# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:05:02 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: N~2~-(cyclohexylsulfonyl)-N-[(1R)-1-(piperidin-1-ylcarbonyl)-3-(pyridinium-4-ylamino)propyl]glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CN[S](=O)(=O)C1CCCCC1)N[C@H](CCNc2cc[nH+]cc2)C(=O)N3CCCCC3
#
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
 I11  I11  N~2~-(cyclohexylsulfonyl)-N-[(1R)-1-(piperidin-1-ylcarbonyl)-3-(pyridinium-4-ylamino)propyl]glycinamide  ligand  68  32  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I11
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
 I11  C1    C  CH2   0  -0.436   6.5297  -1.6361  -0.0959
 I11  C2    C  CH2   0  -0.424   6.2114  -0.1975  -0.4951
 I11  C3    C  CH1   0  -0.463   4.7722   0.1470  -0.1115
 I11  C4    C  CH2   0  -0.428   4.5068  -0.0706   1.3745
 I11  C5    C  CH2   0  -0.435   4.8399  -1.5107   1.7601
 I11  C6    C  CH2   0  -0.434   6.2716  -1.8752   1.3871
 I11  S19   S  S     0   1.391   4.4188   1.8464  -0.6015
 I11  O43   O  OS    0  -0.672   5.2099   2.7436   0.2295
 I11  O44   O  OS    0  -0.672   4.5373   1.9231  -2.0521
 I11  N20   N  NC1   0  -0.746   2.8493   2.1532  -0.2395
 I11  C21   C  CH2   0  -0.392   1.7908   1.4461  -0.9278
 I11  C22   C  C     0   0.541   0.5443   1.4492  -0.0576
 I11  O42   O  O     0  -0.475   0.5318   1.9539   1.0522
 I11  N23   N  NH1   0  -0.626  -0.5111   0.8307  -0.6075
 I11  C24   C  CH1   0  -0.233  -1.8235   0.8997  -0.0192
 I11  C25   C  CH2   0  -0.516  -2.6911  -0.2307  -0.5718
 I11  C26   C  CH2   0  -0.253  -2.1904  -1.5938  -0.1235
 I11  N27   N  NH1   0  -0.670  -3.0864  -2.6277  -0.5996
 I11  C28   C  CR6   0   0.540  -2.9359  -3.9234  -0.3602
 I11  C29   C  CR16  0  -0.427  -3.8908  -4.8592  -0.8338
 I11  C30   C  CR16  0   0.073  -3.7278  -6.1833  -0.5790
 I11  N31   N  NR16  1  -0.598  -2.6655  -6.6238   0.1204
 I11  C32   C  CR16  0   0.075  -1.7369  -5.7759   0.5875
 I11  C33   C  CR16  0  -0.432  -1.8357  -4.4347   0.3709
 I11  C34   C  C     0   0.566  -2.4566   2.2701  -0.3267
 I11  O41   O  O     0  -0.491  -2.0090   2.9340  -1.2502
 I11  N35   N  NT    0  -0.449  -3.4940   2.6684   0.4299
 I11  C36   C  CH2   0  -0.314  -4.1979   3.9084   0.1285
 I11  C37   C  CH2   0  -0.433  -5.6464   3.6205  -0.2449
 I11  C38   C  CH2   0  -0.445  -6.3437   2.8386   0.8629
 I11  C39   C  CH2   0  -0.435  -5.5504   1.5857   1.2187
 I11  C40   C  CH2   0  -0.335  -4.0988   1.9336   1.5314
 I11  H11   H  HCH2  0   0.222   5.9163  -2.3213  -0.6894
 I11  H12   H  HCH2  0   0.243   7.5702  -1.8543  -0.3439
 I11  H21   H  HCH2  0   0.258   6.3599  -0.0660  -1.5676
 I11  H22   H  HCH2  0   0.239   6.8989   0.4821   0.0169
 I11  H3    H  HCH1  0   0.292   4.0868  -0.4703  -0.7025
 I11  H41   H  HCH2  0   0.242   5.1249   0.6146   1.9602
 I11  H42   H  HCH2  0   0.245   3.4634   0.1421   1.6185
 I11  H51   H  HCH2  0   0.222   4.1447  -2.1921   1.2587
 I11  H52   H  HCH2  0   0.243   4.6804  -1.6380   2.8327
 I11  H61   H  HCH2  0   0.237   6.4720  -2.9182   1.6411
 I11  H62   H  HCH2  0   0.217   6.9669  -1.2701   1.9780
 I11  H20   H  HNC1  0   0.415   2.6615   2.3556   0.7374
 I11  H211  H  HCH2  0   0.284   2.0441   0.4050  -1.1555
 I11  H212  H  HCH2  0   0.301   1.5592   1.9305  -1.8789
 I11  H23   H  HNH1  0   0.409  -0.4552   0.5742  -1.5822
 I11  H24   H  HCH1  0   0.291  -1.7085   0.7707   1.0590
 I11  H251  H  HCH2  0   0.279  -3.7193  -0.0982  -0.2313
 I11  H252  H  HCH2  0   0.276  -2.7169  -0.1737  -1.6641
 I11  H261  H  HCH2  0   0.263  -1.1816  -1.7749  -0.5020
 I11  H262  H  HCH2  0   0.258  -2.1396  -1.6234   0.9695
 I11  H27   H  HNH1  0   0.419  -3.9103  -2.3400  -1.1059
 I11  H29   H  HCR6  0   0.312  -4.7553  -4.5305  -1.3934
 I11  H30   H  HCR6  0   0.340  -4.4287  -6.9318  -0.9148
 I11  H31   H  HNR6  0   0.454  -2.5664  -7.6129   0.2994
 I11  H32   H  HCR6  0   0.341  -0.9183  -6.2133   1.1379
 I11  H33   H  HCR6  0   0.316  -1.0654  -3.7910   0.7676
 I11  H361  H  HCH2  0   0.240  -4.1645   4.5419   1.0211
 I11  H362  H  HCH2  0   0.266  -3.6801   4.4358  -0.6671
 I11  H371  H  HCH2  0   0.241  -6.1611   4.5646  -0.4353
 I11  H372  H  HCH2  0   0.225  -5.6669   3.0510  -1.1788
 I11  H381  H  HCH2  0   0.220  -6.4294   3.4731   1.7511
 I11  H382  H  HCH2  0   0.241  -7.3598   2.5734   0.5656
 I11  H391  H  HCH2  0   0.245  -5.9873   1.0834   2.0841
 I11  H392  H  HCH2  0   0.227  -5.5864   0.8764   0.3856
 I11  H401  H  HCH2  0   0.267  -3.5324   1.0383   1.7744
 I11  H402  H  HCH2  0   0.257  -4.0626   2.5711   2.4215

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
 I11  C1   C2    single    1.526  0.020  1.526
 I11  C1   C6    single    1.524  0.020  1.524
 I11  C1   H11   single    0.970  0.020  1.090
 I11  C1   H12   single    0.970  0.020  1.090
 I11  C2   C3    single    1.529  0.020  1.529
 I11  C2   H21   single    0.970  0.020  1.090
 I11  C2   H22   single    0.970  0.020  1.090
 I11  C3   C4    single    1.525  0.020  1.525
 I11  C3   S19   single    1.804  0.020  1.804
 I11  C3   H3    single    0.970  0.020  1.090
 I11  C4   C5    single    1.528  0.020  1.528
 I11  C4   H41   single    0.970  0.020  1.090
 I11  C4   H42   single    0.970  0.020  1.090
 I11  C5   C6    single    1.524  0.020  1.524
 I11  C5   H51   single    0.970  0.020  1.090
 I11  C5   H52   single    0.970  0.020  1.090
 I11  C6   H61   single    0.970  0.020  1.090
 I11  C6   H62   single    0.970  0.020  1.090
 I11  S19  O43   double    1.457  0.020  1.457
 I11  S19  O44   double    1.458  0.020  1.458
 I11  S19  N20   single    1.640  0.020  1.640
 I11  N20  C21   single    1.447  0.020  1.447
 I11  N20  H20   single    0.890  0.020  1.040
 I11  C21  C22   single    1.520  0.020  1.520
 I11  C21  H211  single    0.970  0.020  1.090
 I11  C21  H212  single    0.970  0.020  1.090
 I11  C22  O42   double    1.219  0.020  1.219
 I11  C22  N23   single    1.341  0.020  1.341
 I11  N23  C24   single    1.440  0.020  1.440
 I11  N23  H23   single    0.890  0.020  1.040
 I11  C24  C25   single    1.528  0.020  1.528
 I11  C24  C34   single    1.541  0.020  1.541
 I11  C24  H24   single    0.970  0.020  1.090
 I11  C25  C26   single    1.520  0.020  1.520
 I11  C25  H251  single    0.970  0.020  1.090
 I11  C25  H252  single    0.970  0.020  1.090
 I11  C26  N27   single    1.449  0.020  1.449
 I11  C26  H261  single    0.970  0.020  1.090
 I11  C26  H262  single    0.970  0.020  1.090
 I11  N27  C28   single    1.326  0.020  1.326
 I11  N27  H27   single    0.860  0.020  1.020
 I11  C28  C29   aromatic  1.418  0.020  1.418
 I11  C28  C33   aromatic  1.417  0.020  1.417
 I11  C29  C30   aromatic  1.358  0.020  1.358
 I11  C29  H29   single    0.930  0.020  1.080
 I11  C30  N31   aromatic  1.346  0.020  1.346
 I11  C30  H30   single    0.930  0.020  1.080
 I11  N31  C32   aromatic  1.341  0.020  1.341
 I11  N31  H31   single    0.860  0.020  1.020
 I11  C32  C33   aromatic  1.362  0.020  1.362
 I11  C32  H32   single    0.930  0.020  1.080
 I11  C33  H33   single    0.930  0.020  1.080
 I11  C34  O41   double    1.222  0.020  1.222
 I11  C34  N35   single    1.344  0.020  1.344
 I11  N35  C36   single    1.457  0.020  1.457
 I11  N35  C40   single    1.456  0.020  1.456
 I11  C36  C37   single    1.523  0.020  1.523
 I11  C36  H361  single    0.970  0.020  1.090
 I11  C36  H362  single    0.970  0.020  1.090
 I11  C37  C38   single    1.525  0.020  1.525
 I11  C37  H371  single    0.970  0.020  1.090
 I11  C37  H372  single    0.970  0.020  1.090
 I11  C38  C39   single    1.525  0.020  1.525
 I11  C38  H381  single    0.970  0.020  1.090
 I11  C38  H382  single    0.970  0.020  1.090
 I11  C39  C40   single    1.525  0.020  1.525
 I11  C39  H391  single    0.970  0.020  1.090
 I11  C39  H392  single    0.970  0.020  1.090
 I11  C40  H401  single    0.970  0.020  1.090
 I11  C40  H402  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
 I11  H12   C1   H11   106.60  3.000
 I11  H12   C1   C6    110.56  3.000
 I11  H11   C1   C6    109.54  3.000
 I11  H12   C1   C2    109.13  3.000
 I11  H11   C1   C2    109.35  3.000
 I11  C6    C1   C2    111.53  3.000
 I11  H22   C2   H21   107.43  3.000
 I11  H22   C2   C3    109.53  3.000
 I11  H21   C2   C3    110.35  3.000
 I11  H22   C2   C1    109.39  3.000
 I11  H21   C2   C1    110.03  3.000
 I11  C3    C2   C1    110.06  3.000
 I11  H3    C3   S19   105.18  3.000
 I11  H3    C3   C4    109.66  3.000
 I11  S19   C3   C4    111.41  3.000
 I11  H3    C3   C2    109.07  3.000
 I11  S19   C3   C2    109.18  3.000
 I11  C4    C3   C2    112.09  3.000
 I11  H42   C4   H41   107.36  3.000
 I11  H42   C4   C5    109.60  3.000
 I11  H41   C4   C5    109.42  3.000
 I11  H42   C4   C3    110.86  3.000
 I11  H41   C4   C3    109.53  3.000
 I11  C5    C4   C3    110.03  3.000
 I11  H52   C5   H51   106.53  3.000
 I11  H52   C5   C6    110.48  3.000
 I11  H51   C5   C6    109.60  3.000
 I11  H52   C5   C4    109.03  3.000
 I11  H51   C5   C4    109.43  3.000
 I11  C6    C5   C4    111.63  3.000
 I11  H62   C6   H61   106.61  3.000
 I11  H62   C6   C5    109.41  3.000
 I11  H61   C6   C5    110.12  3.000
 I11  H62   C6   C1    109.32  3.000
 I11  H61   C6   C1    110.19  3.000
 I11  C5    C6   C1    111.09  3.000
 I11  N20   S19  O44   106.72  3.000
 I11  N20   S19  O43   106.18  3.000
 I11  O44   S19  O43   119.42  3.000
 I11  N20   S19  C3    107.69  3.000
 I11  O44   S19  C3    107.70  3.000
 I11  O43   S19  C3    108.60  3.000
 I11  H20   N20  C21   114.82  3.000
 I11  H20   N20  S19   115.26  3.000
 I11  C21   N20  S19   120.25  3.000
 I11  H212  C21  H211  106.83  3.000
 I11  H212  C21  C22   108.89  3.000
 I11  H211  C21  C22   108.09  3.000
 I11  H212  C21  N20   110.65  3.000
 I11  H211  C21  N20   113.21  3.000
 I11  C22   C21  N20   109.06  3.000
 I11  N23   C22  O42   123.78  3.000
 I11  N23   C22  C21   114.18  3.000
 I11  O42   C22  C21   122.03  3.000
 I11  H23   N23  C24   117.21  3.000
 I11  H23   N23  C22   118.00  3.000
 I11  C24   N23  C22   121.84  3.000
 I11  H24   C24  C34   110.21  3.000
 I11  H24   C24  C25   109.23  3.000
 I11  C34   C24  C25   110.63  3.000
 I11  H24   C24  N23   107.57  3.000
 I11  C34   C24  N23   109.61  3.000
 I11  C25   C24  N23   109.52  3.000
 I11  H252  C25  H251  106.44  3.000
 I11  H252  C25  C26   110.43  3.000
 I11  H251  C25  C26   109.10  3.000
 I11  H252  C25  C24   109.63  3.000
 I11  H251  C25  C24   109.40  3.000
 I11  C26   C25  C24   111.70  3.000
 I11  H262  C26  H261  107.37  3.000
 I11  H262  C26  N27   109.73  3.000
 I11  H261  C26  N27   109.81  3.000
 I11  H262  C26  C25   109.52  3.000
 I11  H261  C26  C25   110.53  3.000
 I11  N27   C26  C25   109.84  3.000
 I11  H27   N27  C28   117.51  3.000
 I11  H27   N27  C26   117.81  3.000
 I11  C28   N27  C26   124.59  3.000
 I11  C33   C28  C29   117.20  3.000
 I11  C33   C28  N27   122.28  3.000
 I11  C29   C28  N27   120.52  3.000
 I11  H29   C29  C30   119.31  3.000
 I11  H29   C29  C28   120.70  3.000
 I11  C30   C29  C28   119.98  3.000
 I11  H30   C30  N31   116.57  3.000
 I11  H30   C30  C29   122.68  3.000
 I11  N31   C30  C29   120.75  3.000
 I11  H31   N31  C32   119.30  3.000
 I11  H31   N31  C30   119.34  3.000
 I11  C32   N31  C30   121.36  3.000
 I11  H32   C32  C33   122.36  3.000
 I11  H32   C32  N31   116.52  3.000
 I11  C33   C32  N31   121.12  3.000
 I11  H33   C33  C32   118.49  3.000
 I11  H33   C33  C28   121.92  3.000
 I11  C32   C33  C28   119.59  3.000
 I11  N35   C34  O41   123.15  3.000
 I11  N35   C34  C24   117.93  3.000
 I11  O41   C34  C24   118.91  3.000
 I11  C40   N35  C36   112.66  3.000
 I11  C40   N35  C34   126.65  3.000
 I11  C36   N35  C34   120.56  3.000
 I11  H362  C36  H361  107.56  3.000
 I11  H362  C36  C37   111.45  3.000
 I11  H361  C36  C37   109.77  3.000
 I11  H362  C36  N35   109.54  3.000
 I11  H361  C36  N35   107.99  3.000
 I11  C37   C36  N35   110.44  3.000
 I11  H372  C37  H371  107.00  3.000
 I11  H372  C37  C38   110.17  3.000
 I11  H371  C37  C38   110.76  3.000
 I11  H372  C37  C36   108.99  3.000
 I11  H371  C37  C36   109.11  3.000
 I11  C38   C37  C36   110.71  3.000
 I11  H382  C38  H381  106.79  3.000
 I11  H382  C38  C39   110.38  3.000
 I11  H381  C38  C39   109.12  3.000
 I11  H382  C38  C37   110.64  3.000
 I11  H381  C38  C37   109.15  3.000
 I11  C39   C38  C37   110.67  3.000
 I11  H392  C39  H391  106.97  3.000
 I11  H392  C39  C40   109.58  3.000
 I11  H391  C39  C40   108.86  3.000
 I11  H392  C39  C38   109.74  3.000
 I11  H391  C39  C38   110.78  3.000
 I11  C40   C39  C38   110.83  3.000
 I11  H402  C40  H401  106.29  3.000
 I11  H402  C40  C39   109.31  3.000
 I11  H401  C40  C39   110.73  3.000
 I11  H402  C40  N35   107.90  3.000
 I11  H401  C40  N35   111.62  3.000
 I11  C39   C40  N35   110.82  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
 I11  CONST_01  N31  C30  C29  C28     0.00   0.0  0
 I11  CONST_02  N31  C32  C33  C28     0.00   0.0  0
 I11  CONST_03  C32  C33  C28  C29     0.00   0.0  0
 I11  CONST_04  C32  N31  C30  C29     0.00   0.0  0
 I11  CONST_05  C33  C28  C29  C30     0.00   0.0  0
 I11  CONST_06  C33  C32  N31  C30     0.00   0.0  0
 I11  CONST_07  C30  C29  C28  N27   180.00   0.0  0
 I11  CONST_08  C32  C33  C28  N27   180.00   0.0  0
 I11  CONST_09  H30  C30  C29  C28   180.00   0.0  0
 I11  CONST_10  H32  C32  C33  C28   180.00   0.0  0
 I11  CONST_11  H33  C33  C28  C29   180.00   0.0  0
 I11  CONST_12  H31  N31  C30  C29   180.00   0.0  0
 I11  CONST_13  H29  C29  C30  N31   180.00   0.0  0
 I11  CONST_14  C36  N35  C34  C24   180.00   0.0  0
 I11  CONST_15  C40  N35  C34  C24     0.00   0.0  0
 I11  CONST_16  C36  N35  C34  O41     0.00   0.0  0
 I11  CONST_17  C40  N35  C34  O41   180.00   0.0  0
 I11  CONST_18  C29  C28  N27  C26   180.00   0.0  0
 I11  CONST_19  C33  C28  N27  C26     0.00   0.0  0
 I11  CONST_20  H27  N27  C28  C29     0.00   0.0  0
 I11  CONST_21  C24  N23  C22  C21   180.00   0.0  0
 I11  CONST_22  C24  N23  C22  O42     0.00   0.0  0
 I11  CONST_23  H23  N23  C22  C21     0.00   0.0  0
 I11  Var_01    C4   C5   C6   C1    -55.66  30.0  1
 I11  Var_02    C5   C6   C1   C2     55.67  30.0  1
 I11  Var_03    C6   C1   C2   C3    -55.56  30.0  1
 I11  Var_04    C6   C5   C4   C3     55.54  30.0  1
 I11  Var_05    C38  C37  C36  N35    56.08  30.0  1
 I11  Var_06    C38  C39  C40  N35   -54.96  30.0  1
 I11  Var_07    C39  C40  N35  C36    58.93  30.0  1
 I11  Var_08    C39  C38  C37  C36   -53.44  30.0  1
 I11  Var_09    C40  N35  C36  C37   -59.45  30.0  1
 I11  Var_10    C40  C39  C38  C37    52.80  30.0  1
 I11  Var_11    C21  N20  S19  C3    -65.53  30.0  3
 I11  Var_12    C28  N27  C26  C25  -179.06  30.0  3
 I11  Var_13    C22  C21  N20  S19   156.21  30.0  3
 I11  Var_14    O42  C22  C21  N20    -2.04  30.0  3
 I11  Var_15    N27  C26  C25  C24   176.48  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
 I11  chir_01  C3   C2   C4   S19  negativ
 I11  chir_02  C24  N23  C34  C25  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
 I11  plan-1  N27  0.020
 I11  plan-1  C28  0.020
 I11  plan-1  C29  0.020
 I11  plan-1  C30  0.020
 I11  plan-1  N31  0.020
 I11  plan-1  C32  0.020
 I11  plan-1  C33  0.020
 I11  plan-1  H29  0.020
 I11  plan-1  H30  0.020
 I11  plan-1  H31  0.020
 I11  plan-1  H32  0.020
 I11  plan-1  H33  0.020
 I11  plan-2  C24  0.020
 I11  plan-2  C34  0.020
 I11  plan-2  O41  0.020
 I11  plan-2  N35  0.020
 I11  plan-2  C36  0.020
 I11  plan-2  C40  0.020
 I11  plan-3  C26  0.020
 I11  plan-3  N27  0.020
 I11  plan-3  C28  0.020
 I11  plan-3  H27  0.020
 I11  plan-4  C21  0.020
 I11  plan-4  C22  0.020
 I11  plan-4  O42  0.020
 I11  plan-4  N23  0.020
 I11  plan-4  C24  0.020
 I11  plan-4  H23  0.020

