# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 16:55:39 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 4-({5-bromo-1'-[(2-chlorophenyl)sulfonyl]-2-oxospiro[indole-3,4'-piperidin]-1(2H)-yl}methyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(CN2C(=O)C3(CCN(CC3)[S](=O)(=O)c4ccccc4Cl)c5cc(Br)ccc25)cc1
#
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
 9LV  9LV  '4-({5-bromo-1'-[(2-chlorophenyl)sulfonyl]-2-oxospiro[indole-3,4'-piperidin]-1(2H)-yl}methyl)benzoic acid'  ligand  58  36  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9LV
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
 9LV  C4    C   CR5   0  -0.379   0.2009   0.0955  -0.5769
 9LV  C5    C   CR56  0   0.156  -0.5299  -1.1537  -0.1772
 9LV  C6    C   CR56  0   0.396  -1.8040  -1.1364  -0.7333
 9LV  C7    C   CR6   0  -0.134   5.1944   1.3438  -0.1158
 9LV  C10   C   CH2   0  -0.408   0.5092   0.9624   0.6576
 9LV  C15   C   CR16  0  -0.296  -2.7103  -2.1545  -0.5100
 9LV  C17   C   CR16  0  -0.318  -0.1274  -2.2034   0.6176
 9LV  C20   C   CH2   0  -0.287   1.3780   2.1717   0.3554
 9LV  C21   C   CR6   0  -0.094  -6.4591   1.5552   0.3009
 9LV  C24   C   CR16  0  -0.244  -6.6852   0.9716  -0.9448
 9LV  C26   C   CR6   0   0.092  -4.3061   0.7525  -1.2946
 9LV  O28   O   OH1   0  -0.593  -8.7644   1.7681   0.6717
 9LV  O22   O   O     0  -0.439  -7.3945   2.5158   2.2632
 9LV  C23   C   CR16  0  -0.237  -5.1493   1.7295   0.7400
 9LV  C32   C   CR16  0  -0.270  -4.0843   1.3324  -0.0499
 9LV  N2    N   NR5   0  -0.598  -1.9627   0.0156  -1.4956
 9LV  C3    C   CR5   0   0.606  -0.8304   0.7851  -1.4745
 9LV  O16   O   O     0  -0.438  -0.7002   1.8353  -2.0650
 9LV  N8    N   N     0  -0.597   2.5808   1.7285  -0.3450
 9LV  C19   C   CH2   0  -0.300   2.3468   1.0231  -1.6021
 9LV  C9    C   CH2   0  -0.402   1.5024  -0.2111  -1.3317
 9LV  S1    S   S     0   1.401   3.9565   2.6152  -0.2485
 9LV  O12   O   OS    0  -0.645   3.9208   3.3819   0.9848
 9LV  O13   O   OS    0  -0.646   4.2199   3.3277  -1.4914
 9LV  C30   C   CR16  0  -0.254   6.1695   1.2687  -1.1023
 9LV  C35   C   CR16  0  -0.232   7.1663   0.3088  -1.0270
 9LV  C36   C   CR16  0  -0.248   7.1901  -0.5768   0.0386
 9LV  C34   C   CR16  0  -0.200   6.2211  -0.5089   1.0291
 9LV  C18   C   CR6   0  -0.016   5.2240   0.4501   0.9542
 9LV  CL29  CL  CL    0  -0.088   4.0412   0.4890   2.2082
 9LV  C25   C   CR6   0  -0.119  -1.0353  -3.2373   0.8428
 9LV  BR33  BR  BR    0  -0.048  -0.5160  -4.6936   1.9288
 9LV  C27   C   CR16  0  -0.238  -2.3079  -3.2195   0.2927
 9LV  C31   C   CR16  0  -0.283  -5.6161   0.5731  -1.7288
 9LV  H1    H   HCH2  0   0.267  -0.4168   1.2982   1.1308
 9LV  H2    H   HCH2  0   0.257   1.0255   0.3330   1.3863
 9LV  H3    H   HCR6  0   0.281  -3.7065  -2.1468  -0.9309
 9LV  H4    H   HCR6  0   0.273   0.8635  -2.2242   1.0547
 9LV  H5    H   HCH2  0   0.255   0.8337   2.9130  -0.2353
 9LV  H6    H   HCH2  0   0.279   1.6586   2.6373   1.2970
 9LV  H7    H   HCR6  0   0.270  -7.6899   0.8177  -1.3130
 9LV  H8    H   HOH1  0   0.488  -9.4494   2.0667   1.2883
 9LV  H9    H   HCR6  0   0.268  -4.9549   2.1784   1.7045
 9LV  H10   H   HCR6  0   0.257  -3.0776   1.4805   0.3197
 9LV  H11   H   HCH2  0   0.285  -3.4704  -0.4988  -2.8215
 9LV  H12   H   HCH2  0   0.304  -2.9426   1.1666  -2.8884
 9LV  H13   H   HCH2  0   0.265   1.8730   1.6776  -2.3371
 9LV  H14   H   HCH2  0   0.273   3.2974   0.6931  -2.0241
 9LV  H15   H   HCH2  0   0.259   2.0865  -0.9044  -0.7214
 9LV  H16   H   HCH2  0   0.269   1.2880  -0.7147  -2.2761
 9LV  H17   H   HCR6  0   0.293   6.1519   1.9590  -1.9335
 9LV  H18   H   HCR6  0   0.279   7.9187   0.2559  -1.8012
 9LV  H19   H   HCR6  0   0.284   7.9638  -1.3292   0.1068
 9LV  H20   H   HCR6  0   0.293   6.2386  -1.2009   1.8597
 9LV  H21   H   HCR6  0   0.285  -3.0035  -4.0261   0.4805
 9LV  H22   H   HCR6  0   0.265  -5.8074   0.1150  -2.6918
 9LV  C14   C   CH2   0  -0.379  -3.1703   0.3493  -2.2021
 9LV  C11   C   C     0   0.533  -7.5641   1.9980   1.1850

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
 9LV  BR33  C25  single    1.889  0.020  1.889
 9LV  C27   C25  aromatic  1.386  0.020  1.386
 9LV  C27   C15  aromatic  1.393  0.020  1.393
 9LV  C25   C17  aromatic  1.394  0.020  1.394
 9LV  C15   C6   aromatic  1.381  0.020  1.381
 9LV  O22   C11  double    1.208  0.020  1.208
 9LV  C24   C31  aromatic  1.384  0.020  1.384
 9LV  C24   C21  aromatic  1.394  0.020  1.394
 9LV  C31   C26  aromatic  1.392  0.020  1.392
 9LV  C17   C5   aromatic  1.377  0.020  1.377
 9LV  C6    C5   aromatic  1.390  0.020  1.390
 9LV  C6    N2   single    1.390  0.020  1.390
 9LV  C11   C21  single    1.483  0.020  1.483
 9LV  C11   O28  single    1.326  0.020  1.326
 9LV  C21   C23  aromatic  1.392  0.020  1.392
 9LV  C26   C14  single    1.509  0.020  1.509
 9LV  C26   C32  aromatic  1.391  0.020  1.391
 9LV  C5    C4   single    1.501  0.020  1.501
 9LV  C14   N2   single    1.438  0.020  1.438
 9LV  N2    C3   single    1.369  0.020  1.369
 9LV  C23   C32  aromatic  1.384  0.020  1.384
 9LV  C4    C3   single    1.531  0.020  1.531
 9LV  C4    C10  single    1.540  0.020  1.540
 9LV  C4    C9   single    1.536  0.020  1.536
 9LV  C3    O16  double    1.212  0.020  1.212
 9LV  C10   C20  single    1.519  0.020  1.519
 9LV  C9    C19  single    1.520  0.020  1.520
 9LV  C20   N8   single    1.461  0.020  1.461
 9LV  N8    C19  single    1.460  0.020  1.460
 9LV  N8    S1   single    1.639  0.020  1.639
 9LV  O13   S1   double    1.457  0.020  1.457
 9LV  S1    O12  double    1.453  0.020  1.453
 9LV  S1    C7   single    1.779  0.020  1.779
 9LV  CL29  C18  single    1.724  0.020  1.724
 9LV  C7    C18  aromatic  1.394  0.020  1.394
 9LV  C7    C30  aromatic  1.389  0.020  1.389
 9LV  C18   C34  aromatic  1.385  0.020  1.385
 9LV  C30   C35  aromatic  1.386  0.020  1.386
 9LV  C34   C36  aromatic  1.387  0.020  1.387
 9LV  C35   C36  aromatic  1.386  0.020  1.386
 9LV  C10   H1   single    0.970  0.020  1.090
 9LV  C10   H2   single    0.970  0.020  1.090
 9LV  C15   H3   single    0.930  0.020  1.080
 9LV  C17   H4   single    0.930  0.020  1.080
 9LV  C20   H5   single    0.970  0.020  1.090
 9LV  C20   H6   single    0.970  0.020  1.090
 9LV  C24   H7   single    0.930  0.020  1.080
 9LV  O28   H8   single    0.850  0.020  0.980
 9LV  C23   H9   single    0.930  0.020  1.080
 9LV  C32   H10  single    0.930  0.020  1.080
 9LV  C14   H11  single    0.970  0.020  1.090
 9LV  C14   H12  single    0.970  0.020  1.090
 9LV  C19   H13  single    0.970  0.020  1.090
 9LV  C19   H14  single    0.970  0.020  1.090
 9LV  C9    H15  single    0.970  0.020  1.090
 9LV  C9    H16  single    0.970  0.020  1.090
 9LV  C30   H17  single    0.930  0.020  1.080
 9LV  C35   H18  single    0.930  0.020  1.080
 9LV  C36   H19  single    0.930  0.020  1.080
 9LV  C34   H20  single    0.930  0.020  1.080
 9LV  C27   H21  single    0.930  0.020  1.080
 9LV  C31   H22  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
 9LV  C9    C4   C3    111.88  3.000
 9LV  C9    C4   C10   109.68  3.000
 9LV  C3    C4   C10   110.57  3.000
 9LV  C9    C4   C5    112.17  3.000
 9LV  C10   C4   C5    110.64  3.000
 9LV  C3    C4   C5    101.71  3.000
 9LV  C17   C5   C6    120.55  3.000
 9LV  C6    C5   C4    109.22  3.000
 9LV  C17   C5   C4    130.22  3.000
 9LV  N2    C6   C15   128.64  3.000
 9LV  N2    C6   C5    109.52  3.000
 9LV  C15   C6   C5    121.83  3.000
 9LV  C18   C7   C30   119.69  3.000
 9LV  C30   C7   S1    118.29  3.000
 9LV  C18   C7   S1    122.00  3.000
 9LV  H2    C10  H1    106.77  3.000
 9LV  H2    C10  C20   108.72  3.000
 9LV  H1    C10  C20   109.03  3.000
 9LV  H2    C10  C4    107.76  3.000
 9LV  H1    C10  C4    110.52  3.000
 9LV  C20   C10  C4    113.78  3.000
 9LV  H3    C15  C27   119.72  3.000
 9LV  H3    C15  C6    122.43  3.000
 9LV  C27   C15  C6    117.85  3.000
 9LV  H4    C17  C25   121.08  3.000
 9LV  H4    C17  C5    121.00  3.000
 9LV  C25   C17  C5    117.92  3.000
 9LV  H6    C20  H5    107.83  3.000
 9LV  H6    C20  N8    109.43  3.000
 9LV  H5    C20  N8    110.91  3.000
 9LV  H6    C20  C10   108.43  3.000
 9LV  H5    C20  C10   111.25  3.000
 9LV  N8    C20  C10   108.95  3.000
 9LV  C23   C21  C11   118.40  3.000
 9LV  C23   C21  C24   119.12  3.000
 9LV  C11   C21  C24   122.47  3.000
 9LV  H7    C24  C31   118.93  3.000
 9LV  H7    C24  C21   120.98  3.000
 9LV  C31   C24  C21   120.09  3.000
 9LV  C31   C26  C14   119.11  3.000
 9LV  C14   C26  C32   121.98  3.000
 9LV  C31   C26  C32   118.89  3.000
 9LV  H8    O28  C11   109.90  3.000
 9LV  H9    C23  C32   119.32  3.000
 9LV  H9    C23  C21   120.15  3.000
 9LV  C32   C23  C21   120.53  3.000
 9LV  H10   C32  C23   118.78  3.000
 9LV  H10   C32  C26   120.72  3.000
 9LV  C23   C32  C26   120.50  3.000
 9LV  C3    N2   C14   124.86  3.000
 9LV  C3    N2   C6    111.27  3.000
 9LV  C14   N2   C6    123.87  3.000
 9LV  O16   C3   N2    124.64  3.000
 9LV  O16   C3   C4    127.13  3.000
 9LV  N2    C3   C4    108.23  3.000
 9LV  S1    N8   C19   116.51  3.000
 9LV  S1    N8   C20   119.91  3.000
 9LV  C19   N8   C20   115.30  3.000
 9LV  H14   C19  H13   107.39  3.000
 9LV  H14   C19  C9    107.90  3.000
 9LV  H13   C19  C9    111.43  3.000
 9LV  H14   C19  N8    109.84  3.000
 9LV  H13   C19  N8    111.05  3.000
 9LV  C9    C19  N8    109.16  3.000
 9LV  H16   C9   H15   107.19  3.000
 9LV  H16   C9   C19   109.26  3.000
 9LV  H15   C9   C19   108.52  3.000
 9LV  H16   C9   C4    110.54  3.000
 9LV  H15   C9   C4    107.76  3.000
 9LV  C19   C9   C4    113.35  3.000
 9LV  O13   S1   O12   118.08  3.000
 9LV  O12   S1   N8    108.35  3.000
 9LV  O13   S1   N8    111.47  3.000
 9LV  O12   S1   C7    109.32  3.000
 9LV  O13   S1   C7    106.70  3.000
 9LV  N8    S1   C7    101.64  3.000
 9LV  H17   C30  C35   119.73  3.000
 9LV  H17   C30  C7    120.02  3.000
 9LV  C35   C30  C7    120.25  3.000
 9LV  H18   C35  C36   120.50  3.000
 9LV  H18   C35  C30   119.71  3.000
 9LV  C36   C35  C30   119.79  3.000
 9LV  H19   C36  C34   119.26  3.000
 9LV  H19   C36  C35   120.36  3.000
 9LV  C34   C36  C35   120.38  3.000
 9LV  H20   C34  C18   119.75  3.000
 9LV  H20   C34  C36   120.39  3.000
 9LV  C18   C34  C36   119.87  3.000
 9LV  CL29  C18  C34   118.04  3.000
 9LV  C34   C18  C7    120.03  3.000
 9LV  CL29  C18  C7    121.94  3.000
 9LV  C27   C25  BR33  119.36  3.000
 9LV  C27   C25  C17   121.61  3.000
 9LV  BR33  C25  C17   119.04  3.000
 9LV  H21   C27  C25   120.79  3.000
 9LV  H21   C27  C15   118.97  3.000
 9LV  C25   C27  C15   120.24  3.000
 9LV  H22   C31  C26   119.87  3.000
 9LV  H22   C31  C24   119.25  3.000
 9LV  C26   C31  C24   120.87  3.000
 9LV  H12   C14  H11   106.39  3.000
 9LV  H12   C14  N2    107.91  3.000
 9LV  H11   C14  N2    109.22  3.000
 9LV  H12   C14  C26   109.58  3.000
 9LV  H11   C14  C26   109.98  3.000
 9LV  N2    C14  C26   113.50  3.000
 9LV  O22   C11  O28   123.17  3.000
 9LV  O28   C11  C21   113.09  3.000
 9LV  O22   C11  C21   123.75  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
 9LV  CONST_01  C27   C25  C17  C5      0.00   0.0  0
 9LV  CONST_02  C27   C15  C6   C5      0.00   0.0  0
 9LV  CONST_03  C25   C27  C15  C6      0.00   0.0  0
 9LV  CONST_04  C25   C17  C5   C6      0.00   0.0  0
 9LV  CONST_05  C36   C34  C18  C7      0.00   0.0  0
 9LV  CONST_06  C36   C35  C30  C7      0.00   0.0  0
 9LV  CONST_07  C17   C25  C27  C15     0.00   0.0  0
 9LV  CONST_08  C17   C5   C6   C15     0.00   0.0  0
 9LV  CONST_09  C26   C31  C24  C21     0.00   0.0  0
 9LV  CONST_10  C26   C32  C23  C21     0.00   0.0  0
 9LV  CONST_11  C32   C26  C31  C24     0.00   0.0  0
 9LV  CONST_12  C32   C23  C21  C24     0.00   0.0  0
 9LV  CONST_13  C31   C24  C21  C23     0.00   0.0  0
 9LV  CONST_14  C31   C26  C32  C23     0.00   0.0  0
 9LV  CONST_15  C34   C18  C7   C30     0.00   0.0  0
 9LV  CONST_16  C34   C36  C35  C30     0.00   0.0  0
 9LV  CONST_17  C18   C7   C30  C35     0.00   0.0  0
 9LV  CONST_18  C18   C34  C36  C35     0.00   0.0  0
 9LV  CONST_19  C25   C17  C5   C4    180.00   0.0  0
 9LV  CONST_20  C15   C6   C5   C4    180.00   0.0  0
 9LV  CONST_21  N2    C6   C5   C4      0.00   0.0  0
 9LV  CONST_22  C6    N2   C3   C4      0.00   0.0  0
 9LV  CONST_23  BR33  C25  C17  C5    180.00   0.0  0
 9LV  CONST_24  BR33  C25  C27  C15   180.00   0.0  0
 9LV  CONST_25  C14   C26  C31  C24   180.00   0.0  0
 9LV  CONST_26  C31   C24  C21  C11   180.00   0.0  0
 9LV  CONST_27  C32   C23  C21  C11   180.00   0.0  0
 9LV  CONST_28  C14   C26  C32  C23   180.00   0.0  0
 9LV  CONST_29  C34   C18  C7   S1    180.00   0.0  0
 9LV  CONST_30  C35   C30  C7   S1    180.00   0.0  0
 9LV  CONST_31  CL29  C18  C7   C30   180.00   0.0  0
 9LV  CONST_32  CL29  C18  C34  C36   180.00   0.0  0
 9LV  CONST_33  C14   N2   C3   C4    180.00   0.0  0
 9LV  CONST_34  O16   C3   N2   C6    180.00   0.0  0
 9LV  CONST_35  H4    C17  C5   C4      0.00   0.0  0
 9LV  CONST_36  H3    C15  C6   C5    180.00   0.0  0
 9LV  CONST_37  H21   C27  C15  C6    180.00   0.0  0
 9LV  CONST_38  H20   C34  C18  C7    180.00   0.0  0
 9LV  CONST_39  H18   C35  C30  C7    180.00   0.0  0
 9LV  CONST_40  H22   C31  C24  C21   180.00   0.0  0
 9LV  CONST_41  H10   C32  C23  C21   180.00   0.0  0
 9LV  CONST_42  H9    C23  C21  C24   180.00   0.0  0
 9LV  CONST_43  H7    C24  C31  C26   180.00   0.0  0
 9LV  CONST_44  H19   C36  C35  C30   180.00   0.0  0
 9LV  CONST_45  H17   C30  C35  C36   180.00   0.0  0
 9LV  CONST_46  O16   C3   N2   C14     0.00   0.0  0
 9LV  CONST_47  H8    O28  C11  C21   180.00   0.0  0
 9LV  Var_01    N8    C20  C10  C4    -52.97  30.0  1
 9LV  Var_02    N8    C19  C9   C4     53.67  30.0  1
 9LV  Var_03    C20   C10  C4   C5    173.79  30.0  3
 9LV  Var_04    C19   C9   C4   C5   -173.05  30.0  3
 9LV  Var_05    C10   C4   C5   C6    115.55  30.0  1
 9LV  Var_06    N2    C3   C4   C10  -115.62  30.0  1
 9LV  Var_07    C19   N8   C20  C10    58.75  30.0  1
 9LV  Var_08    C9    C19  N8   C20   -59.25  30.0  1
 9LV  Var_09    C26   C14  N2   C6     71.27  30.0  2
 9LV  Var_10    C20   N8   S1   C7    140.31  30.0  2
 9LV  Var_11    N2    C14  C26  C32    27.84  30.0  2
 9LV  Var_12    C18   C7   S1   N8    -61.95  30.0  2
 9LV  Var_13    O22   C11  C21  C24  -179.37  30.0  2

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
 9LV  plan-1  C7    0.020
 9LV  plan-1  S1    0.020
 9LV  plan-1  C30   0.020
 9LV  plan-1  C35   0.020
 9LV  plan-1  C36   0.020
 9LV  plan-1  C34   0.020
 9LV  plan-1  C18   0.020
 9LV  plan-1  CL29  0.020
 9LV  plan-1  H17   0.020
 9LV  plan-1  H18   0.020
 9LV  plan-1  H19   0.020
 9LV  plan-1  H20   0.020
 9LV  plan-2  C21   0.020
 9LV  plan-2  C24   0.020
 9LV  plan-2  C26   0.020
 9LV  plan-2  C23   0.020
 9LV  plan-2  C32   0.020
 9LV  plan-2  C31   0.020
 9LV  plan-2  H7    0.020
 9LV  plan-2  H9    0.020
 9LV  plan-2  H10   0.020
 9LV  plan-2  H22   0.020
 9LV  plan-2  C14   0.020
 9LV  plan-2  C11   0.020
 9LV  plan-3  C4    0.020
 9LV  plan-3  C5    0.020
 9LV  plan-3  C6    0.020
 9LV  plan-3  C15   0.020
 9LV  plan-3  C17   0.020
 9LV  plan-3  N2    0.020
 9LV  plan-3  C3    0.020
 9LV  plan-3  O16   0.020
 9LV  plan-3  C25   0.020
 9LV  plan-3  BR33  0.020
 9LV  plan-3  C27   0.020
 9LV  plan-3  H3    0.020
 9LV  plan-3  H4    0.020
 9LV  plan-3  H21   0.020
 9LV  plan-3  C14   0.020
 9LV  plan-4  C21   0.020
 9LV  plan-4  O28   0.020
 9LV  plan-4  O22   0.020
 9LV  plan-4  H8    0.020
 9LV  plan-4  C11   0.020

