# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 06:18:37 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (1R,2R,4R)-N-[(2E)-2-iminoethyl]-2-(morpholin-4-ylcarbonyl)-4-(phenylsulfonyl)cyclopentanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=CCNC(=O)[C@@H]1C[C@H](C[C@H]1C(=O)N2CCOCC2)[S](=O)(=O)c3ccccc3
#
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
 QQV  QQV  (1R,2R,4R)-N-[(2E)-2-iminoethyl]-2-(morpholin-4-ylcarbonyl)-4-(phenylsulfonyl)cyclopentanecarboxamide  ligand  53  28  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QQV
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
 QQV  O12   O  OS    0  -0.666  -1.6078  -3.4837  -1.0456
 QQV  S1    S  S     0   1.212  -2.0993  -2.1132  -0.9050
 QQV  O11   O  OS    0  -0.661  -2.1958  -1.2774  -2.1022
 QQV  C13   C  CR6   0  -0.163  -3.6925  -2.1715  -0.1293
 QQV  C24   C  CR16  0  -0.241  -4.6785  -1.2716  -0.5085
 QQV  C27   C  CR16  0  -0.243  -5.9161  -1.3317   0.1164
 QQV  C28   C  CR16  0  -0.233  -6.1537  -2.2776   1.1041
 QQV  C26   C  CR16  0  -0.242  -5.1577  -3.1746   1.4716
 QQV  C25   C  CR16  0  -0.231  -3.9193  -3.1296   0.8517
 QQV  C4    C  CH1   0  -0.431  -1.0495  -1.2856   0.2948
 QQV  C7    C  CH2   0  -0.445  -1.4258   0.1915   0.5012
 QQV  C6    C  CH2   0  -0.441   0.4063  -1.3102  -0.2104
 QQV  C2    C  CH1   0  -0.423   0.9188   0.1010   0.1065
 QQV  C5    C  CH1   0  -0.356  -0.3024   0.9728  -0.1820
 QQV  C9    C  C     0   0.586  -0.1431   2.3757   0.3622
 QQV  N17   N  NH1   0  -0.626  -0.2771   3.3618  -0.5376
 QQV  C21   C  CH2   0  -0.365  -0.0606   4.7540  -0.2223
 QQV  C14   C  C1    0  -0.017   1.3898   5.1293  -0.3363
 QQV  N10   N  N     0  -0.542   1.7527   6.1512  -0.9819
 QQV  O16   O  O     0  -0.495   0.0848   2.5798   1.5471
 QQV  C3    C  C     0   0.599   2.1422   0.4897  -0.7043
 QQV  O15   O  O     0  -0.487   2.0313   1.2495  -1.6577
 QQV  N8    N  NT    0  -0.473   3.3254  -0.0500  -0.3457
 QQV  C19   C  CH2   0  -0.328   4.5418   0.2437  -1.0861
 QQV  C23   C  CH2   0  -0.184   5.6039   0.7702  -0.1369
 QQV  O18   O  O2    0  -0.482   5.8396  -0.1265   0.9265
 QQV  C22   C  CH2   0  -0.173   4.6615  -0.3711   1.6592
 QQV  C20   C  CH2   0  -0.335   3.5612  -0.9404   0.7781
 QQV  HXT   H  H     0   0.228   2.0843   4.4623   0.1820
 QQV  H4    H  HCH1  0   0.333  -1.1548  -1.8623   1.2154
 QQV  H24   H  HCR6  0   0.287  -4.4961  -0.5384  -1.2824
 QQV  H25   H  HCR6  0   0.287  -3.1483  -3.8360   1.1304
 QQV  H27   H  HCR6  0   0.275  -6.6946  -0.6386  -0.1724
 QQV  H28   H  HCR6  0   0.274  -7.1202  -2.3191   1.5885
 QQV  H26   H  HCR6  0   0.276  -5.3453  -3.9147   2.2376
 QQV  H71C  H  HCH2  0   0.279  -2.4086   0.4633   0.1163
 QQV  H72C  H  HCH2  0   0.274  -1.4359   0.3992   1.5710
 QQV  H61C  H  HCH2  0   0.284   0.9799  -2.1013   0.2671
 QQV  H62C  H  HCH2  0   0.271   0.4598  -1.4755  -1.2897
 QQV  H5    H  HCH1  0   0.274  -0.4824   0.9963  -1.2590
 QQV  H2    H  HCH1  0   0.291   1.1300   0.1741   1.1776
 QQV  H17   H  HNH1  0   0.406  -0.3576   3.1134  -1.5101
 QQV  H211  H  HCH2  0   0.272  -0.6531   5.3711  -0.8961
 QQV  H212  H  HCH2  0   0.271  -0.4064   4.9468   0.7950
 QQV  H10   H  H     0   0.347   2.7621   6.2603  -0.9388
 QQV  H191  H  HCH2  0   0.249   4.8947  -0.6720  -1.5722
 QQV  H192  H  HCH2  0   0.271   4.3393   0.9780  -1.8610
 QQV  H201  H  HCH2  0   0.272   2.6643  -1.0740   1.3761
 QQV  H202  H  HCH2  0   0.255   3.8526  -1.9264   0.4020
 QQV  H231  H  HCH2  0   0.245   6.5462   0.8999  -0.6706
 QQV  H232  H  HCH2  0   0.210   5.2930   1.7518   0.2478
 QQV  H221  H  HCH2  0   0.247   4.9057  -1.0830   2.4488
 QQV  H222  H  HCH2  0   0.210   4.3005   0.5527   2.1331

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
 QQV  O12  S1    double    1.463  0.020  1.463
 QQV  S1   O11   double    1.463  0.020  1.463
 QQV  S1   C13   single    1.773  0.020  1.773
 QQV  S1   C4    single    1.796  0.020  1.796
 QQV  C13  C24   aromatic  1.388  0.020  1.388
 QQV  C13  C25   aromatic  1.390  0.020  1.390
 QQV  C24  C27   aromatic  1.388  0.020  1.388
 QQV  C27  C28   aromatic  1.388  0.020  1.388
 QQV  C28  C26   aromatic  1.390  0.020  1.390
 QQV  C26  C25   aromatic  1.386  0.020  1.386
 QQV  C4   C7    single    1.538  0.020  1.538
 QQV  C4   C6    single    1.541  0.020  1.541
 QQV  C7   C5    single    1.529  0.020  1.529
 QQV  C6   C2    single    1.535  0.020  1.535
 QQV  C2   C5    single    1.528  0.020  1.528
 QQV  C2   C3    single    1.518  0.020  1.518
 QQV  C5   C9    single    1.513  0.020  1.513
 QQV  C9   N17   single    1.342  0.020  1.342
 QQV  C9   O16   double    1.224  0.020  1.224
 QQV  N17  C21   single    1.444  0.020  1.444
 QQV  C21  C14   single    1.502  0.020  1.502
 QQV  C14  N10   double    1.262  0.020  1.262
 QQV  C14  HXT   single    0.930  0.020  1.080
 QQV  C3   O15   double    1.224  0.020  1.224
 QQV  C3   N8    single    1.349  0.020  1.349
 QQV  N8   C19   single    1.454  0.020  1.454
 QQV  N8   C20   single    1.453  0.020  1.453
 QQV  C19  C23   single    1.519  0.020  1.519
 QQV  C23  O18   single    1.411  0.020  1.411
 QQV  O18  C22   single    1.409  0.020  1.409
 QQV  C22  C20   single    1.520  0.020  1.520
 QQV  C4   H4    single    0.970  0.020  1.090
 QQV  C24  H24   single    0.930  0.020  1.080
 QQV  C25  H25   single    0.930  0.020  1.080
 QQV  C27  H27   single    0.930  0.020  1.080
 QQV  C28  H28   single    0.930  0.020  1.080
 QQV  C26  H26   single    0.930  0.020  1.080
 QQV  C7   H71C  single    0.970  0.020  1.090
 QQV  C7   H72C  single    0.970  0.020  1.090
 QQV  C6   H61C  single    0.970  0.020  1.090
 QQV  C6   H62C  single    0.970  0.020  1.090
 QQV  C5   H5    single    0.970  0.020  1.090
 QQV  C2   H2    single    0.970  0.020  1.090
 QQV  N17  H17   single    0.860  0.020  1.020
 QQV  C21  H211  single    0.970  0.020  1.090
 QQV  C21  H212  single    0.970  0.020  1.090
 QQV  N10  H10   single    0.890  0.020  1.040
 QQV  C19  H191  single    0.970  0.020  1.090
 QQV  C19  H192  single    0.970  0.020  1.090
 QQV  C20  H201  single    0.970  0.020  1.090
 QQV  C20  H202  single    0.970  0.020  1.090
 QQV  C23  H231  single    0.970  0.020  1.090
 QQV  C23  H232  single    0.970  0.020  1.090
 QQV  C22  H221  single    0.970  0.020  1.090
 QQV  C22  H222  single    0.970  0.020  1.090

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
 QQV  C4    S1   C13   104.37  3.000
 QQV  C4    S1   O11   108.77  3.000
 QQV  C13   S1   O11   108.51  3.000
 QQV  C4    S1   O12   107.43  3.000
 QQV  C13   S1   O12   108.26  3.000
 QQV  O11   S1   O12   118.60  3.000
 QQV  C25   C13  C24   121.60  3.000
 QQV  C25   C13  S1    118.56  3.000
 QQV  C24   C13  S1    119.84  3.000
 QQV  H24   C24  C27   120.13  3.000
 QQV  H24   C24  C13   121.02  3.000
 QQV  C27   C24  C13   118.85  3.000
 QQV  H27   C27  C28   120.23  3.000
 QQV  H27   C27  C24   119.60  3.000
 QQV  C28   C27  C24   120.17  3.000
 QQV  H28   C28  C26   119.80  3.000
 QQV  H28   C28  C27   119.85  3.000
 QQV  C26   C28  C27   120.35  3.000
 QQV  H26   C26  C25   119.61  3.000
 QQV  H26   C26  C28   120.31  3.000
 QQV  C25   C26  C28   120.08  3.000
 QQV  H25   C25  C26   120.02  3.000
 QQV  H25   C25  C13   121.03  3.000
 QQV  C26   C25  C13   118.94  3.000
 QQV  H4    C4   C6    111.05  3.000
 QQV  H4    C4   C7    111.75  3.000
 QQV  C6    C4   C7    106.88  3.000
 QQV  H4    C4   S1    105.28  3.000
 QQV  C6    C4   S1    109.01  3.000
 QQV  C7    C4   S1    112.90  3.000
 QQV  H72C  C7   H71C  106.90  3.000
 QQV  H72C  C7   C5    110.36  3.000
 QQV  H71C  C7   C5    112.16  3.000
 QQV  H72C  C7   C4    108.48  3.000
 QQV  H71C  C7   C4    114.38  3.000
 QQV  C5    C7   C4    104.53  3.000
 QQV  H62C  C6   H61C  107.32  3.000
 QQV  H62C  C6   C2    109.06  3.000
 QQV  H61C  C6   C2    113.71  3.000
 QQV  H62C  C6   C4    111.86  3.000
 QQV  H61C  C6   C4    111.46  3.000
 QQV  C2    C6   C4    103.48  3.000
 QQV  H2    C2   C3    110.50  3.000
 QQV  H2    C2   C5    107.52  3.000
 QQV  C3    C2   C5    113.40  3.000
 QQV  H2    C2   C6    109.15  3.000
 QQV  C3    C2   C6    113.22  3.000
 QQV  C5    C2   C6    102.63  3.000
 QQV  H5    C5   C9    110.61  3.000
 QQV  H5    C5   C2    109.28  3.000
 QQV  C9    C5   C2    112.14  3.000
 QQV  H5    C5   C7    109.29  3.000
 QQV  C9    C5   C7    112.98  3.000
 QQV  C2    C5   C7    102.20  3.000
 QQV  O16   C9   N17   123.06  3.000
 QQV  O16   C9   C5    121.49  3.000
 QQV  N17   C9   C5    115.45  3.000
 QQV  H17   N17  C21   117.44  3.000
 QQV  H17   N17  C9    118.32  3.000
 QQV  C21   N17  C9    123.18  3.000
 QQV  H212  C21  H211  107.71  3.000
 QQV  H212  C21  C14   109.42  3.000
 QQV  H211  C21  C14   109.68  3.000
 QQV  H212  C21  N17   109.05  3.000
 QQV  H211  C21  N17   109.24  3.000
 QQV  C14   C21  N17   111.66  3.000
 QQV  HXT   C14  N10   123.63  3.000
 QQV  HXT   C14  C21   115.14  3.000
 QQV  N10   C14  C21   121.24  3.000
 QQV  H10   N10  C14   110.54  3.000
 QQV  N8    C3   O15   122.33  3.000
 QQV  N8    C3   C2    117.54  3.000
 QQV  O15   C3   C2    120.12  3.000
 QQV  C20   N8   C19   112.45  3.000
 QQV  C20   N8   C3    126.37  3.000
 QQV  C19   N8   C3    121.17  3.000
 QQV  H192  C19  H191  107.97  3.000
 QQV  H192  C19  C23   109.99  3.000
 QQV  H191  C19  C23   110.00  3.000
 QQV  H192  C19  N8    110.10  3.000
 QQV  H191  C19  N8    109.07  3.000
 QQV  C23   C19  N8    109.69  3.000
 QQV  H232  C23  H231  108.02  3.000
 QQV  H232  C23  O18   110.55  3.000
 QQV  H231  C23  O18   107.47  3.000
 QQV  H232  C23  C19   109.30  3.000
 QQV  H231  C23  C19   109.85  3.000
 QQV  O18   C23  C19   111.56  3.000
 QQV  C22   O18  C23   111.27  3.000
 QQV  H222  C22  H221  108.06  3.000
 QQV  H222  C22  C20   109.08  3.000
 QQV  H221  C22  C20   109.71  3.000
 QQV  H222  C22  O18   110.67  3.000
 QQV  H221  C22  O18   107.61  3.000
 QQV  C20   C22  O18   111.64  3.000
 QQV  H202  C20  H201  107.34  3.000
 QQV  H202  C20  C22   110.10  3.000
 QQV  H201  C20  C22   108.94  3.000
 QQV  H202  C20  N8    109.23  3.000
 QQV  H201  C20  N8    111.55  3.000
 QQV  C22   C20  N8    109.65  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
 QQV  CONST_01  C28  C27  C24  C13    0.00   0.0  0
 QQV  CONST_02  C28  C26  C25  C13    0.00   0.0  0
 QQV  CONST_03  C26  C25  C13  C24    0.00   0.0  0
 QQV  CONST_04  C26  C28  C27  C24    0.00   0.0  0
 QQV  CONST_05  C25  C13  C24  C27    0.00   0.0  0
 QQV  CONST_06  C25  C26  C28  C27    0.00   0.0  0
 QQV  CONST_07  C27  C24  C13  S1   180.00   0.0  0
 QQV  CONST_08  C26  C25  C13  S1   180.00   0.0  0
 QQV  CONST_09  C19  N8   C3   C2   180.00   0.0  0
 QQV  CONST_10  C20  N8   C3   C2     0.00   0.0  0
 QQV  CONST_11  H27  C27  C24  C13  180.00   0.0  0
 QQV  CONST_12  H26  C26  C25  C13  180.00   0.0  0
 QQV  CONST_13  H25  C25  C13  C24  180.00   0.0  0
 QQV  CONST_14  H28  C28  C27  C24  180.00   0.0  0
 QQV  CONST_15  H24  C24  C27  C28  180.00   0.0  0
 QQV  CONST_16  C19  N8   C3   O15    0.00   0.0  0
 QQV  CONST_17  C20  N8   C3   O15  180.00   0.0  0
 QQV  CONST_18  C21  N17  C9   C5   180.00   0.0  0
 QQV  CONST_19  H17  N17  C9   C5     0.00   0.0  0
 QQV  CONST_20  O16  C9   N17  C21    0.00   0.0  0
 QQV  Var_01    O18  C23  C19  N8    55.48  30.0  1
 QQV  Var_02    O18  C22  C20  N8   -55.41  30.0  1
 QQV  Var_03    C22  C20  N8   C19   53.77  30.0  1
 QQV  Var_04    C20  N8   C19  C23  -53.87  30.0  1
 QQV  Var_05    C20  C22  O18  C23   58.43  30.0  1
 QQV  Var_06    C4   S1   C13  C24  102.06  30.0  2
 QQV  Var_07    C14  C21  N17  C9    85.28  30.0  3
 QQV  Var_08    N10  C14  C21  N17  130.95  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
 QQV  chir_01  C4  S1  C7  C6  positiv
 QQV  chir_02  C2  C3  C5  C6  negativ
 QQV  chir_03  C5  C7  C2  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
 QQV  plan-1  S1   0.020
 QQV  plan-1  C13  0.020
 QQV  plan-1  C24  0.020
 QQV  plan-1  C27  0.020
 QQV  plan-1  C28  0.020
 QQV  plan-1  C26  0.020
 QQV  plan-1  C25  0.020
 QQV  plan-1  H24  0.020
 QQV  plan-1  H25  0.020
 QQV  plan-1  H27  0.020
 QQV  plan-1  H28  0.020
 QQV  plan-1  H26  0.020
 QQV  plan-2  C2   0.020
 QQV  plan-2  C3   0.020
 QQV  plan-2  O15  0.020
 QQV  plan-2  N8   0.020
 QQV  plan-2  C19  0.020
 QQV  plan-2  C20  0.020
 QQV  plan-3  C5   0.020
 QQV  plan-3  C9   0.020
 QQV  plan-3  N17  0.020
 QQV  plan-3  C21  0.020
 QQV  plan-3  O16  0.020
 QQV  plan-3  H17  0.020
 QQV  plan-4  C21  0.020
 QQV  plan-4  C14  0.020
 QQV  plan-4  N10  0.020
 QQV  plan-4  HXT  0.020
 QQV  plan-4  H10  0.020

