# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 10:19:11 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: 11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)undecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc2c1cccc2[S](=O)(=O)NCCCCCCCCCCC(O)=O
#
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
 11D  11D  '11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)undecanoic acid'  ligand  63  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_11D
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
 11D  C1    C  CR16   0  -0.289    4.7815   1.1700  -1.7032
 11D  C2    C  CR66   0   0.043    4.6357   1.1219  -0.2981
 11D  C3    C  CR66   0   0.194    4.3624  -0.1257   0.3332
 11D  C4    C  CR6    0  -0.280    4.3006  -1.2816  -0.5010
 11D  C5    C  CR16   0  -0.241    4.4812  -1.2041  -1.8569
 11D  C6    C  CR16   0  -0.249    4.7192   0.0378  -2.4646
 11D  C7    C  CR6    0   0.298    4.7094   2.3217   0.4825
 11D  C8    C  CR16   0  -0.340    4.4198   2.2589   1.8250
 11D  C9    C  CR16   0  -0.229    4.1303   1.0293   2.4365
 11D  C10   C  CR16   0  -0.381    4.1282  -0.1404   1.7291
 11D  N11   N  NT     0  -0.492    5.0410   3.5182  -0.1668
 11D  C12   C  CH3    0  -0.546    4.5524   4.7402   0.4343
 11D  C13   C  CH3    0  -0.545    6.4372   3.6381  -0.5626
 11D  S14   S  S      0   1.368    3.8799  -2.8824   0.1582
 11D  O15   O  OS     0  -0.649    3.8626  -3.8178  -0.9542
 11D  O16   O  OS     0  -0.659    4.7148  -3.1787   1.3123
 11D  N17   N  NC1    0  -0.734    2.3346  -2.7645   0.7130
 11D  C18   C  CH2    0  -0.270    1.3020  -2.2533  -0.1896
 11D  C19   C  CH2    0  -0.447   -0.0404  -2.2586   0.5226
 11D  C20   C  CH2    0  -0.421   -1.1347  -1.6050  -0.3109
 11D  C21   C  CH2    0  -0.413   -2.4581  -1.5137   0.4380
 11D  C22   C  CH2    0  -0.413   -3.5455  -0.7818  -0.3372
 11D  C23   C  CH2    0  -0.411   -4.8391  -0.6323   0.4538
 11D  C24   C  CH2    0  -0.410   -5.9237   0.1357  -0.2901
 11D  C25   C  CH2    0  -0.410   -7.1952   0.3205   0.5286
 11D  C26   C  CH2    0  -0.402   -8.2788   1.1039  -0.2024
 11D  C27   C  CH2    0  -0.582   -9.5304   1.2967   0.6375
 11D  C28   C  C      0   0.410  -10.6805   2.0765  -0.0222
 11D  O29   O  O      0  -0.610  -10.5317   2.4514  -1.2020
 11D  O30   O  OC    -1  -0.635  -11.6891   2.2687   0.6908
 11D  H1    H  HCR6   0   0.280    4.9200   2.1273  -2.1855
 11D  H5    H  HCR6   0   0.289    4.4199  -2.0884  -2.4746
 11D  H6    H  HCR6   0   0.272    4.8258   0.0925  -3.5390
 11D  H8    H  HCR6   0   0.271    4.4415   3.1505   2.4369
 11D  H9    H  HCR6   0   0.267    3.9376   1.0064   3.5010
 11D  H10   H  HCR6   0   0.251    3.9661  -1.0617   2.2659
 11D  H12   H  HCH3   0   0.212    5.0940   5.0335   1.3432
 11D  H12A  H  HCH3   0   0.250    4.6600   5.5519  -0.2856
 11D  H12B  H  HCH3   0   0.248    3.4950   4.6476   0.6789
 11D  H13   H  HCH3   0   0.252    6.8115   2.7056  -0.9792
 11D  H13A  H  HCH3   0   0.242    6.5396   4.4098  -1.3264
 11D  H13B  H  HCH3   0   0.223    7.0805   3.9088   0.2848
 11D  HN17  H  HNC1   0   0.408    2.2937  -2.3605   1.6425
 11D  H18   H  HCH2   0   0.235    1.5350  -1.2357  -0.5254
 11D  H18A  H  HCH2   0   0.258    1.2647  -2.8918  -1.0728
 11D  H19   H  HCH2   0   0.237   -0.3190  -3.2845   0.7773
 11D  H19A  H  HCH2   0   0.226    0.0557  -1.7151   1.4691
 11D  H20   H  HCH2   0   0.216   -0.8139  -0.5985  -0.6000
 11D  H20A  H  HCH2   0   0.219   -1.2746  -2.1606  -1.2439
 11D  H21   H  HCH2   0   0.212   -2.8057  -2.5200   0.6959
 11D  H21A  H  HCH2   0   0.209   -2.2914  -0.9994   1.3914
 11D  H22   H  HCH2   0   0.207   -3.1789   0.2112  -0.6209
 11D  H22A  H  HCH2   0   0.208   -3.7488  -1.3082  -1.2763
 11D  H23   H  HCH2   0   0.207   -5.2175  -1.6238   0.7267
 11D  H23A  H  HCH2   0   0.205   -4.6223  -0.1231   1.3998
 11D  H24   H  HCH2   0   0.204   -5.5356   1.1181  -0.5824
 11D  H24A  H  HCH2   0   0.205   -6.1642  -0.3830  -1.2249
 11D  H25   H  HCH2   0   0.202   -7.5868  -0.6618   0.8179
 11D  H25A  H  HCH2   0   0.201   -6.9470   0.8305   1.4667
 11D  H26   H  HCH2   0   0.199   -7.8783   2.0777  -0.5007
 11D  H26A  H  HCH2   0   0.200   -8.5317   0.5874  -1.1330
 11D  H27   H  HCH2   0   0.216   -9.9180   0.3180   0.9460
 11D  H27A  H  HCH2   0   0.214   -9.2682   1.8005   1.5754

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
 11D  C2   C1    aromatic  1.413  0.020  1.413
 11D  C1   C6    aromatic  1.366  0.020  1.366
 11D  C1   H1    single    0.930  0.020  1.080
 11D  C7   C2    aromatic  1.433  0.020  1.433
 11D  C3   C2    aromatic  1.425  0.020  1.425
 11D  C10  C3    aromatic  1.416  0.020  1.416
 11D  C3   C4    aromatic  1.427  0.020  1.427
 11D  S14  C4    single    1.782  0.020  1.782
 11D  C4   C5    aromatic  1.370  0.020  1.370
 11D  C5   C6    aromatic  1.403  0.020  1.403
 11D  C5   H5    single    0.930  0.020  1.080
 11D  C6   H6    single    0.930  0.020  1.080
 11D  C8   C7    aromatic  1.375  0.020  1.375
 11D  C7   N11   single    1.401  0.020  1.401
 11D  C9   C8    aromatic  1.403  0.020  1.403
 11D  C8   H8    single    0.930  0.020  1.080
 11D  C9   C10   aromatic  1.367  0.020  1.367
 11D  C9   H9    single    0.930  0.020  1.080
 11D  C10  H10   single    0.930  0.020  1.080
 11D  C13  N11   single    1.456  0.020  1.456
 11D  N11  C12   single    1.447  0.020  1.447
 11D  C12  H12   single    0.970  0.020  1.090
 11D  C12  H12A  single    0.970  0.020  1.090
 11D  C12  H12B  single    0.970  0.020  1.090
 11D  C13  H13   single    0.970  0.020  1.090
 11D  C13  H13A  single    0.970  0.020  1.090
 11D  C13  H13B  single    0.970  0.020  1.090
 11D  N17  S14   single    1.646  0.020  1.646
 11D  S14  O16   double    1.455  0.020  1.455
 11D  S14  O15   double    1.453  0.020  1.453
 11D  C18  N17   single    1.464  0.020  1.464
 11D  N17  HN17  single    0.890  0.020  1.040
 11D  C18  C19   single    1.520  0.020  1.520
 11D  C18  H18   single    0.970  0.020  1.090
 11D  C18  H18A  single    0.970  0.020  1.090
 11D  C20  C19   single    1.523  0.020  1.523
 11D  C19  H19   single    0.970  0.020  1.090
 11D  C19  H19A  single    0.970  0.020  1.090
 11D  C20  C21   single    1.523  0.020  1.523
 11D  C20  H20   single    0.970  0.020  1.090
 11D  C20  H20A  single    0.970  0.020  1.090
 11D  C22  C21   single    1.523  0.020  1.523
 11D  C21  H21   single    0.970  0.020  1.090
 11D  C21  H21A  single    0.970  0.020  1.090
 11D  C23  C22   single    1.524  0.020  1.524
 11D  C22  H22   single    0.970  0.020  1.090
 11D  C22  H22A  single    0.970  0.020  1.090
 11D  C24  C23   single    1.523  0.020  1.523
 11D  C23  H23   single    0.970  0.020  1.090
 11D  C23  H23A  single    0.970  0.020  1.090
 11D  C25  C24   single    1.524  0.020  1.524
 11D  C24  H24   single    0.970  0.020  1.090
 11D  C24  H24A  single    0.970  0.020  1.090
 11D  C26  C25   single    1.524  0.020  1.524
 11D  C25  H25   single    0.970  0.020  1.090
 11D  C25  H25A  single    0.970  0.020  1.090
 11D  C27  C26   single    1.520  0.020  1.520
 11D  C26  H26   single    0.970  0.020  1.090
 11D  C26  H26A  single    0.970  0.020  1.090
 11D  C28  C27   single    1.538  0.020  1.538
 11D  C27  H27   single    0.970  0.020  1.090
 11D  C27  H27A  single    0.970  0.020  1.090
 11D  O29  C28   deloc     1.247  0.020  1.247
 11D  C28  O30   deloc     1.250  0.020  1.250

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
 11D  H1    C1   C6    119.42  3.000
 11D  H1    C1   C2    119.15  3.000
 11D  C6    C1   C2    121.41  3.000
 11D  C7    C2   C3    120.11  3.000
 11D  C3    C2   C1    119.35  3.000
 11D  C7    C2   C1    120.50  3.000
 11D  C10   C3   C4    124.12  3.000
 11D  C4    C3   C2    117.30  3.000
 11D  C10   C3   C2    118.54  3.000
 11D  S14   C4   C5    116.62  3.000
 11D  C5    C4   C3    121.81  3.000
 11D  S14   C4   C3    121.46  3.000
 11D  H5    C5   C6    119.11  3.000
 11D  H5    C5   C4    120.80  3.000
 11D  C6    C5   C4    120.07  3.000
 11D  H6    C6   C5    119.47  3.000
 11D  H6    C6   C1    120.50  3.000
 11D  C5    C6   C1    120.01  3.000
 11D  N11   C7   C8    122.78  3.000
 11D  N11   C7   C2    118.34  3.000
 11D  C8    C7   C2    118.86  3.000
 11D  H8    C8   C9    118.68  3.000
 11D  H8    C8   C7    120.70  3.000
 11D  C9    C8   C7    120.59  3.000
 11D  H9    C9   C10   119.39  3.000
 11D  H9    C9   C8    118.94  3.000
 11D  C10   C9   C8    121.64  3.000
 11D  H10   C10  C9    118.27  3.000
 11D  H10   C10  C3    121.63  3.000
 11D  C9    C10  C3    120.08  3.000
 11D  C13   N11  C12   111.54  3.000
 11D  C12   N11  C7    116.67  3.000
 11D  C13   N11  C7    115.03  3.000
 11D  H12B  C12  H12A  107.89  3.000
 11D  H12B  C12  H12   108.40  3.000
 11D  H12A  C12  H12   107.40  3.000
 11D  H12B  C12  N11   110.44  3.000
 11D  H12A  C12  N11   108.73  3.000
 11D  H12   C12  N11   113.77  3.000
 11D  H13B  C13  H13A  108.12  3.000
 11D  H13B  C13  H13   107.79  3.000
 11D  H13A  C13  H13   107.82  3.000
 11D  H13B  C13  N11   111.86  3.000
 11D  H13A  C13  N11   109.79  3.000
 11D  H13   C13  N11   111.31  3.000
 11D  N17   S14  O16   106.62  3.000
 11D  O16   S14  O15   118.88  3.000
 11D  N17   S14  O15   107.03  3.000
 11D  O15   S14  C4    107.33  3.000
 11D  O16   S14  C4    109.94  3.000
 11D  N17   S14  C4    106.38  3.000
 11D  HN17  N17  C18   113.43  3.000
 11D  HN17  N17  S14   112.04  3.000
 11D  C18   N17  S14   118.65  3.000
 11D  H18A  C18  H18   107.62  3.000
 11D  H18A  C18  C19   110.33  3.000
 11D  H18   C18  C19   109.54  3.000
 11D  H18A  C18  N17   108.61  3.000
 11D  H18   C18  N17   111.28  3.000
 11D  C19   C18  N17   109.45  3.000
 11D  H19A  C19  H19   106.66  3.000
 11D  H19A  C19  C20   108.84  3.000
 11D  H19   C19  C20   110.31  3.000
 11D  H19A  C19  C18   109.01  3.000
 11D  H19   C19  C18   109.73  3.000
 11D  C20   C19  C18   112.13  3.000
 11D  H20A  C20  H20   106.19  3.000
 11D  H20A  C20  C21   109.78  3.000
 11D  H20   C20  C21   109.22  3.000
 11D  H20A  C20  C19   109.90  3.000
 11D  H20   C20  C19   109.17  3.000
 11D  C21   C20  C19   112.39  3.000
 11D  H21A  C21  H21   105.94  3.000
 11D  H21A  C21  C22   109.02  3.000
 11D  H21   C21  C22   109.56  3.000
 11D  H21A  C21  C20   108.88  3.000
 11D  H21   C21  C20   109.66  3.000
 11D  C22   C21  C20   113.50  3.000
 11D  H22A  C22  H22   106.00  3.000
 11D  H22A  C22  C23   109.55  3.000
 11D  H22   C22  C23   109.24  3.000
 11D  H22A  C22  C21   109.75  3.000
 11D  H22   C22  C21   109.17  3.000
 11D  C23   C22  C21   112.90  3.000
 11D  H23A  C23  H23   105.89  3.000
 11D  H23A  C23  C24   109.16  3.000
 11D  H23   C23  C24   109.39  3.000
 11D  H23A  C23  C22   109.01  3.000
 11D  H23   C23  C22   109.50  3.000
 11D  C24   C23  C22   113.61  3.000
 11D  H24A  C24  H24   105.93  3.000
 11D  H24A  C24  C25   109.43  3.000
 11D  H24   C24  C25   109.28  3.000
 11D  H24A  C24  C23   109.53  3.000
 11D  H24   C24  C23   109.27  3.000
 11D  C25   C24  C23   113.15  3.000
 11D  H25A  C25  H25   105.77  3.000
 11D  H25A  C25  C26   109.41  3.000
 11D  H25   C25  C26   109.47  3.000
 11D  H25A  C25  C24   109.10  3.000
 11D  H25   C25  C24   109.35  3.000
 11D  C26   C25  C24   113.46  3.000
 11D  H26A  C26  H26   105.84  3.000
 11D  H26A  C26  C27   109.85  3.000
 11D  H26   C26  C27   109.83  3.000
 11D  H26A  C26  C25   109.25  3.000
 11D  H26   C26  C25   109.15  3.000
 11D  C27   C26  C25   112.69  3.000
 11D  H27A  C27  H27   104.71  3.000
 11D  H27A  C27  C28   108.22  3.000
 11D  H27   C27  C28   107.98  3.000
 11D  H27A  C27  C26   109.52  3.000
 11D  H27   C27  C26   109.47  3.000
 11D  C28   C27  C26   116.30  3.000
 11D  O30   C28  O29   126.14  3.000
 11D  O30   C28  C27   115.89  3.000
 11D  O29   C28  C27   117.97  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
 11D  CONST_01  C8   C7   C2   C1    180.00   0.0  0
 11D  CONST_02  C10  C3   C2   C1    180.00   0.0  0
 11D  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 11D  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 11D  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 11D  CONST_06  C9   C8   C7   C2      0.00   0.0  0
 11D  CONST_07  C9   C10  C3   C2      0.00   0.0  0
 11D  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 11D  CONST_09  C6   C1   C2   C3      0.00   0.0  0
 11D  CONST_10  C8   C7   C2   C3      0.00   0.0  0
 11D  CONST_11  C8   C9   C10  C3      0.00   0.0  0
 11D  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 11D  CONST_13  C7   C2   C3   C4    180.00   0.0  0
 11D  CONST_14  C9   C10  C3   C4    180.00   0.0  0
 11D  CONST_15  C10  C3   C4   C5    180.00   0.0  0
 11D  CONST_16  C7   C2   C1   C6    180.00   0.0  0
 11D  CONST_17  C10  C3   C2   C7      0.00   0.0  0
 11D  CONST_18  C10  C9   C8   C7      0.00   0.0  0
 11D  CONST_19  N11  C7   C2   C1      0.00   0.0  0
 11D  CONST_20  S14  C4   C3   C2    180.00   0.0  0
 11D  CONST_21  N11  C7   C2   C3    180.00   0.0  0
 11D  CONST_22  S14  C4   C5   C6    180.00   0.0  0
 11D  CONST_23  N11  C7   C8   C9    180.00   0.0  0
 11D  CONST_24  S14  C4   C3   C10     0.00   0.0  0
 11D  CONST_25  H5   C5   C6   C1    180.00   0.0  0
 11D  CONST_26  H6   C6   C1   C2    180.00   0.0  0
 11D  CONST_27  H8   C8   C7   C2    180.00   0.0  0
 11D  CONST_28  H10  C10  C3   C2    180.00   0.0  0
 11D  CONST_29  H1   C1   C2   C3    180.00   0.0  0
 11D  CONST_30  H9   C9   C10  C3    180.00   0.0  0
 11D  Var_01    N17  S14  C4   C3     63.78  30.0  2
 11D  Var_02    C18  N17  S14  C4     52.67  30.0  1
 11D  Var_03    H13  C13  N11  C7     42.04  30.0  3
 11D  Var_04    H12  C12  N11  C7     74.42  30.0  3
 11D  Var_05    C19  C18  N17  S14   178.90  30.0  2
 11D  Var_06    C20  C19  C18  N17   174.12  30.0  3
 11D  Var_07    C21  C20  C19  C18  -175.74  30.0  1
 11D  Var_08    C22  C21  C20  C19   176.19  30.0  3
 11D  Var_09    C23  C22  C21  C20  -176.89  30.0  1
 11D  Var_10    C24  C23  C22  C21   178.20  30.0  1
 11D  Var_11    C25  C24  C23  C22  -178.02  30.0  1
 11D  Var_12    C26  C25  C24  C23   179.25  30.0  1
 11D  Var_13    C27  C26  C25  C24  -179.10  30.0  1
 11D  Var_14    C28  C27  C26  C25  -179.91  30.0  1
 11D  Var_15    O29  C28  C27  C26     2.53  30.0  2

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
 11D  plan-1  C1   0.020
 11D  plan-1  C2   0.020
 11D  plan-1  C3   0.020
 11D  plan-1  C4   0.020
 11D  plan-1  C5   0.020
 11D  plan-1  C6   0.020
 11D  plan-1  C7   0.020
 11D  plan-1  C8   0.020
 11D  plan-1  C9   0.020
 11D  plan-1  C10  0.020
 11D  plan-1  N11  0.020
 11D  plan-1  S14  0.020
 11D  plan-1  H1   0.020
 11D  plan-1  H5   0.020
 11D  plan-1  H6   0.020
 11D  plan-1  H8   0.020
 11D  plan-1  H9   0.020
 11D  plan-1  H10  0.020
 11D  plan-2  C7   0.020
 11D  plan-2  N11  0.020
 11D  plan-2  C12  0.020
 11D  plan-2  C13  0.020
 11D  plan-3  C27  0.020
 11D  plan-3  C28  0.020
 11D  plan-3  O29  0.020
 11D  plan-3  O30  0.020

