# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:58:06 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-{3-[(2S)-4,4-difluoro-2-(pyrrolidin-1-ylcarbonyl)pyrrolidin-1-yl]-3-oxopropyl}-1H-isoindole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC1(F)C[C@H](N(C1)C(=O)CCN2C(=O)c3ccccc3C2=O)C(=O)N4CCCC4
#
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
 X99  X99  2-{3-[(2S)-4,4-difluoro-2-(pyrrolidin-1-ylcarbonyl)pyrrolidin-1-yl]-3-oxopropyl}-1H-isoindole-1,3(2H)-dione  ligand  50  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X99
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
 X99  C     C  C     0   0.595   0.7738  -0.0433  -0.4098
 X99  O     O  O     0  -0.491   1.2015  -0.9750  -1.0755
 X99  C1    C  CH2   0  -0.616  -0.6995   0.1638  -0.1508
 X99  C2    C  CH2   0  -0.297  -1.5430  -0.9493  -0.7569
 X99  N3    N  NR5   0  -0.604  -2.9497  -0.7519  -0.4784
 X99  C4    C  CR5   0   0.578  -3.7984   0.0025  -1.2735
 X99  C5    C  CR5   0   0.578  -3.5961  -1.2568   0.6394
 X99  O6    O  O     0  -0.400  -3.4816   0.5656  -2.2906
 X99  O7    O  O     0  -0.400  -3.0812  -1.9265   1.4986
 X99  C8    C  CR56  0  -0.027  -5.1242  -0.0417  -0.6132
 X99  C9    C  CR16  0  -0.295  -6.3228   0.5305  -0.9810
 X99  C10   C  CR16  0  -0.241  -7.4153   0.3119  -0.1431
 X99  C11   C  CR16  0  -0.241  -7.2937  -0.4530   1.0134
 X99  C12   C  CR16  0  -0.295  -6.0751  -1.0255   1.3747
 X99  C13   C  CR56  0  -0.028  -5.0028  -0.8017   0.5384
 X99  N     N  NT    0  -0.496   1.6097   0.8597   0.1356
 X99  CD    C  CH2   0  -0.373   1.2387   2.0110   0.9283
 X99  CA    C  CH1   0  -0.197   3.0462   0.7034  -0.0152
 X99  CB    C  CH2   0  -0.601   3.6285   1.9042   0.7486
 X99  CG    C  CT    0   0.740   2.4744   2.8789   0.7836
 X99  C3    C  C     0   0.564   3.5148  -0.6032   0.6224
 X99  O1    O  O     0  -0.500   2.9271  -1.0583   1.5941
 X99  F1    F  F     0  -0.343   2.4113   3.5779  -0.3888
 X99  F2    F  F     0  -0.331   2.5774   3.8058   1.7664
 X99  N1    N  NR5   0  -0.473   4.6134  -1.1629   0.1107
 X99  CD1   C  CH2   0  -0.259   5.1669  -2.3903   0.6789
 X99  CA1   C  CH2   0  -0.284   5.4031  -0.6695  -1.0169
 X99  CB1   C  CH2   0  -0.473   6.6993  -1.4626  -0.9037
 X99  CG1   C  CH2   0  -0.488   6.2357  -2.7966  -0.3283
 X99  H1    H  HCH2  0   0.288  -0.8700   0.2202   0.9283
 X99  H1A   H  HCH2  0   0.291  -1.0082   1.1311  -0.5587
 X99  H2    H  HCH2  0   0.278  -1.4151  -0.9945  -1.8367
 X99  H2A   H  HCH2  0   0.278  -1.2555  -1.9192  -0.3559
 X99  H9    H  HCR6  0   0.276  -6.4174   1.1253  -1.8798
 X99  H10   H  HCR6  0   0.279  -8.3747   0.7438  -0.3942
 X99  H11   H  HCR6  0   0.279  -8.1611  -0.6042   1.6417
 X99  H12   H  HCR6  0   0.276  -5.9820  -1.6198   2.2739
 X99  HD    H  HCH2  0   0.292   0.3454   2.5091   0.5516
 X99  HDA   H  HCH2  0   0.275   1.0793   1.7571   1.9806
 X99  HA    H  HCH1  0   0.304   3.3108   0.7512  -1.0736
 X99  HB    H  HCH2  0   0.293   3.8786   1.6302   1.7752
 X99  HBA   H  HCH2  0   0.301   4.5191   2.3157   0.2760
 X99  HD1   H  HCH2  0   0.239   5.5982  -2.1911   1.6638
 X99  HDA1  H  HCH2  0   0.249   4.3924  -3.1473   0.8024
 X99  HA1   H  HCH2  0   0.248   4.8996  -0.8794  -1.9650
 X99  HAA   H  HCH2  0   0.257   5.5741   0.4053  -0.9532
 X99  HB1   H  HCH2  0   0.255   7.2042  -1.5575  -1.8641
 X99  HBA1  H  HCH2  0   0.242   7.3826  -0.9663  -0.2116
 X99  HG    H  HCH2  0   0.254   7.0384  -3.3693   0.1339
 X99  HGA   H  HCH2  0   0.241   5.7963  -3.4134  -1.1155

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
 X99  C    C1    single    1.510  0.020  1.510
 X99  O    C     double    1.222  0.020  1.222
 X99  C1   H1    single    0.970  0.020  1.090
 X99  C1   H1A   single    0.970  0.020  1.090
 X99  C2   C1    single    1.522  0.020  1.522
 X99  C2   N3    single    1.447  0.020  1.447
 X99  C2   H2    single    0.970  0.020  1.090
 X99  C2   H2A   single    0.970  0.020  1.090
 X99  N3   C4    single    1.386  0.020  1.386
 X99  N3   C5    single    1.386  0.020  1.386
 X99  C4   C8    single    1.482  0.020  1.482
 X99  C5   C13   single    1.482  0.020  1.482
 X99  O6   C4    double    1.205  0.020  1.205
 X99  O7   C5    double    1.205  0.020  1.205
 X99  C8   C13   aromatic  1.385  0.020  1.385
 X99  C8   C9    aromatic  1.378  0.020  1.378
 X99  C9   C10   aromatic  1.394  0.020  1.394
 X99  C9   H9    single    0.930  0.020  1.080
 X99  C10  C11   aromatic  1.392  0.020  1.392
 X99  C10  H10   single    0.930  0.020  1.080
 X99  C11  H11   single    0.930  0.020  1.080
 X99  C12  C11   aromatic  1.394  0.020  1.394
 X99  C12  H12   single    0.930  0.020  1.080
 X99  C13  C12   aromatic  1.378  0.020  1.378
 X99  N    CD    single    1.446  0.020  1.446
 X99  CD   HD    single    0.970  0.020  1.090
 X99  CD   HDA   single    0.970  0.020  1.090
 X99  CA   N     single    1.453  0.020  1.453
 X99  CA   CB    single    1.538  0.020  1.538
 X99  CA   HA    single    0.970  0.020  1.090
 X99  CB   CG    single    1.511  0.020  1.511
 X99  CB   HB    single    0.970  0.020  1.090
 X99  CB   HBA   single    0.970  0.020  1.090
 X99  CG   CD    single    1.517  0.020  1.517
 X99  CG   F1    single    1.366  0.020  1.366
 X99  C3   CA    single    1.528  0.020  1.528
 X99  C3   O1    double    1.223  0.020  1.223
 X99  F2   CG    single    1.355  0.020  1.355
 X99  N1   CD1   single    1.461  0.020  1.461
 X99  N1   CA1   single    1.462  0.020  1.462
 X99  CD1  CG1   single    1.524  0.020  1.524
 X99  CA1  CB1   single    1.524  0.020  1.524
 X99  CB1  CG1   single    1.525  0.020  1.525
 X99  CD1  HD1   single    0.970  0.020  1.090
 X99  CD1  HDA1  single    0.970  0.020  1.090
 X99  CA1  HA1   single    0.970  0.020  1.090
 X99  CA1  HAA   single    0.970  0.020  1.090
 X99  CB1  HB1   single    0.970  0.020  1.090
 X99  CB1  HBA1  single    0.970  0.020  1.090
 X99  CG1  HG    single    0.970  0.020  1.090
 X99  CG1  HGA   single    0.970  0.020  1.090
 X99  C    N     single    1.346  0.020  1.346
 X99  C3   N1    single    1.335  0.020  1.335

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
 X99  N     C    C1   116.39  3.000
 X99  N     C    O    120.98  3.000
 X99  C1    C    O    122.63  3.000
 X99  H1A   C1   H1   106.15  3.000
 X99  H1A   C1   C2   109.97  3.000
 X99  H1    C1   C2   110.12  3.000
 X99  C2    C1   C    111.84  3.000
 X99  H1A   C1   C    109.42  3.000
 X99  H1    C1   C    109.16  3.000
 X99  H2A   C2   H2   107.31  3.000
 X99  H2A   C2   N3   107.90  3.000
 X99  H2    C2   N3   108.11  3.000
 X99  H2A   C2   C1   111.01  3.000
 X99  H2    C2   C1   111.12  3.000
 X99  N3    C2   C1   111.23  3.000
 X99  C5    N3   C4   112.04  3.000
 X99  C5    N3   C2   123.96  3.000
 X99  C4    N3   C2   123.97  3.000
 X99  C8    C4   O6   128.70  3.000
 X99  O6    C4   N3   125.28  3.000
 X99  C8    C4   N3   106.02  3.000
 X99  C13   C5   O7   128.68  3.000
 X99  O7    C5   N3   125.31  3.000
 X99  C13   C5   N3   106.01  3.000
 X99  C13   C8   C9   121.73  3.000
 X99  C9    C8   C4   130.30  3.000
 X99  C13   C8   C4   107.96  3.000
 X99  H9    C9   C10  121.13  3.000
 X99  H9    C9   C8   121.74  3.000
 X99  C10   C9   C8   117.13  3.000
 X99  H10   C10  C11  119.32  3.000
 X99  H10   C10  C9   119.54  3.000
 X99  C11   C10  C9   121.14  3.000
 X99  H11   C11  C12  119.54  3.000
 X99  C12   C11  C10  121.16  3.000
 X99  H11   C11  C10  119.30  3.000
 X99  H12   C12  C13  121.78  3.000
 X99  C13   C12  C11  117.14  3.000
 X99  H12   C12  C11  121.08  3.000
 X99  C12   C13  C8   121.69  3.000
 X99  C12   C13  C5   130.34  3.000
 X99  C8    C13  C5   107.96  3.000
 X99  CA    N    CD   113.34  3.000
 X99  CA    N    C    119.99  3.000
 X99  CD    N    C    126.65  3.000
 X99  HDA   CD   HD   108.61  3.000
 X99  HDA   CD   CG   110.07  3.000
 X99  HD    CD   CG   111.91  3.000
 X99  CG    CD   N    101.20  3.000
 X99  HDA   CD   N    112.32  3.000
 X99  HD    CD   N    112.62  3.000
 X99  HA    CA   C3   111.57  3.000
 X99  C3    CA   CB   110.15  3.000
 X99  HA    CA   CB   110.83  3.000
 X99  C3    CA   N    110.61  3.000
 X99  HA    CA   N    109.60  3.000
 X99  CB    CA   N    103.82  3.000
 X99  HBA   CB   HB   108.40  3.000
 X99  HBA   CB   CG   113.01  3.000
 X99  HB    CB   CG   108.37  3.000
 X99  HBA   CB   CA   112.90  3.000
 X99  HB    CB   CA   110.98  3.000
 X99  CG    CB   CA   103.06  3.000
 X99  F2    CG   F1   106.02  3.000
 X99  F2    CG   CB   113.58  3.000
 X99  F1    CG   CB   110.21  3.000
 X99  F2    CG   CD   112.59  3.000
 X99  F1    CG   CD   109.69  3.000
 X99  CB    CG   CD   104.79  3.000
 X99  N1    C3   O1   122.94  3.000
 X99  N1    C3   CA   116.81  3.000
 X99  O1    C3   CA   120.16  3.000
 X99  CA1   N1   CD1  112.25  3.000
 X99  CA1   N1   C3   126.76  3.000
 X99  CD1   N1   C3   120.98  3.000
 X99  HDA1  CD1  HD1  107.74  3.000
 X99  HDA1  CD1  CG1  112.83  3.000
 X99  HD1   CD1  CG1  111.55  3.000
 X99  HDA1  CD1  N1   110.99  3.000
 X99  HD1   CD1  N1   110.28  3.000
 X99  CG1   CD1  N1   103.45  3.000
 X99  HAA   CA1  HA1  108.18  3.000
 X99  HAA   CA1  CB1  112.05  3.000
 X99  HA1   CA1  CB1  110.86  3.000
 X99  HAA   CA1  N1   111.86  3.000
 X99  HA1   CA1  N1   110.79  3.000
 X99  CB1   CA1  N1   103.09  3.000
 X99  HBA1  CB1  HB1  107.97  3.000
 X99  HBA1  CB1  CG1  110.41  3.000
 X99  HB1   CB1  CG1  113.42  3.000
 X99  HBA1  CB1  CA1  110.04  3.000
 X99  HB1   CB1  CA1  111.97  3.000
 X99  CG1   CB1  CA1  102.98  3.000
 X99  HGA   CG1  HG   107.79  3.000
 X99  HGA   CG1  CB1  110.14  3.000
 X99  HG    CG1  CB1  113.33  3.000
 X99  HGA   CG1  CD1  110.17  3.000
 X99  HG    CG1  CD1  112.13  3.000
 X99  CB1   CG1  CD1  103.26  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
 X99  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 X99  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 X99  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 X99  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 X99  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 X99  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 X99  CONST_07  C8   C4   N3   C5      0.00   0.0  0
 X99  CONST_08  CD1  N1   C3   CA    180.00   0.0  0
 X99  CONST_09  CA1  N1   C3   CA      0.00   0.0  0
 X99  CONST_10  C8   C4   N3   C2    180.00   0.0  0
 X99  CONST_11  O6   C4   N3   C5    180.00   0.0  0
 X99  CONST_12  H9   C9   C8   C4      0.00   0.0  0
 X99  CONST_13  H12  C12  C13  C5      0.00   0.0  0
 X99  CONST_14  H10  C10  C9   C8    180.00   0.0  0
 X99  CONST_15  H11  C11  C10  C9    180.00   0.0  0
 X99  CONST_16  CD   N    C    O     180.00   0.0  0
 X99  CONST_17  CA   N    C    O       0.00   0.0  0
 X99  CONST_18  CD   N    C    C1      0.00   0.0  0
 X99  CONST_19  CA   N    C    C1    180.00   0.0  0
 X99  CONST_20  CD1  N1   C3   O1      0.00   0.0  0
 X99  CONST_21  CA1  N1   C3   O1    180.00   0.0  0
 X99  CONST_22  O6   C4   N3   C2      0.00   0.0  0
 X99  Var_01    CB   CG   CD   N     -35.55  30.0  1
 X99  Var_02    CA   CB   CG   CD     35.63  30.0  1
 X99  Var_03    CG   CD   N    CA     22.73  30.0  1
 X99  Var_04    CB1  CG1  CD1  N1     30.03  30.0  1
 X99  Var_05    CG1  CB1  CA1  N1     32.42  30.0  1
 X99  Var_06    CB1  CA1  N1   CD1   -14.20  30.0  1
 X99  Var_07    CA1  CB1  CG1  CD1   -38.92  30.0  1
 X99  Var_08    CG1  CD1  N1   CA1    -9.98  30.0  1
 X99  Var_09    C4   N3   C2   C1     87.58  30.0  3
 X99  Var_10    N3   C2   C1   C     178.86  30.0  1
 X99  Var_11    N    C    C1   C2   -177.28  30.0  1

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
 X99  chir_01  CA  N  CB  C3  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
 X99  plan-1  C    0.020
 X99  plan-1  O    0.020
 X99  plan-1  C1   0.020
 X99  plan-1  N    0.020
 X99  plan-1  CD   0.020
 X99  plan-1  CA   0.020
 X99  plan-2  C2   0.020
 X99  plan-2  N3   0.020
 X99  plan-2  C4   0.020
 X99  plan-2  C5   0.020
 X99  plan-2  O6   0.020
 X99  plan-2  O7   0.020
 X99  plan-2  C8   0.020
 X99  plan-2  C9   0.020
 X99  plan-2  C10  0.020
 X99  plan-2  C11  0.020
 X99  plan-2  C12  0.020
 X99  plan-2  C13  0.020
 X99  plan-2  H9   0.020
 X99  plan-2  H10  0.020
 X99  plan-2  H11  0.020
 X99  plan-2  H12  0.020
 X99  plan-3  CA   0.020
 X99  plan-3  C3   0.020
 X99  plan-3  O1   0.020
 X99  plan-3  N1   0.020
 X99  plan-3  CD1  0.020
 X99  plan-3  CA1  0.020

