# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:43:32 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (3S)-1-(4-{[(2,3,5,6-tetramethylphenyl)sulfonyl]amino}naphthalen-1-yl)pyrrolidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(C)c(c1C)[S](=O)(=O)Nc2ccc(N3CC[C@@H](C3)C(O)=O)c4ccccc24
#
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
 51M  51M  '(3S)-1-(4-{[(2,3,5,6-tetramethylphenyl)sulfonyl]amino}naphthalen-1-yl)pyrrolidine-3-carboxylic acid'  ligand  60  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_51M
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
 51M  C1   C  CR16  0  -0.256  -0.4912   0.4874  -2.4568
 51M  C2   C  CR16  0  -0.368  -1.7534   0.6477  -1.8632
 51M  C3   C  CR6   0   0.302  -2.0818  -0.0286  -0.7113
 51M  C7   C  CR16  0  -0.299   1.0364  -2.0480  -0.1980
 51M  C8   C  CR16  0  -0.247   0.6722  -2.8360   0.8588
 51M  C9   C  CR16  0  -0.256  -0.6256  -2.7473   1.3933
 51M  C10  C  CR16  0  -0.307  -1.5179  -1.8467   0.8788
 51M  C12  C  CH2   0  -0.294  -4.3921   0.8003  -0.7253
 51M  C13  C  CH1   0  -0.394  -5.4789   0.8588   0.3446
 51M  C14  C  CH2   0  -0.458  -4.6928   0.8779   1.6872
 51M  C15  C  CH2   0  -0.309  -3.2289   0.8288   1.2618
 51M  C16  C  C     0   0.553  -6.4152  -0.3211   0.2992
 51M  O17  O  OH1   0  -0.595  -7.4185  -0.1697   1.1588
 51M  C21  C  CR6   0  -0.317   3.1140   0.5262  -0.1598
 51M  C24  C  CR6   0   0.081   4.1237  -0.3930   0.1853
 51M  C27  C  CR6   0   0.087   2.7398   1.0905   2.1427
 51M  C31  C  CH3   0  -0.743   2.0248   1.8296   3.2384
 51M  C4   C  CR6   0   0.166   0.4566  -0.3286  -1.9026
 51M  C5   C  CR66  0   0.045  -1.1589  -0.9904  -0.1873
 51M  C6   C  CR66  0   0.154   0.1326  -1.1192  -0.7628
 51M  N11  N  NT    0  -0.508  -3.2868   0.1632  -0.0381
 51M  O18  O  O     0  -0.436  -6.2919  -1.2945  -0.4004
 51M  N19  N  NC1   0  -0.819   1.7619  -0.3200  -2.4585
 51M  S20  S  S     0   1.340   2.8320   0.8370  -1.9069
 51M  O22  O  OS    0  -0.634   2.1830   2.1246  -2.0619
 51M  O23  O  OS    0  -0.649   4.0642   0.6199  -2.6457
 51M  C25  C  CR6   0   0.088   4.4803  -0.4954   1.5340
 51M  C26  C  CR16  0  -0.330   3.8035   0.2678   2.4723
 51M  C28  C  CR6   0   0.102   2.3528   1.2169   0.8014
 51M  C29  C  CH3   0  -0.729   4.8261  -1.3150  -0.7786
 51M  H1   H  HCR6  0   0.266  -0.2486   1.0568  -3.3438
 51M  H2   H  HCR6  0   0.268  -2.4427   1.3494  -2.3120
 51M  H3   H  HCR6  0   0.232   2.0306  -2.1573  -0.6077
 51M  H4   H  HCR6  0   0.257   1.3788  -3.5432   1.2728
 51M  H5   H  HCR6  0   0.257  -0.9217  -3.4016   2.2028
 51M  H6   H  HCR6  0   0.265  -2.5274  -1.8096   1.2650
 51M  H7   H  HCH2  0   0.262  -4.6806   0.2411  -1.6149
 51M  H8   H  HCH2  0   0.229  -4.1554   1.8275  -1.0373
 51M  H9   H  HCH1  0   0.300  -6.0772   1.7662   0.2405
 51M  H10  H  HCH2  0   0.259  -4.9151   1.7676   2.2727
 51M  H11  H  HCH2  0   0.257  -4.9329   0.0156   2.3103
 51M  H12  H  HCH2  0   0.231  -2.8203   1.8442   1.1556
 51M  H13  H  HCH2  0   0.259  -2.6022   0.2934   1.9731
 51M  H14  H  HOH1  0   0.480  -7.9893  -0.9526   1.1450
 51M  H15  H  HCH3  0   0.249   6.5108  -1.2394   1.4523
 51M  H16  H  HCH3  0   0.255   5.7824  -1.2603   3.0542
 51M  H17  H  HCH3  0   0.250   5.3183  -2.4621   1.8595
 51M  H18  H  HCH3  0   0.247   1.0038   1.4662   3.3756
 51M  H19  H  HCH3  0   0.255   2.5438   1.7057   4.1875
 51M  H20  H  HCH3  0   0.248   1.9573   2.8993   3.0346
 51M  H21  H  HCH3  0   0.254   1.3750   3.1170   0.4685
 51M  H22  H  HCH3  0   0.266   0.6005   1.7853  -0.3732
 51M  H23  H  HCH3  0   0.241   0.4249   1.9357   1.3513
 51M  H24  H  HNC1  0   0.417   2.2001  -1.2186  -2.6297
 51M  H25  H  HCR6  0   0.248   4.1018   0.1955   3.5124
 51M  H26  H  HCH3  0   0.268   5.7534  -0.8820  -1.1553
 51M  H27  H  HCH3  0   0.254   5.0870  -2.2406  -0.2702
 51M  H28  H  HCH3  0   0.231   4.2324  -1.6024  -1.6408
 51M  C30  C  CH3   0  -0.747   5.5799  -1.4106   1.9948
 51M  C32  C  CH3   0  -0.728   1.1298   2.0550   0.5304

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
 51M  O18  C16  double    1.205  0.020  1.205
 51M  O17  C16  single    1.330  0.020  1.330
 51M  C16  C13  single    1.507  0.020  1.507
 51M  C13  C14  single    1.556  0.020  1.556
 51M  C13  C12  single    1.526  0.020  1.526
 51M  C14  C15  single    1.525  0.020  1.525
 51M  C12  N11  single    1.449  0.020  1.449
 51M  C15  N11  single    1.462  0.020  1.462
 51M  N11  C3   single    1.394  0.020  1.394
 51M  C2   C3   aromatic  1.376  0.020  1.376
 51M  C2   C1   aromatic  1.404  0.020  1.404
 51M  C30  C25  single    1.503  0.020  1.503
 51M  C3   C5   aromatic  1.432  0.020  1.432
 51M  C26  C25  aromatic  1.386  0.020  1.386
 51M  C26  C27  aromatic  1.385  0.020  1.385
 51M  C31  C27  single    1.503  0.020  1.503
 51M  C25  C24  aromatic  1.399  0.020  1.399
 51M  C1   C4   aromatic  1.368  0.020  1.368
 51M  C27  C28  aromatic  1.402  0.020  1.402
 51M  C5   C10  aromatic  1.414  0.020  1.414
 51M  C5   C6   aromatic  1.420  0.020  1.420
 51M  C24  C29  single    1.508  0.020  1.508
 51M  C24  C21  aromatic  1.408  0.020  1.408
 51M  C10  C9   aromatic  1.368  0.020  1.368
 51M  C28  C21  aromatic  1.407  0.020  1.407
 51M  C28  C32  single    1.507  0.020  1.507
 51M  C4   C6   aromatic  1.424  0.020  1.424
 51M  C4   N19  single    1.419  0.020  1.419
 51M  C21  S20  single    1.797  0.020  1.797
 51M  C6   C7   aromatic  1.414  0.020  1.414
 51M  N19  S20  single    1.670  0.020  1.670
 51M  C9   C8   aromatic  1.406  0.020  1.406
 51M  S20  O22  double    1.450  0.020  1.450
 51M  S20  O23  double    1.453  0.020  1.453
 51M  C7   C8   aromatic  1.368  0.020  1.368
 51M  C1   H1   single    0.930  0.020  1.080
 51M  C2   H2   single    0.930  0.020  1.080
 51M  C7   H3   single    0.930  0.020  1.080
 51M  C8   H4   single    0.930  0.020  1.080
 51M  C9   H5   single    0.930  0.020  1.080
 51M  C10  H6   single    0.930  0.020  1.080
 51M  C12  H7   single    0.970  0.020  1.090
 51M  C12  H8   single    0.970  0.020  1.090
 51M  C13  H9   single    0.970  0.020  1.090
 51M  C14  H10  single    0.970  0.020  1.090
 51M  C14  H11  single    0.970  0.020  1.090
 51M  C15  H12  single    0.970  0.020  1.090
 51M  C15  H13  single    0.970  0.020  1.090
 51M  O17  H14  single    0.850  0.020  0.980
 51M  C30  H15  single    0.970  0.020  1.090
 51M  C30  H16  single    0.970  0.020  1.090
 51M  C30  H17  single    0.970  0.020  1.090
 51M  C31  H18  single    0.970  0.020  1.090
 51M  C31  H19  single    0.970  0.020  1.090
 51M  C31  H20  single    0.970  0.020  1.090
 51M  C32  H21  single    0.970  0.020  1.090
 51M  C32  H22  single    0.970  0.020  1.090
 51M  C32  H23  single    0.970  0.020  1.090
 51M  N19  H24  single    0.890  0.020  1.040
 51M  C26  H25  single    0.930  0.020  1.080
 51M  C29  H26  single    0.970  0.020  1.090
 51M  C29  H27  single    0.970  0.020  1.090
 51M  C29  H28  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
 51M  H1   C1   C4   119.40  3.000
 51M  H1   C1   C2   119.23  3.000
 51M  C4   C1   C2   121.31  3.000
 51M  H2   C2   C3   120.96  3.000
 51M  H2   C2   C1   118.15  3.000
 51M  C3   C2   C1   120.84  3.000
 51M  N11  C3   C5   118.22  3.000
 51M  C5   C3   C2   118.86  3.000
 51M  N11  C3   C2   122.91  3.000
 51M  H3   C7   C6   120.20  3.000
 51M  H3   C7   C8   118.66  3.000
 51M  C6   C7   C8   121.14  3.000
 51M  H4   C8   C9   119.90  3.000
 51M  H4   C8   C7   119.89  3.000
 51M  C9   C8   C7   120.21  3.000
 51M  H5   C9   C10  120.05  3.000
 51M  H5   C9   C8   119.91  3.000
 51M  C10  C9   C8   120.03  3.000
 51M  H6   C10  C5   119.05  3.000
 51M  H6   C10  C9   119.80  3.000
 51M  C5   C10  C9   121.11  3.000
 51M  H8   C12  H7   107.75  3.000
 51M  H8   C12  N11  112.41  3.000
 51M  H7   C12  N11  111.32  3.000
 51M  H8   C12  C13  108.45  3.000
 51M  H7   C12  C13  113.79  3.000
 51M  N11  C12  C13  103.15  3.000
 51M  H9   C13  C16  107.90  3.000
 51M  H9   C13  C14  110.42  3.000
 51M  C16  C13  C14  110.46  3.000
 51M  H9   C13  C12  110.81  3.000
 51M  C14  C13  C12  104.22  3.000
 51M  C16  C13  C12  113.04  3.000
 51M  H11  C14  H10  107.11  3.000
 51M  H11  C14  C15  110.19  3.000
 51M  H10  C14  C15  111.87  3.000
 51M  H11  C14  C13  111.84  3.000
 51M  H10  C14  C13  111.79  3.000
 51M  C15  C14  C13  104.11  3.000
 51M  H13  C15  H12  107.65  3.000
 51M  H13  C15  N11  112.33  3.000
 51M  H12  C15  N11  110.44  3.000
 51M  H13  C15  C14  112.72  3.000
 51M  H12  C15  C14  110.73  3.000
 51M  N11  C15  C14  102.99  3.000
 51M  O18  C16  O17  122.99  3.000
 51M  O17  C16  C13  111.11  3.000
 51M  O18  C16  C13  125.90  3.000
 51M  H14  O17  C16  110.07  3.000
 51M  C28  C21  S20  119.63  3.000
 51M  S20  C21  C24  117.63  3.000
 51M  C28  C21  C24  122.73  3.000
 51M  C29  C24  C25  116.94  3.000
 51M  C29  C24  C21  125.20  3.000
 51M  C25  C24  C21  117.83  3.000
 51M  C28  C27  C26  119.57  3.000
 51M  C28  C27  C31  121.47  3.000
 51M  C26  C27  C31  118.96  3.000
 51M  H20  C31  H19  107.69  3.000
 51M  H20  C31  H18  106.96  3.000
 51M  H19  C31  H18  107.35  3.000
 51M  H20  C31  C27  112.06  3.000
 51M  H19  C31  C27  110.66  3.000
 51M  H18  C31  C27  111.88  3.000
 51M  N19  C4   C6   121.74  3.000
 51M  N19  C4   C1   118.37  3.000
 51M  C6   C4   C1   119.85  3.000
 51M  C6   C5   C10  118.80  3.000
 51M  C6   C5   C3   119.92  3.000
 51M  C10  C5   C3   121.26  3.000
 51M  C5   C6   C4   118.74  3.000
 51M  C4   C6   C7   122.61  3.000
 51M  C5   C6   C7   118.63  3.000
 51M  C15  N11  C12  104.58  3.000
 51M  C15  N11  C3   117.27  3.000
 51M  C12  N11  C3   119.40  3.000
 51M  H24  N19  S20  113.13  3.000
 51M  H24  N19  C4   117.27  3.000
 51M  S20  N19  C4   117.67  3.000
 51M  O23  S20  O22  117.24  3.000
 51M  O23  S20  N19  105.78  3.000
 51M  O22  S20  N19  107.04  3.000
 51M  O23  S20  C21  109.60  3.000
 51M  O22  S20  C21  109.13  3.000
 51M  N19  S20  C21  107.58  3.000
 51M  C26  C25  C30  119.01  3.000
 51M  C26  C25  C24  119.21  3.000
 51M  C30  C25  C24  121.78  3.000
 51M  H25  C26  C25  118.58  3.000
 51M  H25  C26  C27  118.64  3.000
 51M  C25  C26  C27  122.76  3.000
 51M  C32  C28  C27  116.50  3.000
 51M  C32  C28  C21  126.09  3.000
 51M  C27  C28  C21  117.39  3.000
 51M  H28  C29  H27  106.09  3.000
 51M  H28  C29  H26  107.20  3.000
 51M  H27  C29  H26  107.18  3.000
 51M  H28  C29  C24  114.52  3.000
 51M  H27  C29  C24  109.47  3.000
 51M  H26  C29  C24  111.97  3.000
 51M  H17  C30  H16  107.33  3.000
 51M  H17  C30  H15  107.09  3.000
 51M  H16  C30  H15  107.67  3.000
 51M  H17  C30  C25  111.90  3.000
 51M  H16  C30  C25  110.51  3.000
 51M  H15  C30  C25  112.10  3.000
 51M  H23  C32  H22  106.61  3.000
 51M  H23  C32  H21  107.15  3.000
 51M  H22  C32  H21  107.77  3.000
 51M  H23  C32  C28  109.21  3.000
 51M  H22  C32  C28  114.13  3.000
 51M  H21  C32  C28  111.65  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
 51M  CONST_01  C5   C3   C2   C1      0.00   0.0  0
 51M  CONST_02  C5   C6   C4   C1      0.00   0.0  0
 51M  CONST_03  C7   C6   C4   C1    180.00   0.0  0
 51M  CONST_04  C10  C5   C3   C2    180.00   0.0  0
 51M  CONST_05  C6   C5   C3   C2      0.00   0.0  0
 51M  CONST_06  C6   C4   C1   C2      0.00   0.0  0
 51M  CONST_07  C4   C1   C2   C3      0.00   0.0  0
 51M  CONST_08  C9   C10  C5   C3    180.00   0.0  0
 51M  CONST_09  C4   C6   C5   C3      0.00   0.0  0
 51M  CONST_10  C7   C6   C5   C3    180.00   0.0  0
 51M  CONST_11  C10  C5   C6   C7      0.00   0.0  0
 51M  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 51M  CONST_13  C5   C10  C9   C8      0.00   0.0  0
 51M  CONST_14  C5   C6   C7   C8      0.00   0.0  0
 51M  CONST_15  C4   C6   C7   C8    180.00   0.0  0
 51M  CONST_16  C6   C5   C10  C9      0.00   0.0  0
 51M  CONST_17  C6   C7   C8   C9      0.00   0.0  0
 51M  CONST_18  C4   C6   C5   C10   180.00   0.0  0
 51M  CONST_19  C26  C25  C24  C21     0.00   0.0  0
 51M  CONST_20  C26  C27  C28  C21     0.00   0.0  0
 51M  CONST_21  C27  C26  C25  C24     0.00   0.0  0
 51M  CONST_22  C27  C28  C21  C24     0.00   0.0  0
 51M  CONST_23  C28  C27  C26  C25     0.00   0.0  0
 51M  CONST_24  C28  C21  C24  C25     0.00   0.0  0
 51M  CONST_25  N11  C3   C2   C1    180.00   0.0  0
 51M  CONST_26  N11  C3   C5   C10     0.00   0.0  0
 51M  CONST_27  N11  C3   C5   C6    180.00   0.0  0
 51M  CONST_28  N19  C4   C1   C2    180.00   0.0  0
 51M  CONST_29  N19  C4   C6   C7      0.00   0.0  0
 51M  CONST_30  C30  C25  C24  C21   180.00   0.0  0
 51M  CONST_31  C31  C27  C28  C21   180.00   0.0  0
 51M  CONST_32  C32  C28  C21  C24   180.00   0.0  0
 51M  CONST_33  C30  C25  C26  C27   180.00   0.0  0
 51M  CONST_34  S20  C21  C28  C27   180.00   0.0  0
 51M  CONST_35  C25  C26  C27  C31   180.00   0.0  0
 51M  CONST_36  C26  C27  C28  C32   180.00   0.0  0
 51M  CONST_37  N19  C4   C6   C5    180.00   0.0  0
 51M  CONST_38  C25  C24  C21  S20   180.00   0.0  0
 51M  CONST_39  C29  C24  C25  C26   180.00   0.0  0
 51M  CONST_40  C29  C24  C21  C28   180.00   0.0  0
 51M  CONST_41  H1   C1   C2   C3    180.00   0.0  0
 51M  CONST_42  H6   C10  C5   C3      0.00   0.0  0
 51M  CONST_43  H5   C9   C8   C7    180.00   0.0  0
 51M  CONST_44  H3   C7   C8   C9    180.00   0.0  0
 51M  CONST_45  H4   C8   C9   C10   180.00   0.0  0
 51M  CONST_46  H25  C26  C25  C24   180.00   0.0  0
 51M  CONST_47  H2   C2   C1   C4    180.00   0.0  0
 51M  CONST_51  H14  O17  C16  C13   180.00   0.0  0
 51M  Var_01    C12  N11  C3   C2     17.40  30.0  3
 51M  Var_02    C13  C12  N11  C3   -178.31  30.0  1
 51M  Var_03    C14  C15  N11  C3    179.49  30.0  1
 51M  Var_04    N11  C15  C14  C13   -26.21  30.0  1
 51M  Var_05    C4   N19  S20  C21    63.41  30.0  1
 51M  Var_06    N19  S20  C21  C24    86.48  30.0  2
 51M  Var_07    H26  C29  C24  C21    93.79  30.0  2
 51M  Var_08    H21  C32  C28  C21   -97.64  30.0  2
 51M  Var_09    H15  C30  C25  C24    53.21  30.0  2
 51M  Var_10    H18  C31  C27  C26  -112.45  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
 51M  chir_01  C13  C16  C14  C12  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
 51M  plan-1  C21  0.020
 51M  plan-1  C24  0.020
 51M  plan-1  C27  0.020
 51M  plan-1  C31  0.020
 51M  plan-1  S20  0.020
 51M  plan-1  C25  0.020
 51M  plan-1  C26  0.020
 51M  plan-1  C28  0.020
 51M  plan-1  C29  0.020
 51M  plan-1  H25  0.020
 51M  plan-1  C30  0.020
 51M  plan-1  C32  0.020
 51M  plan-2  C1   0.020
 51M  plan-2  C2   0.020
 51M  plan-2  C3   0.020
 51M  plan-2  C7   0.020
 51M  plan-2  C8   0.020
 51M  plan-2  C9   0.020
 51M  plan-2  C10  0.020
 51M  plan-2  C4   0.020
 51M  plan-2  C5   0.020
 51M  plan-2  C6   0.020
 51M  plan-2  N11  0.020
 51M  plan-2  N19  0.020
 51M  plan-2  H1   0.020
 51M  plan-2  H2   0.020
 51M  plan-2  H3   0.020
 51M  plan-2  H4   0.020
 51M  plan-2  H5   0.020
 51M  plan-2  H6   0.020
 51M  plan-3  C4   0.020
 51M  plan-3  N19  0.020
 51M  plan-3  S20  0.020
 51M  plan-3  H24  0.020
 51M  plan-4  C13  0.020
 51M  plan-4  C16  0.020
 51M  plan-4  O17  0.020
 51M  plan-4  O18  0.020
 51M  plan-4  H14  0.020

