# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:11:39 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (2S)-(4-{3-[(4,5-dichloro-1-methyl-1H-indole-2-carbonyl)amino]oxetan-3-yl}phenyl)(pyridin-3-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(cc2c(Cl)c(Cl)ccc12)C(=O)NC3(COC3)c4ccc(cc4)[C@H](C(O)=O)c5cccnc5
#
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
 ONS  ONS  '(2S)-(4-{3-[(4,5-dichloro-1-methyl-1H-indole-2-carbonyl)amino]oxetan-3-yl}phenyl)(pyridin-3-yl)acetic acid'  ligand  55  35  .  2021-08-17  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ONS
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
 ONS  O2   O   OC    -1  -0.594  -3.1661   3.4864   0.5060
 ONS  C19  C   C      0   0.453  -4.3476   3.1016   0.5483
 ONS  O3   O   O      0  -0.584  -5.3206   3.6962   1.0415
 ONS  C18  C   CH1    0  -0.625  -4.6314   1.7413  -0.1558
 ONS  C20  C   CR6    0   0.127  -5.9838   1.1645   0.1588
 ONS  C21  C   CR16   0  -0.125  -6.8687   0.8362  -0.8615
 ONS  N2   N   N      0  -0.404  -8.0681   0.2935  -0.6747
 ONS  C22  C   CR16   0  -0.079  -8.4461   0.0472   0.5717
 ONS  C23  C   CR16   0  -0.326  -7.6478   0.3340   1.6715
 ONS  C24  C   CR16   0  -0.180  -6.4036   0.9014   1.4600
 ONS  C15  C   C      0   0.192  -3.5587   0.7061   0.0827
 ONS  C16  C   C1     0  -0.296  -3.1339  -0.1098  -0.9620
 ONS  C17  C   C1     0  -0.271  -2.2011  -1.1155  -0.7572
 ONS  C14  C   C1     0  -0.302  -3.0108   0.4862   1.3441
 ONS  C13  C   C1     0  -0.286  -2.0818  -0.5219   1.5540
 ONS  C12  C   C      0   0.067  -1.6717  -1.3425   0.5082
 ONS  C9   C   C      0  -0.002  -0.6116  -2.3977   0.7053
 ONS  C10  C   C      0  -0.124  -0.9258  -3.7691   0.0637
 ONS  O1   O   O      0  -0.503  -1.0038  -4.3982   1.3425
 ONS  C11  C   C      0  -0.122  -0.6808  -3.1900   2.0307
 ONS  N1   N   NH1    0  -0.676   0.6541  -1.7834   0.3618
 ONS  C8   C   C      0   0.505   1.8486  -2.4046   0.3534
 ONS  O    O   O      0  -0.470   2.0209  -3.5658   0.6892
 ONS  C6   C   CR5    0   0.265   2.9619  -1.5622  -0.1433
 ONS  C7   C   CR15   0  -0.419   2.9079  -0.6020  -1.1208
 ONS  N    N   NR5    0  -0.576   4.2559  -1.7351   0.2781
 ONS  C25  C   CH3    0  -0.527   4.7325  -2.6307   1.3127
 ONS  C5   C   CR5    0   0.368   5.0541  -0.8871  -0.4304
 ONS  C    C   C1     0  -0.310   6.4344  -0.6861  -0.3698
 ONS  C1   C   C1     0  -0.247   6.9840   0.2468  -1.2184
 ONS  C4   C   CR5    0   0.188   4.2379  -0.1594  -1.3221
 ONS  C3   C   C      0  -0.133   4.8248   0.7808  -2.1749
 ONS  CL   CL  CL     0  -0.099   3.8258   1.6608  -3.2625
 ONS  C2   C   C      0  -0.036   6.1878   0.9768  -2.1176
 ONS  CL1  CL  CL     0  -0.107   6.9509   2.1275  -3.1539
 ONS  H2   H   HCH1   0   0.274  -4.6201   1.9651  -1.2299
 ONS  H3   H   HCR6   0   0.249  -6.5843   1.0260  -1.8930
 ONS  H4   H   HCR6   0   0.258  -9.4254  -0.3991   0.7071
 ONS  H5   H   HCR6   0   0.265  -8.0014   0.1189   2.6708
 ONS  H6   H   HCR6   0   0.254  -5.7665   1.1313   2.3045
 ONS  H7   H   H      0   0.248  -3.5407   0.0400  -1.9554
 ONS  H8   H   H      0   0.258  -1.8907  -1.7278  -1.5962
 ONS  H9   H   H      0   0.247  -3.3024   1.1057   2.1833
 ONS  H10  H   H      0   0.257  -1.6744  -0.6593   2.5486
 ONS  H11  H   H      0   0.224  -1.8769  -3.8084  -0.4742
 ONS  H12  H   H      0   0.229  -0.1454  -4.1882  -0.5731
 ONS  H13  H   H      0   0.229   0.2554  -3.2509   2.5881
 ONS  H14  H   H      0   0.223  -1.4759  -2.8801   2.7135
 ONS  H15  H   HNH1   0   0.416   0.6401  -0.7910   0.1856
 ONS  H16  H   HCR5   0   0.274   2.0295  -0.2829  -1.6589
 ONS  H17  H   HCH3   0   0.260   4.8891  -3.6361   0.9275
 ONS  H18  H   HCH3   0   0.261   5.6752  -2.2526   1.6985
 ONS  H19  H   HCH3   0   0.265   4.0290  -2.6711   2.1380
 ONS  H20  H   H      0   0.284   7.0698  -1.2387   0.3083
 ONS  H21  H   H      0   0.285   8.0500   0.4261  -1.1998

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
 ONS  N2   C21  aromatic  1.330  0.020  1.330
 ONS  N2   C22  aromatic  1.326  0.020  1.326
 ONS  C21  C20  aromatic  1.390  0.020  1.390
 ONS  O3   C19  deloc     1.242  0.020  1.242
 ONS  C22  C23  aromatic  1.389  0.020  1.389
 ONS  C18  C20  single    1.504  0.020  1.504
 ONS  C18  C19  single    1.558  0.020  1.558
 ONS  C18  C15  single    1.510  0.020  1.510
 ONS  C20  C24  aromatic  1.392  0.020  1.392
 ONS  C19  O2   deloc     1.243  0.020  1.243
 ONS  C14  C15  aromatic  1.393  0.020  1.393
 ONS  C14  C13  aromatic  1.387  0.020  1.387
 ONS  C15  C16  aromatic  1.392  0.020  1.392
 ONS  C23  C24  aromatic  1.384  0.020  1.384
 ONS  C13  C12  aromatic  1.391  0.020  1.391
 ONS  C25  N    single    1.449  0.020  1.449
 ONS  O    C8   double    1.221  0.020  1.221
 ONS  C16  C17  aromatic  1.387  0.020  1.387
 ONS  C12  C17  aromatic  1.390  0.020  1.390
 ONS  C12  C9   single    1.509  0.020  1.509
 ONS  C11  C9   single    1.546  0.020  1.546
 ONS  C11  O1   single    1.427  0.020  1.427
 ONS  C8   C6   single    1.482  0.020  1.482
 ONS  C8   N1   single    1.346  0.020  1.346
 ONS  N    C6   aromatic  1.372  0.020  1.372
 ONS  N    C5   aromatic  1.363  0.020  1.363
 ONS  C9   N1   single    1.448  0.020  1.448
 ONS  C9   C10  single    1.546  0.020  1.546
 ONS  O1   C10  single    1.427  0.020  1.427
 ONS  C6   C7   aromatic  1.371  0.020  1.371
 ONS  C    C5   aromatic  1.396  0.020  1.396
 ONS  C    C1   aromatic  1.376  0.020  1.376
 ONS  C5   C4   aromatic  1.411  0.020  1.411
 ONS  C7   C4   aromatic  1.416  0.020  1.416
 ONS  C1   C2   aromatic  1.405  0.020  1.405
 ONS  C4   C3   aromatic  1.398  0.020  1.398
 ONS  C2   C3   aromatic  1.378  0.020  1.378
 ONS  C2   CL1  single    1.726  0.020  1.726
 ONS  C3   CL   single    1.719  0.020  1.719
 ONS  C18  H2   single    0.970  0.020  1.090
 ONS  C21  H3   single    0.930  0.020  1.080
 ONS  C22  H4   single    0.930  0.020  1.080
 ONS  C23  H5   single    0.930  0.020  1.080
 ONS  C24  H6   single    0.930  0.020  1.080
 ONS  C16  H7   single    0.930  0.020  1.080
 ONS  C17  H8   single    0.930  0.020  1.080
 ONS  C14  H9   single    0.930  0.020  1.080
 ONS  C13  H10  single    0.930  0.020  1.080
 ONS  C10  H11  single    0.970  0.020  1.090
 ONS  C10  H12  single    0.970  0.020  1.090
 ONS  C11  H13  single    0.970  0.020  1.090
 ONS  C11  H14  single    0.970  0.020  1.090
 ONS  N1   H15  single    0.860  0.020  1.020
 ONS  C7   H16  single    0.930  0.020  1.080
 ONS  C25  H17  single    0.970  0.020  1.090
 ONS  C25  H18  single    0.970  0.020  1.090
 ONS  C25  H19  single    0.970  0.020  1.090
 ONS  C    H20  single    0.930  0.020  1.080
 ONS  C1   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
 ONS  C18  C19  O3   117.04  3.000
 ONS  C18  C19  O2   115.35  3.000
 ONS  O3   C19  O2   127.56  3.000
 ONS  H2   C18  C15  106.69  3.000
 ONS  H2   C18  C20  107.00  3.000
 ONS  C15  C18  C20  110.06  3.000
 ONS  H2   C18  C19  105.22  3.000
 ONS  C15  C18  C19  113.45  3.000
 ONS  C20  C18  C19  113.85  3.000
 ONS  C24  C20  C21  116.71  3.000
 ONS  C24  C20  C18  122.63  3.000
 ONS  C21  C20  C18  120.64  3.000
 ONS  H3   C21  N2   116.14  3.000
 ONS  H3   C21  C20  119.27  3.000
 ONS  N2   C21  C20  124.58  3.000
 ONS  C22  N2   C21  117.71  3.000
 ONS  H4   C22  C23  120.34  3.000
 ONS  H4   C22  N2   116.82  3.000
 ONS  C23  C22  N2   122.85  3.000
 ONS  H5   C23  C24  121.11  3.000
 ONS  H5   C23  C22  120.18  3.000
 ONS  C24  C23  C22  118.71  3.000
 ONS  H6   C24  C23  119.80  3.000
 ONS  H6   C24  C20  120.76  3.000
 ONS  C23  C24  C20  119.43  3.000
 ONS  C14  C15  C16  117.85  3.000
 ONS  C16  C15  C18  120.01  3.000
 ONS  C14  C15  C18  122.06  3.000
 ONS  H7   C16  C17  119.21  3.000
 ONS  H7   C16  C15  119.49  3.000
 ONS  C17  C16  C15  121.29  3.000
 ONS  H8   C17  C12  120.21  3.000
 ONS  H8   C17  C16  119.20  3.000
 ONS  C12  C17  C16  120.59  3.000
 ONS  H9   C14  C13  118.61  3.000
 ONS  H9   C14  C15  120.37  3.000
 ONS  C13  C14  C15  121.02  3.000
 ONS  H10  C13  C12  120.29  3.000
 ONS  H10  C13  C14  118.88  3.000
 ONS  C12  C13  C14  120.83  3.000
 ONS  C9   C12  C13  121.43  3.000
 ONS  C9   C12  C17  120.04  3.000
 ONS  C13  C12  C17  118.40  3.000
 ONS  N1   C9   C11  117.38  3.000
 ONS  N1   C9   C10  117.09  3.000
 ONS  C11  C9   C10   83.80  3.000
 ONS  C10  C9   C12  115.05  3.000
 ONS  N1   C9   C12  106.64  3.000
 ONS  C11  C9   C12  116.05  3.000
 ONS  H12  C10  H11  108.74  3.000
 ONS  H12  C10  O1   113.13  3.000
 ONS  H11  C10  O1   112.18  3.000
 ONS  H12  C10  C9   115.95  3.000
 ONS  H11  C10  C9   114.37  3.000
 ONS  O1   C10  C9    91.73  3.000
 ONS  C11  O1   C10   92.67  3.000
 ONS  H14  C11  H13  108.72  3.000
 ONS  H14  C11  O1   112.12  3.000
 ONS  H13  C11  O1   113.15  3.000
 ONS  H14  C11  C9   115.02  3.000
 ONS  H13  C11  C9   115.35  3.000
 ONS  O1   C11  C9    91.75  3.000
 ONS  H15  N1   C8   117.75  3.000
 ONS  H15  N1   C9   116.54  3.000
 ONS  C8   N1   C9   125.53  3.000
 ONS  C6   C8   O    121.79  3.000
 ONS  C6   C8   N1   113.97  3.000
 ONS  O    C8   N1   124.21  3.000
 ONS  N    C6   C7   110.14  3.000
 ONS  C7   C6   C8   127.41  3.000
 ONS  N    C6   C8   122.28  3.000
 ONS  H16  C7   C4   126.99  3.000
 ONS  H16  C7   C6   126.51  3.000
 ONS  C4   C7   C6   106.45  3.000
 ONS  C5   N    C25  124.27  3.000
 ONS  C5   N    C6   108.31  3.000
 ONS  C25  N    C6   127.41  3.000
 ONS  H19  C25  H18  107.78  3.000
 ONS  H19  C25  H17  109.16  3.000
 ONS  H18  C25  H17  108.81  3.000
 ONS  H19  C25  N    110.66  3.000
 ONS  H18  C25  N    108.90  3.000
 ONS  H17  C25  N    111.45  3.000
 ONS  C4   C5   C    121.67  3.000
 ONS  C4   C5   N    108.10  3.000
 ONS  C    C5   N    130.23  3.000
 ONS  H20  C    C1   119.91  3.000
 ONS  H20  C    C5   122.32  3.000
 ONS  C1   C    C5   117.76  3.000
 ONS  H21  C1   C2   118.91  3.000
 ONS  H21  C1   C    119.72  3.000
 ONS  C2   C1   C    121.37  3.000
 ONS  C3   C4   C5   119.30  3.000
 ONS  C3   C4   C7   133.71  3.000
 ONS  C5   C4   C7   106.99  3.000
 ONS  C2   C3   CL   121.89  3.000
 ONS  CL   C3   C4   119.08  3.000
 ONS  C2   C3   C4   119.03  3.000
 ONS  CL1  C2   C3   120.46  3.000
 ONS  CL1  C2   C1   118.68  3.000
 ONS  C3   C2   C1   120.87  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
 ONS  CONST_01  C22  N2   C21  C20     0.00   0.0  0
 ONS  CONST_02  C22  C23  C24  C20     0.00   0.0  0
 ONS  CONST_03  C23  C22  N2   C21     0.00   0.0  0
 ONS  CONST_04  C23  C24  C20  C21     0.00   0.0  0
 ONS  CONST_05  C24  C20  C21  N2      0.00   0.0  0
 ONS  CONST_06  C24  C23  C22  N2      0.00   0.0  0
 ONS  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 ONS  CONST_08  C12  C17  C16  C15     0.00   0.0  0
 ONS  CONST_09  C13  C14  C15  C16     0.00   0.0  0
 ONS  CONST_10  C13  C12  C17  C16     0.00   0.0  0
 ONS  CONST_11  C14  C15  C16  C17     0.00   0.0  0
 ONS  CONST_12  C14  C13  C12  C17     0.00   0.0  0
 ONS  CONST_13  C    C5   N    C6    180.00   0.0  0
 ONS  CONST_14  C4   C5   N    C6      0.00   0.0  0
 ONS  CONST_15  C5   C4   C7   C6      0.00   0.0  0
 ONS  CONST_16  C3   C4   C7   C6    180.00   0.0  0
 ONS  CONST_17  C5   N    C6   C7      0.00   0.0  0
 ONS  CONST_18  N    C5   C4   C7      0.00   0.0  0
 ONS  CONST_19  C    C5   C4   C7    180.00   0.0  0
 ONS  CONST_20  C2   C3   C4   C7    180.00   0.0  0
 ONS  CONST_21  C4   C7   C6   N       0.00   0.0  0
 ONS  CONST_22  C1   C    C5   N     180.00   0.0  0
 ONS  CONST_23  C3   C4   C5   N     180.00   0.0  0
 ONS  CONST_24  C2   C1   C    C5      0.00   0.0  0
 ONS  CONST_25  C2   C3   C4   C5      0.00   0.0  0
 ONS  CONST_26  C3   C4   C5   C       0.00   0.0  0
 ONS  CONST_27  C3   C2   C1   C       0.00   0.0  0
 ONS  CONST_28  C4   C5   C    C1      0.00   0.0  0
 ONS  CONST_29  C4   C3   C2   C1      0.00   0.0  0
 ONS  CONST_30  C9   C12  C17  C16   180.00   0.0  0
 ONS  CONST_31  C9   C12  C13  C14   180.00   0.0  0
 ONS  CONST_32  N2   C21  C20  C18   180.00   0.0  0
 ONS  CONST_33  C23  C24  C20  C18   180.00   0.0  0
 ONS  CONST_34  C13  C14  C15  C18   180.00   0.0  0
 ONS  CONST_35  C17  C16  C15  C18   180.00   0.0  0
 ONS  CONST_36  C5   N    C6   C8    180.00   0.0  0
 ONS  CONST_37  C4   C7   C6   C8    180.00   0.0  0
 ONS  CONST_38  C25  N    C6   C7    180.00   0.0  0
 ONS  CONST_39  CL   C3   C4   C7      0.00   0.0  0
 ONS  CONST_40  C    C5   N    C25     0.00   0.0  0
 ONS  CONST_41  C4   C5   N    C25   180.00   0.0  0
 ONS  CONST_42  CL   C3   C4   C5    180.00   0.0  0
 ONS  CONST_43  CL1  C2   C1   C     180.00   0.0  0
 ONS  CONST_44  CL   C3   C2   C1    180.00   0.0  0
 ONS  CONST_45  CL1  C2   C3   C4    180.00   0.0  0
 ONS  CONST_46  H5   C23  C24  C20   180.00   0.0  0
 ONS  CONST_47  H4   C22  N2   C21   180.00   0.0  0
 ONS  CONST_48  H6   C24  C20  C21   180.00   0.0  0
 ONS  CONST_49  H3   C21  N2   C22   180.00   0.0  0
 ONS  CONST_50  H10  C13  C14  C15   180.00   0.0  0
 ONS  CONST_51  H8   C17  C16  C15   180.00   0.0  0
 ONS  CONST_52  H9   C14  C15  C16   180.00   0.0  0
 ONS  CONST_53  H7   C16  C15  C14   180.00   0.0  0
 ONS  CONST_54  H16  C7   C6   N     180.00   0.0  0
 ONS  CONST_55  H20  C    C5   N       0.00   0.0  0
 ONS  CONST_56  H21  C1   C    C5    180.00   0.0  0
 ONS  CONST_57  C6   C8   N1   C9    180.00   0.0  0
 ONS  CONST_58  O    C8   N1   C9      0.00   0.0  0
 ONS  CONST_59  H15  N1   C8   C6      0.00   0.0  0
 ONS  Var_01    H13  C11  O1   C10  -117.00  30.0  1
 ONS  Var_02    H11  C10  O1   C11  -118.89  30.0  1
 ONS  Var_03    N    C6   C8   N1    151.07  30.0  2
 ONS  Var_04    H17  C25  N    C6     83.90  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
 ONS  chir_01  C18  C20  C19  C15  negativ
 ONS  chir_02  C9   C10  C11  C12  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
 ONS  plan-1  C18  0.020
 ONS  plan-1  C20  0.020
 ONS  plan-1  C21  0.020
 ONS  plan-1  N2   0.020
 ONS  plan-1  C22  0.020
 ONS  plan-1  C23  0.020
 ONS  plan-1  C24  0.020
 ONS  plan-1  H3   0.020
 ONS  plan-1  H4   0.020
 ONS  plan-1  H5   0.020
 ONS  plan-1  H6   0.020
 ONS  plan-2  C18  0.020
 ONS  plan-2  C15  0.020
 ONS  plan-2  C16  0.020
 ONS  plan-2  C17  0.020
 ONS  plan-2  C14  0.020
 ONS  plan-2  C13  0.020
 ONS  plan-2  C12  0.020
 ONS  plan-2  C9   0.020
 ONS  plan-2  H7   0.020
 ONS  plan-2  H8   0.020
 ONS  plan-2  H9   0.020
 ONS  plan-2  H10  0.020
 ONS  plan-3  C8   0.020
 ONS  plan-3  C6   0.020
 ONS  plan-3  C7   0.020
 ONS  plan-3  N    0.020
 ONS  plan-3  C25  0.020
 ONS  plan-3  C5   0.020
 ONS  plan-3  C    0.020
 ONS  plan-3  C1   0.020
 ONS  plan-3  C4   0.020
 ONS  plan-3  C3   0.020
 ONS  plan-3  CL   0.020
 ONS  plan-3  C2   0.020
 ONS  plan-3  CL1  0.020
 ONS  plan-3  H16  0.020
 ONS  plan-3  H20  0.020
 ONS  plan-3  H21  0.020
 ONS  plan-4  C9   0.020
 ONS  plan-4  N1   0.020
 ONS  plan-4  C8   0.020
 ONS  plan-4  O    0.020
 ONS  plan-4  C6   0.020
 ONS  plan-4  H15  0.020
 ONS  plan-5  O2   0.020
 ONS  plan-5  C19  0.020
 ONS  plan-5  O3   0.020
 ONS  plan-5  C18  0.020

