# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 13:18:34 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 4-({5-bromo-2-oxo-1'-[(thiophen-2-yl)sulfonyl]spiro[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)c4sccc4)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
 9MV  9MV  '4-({5-bromo-2-oxo-1'-[(thiophen-2-yl)sulfonyl]spiro[indole-3,4'-piperidin]-1(2H)-yl}methyl)benzoic acid'  ligand  54  34  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9MV
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
 9MV  C4    C   CR5    0  -0.357  -0.6176  -0.5707  -1.1457
 9MV  C5    C   CR56   0   0.146  -0.1499   0.7928  -0.7279
 9MV  C6    C   CR56   0   0.401   1.1786   0.9557  -1.1055
 9MV  C7    C   CR5    0  -0.431  -4.4377  -1.0245   0.4420
 9MV  C10   C   CH2    0  -0.417  -0.9377  -1.4269   0.0953
 9MV  C20   C   CH2    0  -0.340  -1.6054  -2.7540  -0.2387
 9MV  C21   C   C      0  -0.109   5.7017  -1.1531   1.0089
 9MV  C22   C   CR15   0  -0.171  -4.7532   0.2054  -0.0574
 9MV  C26   C   C1     0  -0.271   4.5847  -1.9610   0.8011
 9MV  C28   C   CR6    0  -0.123  -0.1220   2.9651   0.2289
 9MV  O31   O   O      0  -0.593   7.6198  -0.6473   2.2893
 9MV  C12   C   C      0   0.396   6.6558  -1.4266   2.1648
 9MV  O24   O   OC    -1  -0.593   6.3889  -2.4073   2.8855
 9MV  C32   C   C1     0  -0.281   3.7086  -1.7166  -0.2435
 9MV  C29   C   C      0   0.113   3.9258  -0.6496  -1.1127
 9MV  N2    N   NR5    0  -0.583   1.6142  -0.1806  -1.7778
 9MV  C3    C   CR5    0   0.611   0.6225  -1.1181  -1.8574
 9MV  O17   O   O      0  -0.449   0.7352  -2.2018  -2.3912
 9MV  N8    N   N      0  -0.548  -2.7676  -2.5838  -1.1097
 9MV  C19   C   CH2    0  -0.331  -2.4701  -1.8626  -2.3464
 9MV  C9    C   CH2    0  -0.422  -1.8301  -0.5052  -2.0889
 9MV  S1    S   S      0   1.392  -4.2674  -2.5228  -0.4513
 9MV  O14   O   OS     0  -0.653  -4.3353  -3.5765   0.5474
 9MV  O15   O   OS     0  -0.642  -5.2159  -2.4805  -1.5490
 9MV  C25   C   CR15   0  -0.189  -4.6835   1.2092   0.9397
 9MV  C23   C   CR15   0  -0.439  -4.3254   0.7108   2.1585
 9MV  S11   S   S2     0   0.285  -4.0771  -0.9786   2.1200
 9MV  C18   C   CR16   0  -0.305  -0.8180   1.7915  -0.0563
 9MV  BR34  BR  BR     0  -0.049  -1.0117   4.3569   1.1456
 9MV  C30   C   CR16   0  -0.237   1.2035   3.1300  -0.1426
 9MV  C16   C   CR16   0  -0.295   1.8748   2.1145  -0.8203
 9MV  C33   C   C1     0  -0.303   5.0405   0.1558  -0.9125
 9MV  C27   C   C1     0  -0.276   5.9187  -0.0943   0.1341
 9MV  H1    H   HCH2   0   0.270  -0.0295  -1.6168   0.6721
 9MV  H2    H   HCH2   0   0.257  -1.5937  -0.8427   0.7450
 9MV  H3    H   HCH2   0   0.283   3.2820   0.5080  -2.8060
 9MV  H4    H   HCH2   0   0.293   2.9550  -1.2077  -2.9499
 9MV  H5    H   HCH2   0   0.279  -0.9134  -3.4181  -0.7587
 9MV  H6    H   HCH2   0   0.286  -1.8956  -3.2659   0.6769
 9MV  H7    H   HCR5   0   0.304  -5.0232   0.3929  -1.0870
 9MV  H8    H   H      0   0.245   4.4049  -2.7926   1.4693
 9MV  H10   H   H      0   0.246   2.8563  -2.3723  -0.3820
 9MV  H11   H   HCH2   0   0.276  -1.8027  -2.5016  -2.9255
 9MV  H12   H   HCH2   0   0.285  -3.3765  -1.7450  -2.9352
 9MV  H13   H   HCH2   0   0.260  -2.5680   0.1645  -1.6435
 9MV  H14   H   HCH2   0   0.272  -1.5441  -0.0555  -3.0418
 9MV  H15   H   HCR5   0   0.290  -4.8980   2.2524   0.7605
 9MV  H16   H   HCR5   0   0.316  -4.2133   1.2510   3.0864
 9MV  H17   H   HCR6   0   0.268  -1.8528   1.6677   0.2419
 9MV  H18   H   HCR6   0   0.284   1.7324   4.0445   0.0888
 9MV  H19   H   HCR6   0   0.278   2.9089   2.2541  -1.1035
 9MV  H20   H   H      0   0.249   5.2238   0.9898  -1.5811
 9MV  H21   H   H      0   0.244   6.7790   0.5469   0.2730
 9MV  C13   C   CH2    0  -0.422   2.9691  -0.3757  -2.2462

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
 9MV  BR34  C28  single    1.889  0.020  1.889
 9MV  C30   C28  aromatic  1.386  0.020  1.386
 9MV  C30   C16  aromatic  1.393  0.020  1.393
 9MV  C28   C18  aromatic  1.394  0.020  1.394
 9MV  C16   C6   aromatic  1.382  0.020  1.382
 9MV  O31   C12  deloc     1.246  0.020  1.246
 9MV  C18   C5   aromatic  1.376  0.020  1.376
 9MV  C26   C32  aromatic  1.385  0.020  1.385
 9MV  C26   C21  aromatic  1.394  0.020  1.394
 9MV  C6    C5   aromatic  1.391  0.020  1.391
 9MV  C6    N2   single    1.390  0.020  1.390
 9MV  C32   C29  aromatic  1.393  0.020  1.393
 9MV  C12   C21  single    1.524  0.020  1.524
 9MV  C12   O24  deloc     1.246  0.020  1.246
 9MV  C21   C27  aromatic  1.390  0.020  1.390
 9MV  C5    C4   single    1.501  0.020  1.501
 9MV  C29   C13  single    1.508  0.020  1.508
 9MV  C29   C33  aromatic  1.390  0.020  1.390
 9MV  C13   N2   single    1.447  0.020  1.447
 9MV  C27   C33  aromatic  1.389  0.020  1.389
 9MV  N2    C3   single    1.367  0.020  1.367
 9MV  C4    C10  single    1.541  0.020  1.541
 9MV  C4    C3   single    1.531  0.020  1.531
 9MV  C4    C9   single    1.538  0.020  1.538
 9MV  C10   C20  single    1.523  0.020  1.523
 9MV  C3    O17  double    1.213  0.020  1.213
 9MV  C9    C19  single    1.523  0.020  1.523
 9MV  C20   N8   single    1.462  0.020  1.462
 9MV  N8    C19  single    1.462  0.020  1.462
 9MV  N8    S1   single    1.639  0.020  1.639
 9MV  O14   S1   double    1.453  0.020  1.453
 9MV  O15   S1   double    1.451  0.020  1.451
 9MV  S1    C7   single    1.753  0.020  1.753
 9MV  C7    C22  aromatic  1.364  0.020  1.364
 9MV  C7    S11  aromatic  1.717  0.020  1.717
 9MV  C22   C25  aromatic  1.417  0.020  1.417
 9MV  S11   C23  aromatic  1.708  0.020  1.708
 9MV  C25   C23  aromatic  1.365  0.020  1.365
 9MV  C10   H1   single    0.970  0.020  1.090
 9MV  C10   H2   single    0.970  0.020  1.090
 9MV  C13   H3   single    0.970  0.020  1.090
 9MV  C13   H4   single    0.970  0.020  1.090
 9MV  C20   H5   single    0.970  0.020  1.090
 9MV  C20   H6   single    0.970  0.020  1.090
 9MV  C22   H7   single    0.930  0.020  1.080
 9MV  C26   H8   single    0.930  0.020  1.080
 9MV  C32   H10  single    0.930  0.020  1.080
 9MV  C19   H11  single    0.970  0.020  1.090
 9MV  C19   H12  single    0.970  0.020  1.090
 9MV  C9    H13  single    0.970  0.020  1.090
 9MV  C9    H14  single    0.970  0.020  1.090
 9MV  C25   H15  single    0.930  0.020  1.080
 9MV  C23   H16  single    0.930  0.020  1.080
 9MV  C18   H17  single    0.930  0.020  1.080
 9MV  C30   H18  single    0.930  0.020  1.080
 9MV  C16   H19  single    0.930  0.020  1.080
 9MV  C33   H20  single    0.930  0.020  1.080
 9MV  C27   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
 9MV  C9    C4   C3    111.64  3.000
 9MV  C9    C4   C10   110.72  3.000
 9MV  C3    C4   C10   110.12  3.000
 9MV  C9    C4   C5    112.20  3.000
 9MV  C3    C4   C5    101.64  3.000
 9MV  C10   C4   C5    110.20  3.000
 9MV  C18   C5   C6    120.74  3.000
 9MV  C6    C5   C4    109.18  3.000
 9MV  C18   C5   C4    130.07  3.000
 9MV  C16   C6   N2    128.86  3.000
 9MV  N2    C6   C5    109.56  3.000
 9MV  C16   C6   C5    121.57  3.000
 9MV  S11   C7   S1    120.04  3.000
 9MV  S11   C7   C22   112.47  3.000
 9MV  S1    C7   C22   127.33  3.000
 9MV  H2    C10  H1    106.14  3.000
 9MV  H2    C10  C20   109.47  3.000
 9MV  H1    C10  C20   109.20  3.000
 9MV  H2    C10  C4    107.85  3.000
 9MV  H1    C10  C4    110.42  3.000
 9MV  C20   C10  C4    113.49  3.000
 9MV  H6    C20  H5    106.49  3.000
 9MV  H6    C20  N8    110.11  3.000
 9MV  H5    C20  N8    106.92  3.000
 9MV  H6    C20  C10   110.02  3.000
 9MV  H5    C20  C10   110.91  3.000
 9MV  N8    C20  C10   112.19  3.000
 9MV  C27   C21  C12   121.09  3.000
 9MV  C27   C21  C26   118.20  3.000
 9MV  C12   C21  C26   120.72  3.000
 9MV  H7    C22  C25   124.05  3.000
 9MV  H7    C22  C7    124.25  3.000
 9MV  C25   C22  C7    111.70  3.000
 9MV  H8    C26  C32   119.76  3.000
 9MV  H8    C26  C21   119.11  3.000
 9MV  C32   C26  C21   121.13  3.000
 9MV  C30   C28  BR34  119.52  3.000
 9MV  C30   C28  C18   121.51  3.000
 9MV  BR34  C28  C18   118.98  3.000
 9MV  O24   C12  O31   126.89  3.000
 9MV  O24   C12  C21   116.49  3.000
 9MV  O31   C12  C21   116.62  3.000
 9MV  H10   C32  C29   120.40  3.000
 9MV  H10   C32  C26   119.13  3.000
 9MV  C29   C32  C26   120.47  3.000
 9MV  C33   C29  C32   118.62  3.000
 9MV  C33   C29  C13   120.78  3.000
 9MV  C32   C29  C13   120.60  3.000
 9MV  C3    N2   C13   124.62  3.000
 9MV  C3    N2   C6    111.18  3.000
 9MV  C13   N2   C6    124.07  3.000
 9MV  O17   C3   N2    124.80  3.000
 9MV  O17   C3   C4    126.81  3.000
 9MV  N2    C3   C4    108.38  3.000
 9MV  S1    N8   C19   120.50  3.000
 9MV  S1    N8   C20   119.49  3.000
 9MV  C19   N8   C20   113.54  3.000
 9MV  H12   C19  H11   106.61  3.000
 9MV  H12   C19  C9    110.22  3.000
 9MV  H11   C19  C9    110.79  3.000
 9MV  H12   C19  N8    109.98  3.000
 9MV  H11   C19  N8    106.54  3.000
 9MV  C9    C19  N8    112.47  3.000
 9MV  H14   C9   H13   106.28  3.000
 9MV  H14   C9   C19   109.25  3.000
 9MV  H13   C9   C19   109.38  3.000
 9MV  H14   C9   C4    110.27  3.000
 9MV  H13   C9   C4    107.99  3.000
 9MV  C19   C9   C4    113.41  3.000
 9MV  O15   S1   O14   120.69  3.000
 9MV  O15   S1   N8    107.17  3.000
 9MV  O14   S1   N8    106.97  3.000
 9MV  O15   S1   C7    107.28  3.000
 9MV  O14   S1   C7    105.36  3.000
 9MV  N8    S1   C7    108.99  3.000
 9MV  H15   C25  C23   123.59  3.000
 9MV  H15   C25  C22   123.91  3.000
 9MV  C23   C25  C22   112.50  3.000
 9MV  H16   C23  S11   119.95  3.000
 9MV  H16   C23  C25   127.75  3.000
 9MV  S11   C23  C25   112.29  3.000
 9MV  C23   S11  C7     91.03  3.000
 9MV  H17   C18  C28   121.09  3.000
 9MV  H17   C18  C5    120.98  3.000
 9MV  C28   C18  C5    117.93  3.000
 9MV  H18   C30  C16   118.99  3.000
 9MV  H18   C30  C28   120.72  3.000
 9MV  C16   C30  C28   120.29  3.000
 9MV  H19   C16  C30   119.62  3.000
 9MV  H19   C16  C6    122.42  3.000
 9MV  C30   C16  C6    117.96  3.000
 9MV  H20   C33  C27   119.75  3.000
 9MV  H20   C33  C29   119.50  3.000
 9MV  C27   C33  C29   120.75  3.000
 9MV  H21   C27  C33   119.52  3.000
 9MV  H21   C27  C21   119.64  3.000
 9MV  C33   C27  C21   120.84  3.000
 9MV  H4    C13  H3    106.89  3.000
 9MV  H4    C13  N2    107.45  3.000
 9MV  H3    C13  N2    108.98  3.000
 9MV  H4    C13  C29   110.78  3.000
 9MV  H3    C13  C29   110.52  3.000
 9MV  N2    C13  C29   112.04  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
 9MV  CONST_01  C30   C28  C18  C5       0.00   0.0  0
 9MV  CONST_02  C30   C16  C6   C5       0.00   0.0  0
 9MV  CONST_03  C28   C30  C16  C6       0.00   0.0  0
 9MV  CONST_04  C28   C18  C5   C6       0.00   0.0  0
 9MV  CONST_05  C23   C25  C22  C7       0.00   0.0  0
 9MV  CONST_06  C25   C23  S11  C7       0.00   0.0  0
 9MV  CONST_07  C29   C32  C26  C21      0.00   0.0  0
 9MV  CONST_08  C29   C33  C27  C21      0.00   0.0  0
 9MV  CONST_09  C23   S11  C7   C22      0.00   0.0  0
 9MV  CONST_10  S11   C23  C25  C22      0.00   0.0  0
 9MV  CONST_11  C33   C29  C32  C26      0.00   0.0  0
 9MV  CONST_12  C33   C27  C21  C26      0.00   0.0  0
 9MV  CONST_13  C27   C21  C26  C32      0.00   0.0  0
 9MV  CONST_14  C27   C33  C29  C32      0.00   0.0  0
 9MV  CONST_15  S11   C7   C22  C25      0.00   0.0  0
 9MV  CONST_16  C16   C30  C28  C18      0.00   0.0  0
 9MV  CONST_17  C16   C6   C5   C18      0.00   0.0  0
 9MV  CONST_18  C28   C18  C5   C4     180.00   0.0  0
 9MV  CONST_19  C16   C6   C5   C4     180.00   0.0  0
 9MV  CONST_20  N2    C6   C5   C4       0.00   0.0  0
 9MV  CONST_21  C6    N2   C3   C4       0.00   0.0  0
 9MV  CONST_22  BR34  C28  C18  C5     180.00   0.0  0
 9MV  CONST_23  C26   C32  C29  C13    180.00   0.0  0
 9MV  CONST_24  C27   C33  C29  C13    180.00   0.0  0
 9MV  CONST_25  C32   C26  C21  C12    180.00   0.0  0
 9MV  CONST_26  C33   C27  C21  C12    180.00   0.0  0
 9MV  CONST_27  C25   C22  C7   S1     180.00   0.0  0
 9MV  CONST_28  C23   S11  C7   S1     180.00   0.0  0
 9MV  CONST_29  C16   C30  C28  BR34   180.00   0.0  0
 9MV  CONST_30  C13   N2   C3   C4     180.00   0.0  0
 9MV  CONST_31  O17   C3   N2   C6     180.00   0.0  0
 9MV  CONST_32  H17   C18  C5   C4       0.00   0.0  0
 9MV  CONST_33  H19   C16  C6   C5     180.00   0.0  0
 9MV  CONST_34  H18   C30  C16  C6     180.00   0.0  0
 9MV  CONST_35  H15   C25  C22  C7     180.00   0.0  0
 9MV  CONST_36  H16   C23  S11  C7     180.00   0.0  0
 9MV  CONST_37  H10   C32  C26  C21    180.00   0.0  0
 9MV  CONST_38  H20   C33  C27  C21    180.00   0.0  0
 9MV  CONST_39  H21   C27  C21  C26    180.00   0.0  0
 9MV  CONST_40  H8    C26  C32  C29    180.00   0.0  0
 9MV  CONST_41  H7    C22  C25  C23    180.00   0.0  0
 9MV  CONST_42  O17   C3   N2   C13      0.00   0.0  0
 9MV  Var_01    N8    C20  C10  C4     -51.41  30.0  1
 9MV  Var_02    N8    C19  C9   C4      51.22  30.0  1
 9MV  Var_03    C20   C10  C4   C5     171.79  30.0  3
 9MV  Var_04    C19   C9   C4   C5    -170.44  30.0  3
 9MV  Var_05    C10   C4   C5   C6     114.58  30.0  1
 9MV  Var_06    N2    C3   C4   C10   -114.98  30.0  1
 9MV  Var_07    C19   N8   C20  C10     55.20  30.0  1
 9MV  Var_08    C9    C19  N8   C20    -55.18  30.0  1
 9MV  Var_09    C29   C13  N2   C6      72.85  30.0  2
 9MV  Var_10    C20   N8   S1   C7      69.59  30.0  1
 9MV  Var_11    N8    S1   C7   C22     82.41  30.0  2
 9MV  Var_12    N2    C13  C29  C32     56.90  30.0  2
 9MV  Var_13    O31   C12  C21  C26   -179.13  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
 9MV  plan-1  C7    0.020
 9MV  plan-1  C22   0.020
 9MV  plan-1  S1    0.020
 9MV  plan-1  C25   0.020
 9MV  plan-1  C23   0.020
 9MV  plan-1  S11   0.020
 9MV  plan-1  H7    0.020
 9MV  plan-1  H15   0.020
 9MV  plan-1  H16   0.020
 9MV  plan-2  C21   0.020
 9MV  plan-2  C26   0.020
 9MV  plan-2  C12   0.020
 9MV  plan-2  C32   0.020
 9MV  plan-2  C29   0.020
 9MV  plan-2  C33   0.020
 9MV  plan-2  C27   0.020
 9MV  plan-2  H8    0.020
 9MV  plan-2  H10   0.020
 9MV  plan-2  H20   0.020
 9MV  plan-2  H21   0.020
 9MV  plan-2  C13   0.020
 9MV  plan-3  C4    0.020
 9MV  plan-3  C5    0.020
 9MV  plan-3  C6    0.020
 9MV  plan-3  C28   0.020
 9MV  plan-3  N2    0.020
 9MV  plan-3  C3    0.020
 9MV  plan-3  O17   0.020
 9MV  plan-3  C18   0.020
 9MV  plan-3  BR34  0.020
 9MV  plan-3  C30   0.020
 9MV  plan-3  C16   0.020
 9MV  plan-3  H17   0.020
 9MV  plan-3  H18   0.020
 9MV  plan-3  H19   0.020
 9MV  plan-3  C13   0.020
 9MV  plan-4  C21   0.020
 9MV  plan-4  O31   0.020
 9MV  plan-4  C12   0.020
 9MV  plan-4  O24   0.020

