# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 05:17:06 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-bromo-4-cyanobenzyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cc(COC(=O)[C@H]2C[C@]3(CN2)C(=O)Nc4ccccc34)ccc1C#N
#
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
 09G  09G  '3-bromo-4-cyanobenzyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate'  ligand  43  27  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_09G
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
 09G  C5   C   CR16  0  -0.262  -5.3678   3.5206   0.5964
 09G  C8   C   CR16  0  -0.267  -6.2501   3.3871  -0.4680
 09G  C23  C   CR16  0  -0.226   3.1554   0.3368  -2.0700
 09G  C3   C   CR16  0  -0.352  -4.5346   2.4611   0.9574
 09G  C24  C   CR16  0  -0.270   2.0952  -0.4986  -1.7809
 09G  C6   C   CR16  0  -0.306  -6.3261   2.2040  -1.2012
 09G  C20  C   CR16  0  -0.269   3.4181  -1.6187  -0.1112
 09G  C22  C   CR6   0   0.064   4.3618   0.1999  -1.3812
 09G  C1   C   CR56  0   0.138  -4.6004   1.2858   0.2391
 09G  C19  C   CR6   0   0.096   2.2204  -1.4805  -0.8018
 09G  C17  C   CR56  0   0.366  -5.4904   1.1692  -0.8277
 09G  C21  C   CR6   0  -0.102   4.4857  -0.7854  -0.4010
 09G  C14  C   CR5   0   0.578  -4.4114  -0.8381  -0.7628
 09G  C9   C   C     0   0.587  -1.0146  -2.1214   0.6310
 09G  C4   C   CH2   0  -0.463  -2.3358   0.0507   0.3867
 09G  C13  C   CH2   0  -0.291  -4.1390  -0.7429   1.7384
 09G  C7   C   CR15  0  -0.179  -1.8948  -1.1142   1.3281
 09G  C2   C   C     0  -0.339  -3.8695  -0.0090   0.3984
 09G  C18  C   CH2   0  -0.247   1.0581  -2.3689  -0.4747
 09G  N26  N   NS    0  -0.231   6.3057   1.7850  -1.9735
 09G  N16  N   NR15  0  -0.744  -5.3631  -0.0957  -1.3891
 09G  N10  N   NR15  0  -0.584  -3.0918  -1.7303   1.8713
 09G  O15  O   O     0  -0.449  -4.0650  -1.9602  -1.0733
 09G  O11  O   O2    0  -0.450   0.1279  -1.5601   0.2557
 09G  BR2  BR  BR    0   0.024   6.0988  -0.9840   0.5327
 09G  H1   H   HCR6  0   0.255  -5.3251   4.4506   1.1475
 09G  H2   H   HCR6  0   0.259  -6.8922   4.2153  -0.7383
 09G  H3   H   HCR6  0   0.296   3.0620   1.0982  -2.8318
 09G  H4   H   HCR6  0   0.255  -3.8437   2.5633   1.7857
 09G  H5   H   HCR6  0   0.280   1.1670  -0.3892  -2.3264
 09G  H6   H   HCR6  0   0.268  -7.0138   2.1069  -2.0308
 09G  H7   H   HCR6  0   0.296   3.5134  -2.3783   0.6536
 09G  H8   H   HCH2  0   0.277  -2.0012   1.0030   0.7974
 09G  H9   H   HCH2  0   0.273  -1.9286  -0.0239  -0.6211
 09G  H10  H   HCH2  0   0.252  -4.0714  -0.0069   2.5450
 09G  H11  H   HCH2  0   0.268  -5.1255  -1.2029   1.7933
 09G  H12  H   HCR5  0   0.288  -1.3022  -0.6816   2.1412
 09G  H13  H   HCH2  0   0.269   0.5907  -2.7439  -1.3874
 09G  H14  H   HCH2  0   0.268   1.3728  -3.2239   0.1257
 09G  H15  H   HNR5  0   0.411  -5.8734  -0.4183  -2.1975
 09G  H16  H   HNR5  0   0.360  -3.3308  -2.5471   1.3214
 09G  O12  O   O     0  -0.438  -1.2908  -3.2762   0.4363
 09G  C25  C   CSP   0   0.042   5.4459   1.0700  -1.6978

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
 09G  N10  C7   single    1.452  0.020  1.452
 09G  N10  C13  single    1.445  0.020  1.445
 09G  C3   C5   aromatic  1.395  0.020  1.395
 09G  C3   C1   aromatic  1.379  0.020  1.379
 09G  C5   C8   aromatic  1.389  0.020  1.389
 09G  C7   C4   single    1.561  0.020  1.561
 09G  C7   C9   single    1.508  0.020  1.508
 09G  C13  C2   single    1.551  0.020  1.551
 09G  C4   C2   single    1.535  0.020  1.535
 09G  C1   C2   single    1.495  0.020  1.495
 09G  C1   C17  aromatic  1.394  0.020  1.394
 09G  C8   C6   aromatic  1.394  0.020  1.394
 09G  C9   O12  double    1.203  0.020  1.203
 09G  C9   O11  single    1.327  0.020  1.327
 09G  C2   C14  single    1.526  0.020  1.526
 09G  O11  C18  single    1.433  0.020  1.433
 09G  BR2  C21  single    1.874  0.020  1.874
 09G  C17  C6   aromatic  1.382  0.020  1.382
 09G  C17  N16  single    1.390  0.020  1.390
 09G  C20  C21  aromatic  1.385  0.020  1.385
 09G  C20  C19  aromatic  1.389  0.020  1.389
 09G  C18  C19  single    1.499  0.020  1.499
 09G  C14  N16  single    1.360  0.020  1.360
 09G  C14  O15  double    1.215  0.020  1.215
 09G  C21  C22  aromatic  1.395  0.020  1.395
 09G  C19  C24  aromatic  1.392  0.020  1.392
 09G  C22  C25  single    1.426  0.020  1.426
 09G  C22  C23  aromatic  1.396  0.020  1.396
 09G  C24  C23  aromatic  1.380  0.020  1.380
 09G  C25  N26  triple    1.152  0.020  1.152
 09G  C5   H1   single    0.930  0.020  1.080
 09G  C8   H2   single    0.930  0.020  1.080
 09G  C23  H3   single    0.930  0.020  1.080
 09G  C3   H4   single    0.930  0.020  1.080
 09G  C24  H5   single    0.930  0.020  1.080
 09G  C6   H6   single    0.930  0.020  1.080
 09G  C20  H7   single    0.930  0.020  1.080
 09G  C4   H8   single    0.970  0.020  1.090
 09G  C4   H9   single    0.970  0.020  1.090
 09G  C13  H10  single    0.970  0.020  1.090
 09G  C13  H11  single    0.970  0.020  1.090
 09G  C7   H12  single    0.970  0.020  1.090
 09G  C18  H13  single    0.970  0.020  1.090
 09G  C18  H14  single    0.970  0.020  1.090
 09G  N16  H15  single    0.860  0.020  1.020
 09G  N10  H16  single    0.890  0.020  1.040

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
 09G  H1   C5   C3   119.83  3.000
 09G  H1   C5   C8   119.87  3.000
 09G  C3   C5   C8   120.30  3.000
 09G  H2   C8   C6   119.06  3.000
 09G  H2   C8   C5   119.65  3.000
 09G  C6   C8   C5   121.29  3.000
 09G  H3   C23  C22  119.43  3.000
 09G  H3   C23  C24  120.50  3.000
 09G  C22  C23  C24  120.07  3.000
 09G  H4   C3   C1   120.60  3.000
 09G  H4   C3   C5   120.46  3.000
 09G  C1   C3   C5   118.94  3.000
 09G  H5   C24  C19  120.19  3.000
 09G  H5   C24  C23  119.47  3.000
 09G  C19  C24  C23  120.33  3.000
 09G  H6   C6   C17  121.64  3.000
 09G  H6   C6   C8   120.94  3.000
 09G  C17  C6   C8   117.42  3.000
 09G  H7   C20  C21  120.15  3.000
 09G  H7   C20  C19  119.80  3.000
 09G  C21  C20  C19  120.04  3.000
 09G  C21  C22  C23  119.51  3.000
 09G  C23  C22  C25  119.19  3.000
 09G  C21  C22  C25  121.30  3.000
 09G  C2   C1   C17  108.73  3.000
 09G  C17  C1   C3   120.02  3.000
 09G  C2   C1   C3   131.23  3.000
 09G  C18  C19  C20  120.07  3.000
 09G  C18  C19  C24  120.11  3.000
 09G  C20  C19  C24  119.81  3.000
 09G  N16  C17  C1   109.07  3.000
 09G  N16  C17  C6   128.90  3.000
 09G  C1   C17  C6   122.03  3.000
 09G  BR2  C21  C22  120.07  3.000
 09G  C22  C21  C20  120.23  3.000
 09G  BR2  C21  C20  119.70  3.000
 09G  O15  C14  N16  125.89  3.000
 09G  O15  C14  C2   126.51  3.000
 09G  N16  C14  C2   107.60  3.000
 09G  O11  C9   O12  123.90  3.000
 09G  O11  C9   C7   110.53  3.000
 09G  O12  C9   C7   125.57  3.000
 09G  H9   C4   H8   107.08  3.000
 09G  H9   C4   C2   112.20  3.000
 09G  H8   C4   C2   109.75  3.000
 09G  H9   C4   C7   113.65  3.000
 09G  H8   C4   C7   109.76  3.000
 09G  C2   C4   C7   104.40  3.000
 09G  H11  C13  H10  107.62  3.000
 09G  H11  C13  N10  111.27  3.000
 09G  H10  C13  N10  110.31  3.000
 09G  H11  C13  C2   113.61  3.000
 09G  H10  C13  C2   107.93  3.000
 09G  N10  C13  C2   106.06  3.000
 09G  H12  C7   N10  109.64  3.000
 09G  H12  C7   C4   107.80  3.000
 09G  N10  C7   C4   108.02  3.000
 09G  H12  C7   C9   106.92  3.000
 09G  C4   C7   C9   112.61  3.000
 09G  N10  C7   C9   111.76  3.000
 09G  C13  C2   C4   101.45  3.000
 09G  C4   C2   C14  111.73  3.000
 09G  C13  C2   C14  109.79  3.000
 09G  C14  C2   C1   102.46  3.000
 09G  C4   C2   C1   117.00  3.000
 09G  C13  C2   C1   114.63  3.000
 09G  H14  C18  H13  108.32  3.000
 09G  H14  C18  O11  110.43  3.000
 09G  H13  C18  O11  110.00  3.000
 09G  H14  C18  C19  111.15  3.000
 09G  H13  C18  C19  110.68  3.000
 09G  O11  C18  C19  106.27  3.000
 09G  H15  N16  C14  123.26  3.000
 09G  H15  N16  C17  124.63  3.000
 09G  C14  N16  C17  112.03  3.000
 09G  H16  N10  C7   109.48  3.000
 09G  H16  N10  C13  109.26  3.000
 09G  C7   N10  C13  105.84  3.000
 09G  C18  O11  C9   117.67  3.000
 09G  N26  C25  C22  180.00  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
 09G  CONST_01  C17  C1   C3   C5     0.00   0.0  0
 09G  CONST_02  C17  C6   C8   C5     0.00   0.0  0
 09G  CONST_03  C1   C3   C5   C8     0.00   0.0  0
 09G  CONST_04  C1   C17  C6   C8     0.00   0.0  0
 09G  CONST_05  C20  C21  C22  C23    0.00   0.0  0
 09G  CONST_06  C20  C19  C24  C23    0.00   0.0  0
 09G  CONST_07  C6   C8   C5   C3     0.00   0.0  0
 09G  CONST_08  C6   C17  C1   C3     0.00   0.0  0
 09G  CONST_09  C21  C20  C19  C24    0.00   0.0  0
 09G  CONST_10  C21  C22  C23  C24    0.00   0.0  0
 09G  CONST_11  C19  C20  C21  C22    0.00   0.0  0
 09G  CONST_12  C19  C24  C23  C22    0.00   0.0  0
 09G  CONST_13  C2   C14  N16  C17    0.00   0.0  0
 09G  CONST_14  C20  C21  C22  C25  180.00   0.0  0
 09G  CONST_15  C24  C23  C22  C25  180.00   0.0  0
 09G  CONST_16  BR2  C21  C22  C23  180.00   0.0  0
 09G  CONST_17  C18  C19  C24  C23  180.00   0.0  0
 09G  CONST_18  BR2  C21  C20  C19  180.00   0.0  0
 09G  CONST_19  C18  C19  C20  C21  180.00   0.0  0
 09G  CONST_20  O15  C14  N16  C17  180.00   0.0  0
 09G  CONST_21  H6   C6   C8   C5   180.00   0.0  0
 09G  CONST_22  H4   C3   C5   C8   180.00   0.0  0
 09G  CONST_23  H2   C8   C5   C3   180.00   0.0  0
 09G  CONST_24  H7   C20  C19  C24  180.00   0.0  0
 09G  CONST_25  H1   C5   C8   C6   180.00   0.0  0
 09G  CONST_26  H5   C24  C19  C20  180.00   0.0  0
 09G  CONST_27  H3   C23  C24  C19  180.00   0.0  0
 09G  CONST_28  H15  N16  C14  C2   180.00   0.0  0
 09G  Var_01    C2   C13  N10  C7    36.54  30.0  1
 09G  Var_02    O11  C18  C19  C24  -73.31  30.0  2
 09G  Var_03    O12  C9   O11  C18    2.79  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
 09G  chir_01  C7  N10  C4  C9   positiv
 09G  chir_02  C2  C4   C1  C14  negativ

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
 09G  plan-1  C23  0.020
 09G  plan-1  C24  0.020
 09G  plan-1  C20  0.020
 09G  plan-1  C22  0.020
 09G  plan-1  C19  0.020
 09G  plan-1  C21  0.020
 09G  plan-1  C18  0.020
 09G  plan-1  N26  0.020
 09G  plan-1  BR2  0.020
 09G  plan-1  H3   0.020
 09G  plan-1  H5   0.020
 09G  plan-1  H7   0.020
 09G  plan-1  C25  0.020
 09G  plan-2  C5   0.020
 09G  plan-2  C8   0.020
 09G  plan-2  C3   0.020
 09G  plan-2  C6   0.020
 09G  plan-2  C1   0.020
 09G  plan-2  C17  0.020
 09G  plan-2  C14  0.020
 09G  plan-2  C2   0.020
 09G  plan-2  N16  0.020
 09G  plan-2  O15  0.020
 09G  plan-2  H1   0.020
 09G  plan-2  H2   0.020
 09G  plan-2  H4   0.020
 09G  plan-2  H6   0.020
 09G  plan-2  H15  0.020
 09G  plan-3  C9   0.020
 09G  plan-3  C7   0.020
 09G  plan-3  O11  0.020
 09G  plan-3  O12  0.020

