# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 19:57:19 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  59  32  .  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_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  C1     0  -0.254  -0.5355   0.3123  -2.4149
 51M  C2   C  C1     0  -0.373  -1.7978   0.3615  -1.8069
 51M  C3   C  C      0   0.326  -2.0768  -0.3791  -0.6768
 51M  C7   C  CR16   0  -0.301   1.1843  -2.2078  -0.2890
 51M  C8   C  CR16   0  -0.251   0.8753  -3.0972   0.7024
 51M  C9   C  CR16   0  -0.259  -0.4321  -3.1523   1.2179
 51M  C10  C  CR16   0  -0.308  -1.3836  -2.2798   0.7641
 51M  C12  C  CH2    0  -0.240  -4.4868   0.2342  -0.5863
 51M  C13  C  CH1    0  -0.428  -5.2430   0.9571   0.5328
 51M  C14  C  CH2    0  -0.445  -4.6384   0.3851   1.8092
 51M  C15  C  CH2    0  -0.283  -3.1833   0.2086   1.4255
 51M  C16  C  C      0   0.424  -6.7717   0.9039   0.4278
 51M  O17  O  OC    -1  -0.611  -7.4079   0.9946   1.4964
 51M  C21  C  CR6    0  -0.314   3.0668   0.6131  -0.1670
 51M  C24  C  CR6    0   0.083   4.1451  -0.2200   0.1886
 51M  C27  C  CR6    0   0.085   2.6775   1.2105   2.1247
 51M  C31  C  CH3    0  -0.744   1.9254   1.9287   3.2095
 51M  C4   C  C      0   0.159   0.4769  -0.4527  -1.9013
 51M  C5   C  CR6    0   0.032  -1.0843  -1.3138  -0.2242
 51M  C6   C  CR6    0   0.158   0.2141  -1.3153  -0.8010
 51M  N11  N  NT     0  -0.545  -3.2609  -0.2691   0.0394
 51M  O18  O  O      0  -0.610  -7.2548   0.8124  -0.7193
 51M  N19  N  NC1    0  -0.820   1.7723  -0.3363  -2.4671
 51M  S20  S  S      0   1.339   2.7650   0.8862  -1.9178
 51M  O22  O  OS     0  -0.635   2.0405   2.1323  -2.0814
 51M  O23  O  OS     0  -0.650   4.0092   0.7382  -2.6542
 51M  C25  C  CR6    0   0.087   4.5225  -0.2610   1.5349
 51M  C26  C  CR16   0  -0.330   3.8016   0.4758   2.4618
 51M  C28  C  CR6    0   0.102   2.2686   1.2729   0.7855
 51M  C29  C  CH3    0  -0.729   4.9001  -1.1100  -0.7663
 51M  H1   H  H      0   0.264  -0.3448   0.9365  -3.2774
 51M  H2   H  H      0   0.264  -2.5285   1.0393  -2.2240
 51M  H3   H  HCR6   0   0.227   2.1863  -2.2076  -0.6947
 51M  H4   H  HCR6   0   0.257   1.6318  -3.7763   1.0732
 51M  H5   H  HCR6   0   0.256  -0.6869  -3.8942   1.9634
 51M  H6   H  HCR6   0   0.265  -2.3960  -2.3529   1.1364
 51M  H7   H  HCH2   0   0.222  -5.0597  -0.6048  -0.9900
 51M  H8   H  HCH2   0   0.223  -4.3000   0.9172  -1.4160
 51M  H9   H  HCH1   0   0.245  -4.9592   2.0183   0.4857
 51M  H10  H  HCH2   0   0.234  -4.7577   1.0388   2.6721
 51M  H11  H  HCH2   0   0.223  -5.0848  -0.5824   2.0540
 51M  H12  H  HCH2   0   0.213  -2.6486   1.1675   1.4829
 51M  H13  H  HCH2   0   0.239  -2.6576  -0.4918   2.0734
 51M  H15  H  HCH3   0   0.249   6.6059  -0.8369   1.4556
 51M  H16  H  HCH3   0   0.256   5.8878  -0.8876   3.0618
 51M  H17  H  HCH3   0   0.250   5.5212  -2.1466   1.8933
 51M  H18  H  HCH3   0   0.248   0.9396   1.4910   3.3817
 51M  H19  H  HCH3   0   0.255   2.4710   1.8807   4.1507
 51M  H20  H  HCH3   0   0.248   1.7690   2.9816   2.9711
 51M  H21  H  HCH3   0   0.253   1.1574   3.0876   0.3912
 51M  H22  H  HCH3   0   0.267   0.4642   1.6675  -0.3767
 51M  H23  H  HCH3   0   0.241   0.3056   1.8854   1.3417
 51M  H24  H  HNC1   0   0.414   2.2748  -1.1950  -2.6624
 51M  H25  H  HCR6   0   0.248   4.1153   0.4535   3.4995
 51M  H26  H  HCH3   0   0.268   5.7579  -0.6035  -1.2092
 51M  H27  H  HCH3   0   0.255   5.2765  -1.9796  -0.2330
 51M  H28  H  HCH3   0   0.230   4.2944  -1.4943  -1.5824
 51M  C30  C  CH3    0  -0.749   5.6949  -1.0747   2.0066
 51M  C32  C  CH3    0  -0.730   0.9885   2.0149   0.5041

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  deloc     1.248  0.020  1.248
 51M  O17  C16  deloc     1.247  0.020  1.247
 51M  C16  C13  single    1.533  0.020  1.533
 51M  C13  C14  single    1.524  0.020  1.524
 51M  C13  C12  single    1.532  0.020  1.532
 51M  C14  C15  single    1.515  0.020  1.515
 51M  C12  N11  single    1.465  0.020  1.465
 51M  C15  N11  single    1.468  0.020  1.468
 51M  N11  C3   single    1.388  0.020  1.388
 51M  C2   C3   aromatic  1.380  0.020  1.380
 51M  C2   C1   aromatic  1.402  0.020  1.402
 51M  C30  C25  single    1.503  0.020  1.503
 51M  C3   C5   aromatic  1.437  0.020  1.437
 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  1.369  0.020  1.369
 51M  C27  C28  aromatic  1.402  0.020  1.402
 51M  C5   C10  aromatic  1.414  0.020  1.414
 51M  C5   C6   aromatic  1.421  0.020  1.421
 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    1.506  0.020  1.506
 51M  C4   C6   aromatic  1.423  0.020  1.423
 51M  C4   N19  single    1.418  0.020  1.418
 51M  C21  S20  single    1.797  0.020  1.797
 51M  C6   C7   aromatic  1.414  0.020  1.414
 51M  N19  S20  single    1.668  0.020  1.668
 51M  C9   C8   aromatic  1.406  0.020  1.406
 51M  S20  O22  double    1.451  0.020  1.451
 51M  S20  O23  double    1.453  0.020  1.453
 51M  C7   C8   aromatic  1.367  0.020  1.367
 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  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   119.42  3.000
 51M  H1   C1   C2   118.97  3.000
 51M  C4   C1   C2   121.52  3.000
 51M  H2   C2   C3   121.08  3.000
 51M  H2   C2   C1   117.61  3.000
 51M  C3   C2   C1   121.23  3.000
 51M  N11  C3   C5   118.57  3.000
 51M  C5   C3   C2   117.89  3.000
 51M  N11  C3   C2   123.54  3.000
 51M  H3   C7   C6   119.99  3.000
 51M  H3   C7   C8   118.80  3.000
 51M  C6   C7   C8   121.20  3.000
 51M  H4   C8   C9   119.98  3.000
 51M  H4   C8   C7   119.92  3.000
 51M  C9   C8   C7   120.09  3.000
 51M  H5   C9   C10  120.12  3.000
 51M  H5   C9   C8   119.89  3.000
 51M  C10  C9   C8   119.99  3.000
 51M  H6   C10  C5   119.01  3.000
 51M  H6   C10  C9   119.59  3.000
 51M  C5   C10  C9   121.35  3.000
 51M  H8   C12  H7   106.82  3.000
 51M  H8   C12  N11  113.36  3.000
 51M  H7   C12  N11  109.42  3.000
 51M  H8   C12  C13  110.16  3.000
 51M  H7   C12  C13  111.91  3.000
 51M  N11  C12  C13  105.26  3.000
 51M  H9   C13  C16  106.74  3.000
 51M  H9   C13  C14  107.20  3.000
 51M  C16  C13  C14  116.10  3.000
 51M  H9   C13  C12  107.26  3.000
 51M  C14  C13  C12  103.82  3.000
 51M  C16  C13  C12  115.20  3.000
 51M  H11  C14  H10  108.01  3.000
 51M  H11  C14  C15  110.23  3.000
 51M  H10  C14  C15  112.07  3.000
 51M  H11  C14  C13  110.96  3.000
 51M  H10  C14  C13  113.26  3.000
 51M  C15  C14  C13  102.28  3.000
 51M  H13  C15  H12  107.16  3.000
 51M  H13  C15  N11  112.20  3.000
 51M  H12  C15  N11  111.03  3.000
 51M  H13  C15  C14  112.81  3.000
 51M  H12  C15  C14  110.63  3.000
 51M  N11  C15  C14  103.07  3.000
 51M  O18  C16  O17  126.55  3.000
 51M  O17  C16  C13  116.58  3.000
 51M  O18  C16  C13  116.84  3.000
 51M  C28  C21  S20  119.53  3.000
 51M  S20  C21  C24  117.67  3.000
 51M  C28  C21  C24  122.74  3.000
 51M  C29  C24  C25  117.20  3.000
 51M  C29  C24  C21  124.93  3.000
 51M  C25  C24  C21  117.83  3.000
 51M  C28  C27  C26  119.54  3.000
 51M  C28  C27  C31  121.50  3.000
 51M  C26  C27  C31  118.96  3.000
 51M  H20  C31  H19  107.66  3.000
 51M  H20  C31  H18  106.96  3.000
 51M  H19  C31  H18  107.35  3.000
 51M  H20  C31  C27  112.05  3.000
 51M  H19  C31  C27  110.62  3.000
 51M  H18  C31  C27  111.96  3.000
 51M  N19  C4   C6   121.81  3.000
 51M  N19  C4   C1   118.68  3.000
 51M  C6   C4   C1   119.50  3.000
 51M  C6   C5   C10  118.45  3.000
 51M  C6   C5   C3   120.27  3.000
 51M  C10  C5   C3   121.24  3.000
 51M  C5   C6   C4   118.83  3.000
 51M  C4   C6   C7   122.41  3.000
 51M  C5   C6   C7   118.73  3.000
 51M  C15  N11  C12  109.61  3.000
 51M  C15  N11  C3   117.89  3.000
 51M  C12  N11  C3   121.36  3.000
 51M  H24  N19  S20  112.91  3.000
 51M  H24  N19  C4   117.38  3.000
 51M  S20  N19  C4   118.19  3.000
 51M  O23  S20  O22  117.25  3.000
 51M  O23  S20  N19  105.54  3.000
 51M  O22  S20  N19  107.17  3.000
 51M  O23  S20  C21  109.53  3.000
 51M  O22  S20  C21  108.92  3.000
 51M  N19  S20  C21  108.02  3.000
 51M  C26  C25  C30  118.91  3.000
 51M  C26  C25  C24  119.19  3.000
 51M  C30  C25  C24  121.89  3.000
 51M  H25  C26  C25  118.59  3.000
 51M  H25  C26  C27  118.61  3.000
 51M  C25  C26  C27  122.78  3.000
 51M  C32  C28  C27  116.64  3.000
 51M  C32  C28  C21  125.92  3.000
 51M  C27  C28  C21  117.41  3.000
 51M  H28  C29  H27  106.17  3.000
 51M  H28  C29  H26  107.33  3.000
 51M  H27  C29  H26  107.36  3.000
 51M  H28  C29  C24  113.91  3.000
 51M  H27  C29  C24  109.56  3.000
 51M  H26  C29  C24  112.15  3.000
 51M  H17  C30  H16  107.31  3.000
 51M  H17  C30  H15  107.12  3.000
 51M  H16  C30  H15  107.70  3.000
 51M  H17  C30  C25  112.02  3.000
 51M  H16  C30  C25  110.45  3.000
 51M  H15  C30  C25  112.02  3.000
 51M  H23  C32  H22  106.50  3.000
 51M  H23  C32  H21  107.07  3.000
 51M  H22  C32  H21  107.83  3.000
 51M  H23  C32  C28  109.32  3.000
 51M  H22  C32  C28  113.93  3.000
 51M  H21  C32  C28  111.84  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  Var_01    C12  N11  C3   C2     23.54  30.0  3
 51M  Var_02    C13  C12  N11  C3   -147.97  30.0  1
 51M  Var_03    C14  C15  N11  C3    172.32  30.0  1
 51M  Var_04    N11  C15  C14  C13   -39.18  30.0  1
 51M  Var_05    C4   N19  S20  C21    61.97  30.0  1
 51M  Var_06    N19  S20  C21  C24    87.39  30.0  2
 51M  Var_07    H26  C29  C24  C21    90.69  30.0  2
 51M  Var_08    H21  C32  C28  C21   -96.48  30.0  2
 51M  Var_09    H15  C30  C25  C24    53.76  30.0  2
 51M  Var_10    H18  C31  C27  C26  -111.74  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

