# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:36:28 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-hydroxy-N~2~-(3-methylbutyl)-N~2~-(naphthalen-2-ylsulfonyl)-D-valinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCN([C@H](C(C)C)C(=O)NO)[S](=O)(=O)c1ccc2ccccc2c1
#
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
 E41  E41  N-hydroxy-N~2~-(3-methylbutyl)-N~2~-(naphthalen-2-ylsulfonyl)-D-valinamide  ligand  55  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E41
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
 E41  O1    O  OH1   0  -0.534  -1.0798   1.4323  -2.3851
 E41  N1    N  NH1   0  -0.374   0.0699   1.0888  -1.7464
 E41  N     N  N     0  -0.585   1.4824  -0.3479   0.4825
 E41  CA    C  CH1   0  -0.202   1.6576   1.0494   0.0537
 E41  C     C  C     0   0.554   0.3416   1.5910  -0.5278
 E41  O     O  O     0  -0.442  -0.4092   2.3236   0.0825
 E41  CB    C  CH1   0  -0.238   2.2583   2.0020   1.0953
 E41  CG1   C  CH3   0  -0.651   3.4617   1.3836   1.7943
 E41  CG2   C  CH3   0  -0.666   2.6707   3.3026   0.4086
 E41  O3    O  OS    0  -0.649   0.5640  -2.1585   1.9247
 E41  O4    O  OS    0  -0.636   0.2731   0.2351   2.6088
 E41  C6    C  CR6   0  -0.216  -1.2398  -0.7257   0.7064
 E41  C7    C  CR16  0  -0.238  -1.4326  -1.5841  -0.4001
 E41  C8    C  CR16  0  -0.313  -2.6069  -1.5318  -1.0942
 E41  C9    C  CR16  0  -0.273  -2.2137   0.1418   1.1113
 E41  C10   C  CR66  0   0.128  -3.4423   0.1974   0.4146
 E41  C11   C  CR66  0   0.101  -3.6435  -0.6453  -0.7079
 E41  C12   C  CR16  0  -0.307  -4.8687  -0.5770  -1.4077
 E41  C13   C  CR16  0  -0.246  -5.8488   0.2898  -1.0052
 E41  C14   C  CR16  0  -0.254  -5.6487   1.1284   0.1109
 E41  C15   C  CR16  0  -0.302  -4.4710   1.0839   0.8062
 E41  C16   C  CH2   0  -0.397   3.5574  -1.5159  -0.2266
 E41  C17   C  CH1   0  -0.237   4.1521  -2.6587  -1.0522
 E41  C18   C  CH2   0  -0.320   2.0513  -1.3825  -0.3925
 E41  C19   C  CH3   0  -0.661   3.9657  -2.4491  -2.5525
 E41  C20   C  CH3   0  -0.651   5.6303  -2.8280  -0.7163
 E41  H1    H  HNH1  0   0.417   0.7712   0.6618  -2.3347
 E41  HA    H  HCH1  0   0.292   2.3844   0.9840  -0.7625
 E41  H181  H  HCH2  0   0.270   1.5946  -2.3427  -0.1626
 E41  H182  H  HCH2  0   0.237   1.7851  -1.1583  -1.4286
 E41  HB    H  HCH1  0   0.245   1.4995   2.2288   1.8433
 E41  HG11  H  HCH3  0   0.214   4.2722   1.1876   1.0894
 E41  HG12  H  HCH3  0   0.235   3.8464   2.0703   2.5493
 E41  HG13  H  HCH3  0   0.232   3.2161   0.4477   2.2923
 E41  HG21  H  HCH3  0   0.237   1.8321   3.8227  -0.0535
 E41  HG22  H  HCH3  0   0.238   3.1141   3.9852   1.1344
 E41  HG23  H  HCH3  0   0.219   3.4196   3.1148  -0.3645
 E41  H7    H  HCR6  0   0.280  -0.6649  -2.2810  -0.7066
 E41  H9    H  HCR6  0   0.281  -2.0619   0.8011   1.9550
 E41  H8    H  HCR6  0   0.274  -2.7568  -2.1835  -1.9456
 E41  H15   H  HCR6  0   0.265  -4.3146   1.7284   1.6623
 E41  H12   H  HCR6  0   0.264  -5.0199  -1.2202  -2.2658
 E41  H13   H  HCR6  0   0.267  -6.7855   0.3344  -1.5450
 E41  H14   H  HCR6  0   0.267  -6.4328   1.8089   0.4153
 E41  H161  H  HCH2  0   0.236   3.7691  -1.6849   0.8323
 E41  H162  H  HCH2  0   0.220   4.0578  -0.5806  -0.5011
 E41  H17   H  HCH1  0   0.220   3.6345  -3.5829  -0.7679
 E41  H191  H  HCH3  0   0.229   2.9155  -2.4399  -2.8474
 E41  H192  H  HCH3  0   0.216   4.4089  -1.5019  -2.8696
 E41  H193  H  HCH3  0   0.231   4.4496  -3.2466  -3.1189
 E41  H201  H  HCH3  0   0.226   5.7790  -3.0224   0.3472
 E41  H202  H  HCH3  0   0.227   6.0656  -3.6604  -1.2715
 E41  H203  H  HCH3  0   0.215   6.1947  -1.9283  -0.9725
 E41  H1O   H  HOH1  0   0.474  -1.6959   0.7008  -2.2351
 E41  S1    S  S     0   1.386   0.3133  -0.7721   1.5636

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
 E41  O1   N1    single    1.359  0.020  1.359
 E41  N1   C     single    1.346  0.020  1.346
 E41  N    CA    single    1.472  0.020  1.472
 E41  N    S1    single    1.648  0.020  1.648
 E41  N    C18   single    1.470  0.020  1.470
 E41  CA   C     single    1.537  0.020  1.537
 E41  CA   CB    single    1.534  0.020  1.534
 E41  C    O     double    1.214  0.020  1.214
 E41  CB   CG1   single    1.523  0.020  1.523
 E41  CB   CG2   single    1.527  0.020  1.527
 E41  S1   O3    double    1.454  0.020  1.454
 E41  S1   O4    double    1.452  0.020  1.452
 E41  S1   C6    single    1.775  0.020  1.775
 E41  C6   C7    aromatic  1.414  0.020  1.414
 E41  C6   C9    aromatic  1.366  0.020  1.366
 E41  C7   C8    aromatic  1.365  0.020  1.365
 E41  C8   C11   aromatic  1.418  0.020  1.418
 E41  C9   C10   aromatic  1.413  0.020  1.413
 E41  C10  C11   aromatic  1.418  0.020  1.418
 E41  C10  C15   aromatic  1.413  0.020  1.413
 E41  C11  C12   aromatic  1.413  0.020  1.413
 E41  C12  C13   aromatic  1.369  0.020  1.369
 E41  C13  C14   aromatic  1.410  0.020  1.410
 E41  C14  C15   aromatic  1.368  0.020  1.368
 E41  C16  C17   single    1.530  0.020  1.530
 E41  C16  C18   single    1.521  0.020  1.521
 E41  C17  C19   single    1.526  0.020  1.526
 E41  C17  C20   single    1.525  0.020  1.525
 E41  O1   H1O   single    0.850  0.020  0.980
 E41  N1   H1    single    0.860  0.020  1.020
 E41  CA   HA    single    0.970  0.020  1.090
 E41  C18  H181  single    0.970  0.020  1.090
 E41  C18  H182  single    0.970  0.020  1.090
 E41  CB   HB    single    0.970  0.020  1.090
 E41  CG1  HG11  single    0.970  0.020  1.090
 E41  CG1  HG12  single    0.970  0.020  1.090
 E41  CG1  HG13  single    0.970  0.020  1.090
 E41  CG2  HG21  single    0.970  0.020  1.090
 E41  CG2  HG22  single    0.970  0.020  1.090
 E41  CG2  HG23  single    0.970  0.020  1.090
 E41  C7   H7    single    0.930  0.020  1.080
 E41  C9   H9    single    0.930  0.020  1.080
 E41  C8   H8    single    0.930  0.020  1.080
 E41  C15  H15   single    0.930  0.020  1.080
 E41  C12  H12   single    0.930  0.020  1.080
 E41  C13  H13   single    0.930  0.020  1.080
 E41  C14  H14   single    0.930  0.020  1.080
 E41  C16  H161  single    0.970  0.020  1.090
 E41  C16  H162  single    0.970  0.020  1.090
 E41  C17  H17   single    0.970  0.020  1.090
 E41  C19  H191  single    0.970  0.020  1.090
 E41  C19  H192  single    0.970  0.020  1.090
 E41  C19  H193  single    0.970  0.020  1.090
 E41  C20  H201  single    0.970  0.020  1.090
 E41  C20  H202  single    0.970  0.020  1.090
 E41  C20  H203  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
 E41  H1O   O1   N1    105.93  3.000
 E41  H1    N1   C     123.02  3.000
 E41  H1    N1   O1    114.86  3.000
 E41  C     N1   O1    120.13  3.000
 E41  C18   N    S1    118.95  3.000
 E41  C18   N    CA    116.66  3.000
 E41  S1    N    CA    121.33  3.000
 E41  HA    CA   CB    106.46  3.000
 E41  HA    CA   C     107.90  3.000
 E41  CB    CA   C     111.92  3.000
 E41  HA    CA   N     103.86  3.000
 E41  CB    CA   N     115.99  3.000
 E41  C     CA   N     110.04  3.000
 E41  O     C    CA    123.51  3.000
 E41  O     C    N1    123.76  3.000
 E41  CA    C    N1    112.57  3.000
 E41  HB    CB   CG2   108.63  3.000
 E41  HB    CB   CG1   108.65  3.000
 E41  CG2   CB   CG1   109.81  3.000
 E41  HB    CB   CA    108.83  3.000
 E41  CG2   CB   CA    109.23  3.000
 E41  CG1   CB   CA    111.65  3.000
 E41  HG13  CG1  HG12  107.71  3.000
 E41  HG13  CG1  HG11  107.98  3.000
 E41  HG12  CG1  HG11  107.34  3.000
 E41  HG13  CG1  CB    112.40  3.000
 E41  HG12  CG1  CB    109.92  3.000
 E41  HG11  CG1  CB    111.29  3.000
 E41  HG23  CG2  HG22  107.45  3.000
 E41  HG23  CG2  HG21  108.03  3.000
 E41  HG22  CG2  HG21  107.24  3.000
 E41  HG23  CG2  CB    110.90  3.000
 E41  HG22  CG2  CB    110.09  3.000
 E41  HG21  CG2  CB    112.91  3.000
 E41  C9    C6   C7    121.37  3.000
 E41  C9    C6   S1    119.84  3.000
 E41  C7    C6   S1    118.79  3.000
 E41  H7    C7   C8    119.43  3.000
 E41  H7    C7   C6    121.10  3.000
 E41  C8    C7   C6    119.48  3.000
 E41  H8    C8   C11   119.31  3.000
 E41  H8    C8   C7    119.73  3.000
 E41  C11   C8   C7    120.96  3.000
 E41  H9    C9   C10   118.85  3.000
 E41  H9    C9   C6    121.23  3.000
 E41  C10   C9   C6    119.91  3.000
 E41  C15   C10  C11   119.26  3.000
 E41  C15   C10  C9    121.39  3.000
 E41  C11   C10  C9    119.35  3.000
 E41  C12   C11  C10   119.12  3.000
 E41  C12   C11  C8    121.97  3.000
 E41  C10   C11  C8    118.92  3.000
 E41  H12   C12  C13   120.60  3.000
 E41  H12   C12  C11   119.01  3.000
 E41  C13   C12  C11   120.39  3.000
 E41  H13   C13  C14   119.55  3.000
 E41  H13   C13  C12   119.95  3.000
 E41  C14   C13  C12   120.50  3.000
 E41  H14   C14  C15   120.08  3.000
 E41  H14   C14  C13   119.59  3.000
 E41  C15   C14  C13   120.33  3.000
 E41  H15   C15  C14   120.44  3.000
 E41  H15   C15  C10   119.16  3.000
 E41  C14   C15  C10   120.40  3.000
 E41  H162  C16  H161  106.63  3.000
 E41  H162  C16  C18   110.49  3.000
 E41  H161  C16  C18   108.12  3.000
 E41  H162  C16  C17   108.96  3.000
 E41  H161  C16  C17   109.38  3.000
 E41  C18   C16  C17   113.05  3.000
 E41  H17   C17  C20   107.86  3.000
 E41  H17   C17  C19   108.23  3.000
 E41  C20   C17  C19   110.49  3.000
 E41  H17   C17  C16   107.82  3.000
 E41  C20   C17  C16   109.93  3.000
 E41  C19   C17  C16   112.35  3.000
 E41  H182  C18  H181  106.21  3.000
 E41  H182  C18  C16   111.26  3.000
 E41  H181  C18  C16   108.38  3.000
 E41  H182  C18  N     109.01  3.000
 E41  H181  C18  N     109.45  3.000
 E41  C16   C18  N     112.34  3.000
 E41  H193  C19  H192  107.64  3.000
 E41  H193  C19  H191  107.02  3.000
 E41  H192  C19  H191  107.74  3.000
 E41  H193  C19  C17   110.84  3.000
 E41  H192  C19  C17   110.78  3.000
 E41  H191  C19  C17   112.61  3.000
 E41  H203  C20  H202  107.62  3.000
 E41  H203  C20  H201  107.75  3.000
 E41  H202  C20  H201  107.80  3.000
 E41  H203  C20  C17   110.95  3.000
 E41  H202  C20  C17   111.06  3.000
 E41  H201  C20  C17   111.49  3.000
 E41  C6    S1   O4    107.78  3.000
 E41  C6    S1   O3    107.20  3.000
 E41  O4    S1   O3    119.16  3.000
 E41  C6    S1   N     107.29  3.000
 E41  O4    S1   N     108.26  3.000
 E41  O3    S1   N     106.62  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
 E41  CONST_01  C11   C8   C7   C6     0.00   0.0  0
 E41  CONST_02  C11   C10  C9   C6     0.00   0.0  0
 E41  CONST_03  C15   C10  C9   C6   180.00   0.0  0
 E41  CONST_04  C10   C9   C6   C7     0.00   0.0  0
 E41  CONST_05  C10   C11  C8   C7     0.00   0.0  0
 E41  CONST_06  C12   C11  C8   C7   180.00   0.0  0
 E41  CONST_07  C9    C6   C7   C8     0.00   0.0  0
 E41  CONST_08  C9    C10  C11  C8     0.00   0.0  0
 E41  CONST_09  C15   C10  C11  C8   180.00   0.0  0
 E41  CONST_10  C13   C12  C11  C8   180.00   0.0  0
 E41  CONST_11  C12   C11  C10  C9   180.00   0.0  0
 E41  CONST_12  C14   C15  C10  C9   180.00   0.0  0
 E41  CONST_13  C13   C12  C11  C10    0.00   0.0  0
 E41  CONST_14  C13   C14  C15  C10    0.00   0.0  0
 E41  CONST_15  C14   C15  C10  C11    0.00   0.0  0
 E41  CONST_16  C14   C13  C12  C11    0.00   0.0  0
 E41  CONST_17  C15   C10  C11  C12    0.00   0.0  0
 E41  CONST_18  C15   C14  C13  C12    0.00   0.0  0
 E41  CONST_19  C8    C7   C6   S1   180.00   0.0  0
 E41  CONST_20  C10   C9   C6   S1   180.00   0.0  0
 E41  CONST_21  H8    C8   C7   C6   180.00   0.0  0
 E41  CONST_22  H9    C9   C6   C7   180.00   0.0  0
 E41  CONST_23  H12   C12  C11  C8     0.00   0.0  0
 E41  CONST_24  H7    C7   C6   C9   180.00   0.0  0
 E41  CONST_25  H15   C15  C10  C9     0.00   0.0  0
 E41  CONST_26  H14   C14  C15  C10  180.00   0.0  0
 E41  CONST_27  H13   C13  C12  C11  180.00   0.0  0
 E41  CONST_28  CA    C    N1   O1   180.00   0.0  0
 E41  CONST_29  O     C    N1   O1     0.00   0.0  0
 E41  Var_01    C7    C6   S1   N     61.17  30.0  2
 E41  Var_02    C6    S1   N    CA    74.64  30.0  3
 E41  Var_03    C17   C16  C18  N    175.69  30.0  1
 E41  Var_04    C16   C18  N    CA    77.89  30.0  3
 E41  Var_05    C19   C17  C16  C18   62.80  30.0  3
 E41  Var_06    HG11  CG1  CB   CA    63.01  30.0  3
 E41  Var_07    HG21  CG2  CB   CA    61.04  30.0  3
 E41  Var_08    H191  C19  C17  C16  -63.51  30.0  3
 E41  Var_09    H201  C20  C17  C16   57.91  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
 E41  chir_01  CA  N  C  CB  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
 E41  plan-1  C6   0.020
 E41  plan-1  C7   0.020
 E41  plan-1  C8   0.020
 E41  plan-1  C9   0.020
 E41  plan-1  C10  0.020
 E41  plan-1  C11  0.020
 E41  plan-1  C12  0.020
 E41  plan-1  C13  0.020
 E41  plan-1  C14  0.020
 E41  plan-1  C15  0.020
 E41  plan-1  H7   0.020
 E41  plan-1  H9   0.020
 E41  plan-1  H8   0.020
 E41  plan-1  H15  0.020
 E41  plan-1  H12  0.020
 E41  plan-1  H13  0.020
 E41  plan-1  H14  0.020
 E41  plan-1  S1   0.020
 E41  plan-2  O1   0.020
 E41  plan-2  N1   0.020
 E41  plan-2  CA   0.020
 E41  plan-2  C    0.020
 E41  plan-2  O    0.020
 E41  plan-2  H1   0.020

