# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 03:06:10 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2R)-2-[3-chloro-4-(methylsulfonyl)phenyl]-3-[(1R)-3-oxocyclopentyl]-N-(pyrazin-2-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc(cc1Cl)[C@@H](C[C@H]2CCC(=O)C2)C(=O)Nc3cnccn3
#
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
 2N8  2N8  (2R)-2-[3-chloro-4-(methylsulfonyl)phenyl]-3-[(1R)-3-oxocyclopentyl]-N-(pyrazin-2-yl)propanamide  ligand  48  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2N8
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
 2N8  O29   O   OS    0  -0.660  -4.6427  -2.1932   1.6307
 2N8  S27   S   S     0   1.218  -4.3840  -1.8112   0.2453
 2N8  O30   O   OS    0  -0.658  -4.4542  -2.8453  -0.7798
 2N8  C28   C   CH3   0  -0.788  -5.4959  -0.4886  -0.1684
 2N8  C23   C   CR6   0  -0.159  -2.7619  -1.0685   0.1980
 2N8  C22   C   CR16  0  -0.238  -2.0842  -0.9134   1.4014
 2N8  C21   C   CR16  0  -0.270  -0.8067  -0.3843   1.4268
 2N8  C24   C   CR6   0  -0.003  -2.1409  -0.6797  -0.9846
 2N8  CL26  CL  CL    0  -0.089  -2.9205  -0.8147  -2.5183
 2N8  C25   C   CR16  0  -0.248  -0.8641  -0.1435  -0.9557
 2N8  C10   C   CR6   0   0.165  -0.1826   0.0061   0.2457
 2N8  C9    C   CH1   0  -0.519   1.2085   0.5850   0.2300
 2N8  C8    C   CH2   0  -0.416   1.4078   1.7126   1.2561
 2N8  C3    C   CH1   0  -0.258   0.4306   2.8630   1.0784
 2N8  C4    C   CH2   0  -0.436   0.6774   4.0102   2.0689
 2N8  C5    C   CH2   0  -0.573  -0.0695   5.1927   1.4624
 2N8  C1    C   C     0   0.407   0.0010   4.9622  -0.0320
 2N8  O6    O   O     0  -0.404  -0.2902   5.7664  -0.8840
 2N8  C2    C   CH2   0  -0.572   0.4939   3.5521  -0.2847
 2N8  C11   C   C     0   0.598   2.2308  -0.5139   0.5007
 2N8  O13   O   O     0  -0.439   2.1353  -1.2661   1.4479
 2N8  N14   N   NH1   0  -0.716   3.2557  -0.5409  -0.3907
 2N8  C15   C   CR6   0   0.446   4.3712  -1.3675  -0.4192
 2N8  N16   N   N     0  -0.398   5.1937  -1.1106  -1.4253
 2N8  C17   C   CR16  0  -0.101   6.2849  -1.8503  -1.5348
 2N8  C18   C   CR16  0  -0.114   6.5662  -2.8619  -0.6316
 2N8  N19   N   N     0  -0.346   5.7429  -3.1210   0.3752
 2N8  C20   C   CR16  0  -0.125   4.6478  -2.3909   0.4980
 2N8  H1    H   HCH3  0   0.300  -5.4078   0.2954   0.5797
 2N8  H2    H   HCH3  0   0.288  -5.2734  -0.1005  -1.1585
 2N8  H3    H   HCH3  0   0.316  -6.5014  -0.9086  -0.1535
 2N8  H4    H   HCR6  0   0.294  -2.5563  -1.2049   2.3288
 2N8  H5    H   HCR6  0   0.275  -0.3094  -0.2706   2.3793
 2N8  H6    H   HCR6  0   0.292  -0.3977   0.1577  -1.8849
 2N8  H7    H   HCH1  0   0.298   1.3895   0.9970  -0.7664
 2N8  H8    H   HCH2  0   0.258   1.3252   1.3127   2.2700
 2N8  H9    H   HCH2  0   0.256   2.4286   2.0938   1.1532
 2N8  H10   H   HCH1  0   0.253  -0.5905   2.4980   1.2352
 2N8  H11   H   HCH2  0   0.251   0.3460   3.7637   3.0771
 2N8  H12   H   HCH2  0   0.234   1.7480   4.2290   2.1194
 2N8  H13   H   HCH2  0   0.278  -1.1278   5.1732   1.7457
 2N8  H14   H   HCH2  0   0.277   0.3175   6.1740   1.7388
 2N8  H15   H   HCH2  0   0.277   1.5327   3.6235  -0.6334
 2N8  H16   H   HCH2  0   0.279  -0.0786   3.0693  -1.0787
 2N8  H17   H   HNH1  0   0.420   3.2375   0.1249  -1.1504
 2N8  H18   H   HCR6  0   0.282   6.9525  -1.6338  -2.3598
 2N8  H19   H   HCR6  0   0.279   7.4615  -3.4637  -0.7232
 2N8  H20   H   HCR6  0   0.291   3.9877  -2.6159   1.3215

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
 2N8  CL26  C24  single    1.726  0.020  1.726
 2N8  O29   S27  double    1.460  0.020  1.460
 2N8  O30   S27  double    1.458  0.020  1.458
 2N8  S27   C23  single    1.785  0.020  1.785
 2N8  S27   C28  single    1.777  0.020  1.777
 2N8  C24   C23  aromatic  1.391  0.020  1.391
 2N8  C24   C25  aromatic  1.385  0.020  1.385
 2N8  C23   C22  aromatic  1.390  0.020  1.390
 2N8  C25   C10  aromatic  1.389  0.020  1.389
 2N8  C4    C5   single    1.524  0.020  1.524
 2N8  C4    C3   single    1.536  0.020  1.536
 2N8  O13   C11  double    1.213  0.020  1.213
 2N8  C22   C21  aromatic  1.383  0.020  1.383
 2N8  C10   C21  aromatic  1.392  0.020  1.392
 2N8  C10   C9   single    1.507  0.020  1.507
 2N8  C5    C1   single    1.514  0.020  1.514
 2N8  C3    C8   single    1.520  0.020  1.520
 2N8  C3    C2   single    1.529  0.020  1.529
 2N8  C8    C9   single    1.538  0.020  1.538
 2N8  C11   C9   single    1.525  0.020  1.525
 2N8  C11   N14  single    1.359  0.020  1.359
 2N8  C20   N19  aromatic  1.322  0.020  1.322
 2N8  C20   C15  aromatic  1.402  0.020  1.402
 2N8  N19   C18  aromatic  1.326  0.020  1.326
 2N8  C1    C2   single    1.515  0.020  1.515
 2N8  C1    O6   double    1.207  0.020  1.207
 2N8  N14   C15  single    1.389  0.020  1.389
 2N8  C15   N16  aromatic  1.325  0.020  1.325
 2N8  C18   C17  aromatic  1.385  0.020  1.385
 2N8  N16   C17  aromatic  1.323  0.020  1.323
 2N8  C28   H1   single    0.970  0.020  1.090
 2N8  C28   H2   single    0.970  0.020  1.090
 2N8  C28   H3   single    0.970  0.020  1.090
 2N8  C22   H4   single    0.930  0.020  1.080
 2N8  C21   H5   single    0.930  0.020  1.080
 2N8  C25   H6   single    0.930  0.020  1.080
 2N8  C9    H7   single    0.970  0.020  1.090
 2N8  C8    H8   single    0.970  0.020  1.090
 2N8  C8    H9   single    0.970  0.020  1.090
 2N8  C3    H10  single    0.970  0.020  1.090
 2N8  C4    H11  single    0.970  0.020  1.090
 2N8  C4    H12  single    0.970  0.020  1.090
 2N8  C5    H13  single    0.970  0.020  1.090
 2N8  C5    H14  single    0.970  0.020  1.090
 2N8  C2    H15  single    0.970  0.020  1.090
 2N8  C2    H16  single    0.970  0.020  1.090
 2N8  N14   H17  single    0.860  0.020  1.020
 2N8  C17   H18  single    0.930  0.020  1.080
 2N8  C18   H19  single    0.930  0.020  1.080
 2N8  C20   H20  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
 2N8  C23   S27  C28   104.65  3.000
 2N8  C28   S27  O30   109.52  3.000
 2N8  C23   S27  O30   108.69  3.000
 2N8  C28   S27  O29   107.75  3.000
 2N8  C23   S27  O29   107.16  3.000
 2N8  O30   S27  O29   118.23  3.000
 2N8  H3    C28  H2    109.82  3.000
 2N8  H3    C28  H1    110.07  3.000
 2N8  H2    C28  H1    110.66  3.000
 2N8  H3    C28  S27   106.70  3.000
 2N8  H2    C28  S27   110.49  3.000
 2N8  H1    C28  S27   109.02  3.000
 2N8  C24   C23  C22   119.16  3.000
 2N8  C22   C23  S27   117.82  3.000
 2N8  C24   C23  S27   122.99  3.000
 2N8  H4    C22  C21   119.40  3.000
 2N8  H4    C22  C23   119.99  3.000
 2N8  C21   C22  C23   120.60  3.000
 2N8  H5    C21  C10   120.81  3.000
 2N8  H5    C21  C22   118.79  3.000
 2N8  C10   C21  C22   120.39  3.000
 2N8  C25   C24  CL26  117.73  3.000
 2N8  C25   C24  C23   120.13  3.000
 2N8  CL26  C24  C23   122.14  3.000
 2N8  H6    C25  C10   120.07  3.000
 2N8  H6    C25  C24   119.14  3.000
 2N8  C10   C25  C24   120.79  3.000
 2N8  C9    C10  C25   119.03  3.000
 2N8  C9    C10  C21   122.05  3.000
 2N8  C25   C10  C21   118.93  3.000
 2N8  H7    C9   C11   108.81  3.000
 2N8  H7    C9   C8    108.08  3.000
 2N8  C11   C9   C8    108.85  3.000
 2N8  H7    C9   C10   107.89  3.000
 2N8  C11   C9   C10   109.89  3.000
 2N8  C8    C9   C10   113.23  3.000
 2N8  H9    C8   H8    106.56  3.000
 2N8  H9    C8   C3    108.97  3.000
 2N8  H8    C8   C3    109.68  3.000
 2N8  H9    C8   C9    108.27  3.000
 2N8  H8    C8   C9    109.93  3.000
 2N8  C3    C8   C9    113.19  3.000
 2N8  H10   C3   C2    108.44  3.000
 2N8  H10   C3   C4    107.84  3.000
 2N8  C2    C3   C4    103.40  3.000
 2N8  H10   C3   C8    109.29  3.000
 2N8  C2    C3   C8    114.76  3.000
 2N8  C4    C3   C8    112.75  3.000
 2N8  H12   C4   H11   107.47  3.000
 2N8  H12   C4   C5    110.04  3.000
 2N8  H11   C4   C5    113.24  3.000
 2N8  H12   C4   C3    109.67  3.000
 2N8  H11   C4   C3    112.27  3.000
 2N8  C5    C4   C3    104.13  3.000
 2N8  H14   C5   H13   107.05  3.000
 2N8  H14   C5   C1    111.76  3.000
 2N8  H13   C5   C1    107.31  3.000
 2N8  H14   C5   C4    115.04  3.000
 2N8  H13   C5   C4    110.88  3.000
 2N8  C1    C5   C4    104.58  3.000
 2N8  C2    C1   O6    125.51  3.000
 2N8  O6    C1   C5    125.74  3.000
 2N8  C2    C1   C5    108.76  3.000
 2N8  H16   C2   H15   107.09  3.000
 2N8  H16   C2   C1    111.25  3.000
 2N8  H15   C2   C1    107.47  3.000
 2N8  H16   C2   C3    115.31  3.000
 2N8  H15   C2   C3    110.59  3.000
 2N8  C1    C2   C3    104.92  3.000
 2N8  N14   C11  O13   124.01  3.000
 2N8  N14   C11  C9    113.80  3.000
 2N8  O13   C11  C9    122.18  3.000
 2N8  H17   N14  C15   113.04  3.000
 2N8  H17   N14  C11   117.82  3.000
 2N8  C15   N14  C11   129.14  3.000
 2N8  C20   C15  N16   121.06  3.000
 2N8  N16   C15  N14   113.51  3.000
 2N8  C20   C15  N14   125.42  3.000
 2N8  C17   N16  C15   117.82  3.000
 2N8  H18   C17  C18   121.17  3.000
 2N8  H18   C17  N16   117.37  3.000
 2N8  C18   C17  N16   121.47  3.000
 2N8  H19   C18  N19   117.97  3.000
 2N8  H19   C18  C17   121.25  3.000
 2N8  N19   C18  C17   120.77  3.000
 2N8  C20   N19  C18   118.49  3.000
 2N8  H20   C20  N19   117.55  3.000
 2N8  H20   C20  C15   122.06  3.000
 2N8  N19   C20  C15   120.39  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
 2N8  CONST_01  C10   C25  C24  C23     0.00   0.0  0
 2N8  CONST_02  C10   C21  C22  C23     0.00   0.0  0
 2N8  CONST_03  C25   C24  C23  C22     0.00   0.0  0
 2N8  CONST_04  C25   C10  C21  C22     0.00   0.0  0
 2N8  CONST_05  C24   C23  C22  C21     0.00   0.0  0
 2N8  CONST_06  C24   C25  C10  C21     0.00   0.0  0
 2N8  CONST_07  C18   N19  C20  C15     0.00   0.0  0
 2N8  CONST_08  C18   C17  N16  C15     0.00   0.0  0
 2N8  CONST_09  N19   C20  C15  N16     0.00   0.0  0
 2N8  CONST_10  N19   C18  C17  N16     0.00   0.0  0
 2N8  CONST_11  C20   N19  C18  C17     0.00   0.0  0
 2N8  CONST_12  C20   C15  N16  C17     0.00   0.0  0
 2N8  CONST_13  C25   C24  C23  S27   180.00   0.0  0
 2N8  CONST_14  C21   C22  C23  S27   180.00   0.0  0
 2N8  CONST_15  CL26  C24  C23  C22   180.00   0.0  0
 2N8  CONST_16  C9    C10  C21  C22   180.00   0.0  0
 2N8  CONST_17  C9    C10  C25  C24   180.00   0.0  0
 2N8  CONST_18  C10   C25  C24  CL26  180.00   0.0  0
 2N8  CONST_19  N19   C20  C15  N14   180.00   0.0  0
 2N8  CONST_20  C17   N16  C15  N14   180.00   0.0  0
 2N8  CONST_21  H6    C25  C24  C23   180.00   0.0  0
 2N8  CONST_22  H5    C21  C22  C23   180.00   0.0  0
 2N8  CONST_23  H4    C22  C23  C24   180.00   0.0  0
 2N8  CONST_24  H18   C17  N16  C15   180.00   0.0  0
 2N8  CONST_25  H20   C20  C15  N16   180.00   0.0  0
 2N8  CONST_26  H19   C18  C17  N16   180.00   0.0  0
 2N8  CONST_27  C20   C15  N14  C11     0.00   0.0  0
 2N8  CONST_28  N16   C15  N14  C11   180.00   0.0  0
 2N8  CONST_29  H17   N14  C15  N16     0.00   0.0  0
 2N8  CONST_30  C15   N14  C11  C9    180.00   0.0  0
 2N8  CONST_31  C15   N14  C11  O13     0.00   0.0  0
 2N8  Var_01    C1    C5   C4   C3    -30.98  30.0  1
 2N8  Var_02    C5    C1   C2   C3     11.59  30.0  1
 2N8  Var_03    C2    C1   C5   C4     12.10  30.0  1
 2N8  Var_04    C24   C23  S27  O29   174.78  30.0  2
 2N8  Var_05    H1    C28  S27  C23   -61.40  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
 2N8  chir_01  C9  C10  C8  C11  negativ
 2N8  chir_02  C3  C4   C8  C2   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
 2N8  plan-1  S27   0.020
 2N8  plan-1  C23   0.020
 2N8  plan-1  C22   0.020
 2N8  plan-1  C21   0.020
 2N8  plan-1  C24   0.020
 2N8  plan-1  CL26  0.020
 2N8  plan-1  C25   0.020
 2N8  plan-1  C10   0.020
 2N8  plan-1  C9    0.020
 2N8  plan-1  H4    0.020
 2N8  plan-1  H5    0.020
 2N8  plan-1  H6    0.020
 2N8  plan-2  N14   0.020
 2N8  plan-2  C15   0.020
 2N8  plan-2  N16   0.020
 2N8  plan-2  C17   0.020
 2N8  plan-2  C18   0.020
 2N8  plan-2  N19   0.020
 2N8  plan-2  C20   0.020
 2N8  plan-2  H18   0.020
 2N8  plan-2  H19   0.020
 2N8  plan-2  H20   0.020
 2N8  plan-3  C5    0.020
 2N8  plan-3  C1    0.020
 2N8  plan-3  O6    0.020
 2N8  plan-3  C2    0.020
 2N8  plan-4  C9    0.020
 2N8  plan-4  C11   0.020
 2N8  plan-4  O13   0.020
 2N8  plan-4  N14   0.020
 2N8  plan-4  C15   0.020
 2N8  plan-4  H17   0.020

