY  CONST_33  H3   C4   C3   C2    180.00   0.0  0
 4OY  CONST_34  H3   C4   C5   C6    180.00   0.0  0
 4OY  CONST_35  H1   C1   C2   C7      0.00   0.0  0
 4OY  CONST_36  H15  C12  C11  C8      0.00   0.0  0
 4OY  CONST_37  H11  C21  C22  C17   180.00   0.0  0
 4OY  CONST_38  H9   C19  C18  C17   180.00   0.0  0
 4OY  CONST_39  H12  C22  C17  C18   180.00   0.0  0
 4OY  CONST_40  H10  C20  C19  C18   180.00   0.0  0
 4OY  CONST_41  H11  C21  C20  C19   180.00   0.0  0
 4OY  CONST_42  H12  C22  C21  C20   180.00   0.0  0
 4OY  CONST_43  H8   C18  C19  C20   180.00   0.0  0
 4OY  CONST_44  H9   C19  C20  C21   180.00   0.0  0
 4OY  CONST_45  H8   C18  C17  C22   180.00   0.0  0
 4OY  CONST_46  H10  C20  C21  C22   180.00   0.0  0
 4OY  CONST_47  H15  C12  S1   C13   180.00   0.0  0
 4OY  CONST_48  H15  C12  C11  C14   180.00   0.0  0
 4OY  CONST_49  H3   C4   C3   C10     0.00   0.0  0
 4OY  CONST_50  C13  N1   C16  C17   180.00   0.0  0
 4OY  CONST_51  S1   C13  N1   C16     0.00   0.0  0
 4OY  CONST_52  C14  C13  N1   C16   180.00   0.0  0
 4OY  CONST_53  H13  N1   C13  C14     0.00   0.0  0
 4OY  CONST_54  H13  N1   C13  S1    180.00   0.0  0
 4OY  CONST_55  C13  N1   C16  O3      0.00   0.0  0
 4OY  CONST_56  H13  N1   C16  C17     0.00   0.0  0
 4OY  CONST_57  H13  N1   C16  O3    180.00   0.0  0
 4OY  Var_01    C8   C7   C2   C1   -162.60  30.0  1
 4OY  Var_02    C9   C10  C3   C4   -163.10  30.0  1
 4OY  Var_03    C8   C7   C2   C3     18.69  30.0  1
 4OY  Var_04    C8   C9   C10  C3    -49.16  30.0  1
 4OY  Var_05    C9   C10  C3   C2     18.00  30.0  1
 4OY  Var_06    H5   C7   C2   C1    -39.38  30.0  1
 4OY  Var_07    H6   C7   C2   C1     76.54  30.0  1
 4OY  Var_08    H18  C10  C3   C4    -39.64  30.0  1
 4OY  Var_09    H19  C10  C3   C4     75.48  30.0  1
 4OY  Var_10    H5   C7   C2   C3    141.92  30.0  1
 4OY  Var_11    H6   C7   C2   C3   -102.16  30.0  1
 4OY  Var_12    H16  C9   C10  C3     72.26  30.0  1
 4OY  Var_13    H17  C9   C10  C3   -171.06  30.0  1
 4OY  Var_14    H18  C10  C3   C2    141.46  30.0  1
 4OY  Var_15    H19  C10  C3   C2   -103.42  30.0  1
 4OY  Var_16    H18  C10  C9   C8   -172.21  30.0  1
 4OY  Var_17    H19  C10  C9   C8     72.04  30.0  1
 4OY  Var_18    C11  C14  C15  O1     -0.39  30.0  2
 4OY  Var_19    C13  C14  C15  O1    178.46  30.0  2
 4OY  Var_20    C22  C17  C16  O3   -179.21  30.0  2
 4OY  Var_21    C18  C17  C16  O3      0.49  30.0  2
 4OY  Var_22    N1   C16  C17  C18  -179.67  30.0  2
 4OY  Var_23    N1   C16  C17  C22     0.64  30.0  2
 4OY  Var_24    O2   C15  C14  C13    -1.32  30.0  2
 4OY  Var_25    C11  C14  C15  O2    179.83  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
 4OY  chir_01  C8  C7  C9  C11  positiv

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
 4OY  plan-1  C8   0.020
 4OY  plan-1  C13  0.020
 4OY  plan-1  C14  0.020
 4OY  plan-1  C15  0.020
 4OY  plan-1  C11  0.020
 4OY  plan-1  C12  0.020
 4OY  plan-1  S1   0.020
 4OY  plan-1  H15  0.020
 4OY  plan-1  N1   0.020
 4OY  plan-2  C16  0.020
 4OY  plan-2  C17  0.020
 4OY  plan-2  C18  0.020
 4OY  plan-2  C19  0.020
 4OY  plan-2  C20  0.020
 4OY  plan-2  C21  0.020
 4OY  plan-2  C22  0.020
 4OY  plan-2  H8   0.020
 4OY  plan-2  H9   0.020
 4OY  plan-2  H10  0.020
 4OY  plan-2  H11  0.020
 4OY  plan-2  H12  0.020
 4OY  plan-3  C1   0.020
 4OY  plan-3  C5   0.020
 4OY  plan-3  C4   0.020
 4OY  plan-3  C3   0.020
 4OY  plan-3  C2   0.020
 4OY  plan-3  C6   0.020
 4OY  plan-3  C7   0.020
 4OY  plan-3  C10  0.020
 4OY  plan-3  H1   0.020
 4OY  plan-3  H2   0.020
 4OY  plan-3  H3   0.020
 4OY  plan-3  H4   0.020
 4OY  plan-4  O3   0.020
 4OY  plan-4  C16  0.020
 4OY  plan-4  C17  0.020
 4OY  plan-4  C13  0.020
 4OY  plan-4  H13  0.020
 4OY  plan-4  N1   0.020
 4OY  plan-5  C14  0.020
 4OY  plan-5  C15  0.020
 4OY  plan-5  O2   0.020
 4OY  plan-5  O1   0.020

