# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 04:56:30 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (7aS)-7a-(4-cyanobenzyl)-6-(3,5-dichlorophenyl)-5-oxo-2,3,5,7a-tetrahydro-1H-pyrrolizine-7-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)cc(c1)C2=C(C#N)[C@]3(CCCN3C2=O)Cc4ccc(cc4)C#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
 2O7  2O7  (7aS)-7a-(4-cyanobenzyl)-6-(3,5-dichlorophenyl)-5-oxo-2,3,5,7a-tetrahydro-1H-pyrrolizine-7-carbonitrile  ligand  43  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2O7
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
 2O7  C1    C   C     0   0.055   0.6085  3.2288   0.4995
 2O7  C3    C   CH2   0  -0.279  -0.2790  1.1971   1.4561
 2O7  C9    C   CH2   0  -0.419   0.8711  2.0953  -0.4966
 2O7  C12   C   CR5   0   0.548   1.1272  2.8170   2.7401
 2O7  C13   C   CR5   0  -0.012   2.0129  3.9206   2.2453
 2O7  C14   C   CR5   0   0.064   1.7694  4.0759   0.9361
 2O7  C15   C   CSP   0   0.000   2.4350  4.9547   0.0493
 2O7  C20   C   CR6   0  -0.028   4.6747  4.6800   4.7520
 2O7  C21   C   CR16  0  -0.167   4.7600  6.0619   4.6789
 2O7  C24   C   CR16  0  -0.252   3.0199  6.0343   3.0013
 2O7  O28   O   O     0  -0.442   1.1714  2.2878   3.8314
 2O7  C32   C   CR6   0   0.153  -0.9211  5.1658   1.0697
 2O7  C33   C   CR16  0  -0.284  -1.6769  4.8300   2.1921
 2O7  C35   C   CR16  0  -0.222  -1.9333  5.7627   3.1813
 2O7  N2    N   N     0  -0.476   0.3066  2.5050   1.7145
 2O7  C6    C   CH2   0  -0.505  -0.1645  1.0469  -0.0728
 2O7  N16   N   NS    0  -0.212   2.9643  5.6502  -0.7019
 2O7  C17   C   CR6   0   0.038   2.9580  4.6449   3.0880
 2O7  C18   C   CR16  0  -0.240   3.7806  3.9596   3.9794
 2O7  C23   C   CR6   0  -0.028   3.9193  6.7217   3.7972
 2O7  CL26  CL  CL    0  -0.100   3.9893  8.4439   3.6965
 2O7  C29   C   CH2   0  -0.510  -0.5698  4.1270   0.0467
 2O7  C37   C   CR6   0  -0.008  -1.4352  7.0584   3.0506
 2O7  C38   C   CR16  0  -0.224  -0.6979  7.4175   1.9233
 2O7  C40   C   CR16  0  -0.309  -0.4497  6.4720   0.9447
 2O7  C42   C   CSP   0   0.056  -1.6912  8.0250   4.0686
 2O7  N43   N   NS    0  -0.251  -1.8995  8.8084   4.8876
 2O7  H31   H   HCH2  0   0.262  -1.3126  1.1455   1.7986
 2O7  H32   H   HCH2  0   0.263   0.2896  0.4349   1.9900
 2O7  H91   H   HCH2  0   0.264   1.8856  1.7160  -0.3598
 2O7  H92   H   HCH2  0   0.269   0.7611  2.4109  -1.5333
 2O7  H21   H   HCR6  0   0.310   5.4604  6.6093   5.2941
 2O7  H24   H   HCR6  0   0.283   2.3549  6.5748   2.3405
 2O7  H33   H   HCR6  0   0.268  -2.0771  3.8301   2.2964
 2O7  H35   H   HCR6  0   0.283  -2.5185  5.4899   4.0489
 2O7  H61   H   HCH2  0   0.257  -1.1253  1.2468  -0.5477
 2O7  H62   H   HCH2  0   0.273   0.1334  0.0393  -0.3558
 2O7  H18   H   HCR6  0   0.290   3.7413  2.8828   4.0532
 2O7  H291  H   HCH2  0   0.292  -1.4298  3.4863  -0.1598
 2O7  H292  H   HCH2  0   0.283  -0.2926  4.5982  -0.8989
 2O7  H38   H   HCR6  0   0.285  -0.3251  8.4269   1.8126
 2O7  H40   H   HCR6  0   0.273   0.1158  6.7625   0.0679
 2O7  CL27  CL  CL    0  -0.102   5.7144  3.8365   5.8431

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
 2O7  N43   C42   triple    1.152  0.020  1.152
 2O7  C42   C37   single    1.427  0.020  1.427
 2O7  C37   C35   aromatic  1.394  0.020  1.394
 2O7  C37   C38   aromatic  1.394  0.020  1.394
 2O7  C35   C33   aromatic  1.384  0.020  1.384
 2O7  C38   C40   aromatic  1.383  0.020  1.383
 2O7  C33   C32   aromatic  1.394  0.020  1.394
 2O7  C40   C32   aromatic  1.394  0.020  1.394
 2O7  C32   C29   single    1.500  0.020  1.500
 2O7  C29   C1    single    1.549  0.020  1.549
 2O7  CL26  C23   single    1.726  0.020  1.726
 2O7  C23   C24   aromatic  1.384  0.020  1.384
 2O7  C23   C21   aromatic  1.386  0.020  1.386
 2O7  N16   C15   triple    1.152  0.020  1.152
 2O7  C24   C17   aromatic  1.393  0.020  1.393
 2O7  C15   C14   single    1.415  0.020  1.415
 2O7  C21   C20   aromatic  1.386  0.020  1.386
 2O7  C14   C1    single    1.502  0.020  1.502
 2O7  C14   C13   double    1.341  0.020  1.341
 2O7  C17   C13   single    1.459  0.020  1.459
 2O7  C17   C18   aromatic  1.393  0.020  1.393
 2O7  C1    N2    single    1.446  0.020  1.446
 2O7  C1    C9    single    1.532  0.020  1.532
 2O7  C13   C12   single    1.499  0.020  1.499
 2O7  C12   N2    single    1.350  0.020  1.350
 2O7  C12   O28   double    1.214  0.020  1.214
 2O7  N2    C3    single    1.456  0.020  1.456
 2O7  C20   C18   aromatic  1.384  0.020  1.384
 2O7  C20   CL27  single    1.727  0.020  1.727
 2O7  C3    C6    single    1.541  0.020  1.541
 2O7  C9    C6    single    1.533  0.020  1.533
 2O7  C3    H31   single    0.970  0.020  1.090
 2O7  C3    H32   single    0.970  0.020  1.090
 2O7  C9    H91   single    0.970  0.020  1.090
 2O7  C9    H92   single    0.970  0.020  1.090
 2O7  C21   H21   single    0.930  0.020  1.080
 2O7  C24   H24   single    0.930  0.020  1.080
 2O7  C33   H33   single    0.930  0.020  1.080
 2O7  C35   H35   single    0.930  0.020  1.080
 2O7  C6    H61   single    0.970  0.020  1.090
 2O7  C6    H62   single    0.970  0.020  1.090
 2O7  C18   H18   single    0.930  0.020  1.080
 2O7  C29   H291  single    0.970  0.020  1.090
 2O7  C29   H292  single    0.970  0.020  1.090
 2O7  C38   H38   single    0.930  0.020  1.080
 2O7  C40   H40   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
 2O7  C29   C1   N2    112.14  3.000
 2O7  N2    C1   C14   101.50  3.000
 2O7  C29   C1   C14   110.24  3.000
 2O7  N2    C1   C9    102.23  3.000
 2O7  C14   C1   C9    118.29  3.000
 2O7  C29   C1   C9    111.67  3.000
 2O7  H32   C3   H31   107.91  3.000
 2O7  H32   C3   C6    112.27  3.000
 2O7  H31   C3   C6    112.19  3.000
 2O7  H32   C3   N2    109.34  3.000
 2O7  H31   C3   N2    111.59  3.000
 2O7  C6    C3   N2    103.52  3.000
 2O7  H92   C9   H91   108.29  3.000
 2O7  H92   C9   C6    113.13  3.000
 2O7  H91   C9   C6    110.82  3.000
 2O7  H92   C9   C1    112.78  3.000
 2O7  H91   C9   C1    109.57  3.000
 2O7  C6    C9   C1    102.15  3.000
 2O7  N2    C12  O28   127.19  3.000
 2O7  O28   C12  C13   126.60  3.000
 2O7  N2    C12  C13   106.18  3.000
 2O7  C17   C13  C14   128.63  3.000
 2O7  C17   C13  C12   123.90  3.000
 2O7  C14   C13  C12   107.47  3.000
 2O7  C15   C14  C13   126.77  3.000
 2O7  C13   C14  C1    111.03  3.000
 2O7  C15   C14  C1    122.12  3.000
 2O7  N16   C15  C14   180.00  3.000
 2O7  CL27  C20  C18   119.17  3.000
 2O7  CL27  C20  C21   118.88  3.000
 2O7  C18   C20  C21   121.95  3.000
 2O7  H21   C21  C23   120.94  3.000
 2O7  H21   C21  C20   120.97  3.000
 2O7  C23   C21  C20   118.09  3.000
 2O7  H24   C24  C23   120.16  3.000
 2O7  H24   C24  C17   120.58  3.000
 2O7  C23   C24  C17   119.24  3.000
 2O7  C40   C32  C29   120.57  3.000
 2O7  C29   C32  C33   120.62  3.000
 2O7  C40   C32  C33   118.76  3.000
 2O7  H33   C33  C35   119.04  3.000
 2O7  H33   C33  C32   120.04  3.000
 2O7  C35   C33  C32   120.91  3.000
 2O7  H35   C35  C37   120.19  3.000
 2O7  H35   C35  C33   120.25  3.000
 2O7  C37   C35  C33   119.55  3.000
 2O7  C12   N2   C3    125.93  3.000
 2O7  C3    N2   C1    112.61  3.000
 2O7  C12   N2   C1    113.31  3.000
 2O7  H62   C6   H61   107.33  3.000
 2O7  H62   C6   C9    112.10  3.000
 2O7  H61   C6   C9    110.45  3.000
 2O7  H62   C6   C3    111.64  3.000
 2O7  H61   C6   C3    110.42  3.000
 2O7  C9    C6   C3    104.94  3.000
 2O7  C18   C17  C24   120.27  3.000
 2O7  C18   C17  C13   120.52  3.000
 2O7  C24   C17  C13   119.20  3.000
 2O7  H18   C18  C17   120.84  3.000
 2O7  H18   C18  C20   120.29  3.000
 2O7  C17   C18  C20   118.86  3.000
 2O7  CL26  C23  C24   119.23  3.000
 2O7  C24   C23  C21   121.59  3.000
 2O7  CL26  C23  C21   119.18  3.000
 2O7  H292  C29  H291  106.81  3.000
 2O7  H292  C29  C32   110.56  3.000
 2O7  H291  C29  C32   110.54  3.000
 2O7  H292  C29  C1    108.07  3.000
 2O7  H291  C29  C1    108.31  3.000
 2O7  C32   C29  C1    112.36  3.000
 2O7  C42   C37  C38   119.82  3.000
 2O7  C38   C37  C35   120.27  3.000
 2O7  C42   C37  C35   119.90  3.000
 2O7  H38   C38  C40   120.24  3.000
 2O7  H38   C38  C37   120.36  3.000
 2O7  C40   C38  C37   119.40  3.000
 2O7  H40   C40  C38   118.88  3.000
 2O7  H40   C40  C32   120.03  3.000
 2O7  C38   C40  C32   121.08  3.000
 2O7  N43   C42  C37   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
 2O7  CONST_01  C24   C23  C21  C20     0.00   0.0  0
 2O7  CONST_02  C24   C17  C18  C20     0.00   0.0  0
 2O7  CONST_03  C17   C24  C23  C21     0.00   0.0  0
 2O7  CONST_04  C17   C18  C20  C21     0.00   0.0  0
 2O7  CONST_05  C37   C35  C33  C32     0.00   0.0  0
 2O7  CONST_06  C37   C38  C40  C32     0.00   0.0  0
 2O7  CONST_07  C38   C37  C35  C33     0.00   0.0  0
 2O7  CONST_08  C38   C40  C32  C33     0.00   0.0  0
 2O7  CONST_09  C40   C38  C37  C35     0.00   0.0  0
 2O7  CONST_10  C40   C32  C33  C35     0.00   0.0  0
 2O7  CONST_11  C23   C24  C17  C18     0.00   0.0  0
 2O7  CONST_12  C23   C21  C20  C18     0.00   0.0  0
 2O7  CONST_13  C23   C24  C17  C13   180.00   0.0  0
 2O7  CONST_14  C20   C18  C17  C13   180.00   0.0  0
 2O7  CONST_15  C13   C12  N2   C1      0.00   0.0  0
 2O7  CONST_17  CL26  C23  C21  C20   180.00   0.0  0
 2O7  CONST_18  C42   C37  C35  C33   180.00   0.0  0
 2O7  CONST_19  C29   C32  C33  C35   180.00   0.0  0
 2O7  CONST_20  CL26  C23  C24  C17   180.00   0.0  0
 2O7  CONST_21  CL27  C20  C18  C17   180.00   0.0  0
 2O7  CONST_22  CL27  C20  C21  C23   180.00   0.0  0
 2O7  CONST_23  C38   C40  C32  C29   180.00   0.0  0
 2O7  CONST_24  C42   C37  C38  C40   180.00   0.0  0
 2O7  CONST_25  O28   C12  N2   C1    180.00   0.0  0
 2O7  CONST_27  H24   C24  C17  C13     0.00   0.0  0
 2O7  CONST_28  H18   C18  C17  C13     0.00   0.0  0
 2O7  CONST_29  H21   C21  C23  C24   180.00   0.0  0
 2O7  CONST_30  H35   C35  C33  C32   180.00   0.0  0
 2O7  CONST_31  H38   C38  C40  C32   180.00   0.0  0
 2O7  CONST_32  H40   C40  C32  C33   180.00   0.0  0
 2O7  CONST_33  H33   C33  C35  C37   180.00   0.0  0
 2O7  Var_01    C17   C13  C14  C1   -173.63  30.0  1
 2O7  Var_02    C6    C3   N2   C1      7.22  30.0  1
 2O7  Var_03    C3    C6   C9   C1    -33.83  30.0  1
 2O7  Var_04    N2    C3   C6   C9     17.29  30.0  1
 2O7  Var_05    C24   C17  C13  C12  -134.59  30.0  3
 2O7  Var_06    N2    C12  C13  C14    -7.08  30.0  1
 2O7  Var_07    C33   C32  C29  C1    -78.67  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
 2O7  chir_01  C1  C14  N2  C9  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
 2O7  plan-1  C13   0.020
 2O7  plan-1  C20   0.020
 2O7  plan-1  C21   0.020
 2O7  plan-1  C24   0.020
 2O7  plan-1  C17   0.020
 2O7  plan-1  C18   0.020
 2O7  plan-1  C23   0.020
 2O7  plan-1  CL26  0.020
 2O7  plan-1  H21   0.020
 2O7  plan-1  H24   0.020
 2O7  plan-1  H18   0.020
 2O7  plan-1  CL27  0.020
 2O7  plan-2  C32   0.020
 2O7  plan-2  C33   0.020
 2O7  plan-2  C35   0.020
 2O7  plan-2  C29   0.020
 2O7  plan-2  C37   0.020
 2O7  plan-2  C38   0.020
 2O7  plan-2  C40   0.020
 2O7  plan-2  C42   0.020
 2O7  plan-2  N43   0.020
 2O7  plan-2  H33   0.020
 2O7  plan-2  H35   0.020
 2O7  plan-2  H38   0.020
 2O7  plan-2  H40   0.020
 2O7  plan-3  C1    0.020
 2O7  plan-3  C3    0.020
 2O7  plan-3  C12   0.020
 2O7  plan-3  C13   0.020
 2O7  plan-3  O28   0.020
 2O7  plan-3  N2    0.020

