# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:01:06 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: ~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-phenyl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)N1CC[C@]2([C@@H]1c3ccccc3)C(=O)Nc4ccccc24
#
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
 D40  D40  '~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-phenyl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate'  ligand  51  27  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D40
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
 D40  C22  C  CR6   0   0.179  -17.0558  17.0318  -1.8511
 D40  C27  C  CR16  0  -0.322  -16.4042  18.1977  -2.2359
 D40  C26  C  CR16  0  -0.243  -16.7044  19.4125  -1.6335
 D40  C25  C  CR16  0  -0.271  -17.6725  19.4750  -0.6416
 D40  C24  C  CR16  0  -0.242  -18.3323  18.3142  -0.2573
 D40  C23  C  CR16  0  -0.281  -18.0236  17.1026  -0.8557
 D40  C20  C  CH3   0  -0.665  -20.7923  15.9573  -5.3102
 D40  C19  C  CH3   0  -0.652  -19.9285  18.0890  -4.3353
 D40  C18  C  CH3   0  -0.682  -21.3189  16.5807  -2.9222
 D40  C17  C  CT    0   0.195  -20.2888  16.6376  -4.0435
 D40  C1   C  CR16  0  -0.257  -15.9798  15.0303   2.0315
 D40  C2   C  CR16  0  -0.268  -14.7846  15.6594   2.3518
 D40  C3   C  CR16  0  -0.308  -13.8890  16.0484   1.3590
 D40  C4   C  CR56  0   0.372  -14.2388  15.7882   0.0484
 D40  C5   C  CR56  0   0.159  -15.4368  15.1652  -0.2958
 D40  C13  C  CH2   0  -0.435  -15.6508  13.5758  -2.2722
 D40  C12  C  CH2   0  -0.278  -17.1586  13.3696  -2.2486
 D40  C6   C  CR16  0  -0.340  -16.3107  14.7787   0.7007
 D40  C8   C  CR5   0   0.583  -14.1440  15.6365  -2.2228
 D40  C10  C  CH1   0  -0.034  -16.6569  15.7355  -2.5087
 D40  C9   C  CR5   0  -0.385  -15.4795  15.0221  -1.7923
 D40  N7   N  NR15  0  -0.743  -13.5098  16.0603  -1.1036
 D40  N11  N  NT    0  -0.526  -17.6807  14.7001  -2.5345
 D40  O15  O  O     0  -0.517  -19.7210  13.9627  -3.1750
 D40  O16  O  O2    0  -0.488  -19.0228  16.0712  -3.6220
 D40  H1   H  HCR6  0   0.243  -15.6625  18.1635  -3.0257
 D40  H2   H  HCR6  0   0.251  -16.1876  20.3105  -1.9472
 D40  H3   H  HCR6  0   0.251  -17.9146  20.4210  -0.1744
 D40  H4   H  HCR6  0   0.250  -19.0926  18.3508   0.5124
 D40  H5   H  HCR6  0   0.240  -18.5520  16.2110  -0.5446
 D40  H6   H  HCH3  0   0.244  -21.0852  14.9242  -5.1364
 D40  H7   H  HCH3  0   0.231  -21.6651  16.4961  -5.6810
 D40  H8   H  HCH3  0   0.234  -20.0329  15.9769  -6.0935
 D40  H9   H  HCH3  0   0.242  -19.5393  18.5832  -3.4437
 D40  H10  H  HCH3  0   0.234  -19.1741  18.1611  -5.1205
 D40  H11  H  HCH3  0   0.226  -20.8131  18.6318  -4.6691
 D40  H12  H  HCH3  0   0.238  -20.9349  17.0504  -2.0151
 D40  H13  H  HCH3  0   0.237  -22.2077  17.1329  -3.2301
 D40  H14  H  HCH3  0   0.245  -21.6273  15.5648  -2.6850
 D40  H15  H  HCR6  0   0.254  -16.6602  14.7325   2.8181
 D40  H16  H  HCR6  0   0.259  -14.5372  15.8475   3.3884
 D40  H17  H  HCR6  0   0.268  -12.9535  16.5308   1.6098
 D40  H18  H  HCH2  0   0.272  -15.1142  12.8598  -1.6518
 D40  H19  H  HCH2  0   0.263  -15.2792  13.4873  -3.2952
 D40  H20  H  HCH2  0   0.243  -17.5056  13.0067  -1.2783
 D40  H21  H  HCH2  0   0.265  -17.4789  12.6490  -3.0006
 D40  H22  H  HCR6  0   0.258  -17.2470  14.2896   0.4663
 D40  H23  H  HCH1  0   0.275  -16.3244  15.9573  -3.5306
 D40  H24  H  HNR5  0   0.414  -12.6020  16.5013  -1.1139
 D40  O21  O  O     0  -0.448  -13.7346  15.7310  -3.3610
 D40  C14  C  C     0   0.759  -18.8923  14.8508  -3.1225

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
 D40  C20  C17  single    1.523  0.020  1.523
 D40  C19  C17  single    1.524  0.020  1.524
 D40  C17  O16  single    1.450  0.020  1.450
 D40  C17  C18  single    1.524  0.020  1.524
 D40  O16  C14  single    1.325  0.020  1.325
 D40  C14  O15  double    1.216  0.020  1.216
 D40  C14  N11  single    1.355  0.020  1.355
 D40  C27  C26  aromatic  1.389  0.020  1.389
 D40  C27  C22  aromatic  1.390  0.020  1.390
 D40  N11  C12  single    1.458  0.020  1.458
 D40  N11  C10  single    1.456  0.020  1.456
 D40  C12  C13  single    1.522  0.020  1.522
 D40  O21  C8   double    1.213  0.020  1.213
 D40  C10  C22  single    1.507  0.020  1.507
 D40  C10  C9   single    1.552  0.020  1.552
 D40  C26  C25  aromatic  1.387  0.020  1.387
 D40  C13  C9   single    1.533  0.020  1.533
 D40  C22  C23  aromatic  1.390  0.020  1.390
 D40  C8   C9   single    1.532  0.020  1.532
 D40  C8   N7   single    1.354  0.020  1.354
 D40  C9   C5   single    1.504  0.020  1.504
 D40  C25  C24  aromatic  1.389  0.020  1.389
 D40  C23  C24  aromatic  1.386  0.020  1.386
 D40  N7   C4   single    1.390  0.020  1.390
 D40  C5   C4   aromatic  1.393  0.020  1.393
 D40  C5   C6   aromatic  1.381  0.020  1.381
 D40  C4   C3   aromatic  1.381  0.020  1.381
 D40  C6   C1   aromatic  1.394  0.020  1.394
 D40  C3   C2   aromatic  1.392  0.020  1.392
 D40  C1   C2   aromatic  1.388  0.020  1.388
 D40  C27  H1   single    0.930  0.020  1.080
 D40  C26  H2   single    0.930  0.020  1.080
 D40  C25  H3   single    0.930  0.020  1.080
 D40  C24  H4   single    0.930  0.020  1.080
 D40  C23  H5   single    0.930  0.020  1.080
 D40  C20  H6   single    0.970  0.020  1.090
 D40  C20  H7   single    0.970  0.020  1.090
 D40  C20  H8   single    0.970  0.020  1.090
 D40  C19  H9   single    0.970  0.020  1.090
 D40  C19  H10  single    0.970  0.020  1.090
 D40  C19  H11  single    0.970  0.020  1.090
 D40  C18  H12  single    0.970  0.020  1.090
 D40  C18  H13  single    0.970  0.020  1.090
 D40  C18  H14  single    0.970  0.020  1.090
 D40  C1   H15  single    0.930  0.020  1.080
 D40  C2   H16  single    0.930  0.020  1.080
 D40  C3   H17  single    0.930  0.020  1.080
 D40  C13  H18  single    0.970  0.020  1.090
 D40  C13  H19  single    0.970  0.020  1.090
 D40  C12  H20  single    0.970  0.020  1.090
 D40  C12  H21  single    0.970  0.020  1.090
 D40  C6   H22  single    0.930  0.020  1.080
 D40  C10  H23  single    0.970  0.020  1.090
 D40  N7   H24  single    0.860  0.020  1.020

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
 D40  C10  C22  C23  122.71  3.000
 D40  C23  C22  C27  118.81  3.000
 D40  C10  C22  C27  118.46  3.000
 D40  H1   C27  C26  119.44  3.000
 D40  H1   C27  C22  119.74  3.000
 D40  C26  C27  C22  120.81  3.000
 D40  H2   C26  C25  120.19  3.000
 D40  H2   C26  C27  119.78  3.000
 D40  C25  C26  C27  120.03  3.000
 D40  H3   C25  C24  120.30  3.000
 D40  H3   C25  C26  120.27  3.000
 D40  C24  C25  C26  119.43  3.000
 D40  H4   C24  C23  119.53  3.000
 D40  H4   C24  C25  120.13  3.000
 D40  C23  C24  C25  120.34  3.000
 D40  H5   C23  C24  119.17  3.000
 D40  H5   C23  C22  120.26  3.000
 D40  C24  C23  C22  120.57  3.000
 D40  H8   C20  H7   107.70  3.000
 D40  H8   C20  H6   108.61  3.000
 D40  H7   C20  H6   107.93  3.000
 D40  H8   C20  C17  111.03  3.000
 D40  H7   C20  C17  109.06  3.000
 D40  H6   C20  C17  112.35  3.000
 D40  H11  C19  H10  107.93  3.000
 D40  H11  C19  H9   108.31  3.000
 D40  H10  C19  H9   108.15  3.000
 D40  H11  C19  C17  109.93  3.000
 D40  H10  C19  C17  111.36  3.000
 D40  H9   C19  C17  111.05  3.000
 D40  H14  C18  H13  107.66  3.000
 D40  H14  C18  H12  108.69  3.000
 D40  H13  C18  H12  107.66  3.000
 D40  H14  C18  C17  112.77  3.000
 D40  H13  C18  C17  108.92  3.000
 D40  H12  C18  C17  110.96  3.000
 D40  O16  C17  C18  111.21  3.000
 D40  C18  C17  C19  109.66  3.000
 D40  O16  C17  C19  102.79  3.000
 D40  C18  C17  C20  111.82  3.000
 D40  O16  C17  C20  110.85  3.000
 D40  C19  C17  C20  110.14  3.000
 D40  H15  C1   C6   119.67  3.000
 D40  H15  C1   C2   119.90  3.000
 D40  C6   C1   C2   120.42  3.000
 D40  H16  C2   C3   119.17  3.000
 D40  H16  C2   C1   119.78  3.000
 D40  C3   C2   C1   121.05  3.000
 D40  H17  C3   C4   121.53  3.000
 D40  H17  C3   C2   121.02  3.000
 D40  C4   C3   C2   117.46  3.000
 D40  N7   C4   C5   109.49  3.000
 D40  C5   C4   C3   122.43  3.000
 D40  N7   C4   C3   128.07  3.000
 D40  C9   C5   C6   132.35  3.000
 D40  C6   C5   C4   119.41  3.000
 D40  C9   C5   C4   108.22  3.000
 D40  H19  C13  H18  108.22  3.000
 D40  H19  C13  C9   109.37  3.000
 D40  H18  C13  C9   112.76  3.000
 D40  H19  C13  C12  109.92  3.000
 D40  H18  C13  C12  112.97  3.000
 D40  C9   C13  C12  103.51  3.000
 D40  H21  C12  H20  107.45  3.000
 D40  H21  C12  N11  111.28  3.000
 D40  H20  C12  N11  111.32  3.000
 D40  H21  C12  C13  111.72  3.000
 D40  H20  C12  C13  111.93  3.000
 D40  N11  C12  C13  103.18  3.000
 D40  H22  C6   C5   121.19  3.000
 D40  H22  C6   C1   119.58  3.000
 D40  C5   C6   C1   119.22  3.000
 D40  O21  C8   N7   126.36  3.000
 D40  N7   C8   C9   107.55  3.000
 D40  O21  C8   C9   126.09  3.000
 D40  H23  C10  N11  109.89  3.000
 D40  H23  C10  C9   107.04  3.000
 D40  N11  C10  C9   102.40  3.000
 D40  H23  C10  C22  108.22  3.000
 D40  C9   C10  C22  113.25  3.000
 D40  N11  C10  C22  115.67  3.000
 D40  C10  C9   C8   110.32  3.000
 D40  C8   C9   C13  112.81  3.000
 D40  C10  C9   C13  101.79  3.000
 D40  C8   C9   C5   102.52  3.000
 D40  C13  C9   C5   113.85  3.000
 D40  C10  C9   C5   115.92  3.000
 D40  H24  N7   C8   123.33  3.000
 D40  H24  N7   C4   124.45  3.000
 D40  C8   N7   C4   112.21  3.000
 D40  C10  N11  C12  113.19  3.000
 D40  C10  N11  C14  123.86  3.000
 D40  C12  N11  C14  120.46  3.000
 D40  C14  O16  C17  123.75  3.000
 D40  O16  C14  O15  126.11  3.000
 D40  O15  C14  N11  123.15  3.000
 D40  O16  C14  N11  110.74  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
 D40  CONST_01  C25  C26  C27  C22     0.00   0.0  0
 D40  CONST_02  C25  C24  C23  C22     0.00   0.0  0
 D40  CONST_03  C24  C25  C26  C27     0.00   0.0  0
 D40  CONST_04  C24  C23  C22  C27     0.00   0.0  0
 D40  CONST_05  C23  C22  C27  C26     0.00   0.0  0
 D40  CONST_06  C23  C24  C25  C26     0.00   0.0  0
 D40  CONST_07  C4   C5   C6   C1      0.00   0.0  0
 D40  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 D40  CONST_09  C5   C4   C3   C2      0.00   0.0  0
 D40  CONST_10  C5   C6   C1   C2      0.00   0.0  0
 D40  CONST_11  C6   C5   C4   C3      0.00   0.0  0
 D40  CONST_12  C6   C1   C2   C3      0.00   0.0  0
 D40  CONST_13  C10  C22  C27  C26   180.00   0.0  0
 D40  CONST_14  C10  C22  C23  C24   180.00   0.0  0
 D40  CONST_15  C9   C8   N7   C4      0.00   0.0  0
 D40  CONST_16  O21  C8   N7   C4    180.00   0.0  0
 D40  CONST_17  H2   C26  C27  C22   180.00   0.0  0
 D40  CONST_18  H4   C24  C23  C22   180.00   0.0  0
 D40  CONST_19  H3   C25  C26  C27   180.00   0.0  0
 D40  CONST_20  H5   C23  C22  C27   180.00   0.0  0
 D40  CONST_21  H1   C27  C26  C25   180.00   0.0  0
 D40  CONST_22  H17  C3   C2   C1    180.00   0.0  0
 D40  CONST_23  H22  C6   C1   C2    180.00   0.0  0
 D40  CONST_24  H15  C1   C2   C3    180.00   0.0  0
 D40  CONST_25  H16  C2   C3   C4    180.00   0.0  0
 D40  CONST_26  H24  N7   C8   C9    180.00   0.0  0
 D40  Var_01    C10  N11  C12  C13    -9.67  30.0  1
 D40  Var_02    N11  C12  C13  C9     30.84  30.0  1
 D40  Var_03    O16  C14  N11  C12  -162.88  30.0  2
 D40  Var_04    N11  C14  O16  C17  -165.77  30.0  3
 D40  Var_05    H9   C19  C17  C20  -178.41  30.0  3
 D40  Var_06    H12  C18  C17  C20   178.64  30.0  3
 D40  Var_07    H6   C20  C17  C19  -178.49  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
 D40  chir_01  C10  N11  C22  C9   negativ
 D40  chir_02  C9   C8   C13  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
 D40  plan-1  C22  0.020
 D40  plan-1  C27  0.020
 D40  plan-1  C26  0.020
 D40  plan-1  C25  0.020
 D40  plan-1  C24  0.020
 D40  plan-1  C23  0.020
 D40  plan-1  C10  0.020
 D40  plan-1  H1   0.020
 D40  plan-1  H2   0.020
 D40  plan-1  H3   0.020
 D40  plan-1  H4   0.020
 D40  plan-1  H5   0.020
 D40  plan-2  C1   0.020
 D40  plan-2  C2   0.020
 D40  plan-2  C3   0.020
 D40  plan-2  C4   0.020
 D40  plan-2  C5   0.020
 D40  plan-2  C6   0.020
 D40  plan-2  C8   0.020
 D40  plan-2  C9   0.020
 D40  plan-2  N7   0.020
 D40  plan-2  H15  0.020
 D40  plan-2  H16  0.020
 D40  plan-2  H17  0.020
 D40  plan-2  H22  0.020
 D40  plan-2  H24  0.020
 D40  plan-2  O21  0.020
 D40  plan-3  N11  0.020
 D40  plan-3  O15  0.020
 D40  plan-3  O16  0.020
 D40  plan-3  C14  0.020

