# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 23:03:52 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 3-[1'-[(2~{S})-2-(4-chlorophenyl)-3-methyl-butanoyl]spiro[1,3-benzodioxole-2,4'-piperidine]-5-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](C(=O)N1CCC2(CC1)Oc3ccc(CCC(O)=O)cc3O2)c4ccc(Cl)cc4
#
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
 DLB  DLB  '3-[1'-[(2~{S})-2-(4-chlorophenyl)-3-methyl-butanoyl]spiro[1,3-benzodioxole-2,4'-piperidine]-5-yl]propanoic acid'  ligand  60  32  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DLB
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
 DLB  C10  C   CR6   0   0.169   4.3673  -0.1842  -0.2885
 DLB  C11  C   CR16  0  -0.327   4.2179  -1.0749  -1.3466
 DLB  C13  C   CR6   0  -0.056   5.3797  -2.7717  -0.1320
 DLB  C15  C   CR16  0  -0.295   5.0359  -0.6198   0.8540
 DLB  C17  C   CH1   0  -0.206   4.9752   2.2772  -0.4655
 DLB  C18  C   CH3   0  -0.657   5.9516   1.9306  -1.5852
 DLB  C19  C   CH3   0  -0.663   4.4041   3.6743  -0.6951
 DLB  C21  C   CR56  0   0.287  -3.2504   1.7418  -0.6839
 DLB  C22  C   CR56  0   0.330  -3.0762   0.4989  -0.0979
 DLB  C24  C   CR16  0  -0.402  -4.0622  -0.4554  -0.1067
 DLB  C25  C   CR6   0   0.108  -5.2743  -0.1332  -0.7394
 DLB  C26  C   CR16  0  -0.323  -5.4361   1.1154  -1.3257
 DLB  C27  C   CR16  0  -0.340  -4.4223   2.0821  -1.3110
 DLB  C28  C   CH2   0  -0.512  -6.4036  -1.1277  -0.7268
 DLB  C1   C   CH2   0  -0.330   0.6744   1.3845   1.7515
 DLB  C2   C   CH2   0  -0.461  -0.4719   2.2501   1.2361
 DLB  C3   C   CR5   0   0.441  -1.1363   1.6104   0.0352
 DLB  C4   C   CH2   0  -0.443  -0.1222   1.2345  -1.0337
 DLB  C5   C   CH2   0  -0.330   1.0151   0.4117  -0.4386
 DLB  N6   N   NT    0  -0.460   1.6194   1.1096   0.6815
 DLB  C7   C   C     0   0.597   2.9116   1.4935   0.7911
 DLB  O8   O   O     0  -0.494   3.3453   2.0058   1.8147
 DLB  C9   C   CH1   0  -0.465   3.8450   1.2322  -0.3929
 DLB  C12  C   CR16  0  -0.197   4.7182  -2.3672  -1.2792
 DLB  C14  C   CR16  0  -0.195   5.5443  -1.9067   0.9392
 DLB  CL   CL  CL    0  -0.132   6.0143  -4.3830  -0.0348
 DLB  O20  O   O     0  -0.497  -2.1279   2.4830  -0.5101
 DLB  O23  O   O     0  -0.494  -1.8421   0.4322   0.4547
 DLB  C29  C   CH2   0  -0.574  -7.2542  -0.9639   0.5283
 DLB  C30  C   C     0   0.551  -8.3870  -1.9476   0.6227
 DLB  O31  O   OH1   0  -0.597  -9.0920  -1.7774   1.7370
 DLB  O32  O   O     0  -0.445  -8.6455  -2.7935  -0.1968
 DLB  H1   H   HCR6  0   0.265   3.7116  -0.7581  -2.2509
 DLB  H2   H   HCR6  0   0.263   5.1686   0.0500   1.6940
 DLB  H3   H   HCH1  0   0.230   5.5214   2.2689   0.4818
 DLB  H4   H   HCH3  0   0.234   6.7370   2.6849  -1.6515
 DLB  H5   H   HCH3  0   0.235   6.4336   0.9657  -1.4299
 DLB  H6   H   HCH3  0   0.215   5.4445   1.8960  -2.5530
 DLB  H7   H   HCH3  0   0.216   3.8611   3.7162  -1.6427
 DLB  H8   H   HCH3  0   0.234   3.7222   3.9832   0.0964
 DLB  H9   H   HCH3  0   0.233   5.2052   4.4130  -0.7432
 DLB  H10  H   HCR6  0   0.264  -3.9134  -1.4236   0.3556
 DLB  H11  H   HCR6  0   0.250  -6.3734   1.3533  -1.8139
 DLB  H12  H   HCR6  0   0.269  -4.5631   3.0503  -1.7728
 DLB  H13  H   HCH2  0   0.254  -7.0272  -0.9939  -1.6125
 DLB  H14  H   HCH2  0   0.253  -6.0042  -2.1427  -0.7725
 DLB  H15  H   HCH2  0   0.279   1.1836   1.8910   2.5651
 DLB  H16  H   HCH2  0   0.255   0.2918   0.4382   2.1460
 DLB  H17  H   HCH2  0   0.266  -1.2061   2.4072   2.0291
 DLB  H18  H   HCH2  0   0.260  -0.0831   3.2276   0.9421
 DLB  H19  H   HCH2  0   0.263  -0.6073   0.6692  -1.8334
 DLB  H20  H   HCH2  0   0.258   0.2811   2.1502  -1.4731
 DLB  H21  H   HCH2  0   0.263   0.6436  -0.5562  -0.0885
 DLB  H22  H   HCH2  0   0.277   1.7437   0.1979  -1.2118
 DLB  H23  H   HCH1  0   0.266   3.2912   1.3186  -1.3319
 DLB  H24  H   HCR6  0   0.280   4.5939  -3.0450  -2.1128
 DLB  H25  H   HCR6  0   0.279   6.0632  -2.2296   1.8315
 DLB  H26  H   HCH2  0   0.286  -6.6366  -1.0630   1.4259
 DLB  H27  H   HCH2  0   0.287  -7.6735   0.0459   0.5736
 DLB  H28  H   HOH1  0   0.479  -9.8146  -2.4215   1.7748

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
 DLB  C28  C25  single    1.505  0.020  1.505
 DLB  C28  C29  single    1.525  0.020  1.525
 DLB  C18  C17  single    1.526  0.020  1.526
 DLB  C24  C25  aromatic  1.405  0.020  1.405
 DLB  C24  C22  aromatic  1.372  0.020  1.372
 DLB  C2   C1   single    1.526  0.020  1.526
 DLB  C2   C3   single    1.514  0.020  1.514
 DLB  O23  C22  single    1.354  0.020  1.354
 DLB  O23  C3   single    1.436  0.020  1.436
 DLB  C25  C26  aromatic  1.389  0.020  1.389
 DLB  C22  C21  aromatic  1.385  0.020  1.385
 DLB  C1   N6   single    1.454  0.020  1.454
 DLB  O32  C30  double    1.206  0.020  1.206
 DLB  C9   C17  single    1.541  0.020  1.541
 DLB  C9   C7   single    1.530  0.020  1.530
 DLB  C9   C10  single    1.513  0.020  1.513
 DLB  C29  C30  single    1.503  0.020  1.503
 DLB  C19  C17  single    1.527  0.020  1.527
 DLB  C3   O20  single    1.429  0.020  1.429
 DLB  C3   C4   single    1.521  0.020  1.521
 DLB  N6   C7   single    1.352  0.020  1.352
 DLB  N6   C5   single    1.451  0.020  1.451
 DLB  C30  O31  single    1.330  0.020  1.330
 DLB  C15  C10  aromatic  1.394  0.020  1.394
 DLB  C15  C14  aromatic  1.386  0.020  1.386
 DLB  C7   O8   double    1.224  0.020  1.224
 DLB  C5   C4   single    1.525  0.020  1.525
 DLB  C26  C27  aromatic  1.401  0.020  1.401
 DLB  C21  O20  single    1.356  0.020  1.356
 DLB  C21  C27  aromatic  1.372  0.020  1.372
 DLB  C10  C11  aromatic  1.391  0.020  1.391
 DLB  C14  C13  aromatic  1.387  0.020  1.387
 DLB  C11  C12  aromatic  1.387  0.020  1.387
 DLB  C13  C12  aromatic  1.385  0.020  1.385
 DLB  C13  CL   single    1.734  0.020  1.734
 DLB  C11  H1   single    0.930  0.020  1.080
 DLB  C15  H2   single    0.930  0.020  1.080
 DLB  C17  H3   single    0.970  0.020  1.090
 DLB  C18  H4   single    0.970  0.020  1.090
 DLB  C18  H5   single    0.970  0.020  1.090
 DLB  C18  H6   single    0.970  0.020  1.090
 DLB  C19  H7   single    0.970  0.020  1.090
 DLB  C19  H8   single    0.970  0.020  1.090
 DLB  C19  H9   single    0.970  0.020  1.090
 DLB  C24  H10  single    0.930  0.020  1.080
 DLB  C26  H11  single    0.930  0.020  1.080
 DLB  C27  H12  single    0.930  0.020  1.080
 DLB  C28  H13  single    0.970  0.020  1.090
 DLB  C28  H14  single    0.970  0.020  1.090
 DLB  C1   H15  single    0.970  0.020  1.090
 DLB  C1   H16  single    0.970  0.020  1.090
 DLB  C2   H17  single    0.970  0.020  1.090
 DLB  C2   H18  single    0.970  0.020  1.090
 DLB  C4   H19  single    0.970  0.020  1.090
 DLB  C4   H20  single    0.970  0.020  1.090
 DLB  C5   H21  single    0.970  0.020  1.090
 DLB  C5   H22  single    0.970  0.020  1.090
 DLB  C9   H23  single    0.970  0.020  1.090
 DLB  C12  H24  single    0.930  0.020  1.080
 DLB  C14  H25  single    0.930  0.020  1.080
 DLB  C29  H26  single    0.970  0.020  1.090
 DLB  C29  H27  single    0.970  0.020  1.090
 DLB  O31  H28  single    0.850  0.020  0.980

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
 DLB  C9   C10  C15  120.98  3.000
 DLB  C15  C10  C11  118.36  3.000
 DLB  C9   C10  C11  120.65  3.000
 DLB  H1   C11  C12  118.77  3.000
 DLB  H1   C11  C10  119.85  3.000
 DLB  C12  C11  C10  121.38  3.000
 DLB  CL   C13  C14  119.53  3.000
 DLB  CL   C13  C12  119.51  3.000
 DLB  C14  C13  C12  120.97  3.000
 DLB  H2   C15  C14  118.80  3.000
 DLB  H2   C15  C10  120.10  3.000
 DLB  C14  C15  C10  121.09  3.000
 DLB  H3   C17  C9   108.69  3.000
 DLB  H3   C17  C19  108.91  3.000
 DLB  C9   C17  C19  110.69  3.000
 DLB  H3   C17  C18  108.32  3.000
 DLB  C19  C17  C18  109.69  3.000
 DLB  C9   C17  C18  110.48  3.000
 DLB  H6   C18  H5   107.66  3.000
 DLB  H6   C18  H4   107.58  3.000
 DLB  H5   C18  H4   107.61  3.000
 DLB  H6   C18  C17  111.11  3.000
 DLB  H5   C18  C17  112.31  3.000
 DLB  H4   C18  C17  110.38  3.000
 DLB  H9   C19  H8   107.43  3.000
 DLB  H9   C19  H7   107.50  3.000
 DLB  H8   C19  H7   107.94  3.000
 DLB  H9   C19  C17  110.59  3.000
 DLB  H8   C19  C17  112.60  3.000
 DLB  H7   C19  C17  110.57  3.000
 DLB  O20  C21  C27  129.05  3.000
 DLB  C27  C21  C22  121.56  3.000
 DLB  O20  C21  C22  109.39  3.000
 DLB  O23  C22  C24  128.56  3.000
 DLB  O23  C22  C21  109.36  3.000
 DLB  C24  C22  C21  122.07  3.000
 DLB  H10  C24  C25  121.05  3.000
 DLB  H10  C24  C22  121.35  3.000
 DLB  C25  C24  C22  117.61  3.000
 DLB  C28  C25  C26  120.68  3.000
 DLB  C26  C25  C24  119.79  3.000
 DLB  C28  C25  C24  119.48  3.000
 DLB  H11  C26  C27  118.64  3.000
 DLB  H11  C26  C25  119.24  3.000
 DLB  C27  C26  C25  122.12  3.000
 DLB  H12  C27  C26  121.26  3.000
 DLB  H12  C27  C21  121.88  3.000
 DLB  C26  C27  C21  116.85  3.000
 DLB  H14  C28  H13  106.80  3.000
 DLB  H14  C28  C29  109.77  3.000
 DLB  H13  C28  C29  109.63  3.000
 DLB  H14  C28  C25  109.85  3.000
 DLB  H13  C28  C25  109.94  3.000
 DLB  C29  C28  C25  110.76  3.000
 DLB  H16  C1   H15  107.30  3.000
 DLB  H16  C1   N6   109.21  3.000
 DLB  H15  C1   N6   109.58  3.000
 DLB  H16  C1   C2   110.46  3.000
 DLB  H15  C1   C2   109.93  3.000
 DLB  N6   C1   C2   110.30  3.000
 DLB  H18  C2   H17  107.82  3.000
 DLB  H18  C2   C3   108.70  3.000
 DLB  H17  C2   C3   109.98  3.000
 DLB  H18  C2   C1   109.34  3.000
 DLB  H17  C2   C1   109.96  3.000
 DLB  C3   C2   C1   110.97  3.000
 DLB  O23  C3   O20  105.74  3.000
 DLB  O20  C3   C4   110.21  3.000
 DLB  O23  C3   C4   109.29  3.000
 DLB  C4   C3   C2   111.68  3.000
 DLB  O20  C3   C2   110.44  3.000
 DLB  O23  C3   C2   109.30  3.000
 DLB  H20  C4   H19  107.64  3.000
 DLB  H20  C4   C5   109.50  3.000
 DLB  H19  C4   C5   109.73  3.000
 DLB  H20  C4   C3   108.76  3.000
 DLB  H19  C4   C3   110.26  3.000
 DLB  C5   C4   C3   110.88  3.000
 DLB  H22  C5   H21  106.38  3.000
 DLB  H22  C5   N6   111.44  3.000
 DLB  H21  C5   N6   108.65  3.000
 DLB  H22  C5   C4   109.24  3.000
 DLB  H21  C5   C4   110.43  3.000
 DLB  N6   C5   C4   110.63  3.000
 DLB  C7   N6   C5   126.64  3.000
 DLB  C5   N6   C1   112.85  3.000
 DLB  C7   N6   C1   120.51  3.000
 DLB  C9   C7   O8   120.16  3.000
 DLB  O8   C7   N6   121.67  3.000
 DLB  C9   C7   N6   118.14  3.000
 DLB  H23  C9   C7   110.00  3.000
 DLB  H23  C9   C17  106.10  3.000
 DLB  C7   C9   C17  111.59  3.000
 DLB  H23  C9   C10  107.94  3.000
 DLB  C7   C9   C10  108.48  3.000
 DLB  C17  C9   C10  112.64  3.000
 DLB  H24  C12  C13  120.70  3.000
 DLB  H24  C12  C11  120.32  3.000
 DLB  C13  C12  C11  118.98  3.000
 DLB  H25  C14  C15  120.25  3.000
 DLB  H25  C14  C13  120.53  3.000
 DLB  C15  C14  C13  119.22  3.000
 DLB  C3   O20  C21  106.83  3.000
 DLB  C3   O23  C22  106.76  3.000
 DLB  H27  C29  H26  105.42  3.000
 DLB  H27  C29  C30  108.21  3.000
 DLB  H26  C29  C30  108.34  3.000
 DLB  H27  C29  C28  110.30  3.000
 DLB  H26  C29  C28  110.53  3.000
 DLB  C30  C29  C28  113.69  3.000
 DLB  O32  C30  O31  123.08  3.000
 DLB  O31  C30  C29  111.62  3.000
 DLB  O32  C30  C29  125.31  3.000
 DLB  H28  O31  C30  110.07  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
 DLB  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 DLB  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 DLB  CONST_03  C14  C15  C10  C11     0.00   0.0  0
 DLB  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 DLB  CONST_05  C12  C11  C10  C15     0.00   0.0  0
 DLB  CONST_06  C12  C13  C14  C15     0.00   0.0  0
 DLB  CONST_07  C25  C24  C22  C21     0.00   0.0  0
 DLB  CONST_08  C25  C26  C27  C21     0.00   0.0  0
 DLB  CONST_09  C26  C25  C24  C22     0.00   0.0  0
 DLB  CONST_10  C26  C27  C21  C22     0.00   0.0  0
 DLB  CONST_11  C27  C26  C25  C24     0.00   0.0  0
 DLB  CONST_12  C27  C21  C22  C24     0.00   0.0  0
 DLB  CONST_13  CL   C13  C12  C11   180.00   0.0  0
 DLB  CONST_14  CL   C13  C14  C15   180.00   0.0  0
 DLB  CONST_15  C28  C25  C24  C22   180.00   0.0  0
 DLB  CONST_16  C28  C25  C26  C27   180.00   0.0  0
 DLB  CONST_17  C14  C15  C10  C9    180.00   0.0  0
 DLB  CONST_18  C12  C11  C10  C9    180.00   0.0  0
 DLB  CONST_19  H25  C14  C15  C10   180.00   0.0  0
 DLB  CONST_20  H24  C12  C11  C10   180.00   0.0  0
 DLB  CONST_21  H2   C15  C10  C11   180.00   0.0  0
 DLB  CONST_22  H1   C11  C12  C13   180.00   0.0  0
 DLB  CONST_23  H10  C24  C22  C21   180.00   0.0  0
 DLB  CONST_24  H11  C26  C27  C21   180.00   0.0  0
 DLB  CONST_25  H12  C27  C21  C22   180.00   0.0  0
 DLB  CONST_26  C9   C7   N6   C1    180.00   0.0  0
 DLB  CONST_27  O8   C7   N6   C1      0.00   0.0  0
 DLB  CONST_28  C9   C7   N6   C5      0.00   0.0  0
 DLB  CONST_29  O8   C7   N6   C5    180.00   0.0  0
 DLB  CONST_30  H28  O31  C30  C29   180.00   0.0  0
 DLB  Var_01    C2   C3   O20  C21  -131.51  30.0  1
 DLB  Var_02    C4   C5   N6   C1     59.60  30.0  1
 DLB  Var_03    C5   N6   C1   C2    -59.75  30.0  1
 DLB  Var_04    C5   C4   C3   C2     51.49  30.0  3
 DLB  Var_05    N6   C1   C2   C3     54.97  30.0  1
 DLB  Var_06    N6   C5   C4   C3    -54.38  30.0  1
 DLB  Var_07    C29  C28  C25  C24    87.24  30.0  3
 DLB  Var_08    C30  C29  C28  C25  -178.75  30.0  3
 DLB  Var_09    O32  C30  C29  C28    -0.72  30.0  3
 DLB  Var_10    H7   C19  C17  C18    60.95  30.0  3
 DLB  Var_11    H4   C18  C17  C19    56.28  30.0  3

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
 DLB  chir_01  C9  C17  C7  C10  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
 DLB  plan-1  C10  0.020
 DLB  plan-1  C11  0.020
 DLB  plan-1  C13  0.020
 DLB  plan-1  C15  0.020
 DLB  plan-1  C9   0.020
 DLB  plan-1  C12  0.020
 DLB  plan-1  C14  0.020
 DLB  plan-1  CL   0.020
 DLB  plan-1  H1   0.020
 DLB  plan-1  H2   0.020
 DLB  plan-1  H24  0.020
 DLB  plan-1  H25  0.020
 DLB  plan-2  C21  0.020
 DLB  plan-2  C22  0.020
 DLB  plan-2  C24  0.020
 DLB  plan-2  C25  0.020
 DLB  plan-2  C26  0.020
 DLB  plan-2  C27  0.020
 DLB  plan-2  C28  0.020
 DLB  plan-2  O20  0.020
 DLB  plan-2  O23  0.020
 DLB  plan-2  H10  0.020
 DLB  plan-2  H11  0.020
 DLB  plan-2  H12  0.020
 DLB  plan-3  C1   0.020
 DLB  plan-3  C5   0.020
 DLB  plan-3  N6   0.020
 DLB  plan-3  C7   0.020
 DLB  plan-3  O8   0.020
 DLB  plan-3  C9   0.020
 DLB  plan-4  C29  0.020
 DLB  plan-4  C30  0.020
 DLB  plan-4  O31  0.020
 DLB  plan-4  O32  0.020
 DLB  plan-4  H28  0.020

